Alteration in successional trajectories of bacterioplankton communities in response to co-exposure of cadmium and phenanthrene in coastal water microcosms

Synthesis of recovery patterns in microbial communities across environments

BACKGROUND

Disturbances alter the diversity and composition of microbial communities. Yet a generalized empirical assessment of microbiome responses to disturbance across different environments is needed to understand the factors driving microbiome recovery, and the role of the environment in driving these patterns.

RESULTS

To this end, we combined null models with Bayesian generalized linear models to examine 86 time series of disturbed mammalian, aquatic, and soil microbiomes up to 50 days following disturbance. Overall, disturbances had the strongest effect on mammalian microbiomes, which lost taxa and later recovered their richness, but not their composition. In contrast, following disturbance, aquatic microbiomes tended away from their pre-disturbance composition over time. Surprisingly, across all environments, we found no evidence of increased compositional dispersion (i.e., variance) following disturbance, in contrast to the expectations of the Anna Karenina Principle.

CONCLUSIONS

This is the first study to systematically compare secondary successional dynamics across disturbed microbiomes, using a consistent temporal scale and modeling approach. Our findings show that the recovery of microbiomes is environment-specific, and helps to reconcile existing, environment-specific research into a unified perspective. Video Abstract.

Changes in Gut Microbiota Structure: A Potential Pathway for Silver Nanoparticles to Affect the Host Metabolism

Silver nanoparticles (AgNPs) are one of the most widely used NPs. Their adverse effects on either the host or its gut microbiota (GM) have been examined. Nevertheless, whether the GM plays any role in AgNP toxicity to the host remains unclear. In the present study, AgNPs were administered to mice by oral gavage once a day for 120 days. A significant dose-dependent accumulation of Ag in the liver was observed, with a steady state reached within 21 days. The AgNPs changed the structure of the GM, mainly with respect to microorganisms involved in the metabolism of energy, amino acids, organic acids, and lipids, as predicted in a PICRUST analysis. Effects of the AgNPs on liver metabolism were also demonstrated, as a KEGG pathway analysis showed the enrichment of pathways responsible for the metabolism of amino acids, purines and pyrimidine, lipids, and energy. More interestingly, the changes in GM structure and liver metabolism were highly correlated, evidenced by the correlation between ∼23% of the differential microorganisms at the genus level and ∼60% of the differential metabolites. This implies that the metabolic variations in liver as affected by AgNPs were partly attributable to NP-induced changes of GM structure. Therefore, our results demonstrate the importance of considering the roles of GM in the toxicity of NPs to the host in evaluations of the health risks of NPs.

A multi-taxonomic framework for assessing relative petrochemical vulnerability of marine biodiversity in the Gulf of Mexico

A fundamental understanding of the impact of petrochemicals and other stressors on marine biodiversity is critical for effective management, restoration, recovery, and mitigation initiatives. As species-specific information on levels of petrochemical exposure and toxicological response are lacking for the majority of marine species, a trait-based assessment to rank species vulnerabilities to petrochemical activities in the Gulf of Mexico can provide a more comprehensive and effective means to prioritize species, habitats, and ecosystems for improved management, restoration and recovery. To initiate and standardize this process, we developed a trait-based framework, applicable to a wide range of vertebrate and invertebrate species, that can be used to rank relative population vulnerabilities of species to petrochemical activities in the Gulf of Mexico. Through expert consultation, 18 traits related to likelihood of exposure, individual sensitivity, and population resilience were identified and defined. The resulting multi-taxonomic petrochemical vulnerability framework can be adapted and applied to a wide variety of species groups and geographic regions. Additional recommendations and guidance on the application of the framework to rank species vulnerabilities under specific petrochemical exposure scenarios, management needs or data limitations are also discussed.

Divergent Patterns of Bacterial Community Structure and Function in Response to Estuarine Output in the Middle of the Bohai Sea

Understanding environment-community relationships under shifting environmental conditions helps uncover mechanisms by which environmental microbial communities manage to improve ecosystem functioning. This study investigated the microbial community and structure near the Yellow Sea River estuary in 12 stations across the middle of the Bohai Sea for over two seasons to elucidate the influence of estuarine output on them. We found that the dominant phyla in all stations were Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, and Planctomycetes. Alpha-diversity increased near the estuary and bacterial community structure differed with variation of spatiotemporal gradients. Among all the environmental factors surveyed, temperature, salinity, phosphate, silicon, nitrate, and total virioplankton abundance played crucial roles in controlling the bacterial community composition. Some inferred that community functions such as carbohydrate, lipid, amino acid metabolism, xenobiotics biodegradation, membrane transport, and environmental adaptation were much higher in winter; energy and nucleotide metabolism were lower in winter. Our results suggested that estuarine output had a great influence on the Bohai Sea environment and changes in the water environmental conditions caused by estuarine output developed distinctive microbial communities in the middle of the Bohai Sea. The distinctive microbial communities in winter demonstrated that the shifting water environment may stimulate changes in the diversity and then strengthen the predicted functions.

Impacts of copper and lead exposure on prokaryotic communities from contaminated contrasted coastal seawaters: the influence of previous metal exposure

Our understanding of environmental factors controlling prokaryotic community is largely hampered by the large environmental variability across spatial scales (e.g. trace metal contamination, nutrient enrichment and physicochemical variations) and the broad diversity of bacterial pre-exposure to environmental factors. In this article, we investigated the specific influence of copper (Cu) and lead (Pb) on prokaryotic communities from the uncontaminated site, using mesocosm experiments. In addition, we studied how pre-exposure (i.e. life history) affects communities, with reference to previous metal exposure on the response of three prokaryotic communities to similar Cu exposition. This study showed a stronger influence of Cu contamination than Pb contamination on prokaryotic diversity and structure. We identified 12 and 34 bacterial families and genera, respectively, contributing to the significant differences observed in community structure between control and spiked conditions. Taken altogether, our results point toward a combination of direct negative responses to Cu contamination and indirect responses mediated by interaction with phytoplankton. These identified responses were largely conditioned by the previous exposure of community to contaminants.

Changes in Bacterioplankton Communities Resulting From Direct and Indirect Interactions With Trace Metal Gradients in an Urbanized Marine Coastal Area

Unraveling the relative importance of both environmental conditions and ecological processes regulating bacterioplankton communities is a central goal in microbial ecology. Marine coastal environments are among the most urbanized areas and as a consequence experience environmental pressures. The highly anthropized Toulon Bay (France) was considered as a model system to investigate shifts in bacterioplankton communities along natural and anthropogenic physicochemical gradients during a 1-month survey. In depth geochemical characterization mainly revealed strong and progressive Cd, Zn, Cu, and Pb contamination gradients between the entrance of the Bay and the north-western anthropized area. On the other hand, low-amplitude natural gradients were observed for other environmental variables. Using 16S rRNA gene sequencing, we observed strong spatial patterns in bacterioplankton taxonomic and predicted function structure along the chemical contamination gradient. Variation partitioning analysis demonstrated that multiple metallic contamination explained the largest part of the spatial biological variations observed, but DOC and salinity were also significant contributors. Network analysis revealed that biotic interactions were far more numerous than direct interactions between microbial groups and environmental variables. This suggests indirect effects of the environment, and especially trace metals, on the community through a few taxonomic groups. These spatial patterns were also partially found for predicted bacterioplankton functions, thus indicating a limited functional redundancy. All these results highlight both potential direct influences of trace metals contamination on coastal bacterioplankton and indirect forcing through biotic interactions and cascading.

Effect of cadmium contamination on the eutrophic secondary pollution of aquatic macrophytes by litter decomposition

The objective of this study was to identify the effect of cadmium (Cd) contamination on the decomposition of aquatic macrophyte litter and its eutrophic secondary pollution. A laboratory experiment was conducted with three treatments: water Cd contamination (Cd-w), litter Cd contamination (Cd-l) and control (CK). The results showed that CK and Cd-w exhibited the typical decomposition dynamics of litter, i.e., early rapid decomposition followed by slow decomposition, while the litter biomass loss (BL) in Cd-l exhibited an approximately linear relationship with time over the 64-day experimental period. The BL in Cd-l was only 10.8% in the initial 4 days, while that in CK and Cd-w was 59.0% and 54.8%, respectively. Cd inhibited the fluctuation of the water chemical oxygen demand (COD) by reducing both the early increase and the subsequent decrease. The increases in water total nitrogen (TN) and total phosphorus (TP) were inhibited by Cd contamination throughout most of the decomposition period. The alterations of litter quality during the plant growth period and of the bacterial community during the litter decomposition period by Cd contamination could explain the variations in litter decomposition rate and its eutrophic secondary pollution during the early and late decomposition stages, respectively. The Cd inhibition of the eutrophic secondary pollution of aquatic macrophytes has great significance for the improved evaluation of Cd contamination.