Unprecedented evidence for high viral abundance and lytic activity in coral reef waters of the South Pacific Ocean

Despite nutrient-depleted conditions, coral reef waters harbor abundant and diverse microbes; as major agents of microbial mortality, viruses are likely to influence microbial processes in these ecosystems. However, little is known about marine viruses in these rapidly changing ecosystems. Here we examined spatial and short-term temporal variability in marine viral abundance (VA) and viral lytic activity across various reef habitats surrounding Moorea Island (French Polynesia) in the South Pacific. Water samples were collected along four regional cross-reef transects and during a time-series in Opunohu Bay. Results revealed high VA (range: 5.6 x 10(6)-3.6 x 10(7) viruses ml(-1)) and lytic viral production (range: 1.5 x 10(9)-9.2 x 10(10) viruses l(-1) d(-1)). Flow cytometry revealed that viral assemblages were composed of three subsets that each displayed distinct spatiotemporal relationships with nutrient concentrations and autotrophic and heterotrophic microbial abundances. The results highlight dynamic shifts in viral community structure and imply that each of these three subsets is ecologically important and likely to infect distinct microbial hosts in reef waters. Based on viral-reduction approach, we estimate that lytic viruses were responsible for the removal of ca. 24-367% of bacterial standing stock d(-1) and the release of ca. 1.0- 62 mu g of organic carbon l(-1) d(-1) in reef waters. Overall, this work demonstrates the highly dynamic distribution of viruses and their critical roles in controlling microbial mortality and nutrient cycling in coral reef water ecosystems

Modeling the Winter–to–Summer Transition of Prokaryotic and Viral Abundance in the Arctic Ocean

One of the challenges in oceanography is to understand the influence of environmental factors on the abundances of prokaryotes and viruses. Generally, conventional statistical methods resolve trends well, but more complex relationships are difficult to explore. In such cases, Artificial Neural Networks (ANNs) offer an alternative way for data analysis. Here, we developed ANN-based models of prokaryotic and viral abundances in the Arctic Ocean. The models were used to identify the best predictors for prokaryotic and viral abundances including cytometrically-distinguishable populations of prokaryotes (high and low nucleic acid cells) and viruses (high- and low-fluorescent viruses) among salinity, temperature, depth, day length, and the concentration of Chlorophyll-a. The best performing ANNs to model the abundances of high and low nucleic acid cells used temperature and Chl-a as input parameters, while the abundances of high- and low-fluorescent viruses used depth, Chl-a, and day length as input parameters. Decreasing viral abundance with increasing depth and decreasing system productivity was captured well by the ANNs. Despite identifying the same predictors for the two populations of prokaryotes and viruses, respectively, the structure of the best performing ANNs differed between high and low nucleic acid cells and between high- and low-fluorescent viruses. Also, the two prokaryotic and viral groups responded differently to changes in the predictor parameters; hence, the cytometric distinction between these populations is ecologically relevant. The models imply that temperature is the main factor explaining most of the variation in the abundances of high nucleic acid cells and total prokaryotes and that the mechanisms governing the reaction to changes in the environment are distinctly different among the prokaryotic and viral populations

Experimental metatranscriptomics reveals the costs and benefits of dissolved organic matter photo‐alteration for freshwater microbes

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156421/2/emi15121_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156421/1/emi15121.pd

Corals and Their Microbiomes Are Differentially Affected by Exposure to Elevated Nutrients and a Natural Thermal Anomaly

Nutrient pollution can increase the prevalence and severity of coral disease and bleaching in ambient temperature conditions or during experimental thermal challenge. However, there have been few opportunities to study the effects of nutrient pollution during natural thermal anomalies. Here we present results from an experiment conducted during the 2014 bleaching event in the Florida Keys, USA, that exposed Agaricia sp. (Undaria) and Siderastrea siderea corals to 3 types of elevated nutrients: nitrogen alone, phosphorous alone, and the combination of nitrogen and phosphorus. Overall, bleaching prevalence and severity was high regardless of treatment, but nitrogen enrichment alone both prolonged bleaching and increased coral mortality in Agaricia corals. At the same time, the elevated temperatures increased the prevalence of Dark Spot Syndrome (DSS), a disease typically associated with cold temperatures in Siderastrea siderea corals. However, nutrient exposure alone did not increase the prevalence or severity of disease, suggesting that thermal stress overwhelms the effects of nutrient pollution on this disease during such an extreme thermal event. Analysis of 78 Siderastrea siderea microbial metagenomes also showed that the thermal event was correlated with significant shifts in the composition and function of the associated microbiomes, and corals with DSS had microbiomes distinct from apparently healthy corals. In particular, we identified shifts in viral, archaeal, and fungal families. These shifts were likely driven by the extreme temperatures or other environmental co-variates occurring during the 2014 bleaching event. However, no microbial taxa were correlated with signs of DSS. Furthermore, although nutrient exposure did not affect microbial alpha diversity, it did significantly affect microbiome beta-diversity, an effect that was independent of time. These results suggest that strong thermal anomalies and local nutrient pollution both interact and act independently to alter coral health in a variety of ways, that ultimately contribute to disease, bleaching, and mortality of reefs in the Florida Keys

Modeling the Winter–to–Summer Transition of Prokaryotic and Viral Abundance in the Arctic Ocean

<div><p>One of the challenges in oceanography is to understand the influence of environmental factors on the abundances of prokaryotes and viruses. Generally, conventional statistical methods resolve trends well, but more complex relationships are difficult to explore. In such cases, Artificial Neural Networks (ANNs) offer an alternative way for data analysis. Here, we developed ANN-based models of prokaryotic and viral abundances in the Arctic Ocean. The models were used to identify the best predictors for prokaryotic and viral abundances including cytometrically-distinguishable populations of prokaryotes (high and low nucleic acid cells) and viruses (high- and low-fluorescent viruses) among salinity, temperature, depth, day length, and the concentration of Chlorophyll-<em>a</em>. The best performing ANNs to model the abundances of high and low nucleic acid cells used temperature and Chl-<em>a</em> as input parameters, while the abundances of high- and low-fluorescent viruses used depth, Chl-<em>a</em>, and day length as input parameters. Decreasing viral abundance with increasing depth and decreasing system productivity was captured well by the ANNs. Despite identifying the same predictors for the two populations of prokaryotes and viruses, respectively, the structure of the best performing ANNs differed between high and low nucleic acid cells and between high- and low-fluorescent viruses. Also, the two prokaryotic and viral groups responded differently to changes in the predictor parameters; hence, the cytometric distinction between these populations is ecologically relevant. The models imply that temperature is the main factor explaining most of the variation in the abundances of high nucleic acid cells and total prokaryotes and that the mechanisms governing the reaction to changes in the environment are distinctly different among the prokaryotic and viral populations.</p> </div

Simulation of prokaryotic abundance.

<p>The figure shows the abundances of (A) HNA, (B) LNA, and (C) total prokaryotic abundance. The ANNs described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052794#pone-0052794-t003" target="_blank">Table 3</a> were used to simulate the abundances of HNA and LNA cells at temperatures ranging from −1.8–2.8°C and Chl-<i>a</i> ranging from 0.01–0.61 µg L⁻¹. Total prokaryotic abundance was computed by summing the simulated abundances of HNA and LNA cells.</p

Unprecedented evidence for high viral abundance and lytic activity in coral reef waters of the South Pacific Ocean.

Despite nutrient-depleted conditions, coral reef waters harbor abundant and diverse microbes; as major agents of microbial mortality, viruses are likely to influence microbial processes in these ecosystems. However, little is known about marine viruses in these rapidly changing ecosystems. Here we examined spatial and short-term temporal variability in marine viral abundance (VA) and viral lytic activity across various reef habitats surrounding Moorea Island (French Polynesia) in the South Pacific. Water samples were collected along four regional cross-reef transects and during a time-series in Opunohu Bay. Results revealed high VA (range: 5.6 × 10(6)-3.6 × 10(7) viruses ml(-1)) and lytic viral production (range: 1.5 × 10(9)-9.2 × 10(10) viruses l(-1) d(-1)). Flow cytometry revealed that viral assemblages were composed of three subsets that each displayed distinct spatiotemporal relationships with nutrient concentrations and autotrophic and heterotrophic microbial abundances. The results highlight dynamic shifts in viral community structure and imply that each of these three subsets is ecologically important and likely to infect distinct microbial hosts in reef waters. Based on viral-reduction approach, we estimate that lytic viruses were responsible for the removal of ca. 24-367% of bacterial standing stock d(-1) and the release of ca. 1.0-62 μg of organic carbon l(-1) d(-1) in reef waters. Overall, this work demonstrates the highly dynamic distribution of viruses and their critical roles in controlling microbial mortality and nutrient cycling in coral reef water ecosystems

Simulation of the abundance of V2 viruses.

<p>The figure shows the abundance of V2 viruses at a depth of (A) 5 m, (B) 50 m, (C) 100 m, (D) 150 m, and (E) 200 m. The ANN described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052794#pone-0052794-t003" target="_blank">Table 3</a> was used to simulate the abundance of V2 viruses at day lengths ranging from 0–24 hours and Chl-<i>a</i> from 0.01–0.61 µg L⁻¹.</p