Increased prokaryotic diversity in the Red Sea deep scattering layer.

BACKGROUND: The diel vertical migration (DVM) of fish provides an active transport of labile dissolved organic matter (DOM) to the deep ocean, fueling the metabolism of heterotrophic bacteria and archaea. We studied the impact of DVM on the mesopelagic prokaryotic diversity of the Red Sea focusing on the mesopelagic deep scattering layer (DSL) between 450-600 m. RESULTS: Despite the general consensus of homogeneous conditions in the mesopelagic layer, we observed variability in physico-chemical variables (oxygen, inorganic nutrients, DOC) in the depth profiles. We also identified distinct seasonal indicator prokaryotes inhabiting the DSL, representing between 2% (in spring) to over 10% (in winter) of total 16S rRNA gene sequences. The dominant indicator groups were Alteromonadales in winter, Vibrionales in spring and Microtrichales in summer. Using multidimensional scaling analysis, the DSL samples showed divergence from the surrounding mesopelagic layers and were distributed according to depth (47% of variance explained). We identified the sources of diversity that contribute to the DSL by analyzing the detailed profiles of spring, where 3 depths were sampled in the mesopelagic. On average, 7% was related to the epipelagic, 34% was common among the other mesopelagic waters and 38% was attributable to the DSL, with 21% of species being unique to this layer. CONCLUSIONS: We conclude that the mesopelagic physico-chemical properties shape a rather uniform prokaryotic community, but that the 200 m deep DSL contributes uniquely and in a high proportion to the diversity of the Red Sea mesopelagic.

Temperature enhances the functional diversity of dissolved organic matter utilization by coastal marine bacteria.

Although bulk bacterial metabolism in response to temperature has been determined for different oceanic regions, the impact of temperature on the functional diversity of dissolved organic matter (DOM) utilization has been largely unexplored. Here, we hypothesized that besides modifying the rates of carbon utilization, temperature can also alter the diversity of substrates utilized. The patterns of utilization of 31 model DOM compounds (as represented in Biolog EcoPlate™) by bacterioplankton were assessed using inocula from surface waters of the southern Bay of Biscay continental shelf over 1 year. Bacteria utilized more polymers and carbohydrates in late spring and summer than in winter, likely reflecting changes in substrate availability linked to the release and accumulation of DOM in phytoplankton post-bloom conditions. Seawater temperature correlated positively with the number of substrates utilized (i.e. functional richness) and this relationship was maintained in monthly experimental incubations spanning 3°C below and above in situ values. The enhancement of functional richness with experimental warming displayed a unimodal response to ambient temperature, peaking at 16°C. This temperature acted as a threshold separating nutrient-sufficient from nutrient-deficient conditions at the study site, suggesting that trophic conditions will be critical in the response of microbial DOM utilization to future warming.

High-Frequency Variability of Bacterioplankton in Response to Environmental Drivers in Red Sea Coastal Waters.

Autotrophic and heterotrophic bacterioplankton are essential to the biogeochemistry of tropical ecosystems. However, the processes that govern their dynamics are not well known. We provide here a high-frequency assessment of bacterial community dynamics and concurrent environmental factors in Red Sea coastal waters. Weekly sampling of surface samples during a full annual cycle at an enclosed station revealed high variability in ecological conditions, which reflected in changes of major bacterioplankton communities. Temperature varied between 23 and 34°C during the sampling period. Autotrophic (Synechococcus, 1.7-16.2 × 104 cells mL-1) and heterotrophic bacteria (1.6-4.3 × 105 cells mL-1) showed two maxima in abundance in spring and summer, while minima were found in winter and autumn. Heterotrophic cells with high nucleic acid content (HNA) peaked in July, but their contribution to the total cell counts (35-60%) did not show a clear seasonal pattern. Actively respiring cells (CTC+) contributed between 4 and 51% of the total number of heterotrophic bacteria, while live cells (with intact membrane) consistently accounted for over 90%. Sequenced 16S rRNA amplicons revealed a predominance of Proteobacteria in summer and autumn (>40%) and a smaller contribution in winter (21-24%), with members of the Alphaproteobacteria class dominating throughout the year. The contribution of the Flavobacteriaceae family was highest in winter (21%), while the Rhodobacteraceae contribution was lowest (6%). Temperature, chlorophyll-a, and dissolved organic carbon concentration were the environmental variables with the greatest effects on bacterial abundance and diversity patterns.

Temperature sensitivities of microbial plankton net growth rates are seasonally coherent and linked to nutrient availability.

Recent work suggests that temperature effects on marine heterotrophic bacteria are strongly seasonal, but few attempts have been made to concurrently assess them across trophic levels. Here, we estimated the temperature sensitivities (using activation energies, E) of autotrophic and heterotrophic microbial plankton net growth rates over an annual cycle in NE Atlantic coastal waters. Phytoplankton grew in winter and late autumn (0.41 ± 0.16 SE d-1 ) and decayed in the remaining months (-0.42 ± 0.10 d-1 ). Heterotrophic microbes shared a similar seasonality, with positive net growth for bacteria (0.14-1.48 d-1 ), while nanoflagellates had higher values (> 0.4 d-1 ) in winter and spring relative to the rest of the year (-0.46 to 0.29 d-1 ). Net growth rates activation energies showed similar dynamics in the three groups (-1.07 to 1.51 eV), characterized by maxima in winter, minima in summer and resumed increases in autumn. Microbial plankton E values were significantly correlated with nitrate concentrations as a proxy for nutrient availability. Nutrient-sufficiency (i.e., > 1 µmol l-1 nitrate) resulted in significantly higher activation energies of phytoplankton and heterotrophic nanoflagellates relative to nutrient-limited conditions. We suggest that only within spatio-temporal windows of both moderate bottom-up and top-down controls will temperature have a major enhancing effect on microbial growth.

Low Abundances but High Growth Rates of Coastal Heterotrophic Bacteria in the Red Sea.

Characterized by some of the highest naturally occurring sea surface temperatures, the Red Sea remains unexplored regarding the dynamics of heterotrophic prokaryotes. Over 16 months, we used flow cytometry to characterize the abundance and growth of four physiological groups of heterotrophic bacteria: membrane-intact (Live), high and low nucleic acid content (HNA and LNA) and actively respiring (CTC+) cells in shallow coastal waters. Chlorophyll a, dissolved organic matter (DOC and DON) concentrations, and their fluorescent properties were also measured as proxies of bottom-up control. We performed short-term incubations (6 days) with the whole microbial community (Community treatment), and with the bacterial community only after removing predators by filtration (Filtered treatment). Initial bacterial abundances ranged from 1.46 to 4.80 × 105 cells mL-1. Total specific growth rates in the Filtered treatment ranged from 0.76 to 2.02 d-1. Live and HNA cells displayed similar seasonal patterns, with higher values during late summer and fall (2.13 and 2.33 d-1, respectively) and lower in late spring (1.02 and 1.01 d-1, respectively). LNA cells were outgrown by the other physiological groups (0.33-1.08 d-1) while CTC+ cells (0.28-1.85 d-1) showed weaker seasonality. The Filtered treatment yielded higher bacterial abundances than the Community treatment in all but 2 of the incubations, and carrying capacities peaked in November 2016 (1.04 × 106 cells mL-1), with minimum values (3.61 × 105 cells mL-1) observed in May 2017. The high temperatures experienced from May through October 2016 (33.4 ± 0.4°C) did not constrain the growth of heterotrophic bacteria. Indeed, bacterial growth efficiencies were positively correlated with environmental temperature, reflecting the presence of more labile compounds (high DON concentrations resulting in lower C:N ratios) in summer. The overall high specific growth rates and the consistently higher carrying capacities in the Filtered treatment suggest that strong top-down control by protistan grazers was the likely cause for the low heterotrophic bacteria abundances.

Testing the metabolic theory of ecology with marine bacteria: different temperature sensitivity of major phylogenetic groups during the spring phytoplankton bloom.

Although temperature is a key driver of bacterioplankton metabolism, the effect of ocean warming on different bacterial phylogenetic groups remains unclear. Here, we conducted monthly short-term incubations with natural coastal bacterial communities over an annual cycle to test the effect of experimental temperature on the growth rates and carrying capacities of four phylogenetic groups: SAR11, Rhodobacteraceae, Gammaproteobacteria and Bacteroidetes. SAR11 was the most abundant group year-round as analysed by CARD-FISH, with maximum abundances in summer, while the other taxa peaked in spring. All groups, including SAR11, showed high temperature-sensitivity of growth rates and/or carrying capacities in spring, under phytoplankton bloom or post-bloom conditions. In that season, Rhodobacteraceae showed the strongest temperature response in growth rates, estimated here as activation energy (E, 1.43 eV), suggesting an advantage to outcompete other groups under warmer conditions. In summer E values were in general lower than 0.65 eV, the value predicted by the Metabolic Theory of Ecology (MTE). Contrary to MTE predictions, carrying capacity tended to increase with warming for all bacterial groups. Our analysis confirms that resource availability is key when addressing the temperature response of heterotrophic bacterioplankton. We further show that even under nutrient-sufficient conditions, warming differentially affected distinct bacterioplankton taxa.

Temperature dependences of growth rates and carrying capacities of marine bacteria depart from metabolic theoretical predictions.

Using the metabolic theory of ecology (MTE) framework, we evaluated over a whole annual cycle the monthly responses to temperature of the growth rates (µ) and carrying capacities (K) of heterotrophic bacterioplankton at a temperate coastal site. We used experimental incubations spanning 6ºC with bacterial physiological groups identified by flow cytometry according to membrane integrity (live), nucleic acid content (HNA and LNA) and respiratory activity (CTC+). The temperature dependence of µ at the exponential phase of growth was summarized by the activation energy (E), which was variable (-0.52 to 0.72 eV) but followed a seasonal pattern, only reaching the hypothesized value for aerobic heterotrophs of 0.65 eV during the spring bloom for the most active bacterial groups (live, HNA, CTC+). K (i.e. maximum experimental abundance) peaked at 4 × 10(6) cells mL(-1) and generally covaried with µ but, contrary to MTE predictions, it did not decrease consistently with temperature. In the case of live cells, the responses of µ and K to temperature were positively correlated and related to seasonal changes in substrate availability, indicating that the responses of bacteria to warming are far from homogeneous and poorly explained by MTE at our site.