Ian Hewson

Cornell University, Ithaca, New York, United States

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Publications (62)283 Total impact

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    ABSTRACT: Intense annual spring phytoplankton blooms and thermohaline stratification lead to anoxia in Chesapeake Bay bottom waters. Once oxygen becomes depleted in the system, microbial communities use energetically favorable alternative electron acceptors for respiration. The extent to which changes in respiration are reflected in community gene expression have only recently been investigated. Metatranscriptomes prepared from near-bottom water plankton over a four month time series in central Chesapeake Bay demonstrated changes consistent with terminal electron acceptor availability. The frequency of respiration-related genes in metatranscriptomes was examined by BLASTx against curated databases of genes intimately and exclusively involved in specific electron acceptor utilization pathways. The relative expression of genes involved in denitrification and dissimilatory nitrate reduction to ammonium were coincident with changes in nitrate, nitrite and ammonium concentrations. Dissimilatory iron and manganese reduction transcript ratios increase during anoxic conditions and corresponded with the highest soluble reactive phosphate and manganese concentrations. The sulfide concentration peaked in late July and early August and also matched dissimilatory sulfate reduction transcript ratios. We show that rather than abrupt transitions between terminal electron acceptors, there seems to be substantial overlap in time and space of these various anaerobic respiratory processes in Chesapeake Bay. This article is protected by copyright. All rights reserved.
    Environmental Microbiology 12/2014; · 6.24 Impact Factor
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    ABSTRACT: Populations of at least 20 asteroid species on the Northeast Pacific Coast have recently experienced an extensive outbreak of sea-star (asteroid) wasting disease (SSWD). The disease leads to behavioral changes, lesions, loss of turgor, limb autotomy, and death charac-terized by rapid degradation ("melting"). Here, we present evidence from experimental challenge studies and field observations that link the mass mortalities to a densovirus (Parvoviridae). Virus-sized ma-terial (i.e., <0.2 μm) from symptomatic tissues that was inoculated into asymptomatic asteroids consistently resulted in SSWD signs whereas animals receiving heat-killed (i.e., control) virus-sized inoc-ulum remained asymptomatic. Viral metagenomic investigations revealed the sea star-associated densovirus (SSaDV) as the most likely candidate virus associated with tissues from symptomatic asteroids. Quantification of SSaDV during transmission trials indi-cated that progression of SSWD paralleled increased SSaDV load. In field surveys, SSaDV loads were more abundant in symptomatic than in asymptomatic asteroids. SSaDV could be detected in plank-ton, sediments and in nonasteroid echinoderms, providing a possible mechanism for viral spread. SSaDV was detected in museum speci-mens of asteroids from 1942, suggesting that it has been present on the North American Pacific Coast for at least 72 y. SSaDV is therefore the most promising candidate disease agent responsible for asteroid mass mortality. virus | Asteroidea | disease | densovirus | wasting
    Proceedings of the National Academy of Sciences 11/2014; · 9.81 Impact Factor
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    ABSTRACT: Background/Question/Methods Skin microbial communities provide protection against pathogens, and regulate physiological processes and immune responses. We hypothesized that ontogenetic and seasonal shifts can alter the balance between “protective” and “harmful” bacteria (also known as dysbiosis), leading to increased rates of infection to pathogens. To test our hypothesis, we examined the transition of skin microbial communities between periods of immunesupression, either caused by development or environmental stress, in declining amphibians affected by the pathogenic fungus Batrachochytrium dendrobatidis. We used automated ribosomal intergenic spacer analyses (ARISA) and Illumina MiSeq sequencing to quantify microbial diversity and composition in Eleutherodactylus coqui and Lithobates yavapaiensis, two anurans with well-characterized infection dynamics but different life histories. Results/Conclusions Using ARISA, we found similar responses in both species where immune-suppressed hosts (juveniles and winter-collected frogs) exhibited increased operational taxonomic unit (OTU) richness, diversity, and evenness. In addition, skin microbial community structure overlapped very little between ages in E. coqui and seasons in L. yavapaiensis, suggesting drastic shifts driven by the addition or loss of specific OTUs or by changes in their relative abundances. Juvenile E. coqui frogs lost eight unique OTUs not present in adults, whereas adult L. yavapaiensis gained 13 unique OTUs from summer to winter. By amplifying the V4 region of 16S ribosomal RNA, we found significant differences in core microbiota for E. coqui. Acinetobacter johnsonii formed part of the core microbiome of juveniles, whereas Pseudomonadaceae dominated in adults. Unfortunately, due to insufficient template material, we were only able to sequence four winter-collected L. yavapaiensis, precluding phylotype analyses between seasons. Our findings indicate that immune suppression during susceptible states is accompanied by the addition of new microbial taxa which causes skin dysbioses in amphibians. Identifying whether these microbial community changes promote health or disease requires further functional investigation, particularly if future conservation strategies are to include the use of probiotics in successful disease mitigation.
    99th ESA Annual Convention 2014; 08/2014
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    ABSTRACT: Cyanobacteria are biogeochemically significant constituents of coral reef ecosystems, however, little is known about biotic and abiotic factors influencing the abundance and composition of cyanobacterial communities in fringing coral reef waters. To understand patterns of cyanobacterial biogeography in relation to coastal environmental factors, we examined the diversity of planktonic and benthic cyanobacteria at 12 sites along the west coast of Hawaii's Big Island. We found distinct cyanobacterial communities in sediments compared to the water column. In both sediments and water, community structure was strongly related to overall biomass (chlorophyll a concentration), though both these communities corresponded to different sets of biotic/abiotic variables. To examine the influence of freshwater input on planktonic cyanobacterial communities, we conducted a mesocosm experiment where seawater was amended with freshwater from two sources representing high- and low-human population influence. Planktonic cyanobacterial abundance decreased over time in mesocosms, though chlorophyll a concentration significantly increased with time, indicating cyanobacteria were likely outcompeted by other phytoplankton in incubations. Our results show that cyanobacterial community structure may be affected by runoff from terrestrial habitats, but that the composition of cyanobacterial communities inhabiting these locations are also structured by factors not measured in this study.This article is protected by copyright. All rights reserved.
    FEMS Microbiology Ecology 04/2014; · 3.56 Impact Factor
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    ABSTRACT: A sea star wasting disase epizootic was first noted in June 2013 and continues to present (February 2014) and involves 12 species of sea stars (Asteroidea) on the Pacific Coast. This is leading to localized mass mortality events in some species and locations. The dominant species affected are Pycnopodia helianthoides, Evasterias troschelli and Pisaster ochraceus. Mortalities and signs of wasting were first reported in Pisaster ochraceus on the outer coast of Washington State, followed by mass mortality of Pycnopodia helianthoides north of Vancouver BC. By mid September, Pisaster ochraceus were affected in Central California and a mass mortality event involving 12 species of stars occurred in November in Central California. Localized mass mortality events continue in Washington State, British Columbia, Central and southern California waters. Diversity of viruses and bacteria in diseased and healthy sea stars are being investigated in the Hewson lab using metagenomics, community fingerprinting of bacteria and quantification of constituent genotypes. Histology and preliminary bacterial metagenomics allows us to rule out fungi, protozoans, larger parasites and ricketsial bacteria as causative. Infection experiments are underway to test different fractions.
    Ocean Sciences Meeting, Honolulu, Hawaii USA; 02/2014
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    ABSTRACT: Our goal is to strengthen the foundations of metaproteomics as a microbial community analysis tool that links the functional identity of actively expressed gene products with host phylogeny. We used shotgun metaproteomics to survey waters in six disparate aquatic habitats (Cayuga Lake, NY; Oneida Lake, NY; Gulf of Maine; Chesapeake Bay, MD; Gulf of Mexico; and the South Pacific). Peptide pools prepared from filter-gathered microbial biomass, analyzed by nano-liquid chromatography-mass spectrometry (MS/MS) generating 9,693 ± 1,073 mass spectra identified 326 ± 107 bacterial proteins per sample. Distribution of proteobacterial (Alpha and Beta) and cyanobacterial (Prochlorococcus and Synechococcus spp.) protein hosts across all six samples was consistent with the previously published biogeography for these microorganisms. Marine samples were enriched in transport proteins (TRAP-type for dicarboxylates and ATP binding cassette (ABC)-type for amino acids and carbohydrates) compared with the freshwater samples. We were able to match in situ expression of many key proteins catalyzing C-, N-, and S-cycle processes with their bacterial hosts across all six habitats. Pelagibacter was identified as the host of ABC-type sugar-, organic polyanion-, and glycine betaine-transport proteins; this extends previously published studies of Pelagibacter's in situ biogeochemical role in marine C- and N-metabolism. Proteins matched to Ruegeria confirmed these organism's role in marine waters oxidizing both carbon monoxide and sulfide. By documenting both processes expressed in situ and the identity of host cells, metaproteomics tested several existing hypotheses about ecophysiological processes and provided fodder for new ones.
    Microbial Ecology 01/2014; · 3.28 Impact Factor
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    ABSTRACT: To assess the effects of seasonal oxygen transition on microbial metabolism, we measured spatiotemporal changes in total dissolved inorganic carbon, respiratory products, and geochemical constituents in the mesohaline region of Chesapeake Bay from May to October 2010. Vertical redox zonation was examined, and a spatial transect survey was also conducted from the southern to northern limit of the mesohaline region in July providing an alternative approach for assessing the temporal dynamics of oxygen transition. The transitions from oxic to hypoxic to anoxic and back to oxic were illustrated by the pattern of nitrogen redox species. Respiration, measured from changes in total dissolved inorganic carbon (∆DIC) and dissolved oxygen (∆DO) during incubations, had an average respiratory quotient (∆DIC/∆DO) of 1.04 ± 0.06 under oxic conditions and 1.58 ± 0.48 under hypoxic conditions. The difference in the respiratory quotients suggested that oxygen-based respiration measurements would underestimate community respiration rates in hypoxic conditions. In the present study, we observed within the surface-mixed layer three- to sevenfold differences in temporal and vertical variation of community respiration, while net respiration across oxyclines and anaerobic respiration in deep waters had lower rates and variability. In some anoxic samples, there was a net decrease in dissolved inorganic carbon that was exacerbated with experimental augmentation of terminal electron acceptors. Potential carbon fixation rates of chemoautotrophs within and below oxyclines were estimated and ranged from 0.63 to 116.9 mg C m−2 day−1 depending on growth conditions. These results indicate that anaerobic metabolism during the seasonal anoxic transition and at oxic/anoxic interface can play an important role in the estuarine carbon cycle.
    Estuaries and Coasts. 01/2014;
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    ABSTRACT: Echinoderms are important constituents of marine ecosystems, where they may influence the recruitment success of benthic flora and fauna, and are important consumers of detritus and plant materials. There are currently no described viruses of echinoderms. We used a viral metagenomic approach to examine viral consortia within three urchins - Colobocentrotus atratus, Tripneustes gratilla, and Echinometra mathaei - which are common constituents of reef communities in the Hawaiian archipelago. Metagenomic libraries revealed the presence of bacteriophage and densoviruses (Parvoviridae) in tissues of all three urchins. Densoviruses are typically known to infect terrestrial and aquatic arthropods. Urchin-associated densoviruses were detected by qPCR in all tissues tested, and were also detected in filtered suspended matter (> 0.2µm) from plankton and in sediments at several locations near to where urchins were collected for metagenomic analysis. This is the first report of echinoderm-associated viruses, which extends the known host range of parvoviruses.
    Journal of General Virology 12/2013; · 3.13 Impact Factor
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    ABSTRACT: We used metatranscriptomics to study the gene transcription patterns of microbial plankton (0.2 - 64 μm) at a mesohaline station in Chesapeake Bay under transitions from oxic to anoxic waters in spring, and anoxic to oxic waters in autumn. Samples were collected from surface [i.e. above pycnocline] waters (3m) and waters beneath the pycnocline (16 - 22 m) in both 2010 and 2011. Metatranscriptome profiles based on function and potential phylogeny were different between 2010 and 2011, and strongly variable in 2011. This difference in variability corresponded with a highly variable ratio of eukaryotic to bacterial sequences (0.3 - 5.5), reflecting transient algal blooms in 2011 that were absent in 2010. The similarity between metatranscriptomes changed at a lower rate during the transition from oxic to anoxic waters than after the return to oxic conditions. Transcripts related to photosynthesis and low-affinity cytochrome oxidases were significantly higher in shallow than in deep waters, while in deep water genes involved in anaerobic metabolism, particularly sulfate reduction, succinyl to propionyl CoA conversion, and menaquinone synthesis were enriched relative to shallow waters. Expected transitions in metabolism between oxic and anoxic deep waters were reflected in elevated anaerobic respiratory reductases and utilization of propenediol and acetoin. The percentage of archaeal transcripts increased in both years in late summer (0.1 - 4.4 % of all transcripts in 2010 and from 0.1 to 6.2 % in 2011). Denitrification-related genes were expressed in a predicted pattern during the oxic-anoxic transition. Overall, our data suggest that Chesapeake Bay microbial assemblages express gene suites differently in shallow and deep waters, and that differences in deep waters reflect variable redox states.
    Applied and Environmental Microbiology 10/2013; · 3.95 Impact Factor
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    ABSTRACT: The benthic amphipod Diporeia is an ecologically and biogeochemically important constituent of deep freshwater lakes in North America. The proliferation of dreissenid mussels in the mid-1990s coincided with a sharp decrease in Diporeia populations in several Laurentian Great Lakes; however the ultimate cause and mechanisms of their decline are still unknown. Here we examined the composition of DNA viruses associated with Diporeia collected from populations of Lake Michigan that had declined and stable populations in Lake Superior and Owasco Lake (Finger Lake in central New York State). Viral metagenomic libraries from Owasco Lake and Lake Superior were comprised primarily of bacteriophages, which may infect bacteria within the amphipod microbiome. In contrast, the metagenomic library from Lake Michigan contained well-represented ssDNA circular viral genomes. The prevalence and viral load of one putative Type V ssDNA circular virus (LM29173) that recruited almost 30% of total viral sequence reads in the Lake Michigan library was analyzed by quantitative PCR. The prevalence of LM29173 was over two orders of magnitude greater in Lake Michigan compared to the other two lakes. Although further research is necessary to establish the pathology and epidemiological extent of viral-Diporeia interactions, our data suggest that viruses may be numerically significant constituents of the Diporeia microbiome, and if pathogenic some of these viruses may be a stressor of Great Lakes Diporeia populations. Our data further indicate that special attention should be given to the circovirus that was prevalent in the declining Michigan population but uncommon in the other two lakes.
    Journal of Great Lakes Research 09/2013; 39(3):499–506. · 2.31 Impact Factor
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    ABSTRACT: Trichodesmium surface aggregations shape the co-occurring microbial community by providing organic carbon and nitrogen and surfaces on which microorganisms can aggregate. Rapid collapse of Trichodesmiumaggregations leads to drastic changes in the chemical and physical properties of surrounding waters, eliciting a response from the microbial community and their associated viruses. Three viral metagenomes were constructed from experimentally lysed Trichodesmiumcollected from two locations in the eastern Gulf of Mexico. Trichodesmiumwere either treated with mitomycin C to induce potential lysogens, or incubated in the absence of mitomycin C. Comparative analyses of viral contiguous sequences indicated that viral composition was responsive to treatment type. Cyanophages were more represented within incubations treated with mitomycin C, while gammaproteobacterial phages were more represented within the untreated incubation. The detection of latent bacteriophage integrases in both the chemically treated and untreated incubations suggests that Trichodesmium death may lead to prophage induction within associated microorganisms. While no single cyanophage-like genotype associated with Trichdesmiumlysis could be identified that might point to an infectious Trichodesmiumphage, reads resembling Trichodesmium were recovered. These data reveal a diverse consortium of lytic and temperate phages associated with Trichodesmiumwhose patterns of representation within treated and untreated libraries offer insights into the activities of host and viral communities during Trichodesmium aggregation collapse. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.
    FEMS Microbiology Ecology 02/2013; · 3.56 Impact Factor
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    ABSTRACT: As dominant members of marine mesozooplankton communities, copepods play critical roles in oceanic food webs and biogeochemical cycling. Despite the ecological significance of copepods, little is known regarding the causes of copepod mortality, and up to 35% of total copepod mortality cannot be accounted for by predation alone. Viruses have been established as ecologically important infectious agents in the oceans; however, viral infection has not been investigated in mesozooplankton communities. Here we used molecular and microscopic techniques to document viral infection in natural populations of the calanoid copepods Acartia tonsa (Dana) and Labidocera aestiva (Wheeler) in Tampa Bay, FL. Viral metagenomics revealed previously undocumented viruses in each species, named Acartia tonsa copepod circo-like virus (AtCopCV) and Labidocera aestiva copepod circo-like virus (LaCopCV). LaCopCV was found to be extremely prevalent and abundant in L. aestiva populations, with up to 100% prevalence in some samples and average viral loads of 1.13 × 10(5) copies per individual. LaCopCV transcription was also detected in the majority of L. aestiva individuals, indicating viral activity. AtCopCV was sporadically detected in A. tonsa populations year-round, suggesting temporal variability in viral infection dynamics. Finally, virus-like particles of unknown identity were observed in the connective tissues of A. tonsa and L. aestiva by transmission electron microscopy, demonstrating that viruses were actively proliferating in copepod connective tissue as opposed to infecting gut contents, parasites, or symbionts. Taken together, these results provide strong independent lines of evidence for active viral infection in dominant copepod species, indicating that viruses may significantly influence mesozooplankton ecology.
    Proceedings of the National Academy of Sciences 01/2013; · 9.81 Impact Factor
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    ABSTRACT: Aquatic viruses play important roles in the biogeochemistry and ecology of lacustrine ecosystems; however, their composition, dynamics, and interactions with viruses of terrestrial origin are less extensively studied. We used a viral shotgun metagenomic approach to elucidate candidate autochthonous (i.e., produced within the lake) and allochthonous (i.e., washed in from other habitats) viral genotypes for a comparative study of their dynamics in lake waters. Based on shotgun metagenomes prepared from catchment soil and freshwater samples from two contrasting lakes (Cayuga Lake and Fayetteville Green Lake), we selected two putatively autochthonous viral genotypes (phycodnaviruses likely infecting algae and cyanomyoviruses likely infecting picocyanobacteria) and two putatively allochthonous viral genotypes (geminiviruses likely infecting terrestrial plants and circoviruses infecting unknown hosts but common in soil libraries) for analysis by genotype-specific quantitative PCR (TaqMan) applied to DNAs from viruses in the viral size fraction of lake plankton, i.e., 0.2 μm > virus > 0.02 μm. The abundance of autochthonous genotypes largely reflected expected host abundance, while the abundance of allochthonous genotypes corresponded with rainfall and storm events in the respective catchments, suggesting that viruses with these genotypes may have been transported to the lake in runoff. The decay rates of allochthonous and autochthonous genotypes, assessed in incubations where all potential hosts were killed, were generally lower (0.13 to 1.50% h(-1)) than those reported for marine virioplankton but similar to those for freshwater virioplankton. Both allochthonous and autochthonous viral genotypes were detected at higher concentrations in subsurface sediments than at the water-sediment interface. Our data indicate that putatively allochthonous viruses are present in lake plankton and sediments, where their temporal dynamics reflect active transport to the lake during hydrological events and then decay once there.
    Applied and Environmental Microbiology 07/2012; 78(18):6583-91. · 3.95 Impact Factor
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    ABSTRACT: We investigated the abundance and assemblage variability of bacteria in 10 spatially distinct freshwater pools on Appledore Island, Gulf of Maine. Assemblages were strongly heterogeneous between pools separated by even short distances. To gain insight into factors that may lead to the establishment of novel assemblages, we conducted an ecosystem-open choromophoric dissolved organic matter (CDOM) enrichment experiment within mesocosms inoculated with a standardized microbial community and observed patterns of their composition over time. Assemblages were strongly divergent from each other in composition after only 3 days of incubation. Divergence among mesocosms was significantly higher with increasing levels of CDOM. CDOM addition initially had a strong positive impact on bacterial operation taxonomic unit (OTU) richness and negative impact on bacterial OTU evenness, but no impact on total bacterial abundance, suggesting that factors controlling abundance are decoupled from those influencing overall composition.
    FEMS Microbiology Ecology 01/2012; 80(2):501-8. · 3.56 Impact Factor
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    ABSTRACT: The diversity and function of viruses in coral holobionts has only recently received attention. The non-reef building gorgonian octocoral, Gorgonia ventalina, is a major constituent of Caribbean reefs. We investigated viral communities associated with G. ventalina tissues to understand their role in gorgonian ecology. Pyrosequencing was used to prepare a total of 514,632 sequence reads of DNA- and RNA-based mixed-community viral genomes (metaviromes). RNA viral assemblages were comprised of primarily unidentifiable reads, with most matching host transcripts and other RNA metaviromes. DNA metaviromes were similar between healthy and diseased tissues and comprised of contiguous sequences (contigs) that matched primarily metazoan and bacterial proteins. Only ~5% of contigs matched viral proteins that were primarily cyanophage and viruses of Chlorella and Ostreococcus. Our results confirm that DNA and RNA viruses comprise a component of the gorgonian holobiont, suggesting that they may play a role in the ecology of G. ventalina.
    Coral Reefs 01/2012; 31(2):487-491. · 3.66 Impact Factor
  • Mary Beth Wilhelm, Ian Hewson
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    ABSTRACT: The Fayetteville Green Lake is a small (0.258 km) meromictic marl lake that is host to a thrombolitic bioherm inhabited by coccoid and filamentous cyanobacteria. To date there has been only limited study of bioherm cyanobacterial community ecology, and none focusing on their molecular diversity. Samples of the bioherm were collected along vertical and spatial transects on a portion of the thrombolite in early fall 2010. Cyanobacterial assemblage spatial variability and operational taxonomic unit composition was analyzed by automated rRNA intergenic spacer analysis (ARISA). A total of 123 cyanobacterial ARISA operational taxonomic units were observed across all fingerprints. Cyanobacterial assemblages were variable across depth and spatial gradients, and may be structured by gradients in light availability and habitat stability. Cyanobacterial community fingerprints were more taxonomic unit rich, diverse, and had greater fingerprint similarity in deeper samples than those at the surface. Several operational taxonomic units were common to all samples taken, while the majority of assemblage components were heterogeneous between transects and depths. Hence, our results suggest that cyanobacterial communities on the thrombolite in Green Lake represent a mixture of taxa that are selected for by prevailing physicochemical conditions, while other taxa are selected for on spatial scales of meters and may represent more specialized cyanobacteria on the thrombolite. Moreover, our data suggest that the depth-dependent structure of bioherm cyanobacterial assemblages may be a consequence of habitat conditions, which may include light intensity and quality, temperature variation and habitat stability.
    Geomicrobiology Journal - GEOMICROBIOL J. 01/2012;
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    ABSTRACT: 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 stations, numbers were enhanced by organic carbon added as simple sugars, a combination of iron and an organic chelator, or iron added with phosphate. At stations nearest the equator, the nutrient-limiting growth was not apparent. Maximum net growth rates for UCYN-A, C. watsonii and γ-24774A11 were 0.19, 0.61 and 0.52 d(-1), respectively, which are the first known empirical growth rates reported for the uncultivated UCYN-A and the γ-24774A11. The addition of N enhanced total phytoplankton biomass up to 5-fold, and the non-N(2)-fixing Synechococcus was among the groups that responded favorably to N addition. Nitrogen was the major nutrient-limiting phytoplankton biomass in the Western South Pacific Ocean, while availability of organic carbon or iron and organic chelator appear to limit abundances of unicellular diazotrophs. Lack of phytoplankton response to nutrient additions in the Pacific warm pool waters suggests diazotroph growth in this area is controlled by different factors than in the higher latitudes, which may partially explain previously observed variability in community composition in the region.
    The ISME Journal 11/2011; 6(4):733-44. · 8.95 Impact Factor
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    ABSTRACT: In the course of analyzing 9,522,746 pyrosequencing reads from 23 stations in the Southwestern Pacific and equatorial Atlantic oceans, it came to our attention that misannotations of rRNA as proteins is now so widespread that false positive matching of rRNA pyrosequencing reads to the National Center for Biotechnology Information (NCBI) non-redundant protein database approaches 90%. One conserved portion of 23S rRNA was consistently misannotated often enough to prompt curators at Pfam to create a spurious protein family. Detailed examination of the annotation history of each seed sequence in the spurious Pfam protein family (PF10695, 'Cw-hydrolase') uncovered issues in the standard operating procedures and quality assurance programs of major sequencing centers, and other issues relating to the curation practices of those managing public databases such as GenBank and SwissProt. We offer recommendations for all these issues, and recommend as well that workers in the field of metatranscriptomics take extra care to avoid including false positive matches in their datasets.
    Nucleic Acids Research 07/2011; 39(20):8792-802. · 8.81 Impact Factor
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    ABSTRACT: Viruses in aquatic ecosystems comprise those produced by both autochthonous and allochthonous host taxa. However, there is little information on the diversity and abundance of viruses of allochthonous origin, particularly from non-anthropogenic sources, in freshwater and marine ecosystems. We investigated the presence of nucleopolyhedroviruses (NPV) (Baculovirus), which commonly infect terrestrial lepidopteran taxa, across the landscape of Appledore Island, Gulf of Maine. PCR and qPCR primers were developed around a 294-bp fragment of the polyhedrin (polH) gene, which is the major constituent protein of NPV multivirion polyhedral occlusion bodies. polH was successfully amplified from several aquatic habitats, and recovered polH sequences were most similar to known lepidopteran NPV. Using quantitative PCR designed around a cluster of detected sequences, we detected polH in Appledore Island soils, supratidal freshwater ponds, nearshore sediments, near- and offshore plankton, and in floatsam. This diverse set of locations suggests that NPVs are widely dispersed along the terrestrial--marine continuum and that free polyhedra may be washed into ponds and eventually to sea. The putative hosts of detected NPVs were webworms (Hyphantria sp.) which form dense nests in late summer on the dominant Appledore Island vegetation (Prunus virginiana). Our data indicate that viruses of terrestrial origin (i.e., allochthonous viruses) may be dispersed widely in coastal marine habitats. The dispersal of NPV polH and detection within offshore net plankton (>64 μm) demonstrates that terrestrial viruses may interact with larger particles and plankton of coastal marine ecosystem, which further suggests that viral genomic information may be transported between biomes.
    Microbial Ecology 04/2011; 62(1):48-57. · 3.28 Impact Factor
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    ABSTRACT: Microbes have central roles in ocean food webs and global biogeochemical processes, yet specific ecological relationships among these taxa are largely unknown. This is in part due to the dilute, microscopic nature of the planktonic microbial community, which prevents direct observation of their interactions. Here, we use a holistic (that is, microbial system-wide) approach to investigate time-dependent variations among taxa from all three domains of life in a marine microbial community. We investigated the community composition of bacteria, archaea and protists through cultivation-independent methods, along with total bacterial and viral abundance, and physico-chemical observations. Samples and observations were collected monthly over 3 years at a well-described ocean time-series site of southern California. To find associations among these organisms, we calculated time-dependent rank correlations (that is, local similarity correlations) among relative abundances of bacteria, archaea, protists, total abundance of bacteria and viruses and physico-chemical parameters. We used a network generated from these statistical correlations to visualize and identify time-dependent associations among ecologically important taxa, for example, the SAR11 cluster, stramenopiles, alveolates, cyanobacteria and ammonia-oxidizing archaea. Negative correlations, perhaps suggesting competition or predation, were also common. The analysis revealed a progression of microbial communities through time, and also a group of unknown eukaryotes that were highly correlated with dinoflagellates, indicating possible symbioses or parasitism. Possible ‘keystone’ species were evident. The network has statistical features similar to previously described ecological networks, and in network parlance has non-random, small world properties (that is, highly interconnected nodes). This approach provides new insights into the natural history of microbes.Keywords: co-occurrence patterns; stramenopiles; dinoflagellates; SAR11; cyanobacteria; time series
    The ISME Journal 03/2011; 5(9):1414-1425. · 8.95 Impact Factor

Publication Stats

2k Citations
283.00 Total Impact Points

Institutions

  • 2010–2014
    • Cornell University
      • • Department of Microbiology
      • • Department of Ecology and Evolutionary Biology
      • • Department of Microbiology and Immunology
      Ithaca, New York, United States
  • 2006–2011
    • University of California, Santa Cruz
      • Department of Ocean Sciences
      Santa Cruz, CA, United States
  • 2003–2011
    • University of Southern California
      • • Wrigley Institute for Environmental Studies
      • • Division of Marine and Environmental Biology
      • • Department of Biological Sciences
      Los Angeles, CA, United States