Phylogenetic Diversity of Marine Cyanophage Isolates and Natural Virus Communities As Revealed by Sequences of Viral Capsid Assembly Protein Gene G20

Applied and Environmental Microbiology. Apr, 2002  |  Pubmed ID: 11916671

In order to characterize the genetic diversity and phylogenetic affiliations of marine cyanophage isolates and natural cyanophage assemblages, oligonucleotide primers CPS1 and CPS8 were designed to specifically amplify ca. 592-bp fragments of the gene for viral capsid assembly protein g20. Phylogenetic analysis of isolated cyanophages revealed that the marine cyanophages were highly diverse yet more closely related to each other than to enteric coliphage T4. Genetically related marine cyanophage isolates were widely distributed without significant geographic segregation (i.e., no correlation between genetic variation and geographic distance). Cloning and sequencing analysis of six natural virus concentrates from estuarine and oligotrophic offshore environments revealed nine phylogenetic groups in a total of 114 different g20 homologs, with up to six clusters and 29 genotypes encountered in a single sample. The composition and structure of natural cyanophage communities in the estuary and open-ocean samples were different from each other, with unique phylogenetic clusters found for each environment. Changes in clonal diversity were also observed from the surface waters to the deep chlorophyll maximum layer in the open ocean. Only three clusters contained known cyanophage isolates, while the identities of the other six clusters remain unknown. Whether or not these unidentified groups are composed of bacteriophages that infect different Synechococcus groups or other closely related cyanobacteria remains to be determined. The high genetic diversity of marine cyanophage assemblages revealed by the g20 sequences suggests that marine viruses can potentially play important roles in regulating microbial genetic diversity.

Estimation of Biologically Damaging UV Levels in Marine Surface Waters with DNA and Viral Dosimeters

Photochemistry and Photobiology. Sep, 2002  |  Pubmed ID: 12403447

We have surveyed the biologically harmful radiation penetrating the water column along a transect in the western Gulf of Mexico using dosimeters consisting of intact viruses or naked calf-thymus DNA (ctDNA). The indigenous marine bacteriophage PWH3a-P1, which lytically infects the heterotrophic bacterium Vibrio natriegens (strain PWH3a), displayed decay rates for infectivity approaching 1.0 h(-1) in surface waters when deployed in a seawater-based dosimeter. The accumulation of pyrimidine dimers in ctDNA dosimeters provided a strong correlation to these results, with pyrimidine dimers representing more than 0.3% (up to ca 3800 dimers Mb(-1) DNA) of the total DNA in dosimeters exposed to sea surface levels of solar radiation. The results demonstrate a strong correlation between the dimer formation in the DNA dosimeters, the decay rates of viral infectivity and the penetration of UVB radiation into the water column. The decay of viral infectivity attenuated with depth in a manner similar to the decay of solar radiation and was still significant at 10 m in offshore oligotrophic water and at dimer frequencies less than 0.1% (ca 200-300 dimers Mb(-1) DNA).

Toxic Microcystis is Widespread in Lake Erie: PCR Detection of Toxin Genes and Molecular Characterization of Associated Cyanobacterial Communities

Microbial Ecology. Feb, 2006  |  Pubmed ID: 16435169

During the past decade, algae blooms, which include the toxic cyanobacterium Microcystis, have reoccurred in the Laurentian Great Lakes, most commonly in the western basin of Lake Erie. Whereas the western basin is the most impacted by toxic Microcystis in Lake Erie, there has historically been little effort focused on identifying the spatial distribution of Microcystis throughout this lake. To address this lack of knowledge, we have employed a polymerase-chain-reaction-based detection of genes required for synthesis of the toxin microcystin (mcyD and mcyB), as well as 16S rDNA fragments specific to either all Microcystis or all cyanobacteria. Using a multiplex approach, we tested 21 samples from 13 field stations and found that toxigenic Microcystis were present in the western and eastern basins in the summers of 1999, 2000, and 2002 and the central basin in 1999 and 2002. This is the most extensive distribution of Microcystis reported in Lake Erie. Clone libraries (16S rDNA) of these cyanobacterial communities were generated from 7 of the 13 field stations (representing all three basins) to partially characterize this microbial community. These libraries were shown to be dominated by sequences assigned to the Synechococcus and Cyanobium phylogenetic cluster, indicating the importance of picoplankton in this large lake system.

Marine and Freshwater Cyanophages in a Laurentian Great Lake: Evidence from Infectivity Assays and Molecular Analyses of G20 Genes

Applied and Environmental Microbiology. Jul, 2006  |  Pubmed ID: 16820493

While it is well established that viruses play an important role in the structure of marine microbial food webs, few studies have directly addressed their role in large lake systems. As part of an ongoing study of the microbial ecology of Lake Erie, we have examined the distribution and diversity of viruses in this system. One surprising result has been the pervasive distribution of cyanophages that infect the marine cyanobacterial isolate Synechococcus sp. strain WH7803. Viruses that lytically infect this cyanobacterium were identified throughout the western basin of Lake Erie, as well as in locations within the central and eastern basins. Analyses of the gene encoding the g20 viral capsid assembly protein (a conservative phylogenetic marker for the cyanophage) indicate that these viruses, as well as amplicons from natural populations and the ballast of commercial ships, are related to marine cyanophages but in some cases form a unique clade, leaving questions concerning the native hosts of these viruses. The results suggest that cyanophages may be as important in freshwater systems as they are known to be in marine systems.

Diversity of Microcystin-producing Cyanobacteria in Spatially Isolated Regions of Lake Erie

Applied and Environmental Microbiology. Jul, 2006  |  Pubmed ID: 16820510

The diversity of microcystin-producing cyanobacteria in the western basin of Lake Erie was studied using sequence analysis of mcyA gene fragments. Distinct populations of potentially toxic Microcystis and Planktothrix were found in spatially isolated locations. This study highlights previously undocumented diversity of potentially toxic cyanobacteria.

Virus Transport During Infiltration of a Wetting Front into Initially Unsaturated Sand Columns

Environmental Science & Technology. Feb, 2008  |  Pubmed ID: 18351079

We investigated the effect of different flow conditions on the transport of bacteriophage phiX174 in Memphis aquifer sand. Virus transport associated with a wetting front moving into an initially unsaturated horizontal sand column was experimentally compared with that observed under steady-state saturated vertical flow. Results obtained by sectioning the sand columns showthattotal (retained and free) resident virus concentrations decreased approximately exponentially with the travel distance. The rate of decline was similar under both transient unsaturated flow and steady-state saturated flow conditions. Total resident virus concentrations near the inlet were an order of magnitude greater than the virus concentration of the influent solution in both experiments, indicating continuous virus sorption during flow through this zone. Virus retardation was quantified using the ratio of the centroids of the relative saturation and virus concentration versus relative distance functions. The mean retardation factors were 6.43 (coefficient of variation, CV = 14.4%) and 8.22 (CV = 8.22%) for the transient unsaturated and steady-state saturated flow experiments, respectively. Attest indicated no significant difference between these values at P < 0.05. Air-water and air-water-solid interfaces are thought to enhance virus inactivation and sorption to solid particles. The similar retardation factors obtained may be attributable to the reduced presence of these interfaces in the two flow systems investigated as compared to steady-state unsaturated flow experiments in which these interfaces occur throughout the entire column.

Global-scale Processes with a Nanoscale Drive: the Role of Marine Viruses

The ISME Journal. Jun, 2008  |  Pubmed ID: 18385772

Analytical Methods Workgroup Report

Advances in Experimental Medicine and Biology. 2008  |  Pubmed ID: 18461779

Field Methods in the Study of Toxic Cyanobacterial Blooms: Results and Insights from Lake Erie Research

Advances in Experimental Medicine and Biology. 2008  |  Pubmed ID: 18461781

Sound field methodologies are an essential prerequisite in the development of a basic understanding of toxic cyanobacteria blooms. Sample collection, on-site processing, storage and transportation, and subsequent analysis and documentation are all critically dependent on a sound field program that allows the researcher to construct, with minimal uncertainty, linkages between bloom events and cyanotoxin production with the ecology of the studied system. Since 1999, we have collected samples in Lake Erie as part of the MELEE (Microbial Ecology of the Lake Erie Ecosystem) and MERHAB-LGL (Monitoring Event Responses for Harmful Algal Blooms in the Lower Great Lakes) research programs to develop appropriate tools and refine methods necessary to characterize the ecology of the reoccurring cyanobacterial blooms in the systems. Satellite imagery, large ship expeditions, classical and novel molecular tools have been combined to provide insight into both the cyanobacteria responsible for these events as well as into some of the environmental cues that may facilitate the formation of toxic blooms. This information, as well new directions in cyano-specific monitoring will be presented to highlight needs for field program monitoring and/or researching toxic freshwater cyanobacteria.

Actinorhodopsin Genes Discovered in Diverse Freshwater Habitats and Among Cultivated Freshwater Actinobacteria

The ISME Journal. Jun, 2009  |  Pubmed ID: 19242530

Microbial rhodopsins are membrane proteins that utilize a retinal chromophore to harvest sunlight for energetic and photosensory functions. Recently, a group of novel rhodopsin sequences named 'actinorhodopsins' (ActRs) was hypothesized to exist among uncultured planktonic Actinobacteria. ActRs were discovered by mining metagenomic data obtained during the Venter Institute's Global Ocean Sampling expedition, from a hypersaline lagoon, two estuaries and a freshwater lake. On the basis of these findings, and many studies that show Actinobacteria are common inhabitants of lakes, we predicted that ActR genes would likely be present in other freshwater habitats and among the genomes of cultivated Actinobacteria. Using degenerate polymerase chain reaction primers, we discovered an ActR gene present in an actinobacterial isolate of the family Microbacteriaceae. Isolate MWH-Uga1 was cultivated prior to this study from a freshwater pond in Uganda and belongs to a group of Actinobacteria previously identified in freshwater ecosystems. ActR genes were also discovered present in numerous mixed cultures containing freshwater Actinobacteria and among environmental DNA samples obtained from three freshwater sources; a small woodland pond and the Laurentian Great Lakes Superior and Erie. An analysis of small subunit ribosomal RNA genes from metagenomic DNA samples harboring ActR genes suggests that organisms belonging to the acI lineage, an uncultured group of Actinobacteria commonly present in fresh waters, may utilize rhodopsins. The co-occurrence of an acI organism with a specific ActR variant in a mixed culture supports our hypothesis.

Identifying the Source of Unknown Microcystin Genes and Predicting Microcystin Variants by Comparing Genes Within Uncultured Cyanobacterial Cells

Applied and Environmental Microbiology. Jun, 2009  |  Pubmed ID: 19363074

While multiple phylogenetic markers have been used in the culture-independent study of microcystin-producing cyanobacteria, in only a few instances have multiple markers been studied within individual cells, and in all cases these studies have been conducted with cultured isolates. Here, we isolate and evaluate large DNA fragments (>6 kb) encompassing two genes involved in microcystin biosynthesis (mcyA2 and mcyB1) and use them to identify the source of gene fragments found in water samples. Further investigation of these gene loci from individual cyanobacterial cells allowed for improved analysis of the genetic diversity within microcystin producers as well as a method to predict microcystin variants for individuals. These efforts have also identified the source of the novel mcyA genotype previously termed Microcystis-like that is pervasive in the Laurentian Great Lakes and they predict the microcystin variant(s) that it produces.

PAH Biodegradative Genotypes in Lake Erie Sediments: Evidence for Broad Geographical Distribution of Pyrene-degrading Mycobacteria

Environmental Science & Technology. May, 2009  |  Pubmed ID: 19544841

Despite a long history of anthropogenic contamination of Lake Erie sediments, little work has been done to understand the potential for PAH biodegradation by indigenous microbial communities. Pyrene-degrading Mycobacterium are prevalent in many polycyclic aromatic hydrocarbon (PAH)-contaminated freshwater sediments, and are of interest for their ability to degrade environmentally recalcitrant high molecular weight PAHs. This work tested the hypothesis that pyrene-degrading mycobacteria are prevalent in Lake Erie; an additional aim was to gain a baseline picture of the sediment microbial communities through sequencing a 16S rDNA clone library. Biodegradation potential of Lake Erie Mycobacterium populations was assessed through quantification of pyrene dioxygenase genes (nidA) and mycobacteria 16S rDNA genes using quantitative real time PCR. nidA was detected at all seven sampling sites across Lake Erie, with abundances ranging from 2.09 to 70.4 x 10(6) copies per gram sediment, with highest abundances at the most PAH-contaminated site (Cleveland Harbor). This is in contrastto naphthalene dioxygenase genes commonly used as biomarkers of PAH degradation: nahAc (from gamma-proteobacteria) was not detected anywhere, and nagAc (from beta-proteobacteria) was detected only in Cleveland Harbor, despite dominance by proteobacteria in Lake Erie sediment 16S rDNA clone libraries (>50% of clones). The prevalence of Mycobacterium nidA genotypes corroborated previous studies indicating that PAH-degrading mycobacteria have a cosmopolitan distribution and suggests they play an important but overlooked role in natural attenuation and cycling of PAHs in Lake Erie.

Transcriptional Profiling of Saccharomyces Cerevisiae Upon Exposure to Saxitoxin

Environmental Science & Technology. Aug, 2009  |  Pubmed ID: 19731715

Saxitoxin is a potent neurotoxin produced by several species of dinoflagellates and cyanobacteria. The molecular target of saxitoxin in higher eukaryotes is the voltage-gated sodium channel; however, its target in lower eukaryotic organisms remains unknown. The goal of this study was to obtain the transcriptional fingerprint of the model lower eukaryote Saccharomyces cerevisiae upon exposure to saxitoxin to identify potential genes suitable for biomarker development. Microarray analyses identified multiple genes associated with copper and iron homeostasis and sulfur metabolism as significantly differentially expressed upon exposure to saxitoxin; these results were verified with quantitative reverse-transcriptase PCR (qRT-PCR). Additionally, the qRT-PCR assays were used to generate expression profiles in a subset of the differentially regulated genes across multiple exposure times and concentrations, the results of which demonstrated that overall, genes tended to respond in a consistent manner to the toxin. In general, the genes encoding the metallothioneins CUP1 and CRS5 were induced following exposure to saxitoxin, while those encoding the ferric/ cupric reductase FRE1 and the copper uptake transporter CTR1 were repressed. The gene encoding the multicopper ferroxidase FET3, part of the high-affinity iron uptake system, was also induced in all treatments, along with the STR3 gene, which codes for the cystathionine beta-lyase found in the methionine biosynthetic pathway.

Ubiquitous Cyanobacterial Podoviruses in the Global Oceans Unveiled Through Viral DNA Polymerase Gene Sequences

The ISME Journal. Oct, 2010  |  Pubmed ID: 20463765

As a major cyanophage group, cyanobacterial podoviruses are important in regulating the biomass and population structure of picocyanobacteria in the ocean. However, little is known about their biogeography in the open ocean. This study represents the first survey of the biodiversity of cyanopodoviruses in the global oceans based on the viral encoded DNA polymerase (pol) gene. A total of 303 DNA pol sequences were amplified by PCR from 10 virus communities collected in the Atlantic and Pacific oceans and the South China Sea. At least five subclusters of cyanopodoviruses were identified in these samples, and one subcluster (subcluster VIII) was found in all sampling sites and comprised approximately 50% of total sequences. The diversity index based on the DNA pol gene sequences recovered through PCR suggests that cyanopodoviruses are less diverse in these oceanic samples than in a previously studied estuarine environment. Although diverse podoviruses were present in the global ocean, each sample was dominated by one major group of cyanopodoviruses. No clear biogeographic patterns were observed using statistical analysis. A metagenomic analysis based on the Global Ocean Sampling database indicates that other types of cyanopodovirus-like DNA pol sequences were present in the global ocean. Together, our study results suggest that cyanopodoviruses are widely distributed in the ocean but their community composition varies with local environments.

Microbial Production of Recalcitrant Dissolved Organic Matter: Long-term Carbon Storage in the Global Ocean

Nature Reviews. Microbiology. Aug, 2010  |  Pubmed ID: 20601964

The biological pump is a process whereby CO(2) in the upper ocean is fixed by primary producers and transported to the deep ocean as sinking biogenic particles or as dissolved organic matter. The fate of most of this exported material is remineralization to CO(2), which accumulates in deep waters until it is eventually ventilated again at the sea surface. However, a proportion of the fixed carbon is not mineralized but is instead stored for millennia as recalcitrant dissolved organic matter. The processes and mechanisms involved in the generation of this large carbon reservoir are poorly understood. Here, we propose the microbial carbon pump as a conceptual framework to address this important, multifaceted biogeochemical problem.

Application of the Major Capsid Protein As a Marker of the Phylogenetic Diversity of Emiliania Huxleyi Viruses

FEMS Microbiology Ecology. May, 2011  |  Pubmed ID: 21255053

Studies of the Phycodnaviridae have traditionally relied on the DNA polymerase (pol) gene as a biomarker. However, recent investigations have suggested that the major capsid protein (MCP) gene may be a reliable phylogenetic biomarker. We used MCP gene amplicons gathered across the North Atlantic to assess the diversity of Emiliania huxleyi-infecting Phycodnaviridae. Nucleotide sequences were examined across >6000 km of open ocean, with comparisons between concentrates of the virus-size fraction of seawater and of lysates generated by exposing host strains to these same virus concentrates. Analyses revealed that many sequences were only sampled once, while several were over-represented. Analyses also revealed nucleotide sequences distinct from previous coastal isolates. Examination of lysed cultures revealed a new richness in phylogeny, as MCP sequences previously unrepresented within the existing collection of E. huxleyi viruses (EhV) were associated with viruses lysing cultures. Sequences were compared with previously described EhV MCP sequences from the North Sea and a Norwegian Fjord, as well as from the Gulf of Maine. Principal component analysis indicates that location-specific distinctions exist despite the presence of sequences common across these environments. Overall, this investigation provides new sequence data and an assessment on the use of the MCP gene.

Global Gene Expression Profiling in Larval Zebrafish Exposed to Microcystin-LR and Microcystis Reveals Endocrine Disrupting Effects of Cyanobacteria

Environmental Science & Technology. Mar, 2011  |  Pubmed ID: 21280650

Microcystis blooms occur worldwide and threaten aquatic ecosystems and human health. Sublethal effects on early developmental stages of fish are largely unknown, and research has mainly focused on microcystin toxins (such as MC-LR) rather than Microcystis cells. We exposed (96 h) zebrafish larvae to purified MC-LR (0-1000 μg/L) or lyophilized Microcystis aeruginosa containing 4.5 μg/L MC-LR and evaluated changes in global gene expression (Affymetrix GeneChip zebrafish genome arrays). Significant changes in gene expression (≥ 1.7-fold change, p < 0.0001) were determined with Rosetta Resolver 7.0, and ontology analysis was conducted with the DAVID bioinformatics tool. The number of differentially expressed genes relative to control increased with MC-LR concentration and included genes related to known mechanisms of action for MC-LR in mammals and older life stages of fish, as well as genes unique to larval zebrafish. Up-regulation of vitellogenin genes (vtg) (19.2-fold to >100-fold on arrays; 619.3-fold confirmed by quantitative PCR) was observed in Microcystis-exposed larvae but not in larvae exposed to MC-LR. Up-regulation of vtg indicates exposure to estrogenic substance(s) and suggests that Microcystis may be a natural source of environmental estrogens. Concerns about effects of Microcystis blooms may extend beyond those associated with the microcystin toxin.

Niche of Harmful Alga Aureococcus Anophagefferens Revealed Through Ecogenomics

Proceedings of the National Academy of Sciences of the United States of America. Mar, 2011  |  Pubmed ID: 21368207

Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics. Using an ecogenomic approach, we specifically focused on gene sets that may facilitate dominance within the environmental conditions present during blooms. A. anophagefferens possesses a larger genome (56 Mbp) and has more genes involved in light harvesting, organic carbon and nitrogen use, and encoding selenium- and metal-requiring enzymes than competing phytoplankton. Genes for the synthesis of microbial deterrents likely permit the proliferation of this species, with reduced mortality losses during blooms. Collectively, these findings suggest that anthropogenic activities resulting in elevated levels of turbidity, organic matter, and metals have opened a niche within coastal ecosystems that ideally suits the unique genetic capacity of A. anophagefferens and thus, has facilitated the proliferation of this and potentially other HABs.

A Protocol for Enumeration of Aquatic Viruses by Epifluorescence Microscopy Using Anodisc™ 13 Membranes

BMC Microbiology. 2011  |  Pubmed ID: 21787406

Epifluorescence microscopy is a common method used to enumerate virus-like particles (VLP) from environmental samples and relies on the use of filter membranes with pore sizes < 0.02 μm; the most commonly used protocols employ 25 mm Anodisc™ membranes with a built-in support ring. Other filters with small pore sizes exist, including the 13 mm Anodisc™ membranes without a support ring. However, the use of these membranes for viral enumeration has not been previously reported.

Molecular Enumeration of an Ecologically Important Cyanophage in a Laurentian Great Lake

Applied and Environmental Microbiology. Oct, 2011  |  Pubmed ID: 21841023

Considerable research has shown that cyanobacteria and the viruses that infect them (cyanophage) are pervasive and diverse in global lake populations. Few studies have seasonally analyzed freshwater systems, and little is known about the bacterial and viral communities that coexist during the harsh winters of the Laurentian Great Lakes. Here, we employed quantitative PCR to estimate the abundance of cyanomyoviruses in this system, using the portal vertex g20 gene as a proxy for cyanophage abundance and to determine the potential ecological relevance of these viruses. Cyanomyoviruses were abundant in both the summer and the winter observations, with up to 3.1 × 10(6) copies of g20 genes ml(-1) found at several stations and depths in both seasons, representing up to 4.6% of the total virus community. Lake Erie was productive during both our observations, with high chlorophyll a concentrations in the summer (up to 10.3 μg liter(-1)) and winter (up to 5.2 μg liter(-1)). Both bacterial and viral abundances were significantly higher during the summer than during the winter (P < 0.05). Summer bacterial abundances ranged from 3.3 × 10(6) to 1.6 × 10(7) ml(-1) while winter abundances ranged between ∼3.4 × 10(5) and 1.2 × 10(6) ml(-1). Total virus abundances were high during both months, with summer abundances significantly higher at most stations, ranging from 6.5 × 10(7) to 8.8 × 10(7) ml(-1), and with winter abundances ranging from 3.4 × 10(7) to 6.6 × 10(7) ml(-1). This work confirms that putative cyanomyoviruses are ubiquitous in both summer and winter months in this large freshwater lake system and that they are an abundant component of the virioplankton group.

Unraveling the Viral Tapestry (from Inside the Capsid Out)

The ISME Journal. Feb, 2011  |  Pubmed ID: 20555364

Novel Lineages of Prochlorococcus and Synechococcus in the Global Oceans

The ISME Journal. Feb, 2012  |  Pubmed ID: 21955990

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 previously unknown clades of Prochlorococcus and Synechococcus. Six high-light (HL)-adapted Prochlorococcus clades were identified, among which clade HLVI had not been described previously. Prochlorococcus clades HLIII, HLIV and HLV, detected in the Equatorial Pacific samples, could be related to the HNLC clades recently found in the high-nutrient, low-chlorophyll (HNLC), iron-depleted tropical oceans. At least four novel Synechococcus clades (out of six clades in total) in subcluster 5.3 were found in subtropical open oceans and the South China Sea. A niche partitioning with depth was observed in the Synechococcus subcluster 5.3. Members of Synechococcus subcluster 5.2 were dominant in the high-latitude waters (northern Bering Sea and Chukchi Sea), suggesting a possible cold-adaptation of some marine Synechococcus in this subcluster. A distinct shift of the picocyanobacterial community was observed from the Bering Sea to the Chukchi Sea, which reflected the change of water temperature. Our study demonstrates that oceanic systems contain a large pool of diverse picocyanobacteria, and further suggest that new genotypes or ecotypes of picocyanobacteria will continue to emerge, as microbial consortia are explored with advanced sequencing technology.

Viral and Bacterial Abundance and Production in the Western Pacific Ocean and the Relation to Other Oceanic Realms

FEMS Microbiology Ecology. Feb, 2012  |  Pubmed ID: 22092569

We completed a transect through the Western Pacific Warm Pool to examine how environmental variables may influence viral and bacterial abundance and production rates in this globally important oceanic region. Of the variables analyzed, viral abundance and production had the most significant relationship to bacterial cell abundance: viral parameters were not significantly correlated to the measured environmental variables, including temperature. Bacterial production rates were significantly correlated to temperature in open ocean waters, but not in waters close to land masses. Analyses of 16S rRNA gene by pyrosequencing indicated only minor changes in eubacterial community structure across the transect, with α-proteobacteria dominating all sampled populations. Diversity within the prokaryotic community did not correlate directly with viral abundance or activity. Comparisons to two other ocean-scale transects (> 8000 km of open ocean in total) in the Atlantic Ocean indicated that correlations between viral and bacterial abundance and production relative to environmental variables are regime dependent. In particular, correlations to temperature showed remarkable differences across the three transects. Collectively, our observations suggest that seemingly similar oceanic regions may have very different microbial community responses to environmental variables. Our observations and analyses demonstrate that ocean-scale generalizations may not apply in the case of viral ecology.

Production of Viruses During a Spring Phytoplankton Bloom in the South Pacific Ocean Near of New Zealand

FEMS Microbiology Ecology. Mar, 2012  |  Pubmed ID: 22092871

Lagrangian studies of virus activity in pelagic environments over extended temporal scales are rare. To address this, viruses and bacteria were examined during the course of a natural phytoplankton bloom in the pelagic South Pacific Ocean east of New Zealand. Daily samples were collected in a mesoscale eddy from year days 263-278 (September 19th-October 4th, 2008). The productive bloom transitioned from a diatom to a pico- and nanoplankton-dominated system, resulting in chlorophyll a concentrations up to 2.43 μg L(-1) . Virus abundances fluctuated c. 10-fold (1.8 × 10(10) -1.3 × 10(11)  L(-1) ) over 16 days. The production rates of virus particles were high compared with those reported in other marine systems, ranging from 1.4 × 10(10) to 2.1 × 10(11)  L(-1)  day(-1) . Our observations suggest viruses contributed significantly to the mortality of bacteria throughout the bloom, with 19-216% of the bacterial standing stock being lysed daily. This mortality released nutrient elements (N, Fe) that likely helped sustain the bloom through the sampling period. Parametric analyses found significant correlations with both biotic (e.g. potential host abundances) and abiotic parameters (e.g. nutrient concentrations, temperature). These observations demonstrate that viruses may be critical in the extended maintenance of regeneration-driven biological production.

Plasticity of Total and Intracellular Phosphorus Quotas in Microcystis Aeruginosa Cultures and Lake Erie Algal Assemblages

Frontiers in Microbiology. 2012  |  Pubmed ID: 22279445

Blooms of the potentially toxic cyanobacterium Microcystis are common events globally, and as a result significant resources continue to be dedicated to monitoring and controlling these events. Recent studies have shown that a significant proportion of total cell-associated phosphorus (P) in marine phytoplankton can be surface adsorbed; as a result studies completed to date do not accurately report the P demands of these organisms. In this study we measure the total cell-associated and intracellular P as well as growth rates of two toxic strains of Microcystis aeruginosa Kütz grown under a range of P concentrations. The results show that the intracellular P pool in Microcystis represents a percentage of total cell-associated P (50-90%) similar to what has been reported for actively growing algae in marine systems. Intracellular P concentrations (39-147 fg cell(-1)) generally increased with increasing P concentrations in the growth medium, but growth rate and the ratio of total cell-associated to intracellular P remained generally stable. Intracellular P quotas and growth rates in cells grown under the different P treatments illustrate the ability of this organism to successfully respond to changes in ambient P loads, and thus have implications for ecosystem scale productivity models employing P concentrations to predict algal bloom events.

Inhibition of Copper Uptake in Yeast Reveals the Copper Transporter Ctr1p As a Potential Molecular Target of Saxitoxin

Environmental Science & Technology. Feb, 2012  |  Pubmed ID: 22304436

Saxitoxin is a secondary metabolite produced by several species of dinoflagellates and cyanobacteria which targets voltage-gated sodium and potassium channels in higher vertebrates. However, its molecular target in planktonic aquatic community members that co-occur with the toxin producers remains unknown. Previous microarray analysis with yeast identified copper and iron-homeostasis genes as being differentially regulated in response to saxitoxin. This study sought to identify the molecular target in microbial cells by comparing the transcriptional profiles of key copper and iron homeostasis genes (CTR1, FRE1, FET3, CUP1, CRS5) in cells exposed to saxitoxin, excess copper, excess iron, an extracellular Cu(I) chelator, or an intracellular Cu(I) chelator. Protein expression and localization of Ctr1p (copper transporter), Fet3p (multicopper oxidase involved in high-affinity iron uptake), and Aft1p (iron regulator) were also compared among treatments. Combined transcript and protein profiles suggested saxitoxin inhibited copper uptake. This hypothesis was confirmed by intracellular Cu(I) imaging with a selective fluorescent probe for labile copper. Based on the combined molecular and physiological results, a model is presented in which the copper transporter Ctr1p serves as a molecular target of saxitoxin and these observations couched in the context of the eco-evolutionary role this toxin may serve for species that produce it.