Luo
Elaine
Luo
Elaine
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ArticleDiversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean(Springer Nature, 2022-03-02) Luo, Elaine ; Leu, Andy O. ; Eppley, John ; Karl, David M. ; DeLong, Edward F.Sinking particles and particle-associated microbes influence global biogeochemistry through particulate matter export from the surface to the deep ocean. Despite ongoing studies of particle-associated microbes, viruses in these habitats remain largely unexplored. Whether, where, and which viruses might contribute to particle production and export remain open to investigation. In this study, we analyzed 857 virus population genomes associated with sinking particles collected over three years in sediment traps moored at 4000 m in the North Pacific Subtropical Gyre. Particle-associated viruses here were linked to cellular hosts through matches to bacterial and archaeal metagenome-assembled genome (MAG)-encoded prophages or CRISPR spacers, identifying novel viruses infecting presumptive deep-sea bacteria such as Colwellia, Moritella, and Shewanella. We also identified lytic viruses whose abundances correlated with particulate carbon flux and/or were exported from the photic to abyssal ocean, including cyanophages. Our data are consistent with some of the predicted outcomes of the viral shuttle hypothesis, and further suggest that viral lysis of both autotrophic and heterotrophic prokaryotes may play a role in carbon export. Our analyses revealed the diversity and origins of prevalent viruses found on deep-sea sinking particles and identified prospective viral groups for future investigation into processes that govern particle export in the open ocean.
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ArticleA primer for microbiome time-series analysis(Frontiers Media, 2020-04-21) Coenen, Ashley R. ; Hu, Sarah K. ; Luo, Elaine ; Muratore, Daniel ; Weitz, Joshua S.Time-series can provide critical insights into the structure and function of microbial communities. The analysis of temporal data warrants statistical considerations, distinct from comparative microbiome studies, to address ecological questions. This primer identifies unique challenges and approaches for analyzing microbiome time-series. In doing so, we focus on (1) identifying compositionally similar samples, (2) inferring putative interactions among populations, and (3) detecting periodic signals. We connect theory, code and data via a series of hands-on modules with a motivating biological question centered on marine microbial ecology. The topics of the modules include characterizing shifts in community structure and activity, identifying expression levels with a diel periodic signal, and identifying putative interactions within a complex community. Modules are presented as self-contained, open-access, interactive tutorials in R and Matlab. Throughout, we highlight statistical considerations for dealing with autocorrelated and compositional data, with an eye to improving the robustness of inferences from microbiome time-series. In doing so, we hope that this primer helps to broaden the use of time-series analytic methods within the microbial ecology research community.
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ArticleMicrobial sources of exocellular DNA in the ocean(American Society for Microbiology, 2022-03-21) Linney, Morgan D. ; Eppley, John ; Romano, Anna ; Luo, Elaine ; DeLong, Edward F. ; Karl, David M.Exocellular DNA is operationally defined as the fraction of the total DNA pool that passes through a membrane filter (0.1 μm). It is composed of DNA-containing vesicles, viruses, and free DNA and is ubiquitous in all aquatic systems, although the sources, sinks, and ecological consequences are largely unknown. Using a method that provides separation of these three fractions, we compared open ocean depth profiles of DNA associated with each fraction. Pelagibacter-like DNA dominated the vesicle fractions for all samples examined over a depth range of 75 to 500 m. Viral DNA consisted predominantly of myovirus-like and podovirus-like DNA and contained the highest proportion of unannotated sequences. Euphotic zone free DNA (75 to 125 m) contained primarily bacterial and viral sequences, with bacteria dominating samples from the mesopelagic zone (500 to 1,000 m). A high proportion of mesopelagic zone free DNA sequences appeared to originate from surface waters, including a large amount of DNA contributed by high-light Prochlorococcus ecotypes. Throughout the water column, but especially in the mesopelagic zone, the composition of free DNA sequences was not always reflective of cooccurring microbial communities that inhabit the same sampling depth. These results reveal the composition of free DNA in different regions of the water column (euphotic and mesopelagic zones), with implications for dissolved organic matter cycling and export (by way of sinking particles and/or migratory zooplankton) as a delivery mechanism.
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ArticleMarine viral particles reveal an expansive repertoire of phage-parasitizing mobile elements(National Academy of Sciences, 2022-10-18) Eppley, John M. ; Biller, Steven J. ; Luo, Elaine ; Burger, Andrew ; DeLong, Edward F.Phage satellites are mobile genetic elements that propagate by parasitizing bacteriophage replication. We report here the discovery of abundant and diverse phage satellites that were packaged as concatemeric repeats within naturally occurring bacteriophage particles in seawater. These same phage-parasitizing mobile elements were found integrated in the genomes of dominant co-occurring bacterioplankton species. Like known phage satellites, many marine phage satellites encoded genes for integration, DNA replication, phage interference, and capsid assembly. Many also contained distinctive gene suites indicative of unique virus hijacking, phage immunity, and mobilization mechanisms. Marine phage satellite sequences were widespread in local and global oceanic virioplankton populations, reflecting their ubiquity, abundance, and temporal persistence in marine planktonic communities worldwide. Their gene content and putative life cycles suggest they may impact host-cell phage immunity and defense, lateral gene transfer, bacteriophage-induced cell mortality and cellular host and virus productivity. Given that marine phage satellites cannot be distinguished from bona fide viral particles via commonly used microscopic techniques, their predicted numbers (∼3.2 × 10 26 in the ocean) may influence current estimates of virus densities, production, and virus-induced mortality. In total, the data suggest that marine phage satellites have potential to significantly impact the ecology and evolution of bacteria and their viruses throughout the oceans. We predict that any habitat that harbors bacteriophage will also harbor similar phage satellites, making them a ubiquitous feature of most microbiomes on Earth.
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PreprintLight stimulates swimming behavior of larval eastern oysters Crassostrea virginica in turbulent flow( 2017-05) Wheeler, Jeanette D. ; Luo, Elaine ; Helfrich, Karl R. ; Anderson, Erik J. ; Starczak, Victoria R. ; Mullineaux, Lauren S.Planktonic larvae of the eastern oyster Crassostrea virginica are able to regulate their vertical position in the water, but the environmental cues responsible for this regulation, particularly in turbulent settings, remain unclear. We quantified swimming responses of late-stage oyster larvae in a grid-stirred turbulence tank to determine how light affects the swimming behavior of larvae over a range of hydrodynamic conditions similar to their natural coastal environments. We used particle image velocimetry and larval tracking to isolate larval swimming from local flow and to quantify 3 behavioral metrics: vertical swimming direction, proportion of larvae diving, and proportion of larvae swimming helically. We compared these metrics across turbulence levels ranging from still water (ε = 0 cm2 s-3) to estuarine-like conditions (ε = 0.4 cm2 s-3) in light and dark. At all turbulence levels, light had no effect on the proportion of upward swimming larvae, but elicited detectable increases in the proportion of helical swimming and diving behaviors. We further examined the effect of light and turbulence on specific characteristics of helical trajectories, and found that these environmental cues induce changes to both vertical and horizontal velocities of helically swimming larvae, changing the helix geometry. The increased prevalence of these behaviors in light likely plays an ecological role: increased diving in light (in conjunction with turbulence) is a potential mechanism to enhance settlement success, while changes to helical swimming in light may serve an anti-predatory function. Together, these behaviors provide insight into potentially complex larval responses to multiple simultaneous environmental cues.