Adaptations to photoautotrophy associated with seasonal ice cover in a large lake revealed by metatranscriptome analysis of a winter diatom bloom

Edgar, Robyn; Morris, Paul F.; Rozmarynowycz, Mark J.; D’Souza, Nigel; Moniruzzaman, Mohammad; Bourbonniere, Richard A.; Bullerjahn, George S.; Phuntumart, Vipaporn; Wilhelm, Steven W.; McKay, R. Michael L.

doi:10.1016/j.jglr.2016.07.025

Cited by 19 publications

(30 citation statements)

References 68 publications

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“…Seasonal successions of this nature have been well-recorded in Lake Erie, another shallow lake plagued by summer Microcystis blooms (Saxton et al, 2012). Other virus-driven community controls have been hypothesized to occur in Lake Erie, with viral infection of parasitic fungal hosts hypothesized to contribute to the maintenance of winter diatom blooms (Edgar et al, 2016). In both scenarios, viral suppression of a predator or competitor enables a particular species or group to thrive.…”

Section: Resultsmentioning

confidence: 99%

“…Freshwater HABs commonly manifest as a summer bloom of cyanobacteria that follows from a winter/spring population of eukaryotic phytoplankton (Ke et al, 2008;Niu et al, 2011;Edgar et al, 2016). HAB research has historically focused on abiotic "bottom-up" controls, such as nutrient or temperature triggers that stimulate cyanobacterial growth (Tang et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

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The “Neglected Viruses” of Taihu: Abundant Transcripts for Viruses Infecting Eukaryotes and Their Potential Role in Phytoplankton Succession

et al. 2020

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The “Neglected Viruses” of Taihu: Abundant Transcripts for Viruses Infecting Eukaryotes and Their Potential Role in Phytoplankton Succession

et al. 2020

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“…Several other clusters, 310 e.g., A(iii) and B(vii) also contained fungal contigs. While such observations are not definitive, 311 they point to the existence of parasitic relationships resulting in complicated ecological 312 interactions involving unicellular eukaryotes, fungi and fungal viruses in marine ecosystems 313 (Edgar et al, 2016). 314…”

Section: Mcp Gene 283mentioning

confidence: 99%

Virus-Host Infection Dynamics of Marine Single-Celled Eukaryotes Resolved from Metatranscriptomics

Moniruzzaman¹,

Wurch

Alexander

et al. 2016

Preprint

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microbiology 21 22 23 24 25 26 2 | M o n i r u z z a m a n e t a l .Abstract 27Metatranscriptomics has emerged as a tool in microbial ecology that can resolve the functional 28 landscape of both prokaryotes and eukaryotes within a community. In this study, we extend the 29 potential of metatranscriptomics to probe active virus infections and virus-host relationships in 30 marine systems. Polyadenylation-selected RNA-seq data were examined from microbial 31 communities in two productive marine environments: a brown tide bloom event dominated by 32Aureococcus anophagefferens in Quantuck Bay, NY, and a diatom-dominated plankton 33 community in Narragansett Bay, RI. Active infections by diverse giant viruses (NCLDVs) of 34 algal and non-algal hosts were found at both sites. Ongoing infections of A. anophagefferens by 35 a known Mimiviridae (AaV) were observed during both the peak and decline of the bloom. 36Bloom decline was also accompanied by increased activity for viruses other than AaV, including 37 (+) ssRNA viruses. In Narragansett Bay, increased temporal reso′lution revealed active NCLDVs 38 with both 'boom-and-bust' as well as 'steady-state infection'-like ecologies. Statistical co-39 occurrence examinations of the dsDNA, ssRNA and dsRNA markers within the data revealed a 40 broad spectrum of statistically strong and significant virus-host relationships that included both 41 known as well as novel interactions. Our approach offers a method for screening the diversity 42 and dynamics of active viral infections in natural systems and develops links between viruses 43 and their potential hosts in situ. 44 45 3 | M o n i r u z z a m a n e t a l . Significance 46Viruses are important partners in ecosystem scale ecology, yet their study to date is primarily 47 limited to single virus-host infection models in the laboratory or limited to "potential-actions" 48 derived from metagenomics analyses. Using metatranscriptomic sequences from polyadenylated-49 RNA selected samples, we have simultaneously captured information regarding eukaryotic 50 diversity and active infection by viruses with dsDNA genomes, resulting in a statistical 51 opportunity to predict "who is infecting whom". This approach further provides concurrent 52 insight regarding viruses with ssRNA and dsRNA genomes, capturing dynamics for the 53 communities of viruses infecting single-celled eukaryotes. Given the central role of these 54 plankton in global scale processes, our efforts result in a transformational step-forward regarding 55 the study of in situ virus-host interactions. 56 57

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“…On the other hand, there are column‐based extraction and purification kits that utilize various buffer reagents and have been shown to work on e.g., C. vulgaris (Jusoh et al ), Dunaliella tertiolecta (Rismani‐Yazdi et al ), Chaetoceros neogracile (Hwang et al ), and Emiliania huxleyi (Bochenek et al ). In case RNA is extracted from a pooled community sample or used for environmental metatranscriptomics different methods are often applied or combined (Kodama et al ; Edgar et al ; Moniruzzaman et al ).…”

mentioning

confidence: 99%

“…Photosynthetic microorganisms form the base of many food webs, are estimated to provide half of the net primary production on earth (Field et al 1998;Behrenfeld et al 2001) and are an important target in functional ecological research, e.g., freshwater biomonitoring (Wu et al 2017) or investigation of adaption strategies of photoautops in ice-covered lakes (Edgar et al 2016). Economically, areas of application where microalgae seem to be most advantageous are biodiesel production (Chisti 2007;Mata et al 2010), isolation of high valuable compounds (e.g., astaxanthin [Lorenz and Cysewski 2000]), and wastewater treatment (Wang et al 2008).…”

mentioning

confidence: 99%

RNA isolation from taxonomically diverse photosynthetic protists

Mundt

Heinrich²,

Hanelt

2018

Limnology & Ocean Methods

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High quality RNA is a crucial requirement in a variety of analyses including next generation sequencing, microarray, and gene expression studies. A number of protocols for the extraction of ribonucleic acids from algae are currently in use, but different reagents interfere with buffer capacities and therefore lower the success of the isolations. The diversity of microalgae is reflected in a large variety of biomolecules and so far no standard protocol for the extraction of RNA from these highly divergent groups has been assessed. With this study, 11 conventional protocols are compared and an alternative standardized protocol for the isolation of high quality total RNA is proposed. Furthermore, the extraction method is applied on four different microalgae species of the Chlorophyta, Charophyta, Rhodophyta, and a dinoflagellate. We present an optimized RNA extraction method, yielding total RNA of high purity and integrity from all the investigated protists. The protocol provided in this study is cost‐effective and can assist in future functional genomics, covering an essential step when working with RNA from non‐model microorganisms.

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Adaptations to photoautotrophy associated with seasonal ice cover in a large lake revealed by metatranscriptome analysis of a winter diatom bloom

Cited by 19 publications

References 68 publications

The “Neglected Viruses” of Taihu: Abundant Transcripts for Viruses Infecting Eukaryotes and Their Potential Role in Phytoplankton Succession

The “Neglected Viruses” of Taihu: Abundant Transcripts for Viruses Infecting Eukaryotes and Their Potential Role in Phytoplankton Succession

Virus-Host Infection Dynamics of Marine Single-Celled Eukaryotes Resolved from Metatranscriptomics

RNA isolation from taxonomically diverse photosynthetic protists

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