Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities

Background

Environmental shotgun sequencing (metagenomics) provides a new way to study communities in microbial ecology. We here use sequence data from the Global Ocean Sampling (GOS) expedition to investigate toxicant selection pressures revealed by the presence of detoxification genes in marine bacteria. To capture a broad range of potential toxicants we selected detoxification protein families representing systems protecting microorganisms from a variety of stressors, such as metals, organic compounds, antibiotics and oxygen radicals.

Results

Using a bioinformatics procedure based on comparative analysis to finished bacterial genomes we found that the amount of detoxification genes present in marine microorganisms seems surprisingly small. The underrepresentation is particularly evident for toxicant transporters and proteins involved in detoxifying metals. Exceptions are enzymes involved in oxidative stress defense where peroxidase enzymes are more abundant in marine bacteria compared to bacteria in general. In contrast, catalases are almost completely absent from the open ocean environment, suggesting that peroxidases and peroxiredoxins constitute a core line of defense against reactive oxygen species (ROS) in the marine milieu.

Conclusions

We found no indication that detoxification systems would be generally more abundant close to the coast compared to the open ocean. On the contrary, for several of the protein families that displayed a significant geographical distribution, like peroxidase, penicillin binding transpeptidase and divalent ion transport protein, the open ocean samples showed the highest abundance. Along the same lines, the abundance of most detoxification proteins did not increase with estimated pollution. The low level of detoxification systems in marine bacteria indicate that the majority of marine bacteria have a low capacity to adapt to increased pollution. Our study exemplifies the use of metagenomics data in ecotoxicology, and in particular how anthropogenic consequences on life in the sea can be examined.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-749) contains supplementary material, which is available to authorized users.     

Dissolved organic matter (DOM) release by phytoplankton in the contemporary and future ocean

The partitioning of organic matter (OM) between dissolved and particulate phases is an important factor in determining the fate of organic carbon in the ocean. Dissolved organic matter (DOM) release by phytoplankton is a ubiquitous process, resulting in 2–50% of the carbon fixed by photosynthesis leaving the cell. This loss can be divided into two components: passive leakage by diffusion across the cell membrane and the active exudation of DOM into the surrounding environment. At present there is no method to distinguish whether DOM is released via leakage or exudation. Most explanations for exudation remain hypothetical; as while DOM release has been measured extensively, there has been relatively little work to determine why DOM is released. Further research is needed to determine the composition of the DOM released by phytoplankton and to link composition to phytoplankton physiological status and environmental conditions. For example, the causes and physiology of phytoplankton cell death are poorly understood, though cell death increases membrane permeability and presumably DOM release. Recent work has shown that phytoplankton interactions with bacteria are important in determining both the amount and composition of the DOM released. In response to increasing CO₂ in the atmosphere, climate change is creating increasingly stressful conditions for phytoplankton in the surface ocean, including relatively warm water, low pH, low nutrient supply and high light. As ocean physics and chemistry change, it is hypothesized that a greater proportion of primary production will be released directly by phytoplankton into the water as DOM. Changes in the partitioning of primary production between the dissolved and particulate phases will have bottom-up effects on ecosystem structure and function. There is a need for research to determine how these changes affect the fate of organic matter in the ocean, particularly the efficiency of the biological carbon pump.     

Ocean acidification increases the vulnerability of native oysters to predation by invasive snails

There is growing concern that global environmental change might exacerbate the ecological impacts of invasive species by increasing their per capita effects on native species. However, the mechanisms underlying such shifts in interaction strength are poorly understood. Here, we test whether ocean acidification, driven by elevated seawater pCO₂, increases the susceptibility of native Olympia oysters to predation by invasive snails. Oysters raised under elevated pCO₂ experienced a 20% increase in drilling predation. When presented alongside control oysters in a choice experiment, 48% more high-CO₂ oysters were consumed. The invasive snails were tolerant of elevated CO₂ with no change in feeding behaviour. Oysters raised under acidified conditions did not have thinner shells, but were 29–40% smaller than control oysters, and these smaller individuals were consumed at disproportionately greater rates. Reduction in prey size is a common response to environmental stress that may drive increasing per capita effects of stress-tolerant invasive predators.     

Acclimation conditions modify physiological response of the diatom Thalassiosira pseudonana to elevated CO2 concentrations in a nitrate‐limited chemostat

Diatoms are responsible for a large proportion of global carbon fixation, with the possibility that they may fix more carbon under future levels of high CO₂. To determine how increased CO₂ concentrations impact the physiology of the diatom Thalassiosira pseudonana Hasle et Heimdal, nitrate‐limited chemostats were used to acclimate cells to a recent past (333 ± 6 μatm) and two projected future concentrations (476 ± 18 μatm, 816 ± 35 μatm) of CO₂. Samples were harvested under steady‐state growth conditions after either an abrupt (15–16 generations) or a longer acclimation process (33–57 generations) to increased CO₂ concentrations. The use of un‐bubbled chemostat cultures allowed us to calculate the uptake ratio of dissolved inorganic carbon relative to dissolved inorganic nitrogen (DIC:DIN), which was strongly correlated with fCO₂ in the shorter acclimations but not in the longer acclimations. Both CO₂ treatment and acclimation time significantly affected the DIC:DIN uptake ratio. Chlorophyll a per cell decreased under elevated CO₂ and the rates of photosynthesis and respiration decreased significantly under higher levels of CO₂. These results suggest that T. pseudonana shifts carbon and energy fluxes in response to high CO₂ and that acclimation time has a strong effect on the physiological response.     

Marine biodiversity�Cecosystem functions under uncertain environmental futures

Anthropogenic activity is currently leading to dramatic transformations of ecosystems and losses of biodiversity. The recognition that these ecosystems provide services that are essential for human well-being has led to a major interest in the forms of the biodiversity–ecosystem functioning relationship. However, there is a lack of studies examining the impact of climate change on these relationships and it remains unclear how multiple climatic drivers may affect levels of ecosystem functioning. Here, we examine the roles of two important climate change variables, temperature and concentration of atmospheric carbon dioxide, on the relationship between invertebrate species richness and nutrient release in a model benthic estuarine system. We found a positive relationship between invertebrate species richness and the levels of release of NH₄-N into the water column, but no effect of species richness on the release of PO₄-P. Higher temperatures and greater concentrations of atmospheric carbon dioxide had a negative impact on nutrient release. Importantly, we found significant interactions between the climate variables, indicating that reliably predicting the effects of future climate change will not be straightforward as multiple drivers are unlikely to have purely additive effects, resulting in increased levels of uncertainty.     

Microsatellites from the world's heaviest bony fish,the giant Mola mola

We report the isolation and characterization of CA_n microsatellite loci from the Mola mola genome using a variation of the hybrid capture method. Five loci exhibit high levels of heterozygocity and two show significant sequence similarity to genes from the closely related Fugu rubripes. These microsatellite markers should be useful in multidisciplinary efforts to understand population characteristics of the giant ocean sunfish.     

Coupling between Marine Plankton and Freshwater Flow in the Plumes off a Small Estuary

Freshwater discharge from rivers is a powerful forcing agent in coastal ecosystems. It not only generates strong ecological effects in estuaries, but also drives the dynamics of nearshore marine waters where prominent river plumes form biogeochemical hot spots in coastal seas worldwide. Large plumes from major rivers exert important controls on pelagic processes. The majority of estuaries are smaller, however, and the importance of the smaller plumes they generate is unknown. We measured the degree of coupling between freshwater flow and inshore zooplankton in such a plume from a subtropical estuary on the east coast of Australia. Flow regimes encompassed long periods of low freshwater input, punctuated by pulsed freshets that initiated the formation of buoyant, lower‐salinity plumes in the nearshore marine zone. Plumes stimulated phytoplankton biomass in the receiving waters, and ultimately changes in zooplankton assemblages. Zooplankton responded strongly to river discharge: (1) in the absence of substantial freshwater flows and plumes, zooplankton was broadly similar in density and biomass across the estuarine‐marine gradient; (2) freshets that generated significant plumes strongly modified hydrological conditions and lowered zooplankton in the estuarine and nearshore waters, and (3) after the initial freshet, zooplankton in the residual plume was at a higher density in nearshore than shelf waters. We demonstrate that coupling between riverine and coastal pelagic systems operates in small plumes, but that there is substantial temporal variance linked to fluctuations in freshwater delivery. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Uncovering the spatial heterogeneity of Ediacaran carbon cycling

Records of the Ediacaran carbon cycle (635–541 million years ago) include the Shuram excursion (SE), the largest negative carbonate carbon isotope excursion in Earth history (down to ?12‰). The nature of this excursion remains enigmatic given the difficulties of interpreting a perceived extreme global decrease in the δ¹³C of seawater dissolved inorganic carbon. Here, we present carbonate and organic carbon isotope (δ¹³C_carb and δ¹³C_org) records from the Ediacaran Doushantuo Formation along a proximal‐to‐distal transect across the Yangtze Platform of South China as a test of the spatial variation of the SE. Contrary to expectations, our results show that the magnitude and morphology of this excursion and its relationship with coexisting δ¹³C_org are highly heterogeneous across the platform. Integrated geochemical, mineralogical, petrographic, and stratigraphic evidence indicates that the SE is a primary marine signature. Data compilations demonstrate that the SE was also accompanied globally by parallel negative shifts of δ³⁴S of carbonate‐associated sulfate (CAS) and increased ⁸⁷Sr/⁸⁶Sr ratio and coastal CAS concentration, suggesting elevated continental weathering and coastal marine sulfate concentration during the SE. In light of these observations, we propose a heterogeneous oxidation model to explain the high spatial heterogeneity of the SE and coexisting δ¹³C_org records of the Doushantuo, with likely relevance to the SE in other regions. In this model, we infer continued marine redox stratification through the SE but with increased availability of oxidants (e.g., O₂ and sulfate) limited to marginal near‐surface marine environments. Oxidation of limited spatiotemporal extent provides a mechanism to drive heterogeneous oxidation of subsurface reduced carbon mostly in shelf areas. Regardless of the mechanism driving the SE, future models must consider the evidence for spatial heterogeneity in δ¹³C presented in this study.     

基于远洋卫勤保障的护理人员培训知识体系构建

目的 构建一套满足我国远洋卫勤保障任务及需求的护理人员培训知识体系。方法 采用文献分析法、专家访谈法和德尔菲法建立指标体系,运用层次分析法确定各指标权重系数。结果 专家权威系数为0.835,形成包括4个一级指标、13个二级指标和56个三级指标的我国护理人员参与远洋卫勤保障任务的培训知识体系,各条目协调系数为0.296~0.423,差异比较有统计学意义（P＜0.05）。结论 专家意见集中,结果可信,可为参与远洋卫勤保障任务的护理人员培训、考核提供量化的参考依据。