Publications

regulatory rnas in cyanobacteria: developmental decisions, stress responses and a plethora of chromosomally encoded cis-antisense rnas.	cyanobacteria are the only prokaryotes which directly convert solar energy into biomass using oxygenic photosynthesis. therefore, these bacteria are of interest for the production of biofuels, biotechnology and are of tremendous relevance for primary carbon fixation in many ecosystems. mechanisms controlling gene expression cannot be understood entirely without information on the numbers and functions of regulatory rnas. in cyanobacteria, non-coding rnas have been characterized from simple unice ...	2011	21294678
dependence of the cyanobacterium prochlorococcus on hydrogen peroxide scavenging microbes for growth at the ocean's surface.	the phytoplankton community in the oligotrophic open ocean is numerically dominated by the cyanobacterium prochlorococcus, accounting for approximately half of all photosynthesis. in the illuminated euphotic zone where prochlorococcus grows, reactive oxygen species are continuously generated via photochemical reactions with dissolved organic matter. however, prochlorococcus genomes lack catalase and additional protective mechanisms common in other aerobes, and this genus is highly susceptible to ...	2011	21304826
antisense rna protects mrna from rnase e degradation by rna-rna duplex formation during phage infection.	the ecologically important cyanobacterium prochlorococcus possesses the smallest genome among oxyphototrophs, with a reduced suite of protein regulators and a disproportionately high number of regulatory rnas. many of these are asrnas, raising the question whether they modulate gene expression through the protection of mrna from rnase e degradation. to address this question, we produced recombinant rnase e from prochlorococcus sp. med4, which functions optimally at 12?mm mg(2+), ph 9 and 35°c. r ...	2011	21325266
response of prochlorococcus ecotypes to co-culture with diverse marine bacteria.	interactions between microorganisms shape microbial ecosystems. systematic studies of mixed microbes in co-culture have revealed widespread potential for growth inhibition among marine heterotrophic bacteria, but similar synoptic studies have not been done with autotroph/heterotroph pairs, nor have precise descriptions of the temporal evolution of interactions been attempted in a high-throughput system. here, we describe patterns in the outcome of pair-wise co-cultures between two ecologically d ...	2011	21326334
the lipoproteins of cyanobacterial photosystem ii.	photosystem ii (psii) complexes from cyanobacteria and plants perform water splitting and plastoquinone reduction and yet have a different complement of lumenal extrinsic proteins. whereas psii from all organisms has the psbo extrinsic protein, crystal structures of psii from cyanobacteria have psbv and psbu while green algae and higher plants instead contain the extrinsic psbp and psbq subunits. proteomic studies in synechocystis sp. pcc 6803 identified three further extrinsic proteins in the t ...	2011	21349737
molecular environments of divinyl chlorophylls in prochlorococcus and synechocystis: differences in fluorescence properties with chlorophyll replacement.	a marine cyanobacterium, prochlorococcus, is a unique oxygenic photosynthetic organism, which accumulates divinyl chlorophylls instead of the monovinyl chlorophylls. to investigate the molecular environment of pigments after pigment replacement but before optimization of the protein moiety in photosynthetic organisms, we compared the fluorescence properties of the divinyl chl a-containing cyanobacteria, prochlorococcus marinus (ccmp 1986, ccmp 2773 and ccmp 1375), by a synechocystis sp. pcc 6803 ...	2011	21377442
yellowstone lake: high-energy geochemistry and rich bacterial diversity.	yellowstone lake is central to the balanced functioning of the yellowstone ecosystem, yet little is known about the microbial component of its food chain. a remotely operated vehicle provided video documentation (http://www.tbi.montana.edu/media/videos/) and allowed sampling of dilute surface zone waters and enriched lake floor hydrothermal vent fluids. vent emissions contained substantial h(2) s, ch(4) , co(2) and h(2) , although ch(4) and h(2) levels were also significant throughout the lake. ...	2011	21450005
phosphorus-related gene content is similar in prochlorococcus populations from the north pacific and north atlantic oceans.		2011	21474783
high performance liquid chromatographic analysis of phytoplankton pigments using a c(16)-amide column.	in this study, a reverse-phase hplc method incorporating a ternary solvent system was developed to analyze most polar and non-polar chlorophylls and carotenoids present in phytoplankton. the method is based on an rp-c(16)-amide column and provided excellent peak resolution of most taxonomically important pigments and an elution profile different than c(8) or c(18) columns provide. analysis of mixed pigment standards, extracts of phytoplankton monocultures, and field samples showed that this meth ...	2011	21497819
genome reduction by deletion of paralogs in the marine cyanobacterium prochlorococcus.	several isolates of the marine cyanobacterial genus prochlorococcus have smaller genome sizes than those of the closely related genus synechococcus. in order to test whether loss of protein-coding genes has contributed to genome size reduction in prochlorococcus, we reconstructed events of gene family evolution over a strongly supported phylogeny of 12 prochlorococcus genomes and 9 synechococcus genomes. significantly more events both of loss of paralogs within gene families and of loss of entir ...	2011	21531921
transcriptome response of high- and low-light-adapted prochlorococcus strains to changing iron availability.	prochlorococcus contributes significantly to ocean primary productivity. the link between primary productivity and iron in specific ocean regions is well established and iron limitation of prochlorococcus cell division rates in these regions has been shown. however, the extent of ecotypic variation in iron metabolism among prochlorococcus and the molecular basis for differences is not understood. here, we examine the growth and transcriptional response of prochlorococcus strains, med4 and mit931 ...	2011	21562599
phylogenetic characterisation of picoplanktonic populations with high and low nucleic acid content in the north atlantic ocean.	in flow cytometric analyses of marine prokaryotic picoplankton often two populations with distinct differences in their apparent nucleic acid content are discernable, one with a high and one with a low nucleic acid content (hna and lna, respectively). in this study we determined the phylogenetic composition of flow cytometrically sorted hna and lna populations, collected at six stations along a transect across three oceanic provinces from iceland to the azores. catalysed reporter deposition fluo ...	2011	21596506
a freshwater cyanophage whose genome indicates close relationships to photosynthetic marine cyanomyophages.	bacteriophage s-crm01 has been isolated from a freshwater strain of synechococcus and shown to be present in the upper klamath river valley in northern california and oregon. the genome of this lytic t4-like phage has a 178 563 bp circular genetic map with 297 predicted protein-coding genes and 33 trna genes that represent all 20-amino-acid specificities. analyses based on gene sequence and gene content indicate a close phylogenetic relationship to the 'photosynthetic' marine cyanomyophages infe ...	2011	21605306
the diversity of cyanomyovirus populations along a north-south atlantic ocean transect.	viruses that infect the marine cyanobacterium prochlorococcus have the potential to impact the growth, productivity, diversity and abundance of their hosts. in this study, changes in the microdiversity of cyanomyoviruses were investigated in 10 environmental samples taken along a north-south atlantic ocean transect using a myoviral-specific pcr-sequencing approach. phylogenetic analyses of 630 viral g20 clones from this study, with 786 published g20 sequences, revealed that myoviral populations ...	2011	21633395
seasonal expression of the picocyanobacterial phosphonate transporter gene phnd in the sargasso sea.	in phosphorus-limited marine environments, picocyanobacteria (synechococcus and prochlorococcus spp.) can hydrolyze naturally occurring phosphonates as a p source. utilization of 2-aminoethylphosphonate (2-aep) is dependent on expression of the phn genes, encoding functions required for uptake, and c-p bond cleavage. prior work has indicated that expression of picocyanobacterial phnd, encoding the phosphonate binding protein of the phosphonate abc transporter, is a proxy for the assimilation of ...	2010	21687717
genomic island variability facilitates prochlorococcus-virus coexistence.	prochlorococcus cyanobacteria are extremely abundant in the oceans, as are the viruses that infect them. how hosts and viruses coexist in nature remains unclear, although the presence of both susceptible and resistant cells may allow this coexistence. combined whole-genome sequencing and pcr screening technology now enables us to investigate the effect of resistance on genome evolution and the genomic mechanisms behind the long-term coexistence of prochlorococcus and their viruses. here we prese ...	2011	21720364
decrease in the autotrophic-to-heterotrophic biomass ratio of picoplankton in oligotrophic marine waters due to bottle enclosure.	we investigated the effects of bottle enclosure on autotrophic and heterotrophic picoplankton in north and south subtropical atlantic oligotrophic waters, where the biomass and metabolism of the microbial community are dominated by the picoplankton size class. we measured changes in both autotrophic (prochlorococcus, synechococcus, and picoeukaryotes) and heterotrophic picoplankton biomass during three time series experiments and in 16 endpoint experiments over 24 h in light and dark treatments. ...	2011	21742930
non-random assembly of bacterioplankton communities in the subtropical north pacific ocean.	the exploration of bacterial diversity in the global ocean has revealed new taxa and previously unrecognized metabolic potential; however, our understanding of what regulates this diversity is limited. using terminal restriction fragment length polymorphism (t-rflp) data from bacterial small-subunit ribosomal rna genes we show that, independent of depth and time, a large fraction of bacterioplankton co-occurrence patterns are non-random in the oligotrophic north pacific subtropical gyre (npsg). ...	2011	21747815
starpicker: a method for efficient prediction of bacterial srna targets based on a two-step model for hybridization.	bacterial srnas are a class of small regulatory rnas involved in regulation of expression of a variety of genes. most srnas act in trans via base-pairing with target mrnas, leading to repression or activation of translation or mrna degradation. to date, more than 1,000 srnas have been identified. however, direct targets have been identified for only approximately 50 of these srnas. computational predictions can provide candidates for target validation, thereby increasing the speed of srna target ...	2011	21799937
ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern sargasso sea.	there are an estimated 10(30) virioplankton in the world oceans, the majority of which are phages (viruses that infect bacteria). marine phages encompass enormous genetic diversity, affect biogeochemical cycling of elements, and partially control aspects of prokaryotic production and diversity. despite their importance, there is a paucity of data describing virioplankton distributions over time and depth in oceanic systems. a decade of high-resolution time-series data collected from the upper 30 ...	2011	21833038
methods for nitrogenase-like dark operative protochlorophyllide oxidoreductase.	nitrogenase-like dark operative protochlorophyllide oxidoreductase (dpor) is involved in the biosynthesis of chlorophylls and bacteriochlorophylls in gymnosperms, ferns, algae, and photosynthetic bacteria. during protochlorophyllide (pchlide) reduction, the homodimeric subunit chll(2) of dpor transfers electrons on the corresponding heterotetrameric catalytic subunit (chln/chlb)(2). although dpor shares significant amino acid sequence homology to the nitrogenase system, only the initial catalyti ...	2011	21833865
phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism.	cyanophages infecting the marine cyanobacteria prochlorococcus and synechococcus encode and express genes for the photosynthetic light reactions. sequenced cyanophage genomes lack calvin cycle genes, however, suggesting that photosynthetic energy harvested via phage proteins is not used for carbon fixation. we report here that cyanophages carry and express a calvin cycle inhibitor, cp12, whose host homologue directs carbon flux from the calvin cycle to the pentose phosphate pathway (ppp). phage ...	2011	21844365
Iron transporters in marine prokaryotic genomes and metagenomes.	In the pelagic environment, iron is a scarce but essential micronutrient. The iron acquisition capabilities of selected marine bacteria have been investigated, but the recent proliferation of marine prokaryotic genomes and metagenomes offers a more comprehensive picture of microbial iron uptake pathways in the ocean. Searching these data sets, we were able to identify uptake mechanisms for Fe(3+) , Fe(2+) and iron chelates (e.g. siderophore and haem iron complexes). Transport of iron chelates i ...	2011	21883791
Novel lineages of Prochlorococcus and Synechococcus in the global oceans.	Picocyanobacteria represented by Prochlorococcus and Synechococcus have an important role in oceanic carbon fixation and nutrient cycling. In this study, we compared the community composition of picocyanobacteria from diverse marine ecosystems ranging from estuary to open oceans, tropical to polar oceans and surface to deep water, based on the sequences of 16S-23S rRNA internal transcribed spacer (ITS). A total of 1339 ITS sequences recovered from 20 samples unveiled diverse and several previous ...	2011	21955990
sunlight modulates the relative importance of heterotrophic bacteria and picophytoplankton in dmsp-sulphur uptake.	there is a large body of evidence supporting a major role of heterotrophic bacteria in dimethylsulphoniopropionate (dmsp) utilisation as a source of reduced sulphur. however, a role for phototrophic microorganisms has been only recently described and little is known about their contribution to dmsp consumption and the potential modulating effects of sunlight. in an attempt to ascertain the relative quantitative roles of heterotrophic bacteria and picophytoplankton in the osmoheterotrophic uptake ...	2011	21955992
On the culture-independent assessment of the diversity and distribution of Prochlorococcus.	Much of our current knowledge on Prochlorococcus has derived from research on various genetic strains that have successfully been brought into culture. In particular, analyses of the complete genomes of 12 of those isolates have revealed the extent to which these strains differ from each other and the genetic means by which they are adapted to specific environmental niches. However, based on culture-independent studies it is now clear that the strains currently available in diverse culture colle ...	2011	21957972
transcriptional responses of surface water marine microbial assemblages to deep-sea water amendment.	deep-water nutrient injection in the north pacific subtropical gyre provides an aperiodic yet significant source of inorganic nutrients to the nutrient-limiting surface waters, and has been implicated in phytoplankton bloom formation. here we examined short-term transcriptional responses of surface water picoplankton assemblages in a deep-sea water (dsw) mixing experiment. both flow cytometric and transcriptomic analysis indicated stimulation of an alteromonas-like population in the dsw-amended ...	2011	21981709
the minimal genome: a metabolic and environmental comparison.	the field of synthetic biology seeks to apply engineering principles to biology in order to produce novel biological systems. one approach to accomplish this goal is the genome-driven cell engineering approach, which searches for functioning minimal genomes in naturally occurring microorganisms, which can then be used as a template for future systems. currently a prototypical minimal genome has not been discovered. this review analyzes the organisms mycoplasma pneumoniae, pelagibacter ubique, ve ...	2011	21987714
internal and external influences on near-surface microbial community structure in the vicinity of the cape verde islands.	microbial community structure in the subtropical north-east atlantic ocean was compared between 2 years and variation attributed to environmental variables. surface seawater communities were analysed by flow cytometry and fluorescence in situ hybridisation. probes specific to alphaproteobacteria, cyanobacteria, gammaproteobacteria and bacteroidetes identified 67-100% of cells. due to natural variation in the study region due to the occurrence of major currents and islands, data could not be pool ...	2011	21994033
phosphite utilization by the marine picocyanobacterium prochlorococcus mit9301.	primary productivity in the ocean's oligotrophic regions is often limited by phosphorus (p) availability. in low phosphate environments, the prevalence of many genes involved in p acquisition is elevated, suggesting that the ability to effectively access diverse p sources is advantageous for organisms inhabiting these regions. prochlorococcus, the numerically dominant primary producer in the oligotrophic ocean, encodes high-affinity p transporters, p regulatory proteins and enzymes for organic p ...	2011	22004069
evolution of a divinyl chlorophyll-based photosystem in prochlorococcus.	acquisition of new photosynthetic pigments has been a crucial process for the evolution of photosynthesis and photosynthetic organisms. in this process, pigment-binding proteins must evolve to fit new pigments. prochlorococcus is a unique photosynthetic organism that uses divinyl chlorophyll (dvchl) instead of monovinyl chlorophyll. however, cyanobacterial mutants that accumulate dvchl immediately die even under medium-light conditions, suggesting that chlorophyll (chl)-binding proteins had to e ...	2011	22006316
potential for phosphite and phosphonate utilization by prochlorococcus.	phosphonates (pn) are diverse organic phosphorus (p) compounds containing c-p bonds and comprise up to 25% of the high-molecular weight dissolved organic p pool in the open ocean. pn bioavailability was suggested to influence markedly bacterial primary production in low-p areas. using metagenomic data from the global ocean sampling expedition, we show that the main potential microbial contributor in pn utilization in oceanic surface water is the globally important marine primary producer prochlo ...	2011	22011717
Cyanophage tRNAs may have a role in cross-infectivity of oceanic Prochlorococcus and Synechococcus hosts.	Marine cyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic prokaryotes in oceanic environments, and are key contributors to global CO(2) fixation, chlorophyll biomass and primary production. Cyanophages, viruses infecting cyanobacteria, are a major force in the ecology of their hosts. These phages contribute greatly to cyanobacterial mortality, therefore acting as a powerful selective force upon their hosts. Phage reproduction is based on utilizatio ...	2011	22011720
tunable pores for measuring concentrations of synthetic and biological nanoparticle dispersions.	scanning ion occlusion sensing (sios), a technique that uses a tunable pore to detect the passage of individual nano-scale objects, is applied here for the rapid, accurate and direct measurement of synthetic and biological nanoparticle concentrations. sios is able to characterize smaller particles than other direct count techniques such as flow cytometry or coulter counters, and the direct count avoids approximations such as those necessary for turbidity measurements. measurements in a model sys ...	2012	22019099
Codon usage patterns and adaptive evolution of marine unicellular cyanobacteria Synechococcus and Prochlorococcus.	Marine unicellular cyanobacteria, represented by Synechococcus and Prochlorococcus, dominate the total phytoplankton biomass and production in oligotrophic ocean. In this study, we employed comparative genomics approaches to extensively investigate synonymous codon usage bias and evolutionary rates in a large number of closely related species of marine unicellular cyanobacteria. Although these two groups of marine cyanobacteria have a close phylogenetic relationship, we find that they are highly ...	2012	22040764
the response of diatom central carbon metabolism to nitrogen starvation is different from that of green algae and higher plants.	the availability of nitrogen varies greatly in the ocean and limits primary productivity over large areas. diatoms, a group of phytoplankton that are responsible for about 20% of global carbon fixation, respond rapidly to influxes of nitrate and are highly successful in upwelling regions. although recent diatom genome projects have highlighted clues to the success of this group, very little is known about their adaptive response to changing environmental conditions. here, we compare the proteome ...	2011	22065419
oxygen-independent alkane formation by non-heme iron-dependent cyanobacterial aldehyde decarbonylase: investigation of kinetics and requirement for an external electron donor.	cyanobacterial aldehyde decarbonylase (cad) is, structurally, a member of the di-iron carboxylate family of oxygenases. we previously reported that cad from prochlorococcus marinus catalyzes the unusual hydrolysis of aldehydes to produce alkanes and formate in a reaction that requires an external reducing system but does not require oxygen [das et al. (2011) angew. chem. 50, 7148-7152]. here we demonstrate that cads from divergent cyanobacterial classes, including the enzyme from n. puntiformes ...	2011	22074177
analogous nutrient limitations in unicellular diazotrophs and prochlorococcus in the south pacific ocean.	growth limitation of phytoplankton and unicellular nitrogen (n(2)) fixers (diazotrophs) were investigated in the oligotrophic western south pacific ocean. based on change in abundances of nifh or 23s rrna gene copies during nutrient-enrichment experiments, the factors limiting net growth of the unicellular diazotrophs ucyn-a (group a), crocosphaera watsonii, γ-proteobacterium 24774a11, and the non-diazotrophic picocyanobacterium prochlorococcus, varied within the region. at the westernmost stati ...	2011	22094348
ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage.	ProPortal (http://proportal.mit.edu/) is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. Our goal is to provide a source of cross-referenced data across multiple scales of biological organization-from the genome to the ecosystem-embracing the full diversity of ecotypic variation within this microbial taxon, its sister group, Synechococcus and phage that infect them. The site currently contains the genomes of 13 Prochlorococ ...	2012	22102570
biogeography of pelagic bacterioplankton across an antagonistic temperature-salinity gradient in the red sea.	the red sea is a unique marine ecosystem with contrasting gradients of temperature and salinity along its north-to-south axis. it is an extremely oligotrophic environment that is characterized by perpetual year-round water column stratification, high annual solar irradiation, and negligible riverine and precipitation inputs. in this study, we investigated whether the contemporary environmental conditions shape community assemblages by pyrosequencing 16s rrna genes of bacteria in surface water sa ...	2011	22133021
isolation and characterization of the prochlorococcus carboxysome reveal the presence of the novel shell protein csos1d.	cyanobacteria, including members of the genus prochlorococcus, contain icosahedral protein microcompartments known as carboxysomes that encapsulate multiple copies of the co(2)-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) in a thin protein shell that enhances the catalytic performance of the enzyme in part through the action of a shell-associated carbonic anhydrase. however, the exact mechanism by which compartmentation provides a catalytic advantage to the enzyme is n ...	2011	22155772
the tricarboxylic acid cycle in cyanobacteria.	it is generally accepted that cyanobacteria have an incomplete tricarboxylic acid (tca) cycle because they lack 2-oxoglutarate dehydrogenase and thus cannot convert 2-oxoglutarate to succinyl-coenzyme a (coa). genes encoding a novel 2-oxoglutarate decarboxylase and succinic semialdehyde dehydrogenase were identified in the cyanobacterium synechococcus sp. pcc 7002. together, these two enzymes convert 2-oxoglutarate to succinate and thus functionally replace 2-oxoglutarate dehydrogenase and succi ...	2011	22174252
Environmental forcing of nitrogen fixation in the eastern tropical and sub-tropical north atlantic ocean.	During the winter of 2006 we measured nifH gene abundances, dinitrogen (N(2)) fixation rates and carbon fixation rates in the eastern tropical and sub-tropical North Atlantic Ocean. The dominant diazotrophic phylotypes were filamentous cyanobacteria, which may include Trichodesmium and Katagnymene, with up to 10(6) L(-1)nifH gene copies, unicellular group A cyanobacteria with up to 10(5) L(-1)nifH gene copies and gamma A proteobacteria with up to 10(4) L(-1)nifH gene copies. N(2) fixation rates ...	2011	22174940
genome sequences of siphoviruses infecting marine synechococcus unveil a diverse cyanophage group and extensive phage-host genetic exchanges.	investigating the interactions between marine cyanobacteria and their viruses (phages) is important towards understanding the dynamic of ocean's primary productivity. genome sequencing of marine cyanophages has greatly advanced our understanding about their ecology and evolution. among 24 reported genomes of cyanophages that infect marine picocyanobacteria, 17 are from cyanomyoviruses and six from cyanopodoviruses, and only one from cyanosiphovirus (prochlorococcus phage p-ss2). here we present ...	2011	22188618
recombination detection under evolutionary scenarios relevant to functional divergence.	recombination can negatively impact methods designed to detect divergent gene function that rely on explicit knowledge of a gene tree. however, we know little about how recombination detection methods perform under evolutionary scenarios encountered in studies of functional molecular divergence. we use simulation to evaluate false positive rates for six recombination detection methods (geneconv, maxchi, chimera, rdp, gard-sbp, gard-mbp) under evolutionary scenarios that might increase false posi ...	2012	22210457
two strains of crocosphaera watsonii with highly conserved genomes are distinguished by strain-specific features.	unicellular nitrogen-fixing cyanobacteria are important components of marine phytoplankton. although non-nitrogen-fixing marine phytoplankton generally exhibit high gene sequence and genomic diversity, gene sequences of natural populations and isolated strains of crocosphaerawatsonii, one of the two most abundant open ocean unicellular cyanobacteria groups, have been shown to be 98-100% identical. the low sequence diversity in crocosphaera is a dramatic contrast to sympatric species of prochloro ...	2011	22232617
marine viruses exploit their host's two-component regulatory system in response to resource limitation.	phosphorus (p) availability, which often limits productivity in marine ecosystems, shapes the p-acquisition gene content of the marine cyanobacteria prochlorococcus [1-4] and its viruses (cyanophages) [5, 6]. as in other bacteria, in prochlorococcus these genes are regulated by the phor/phob two-component regulatory system that is used to sense and respond to p availability and is typical of signal transduction systems found in diverse organisms [7]. replication of cyanophage genomes requires a ...	2012	22244998