Metal impacts on deep-sea microbial communities and function

Project Information

MIDFun

Grant agreement ID: 101038095

DOI

10.3030/101038095

Project closed

EC signature date 14 April 2021

Start date 1 September 2021

End date 31 August 2023

Funded under

• SPREADING EXCELLENCE AND WIDENING PARTICIPATION

Total cost

€ 147 815,04

EU contribution

€ 147 815,04

Coordinated by

CENTRO INTERDISCIPLINAR DE INVESTIGACAO MARINHA E AMBIENTAL
Portugal

Periodic Reporting for period 1 - MIDFun (Metal impacts on deep-sea microbial communities and function)

Reporting period: 2021-09-01 to 2023-08-31

Summary of the context and overall objectives of the project

Deep-sea mining of earth minerals is expected to grow in the next decades. The increase in deep-sea mining activities may lead to the release of toxic concentrations of metals into the surrounding seabed. Increased concentrations of heavy metals can disturb important ecosystem services provided by microbial communities, such as growth, nutrient cycling activity, and microbial diversity. However, the consequences of metal exposure on microbial ecosystem functions in deep-sea conditions are currently unknown. The overarching goal of this project was to evaluate the impacts of heavy metal exposure on microbial growth, metabolism, and diversity in deep-sea conditions. The following specific objectives were proposed:

1. Determine the effects of heavy metal exposure on growth and N2O reduction metabolism in a model bacterial culture, under deep-sea conditions.
2. Examine the effects of heavy metal exposure on the transcriptome of a model bacterial culture, under deep-sea conditions.
3. Determine the impacts of heavy metal exposure on overall N2O fluxes from deep-sea sediments.
4. Evaluate the impacts of heavy metal exposure on the biological and functional diversity of deep-sea complex microbial communities.

This research applied a mixed experimental approach in controlled conditions to address the stated objectives. Bacterial axenic cultures and complex microbial communities were investigated. Pressurized bioreactors and environmental chamber microcosm experiments were used to test the effects of two representative metals (copper and cadmium) on bacterial growth, metabolic reduction of N2O, expression of functional genes, and genetic and functional diversity. The mining of the deep seafloor is still at an early stage of implementation. This research presented a rare opportunity to assess the environmental risks of an anthropogenic activity before it begins to shape the ecosystem.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

More than 10 pure culture experiments were performed with two deep-sea model isolates under exposure to Cd and Cu and 7 microcosms with deep-sea sediments collected near Pacific seamounts under Cd exposure at five different concentrations. Despite the experiments performed, some data still needs to be processed and analysed after the reporting period. So far, the main findings of this project are.
1) The growth of model deep-sea isolates (Shewanella loihica PV-4 and Thalassospira indica PB8B) was similarly affected by Cd exposure, with growth inhibition observed only with Cd concentrations higher than 25 µM.
2) Under Cu exposure, PV-4 did not show any growth inhibition even at concentrations up to 160 µM, while PB8B growth was inhibited at concentrations higher than 4 µM, showing much higher susceptibility to Cu exposure.
3) Regarding the impacts of the metals in the N2O metabolism of both strains, contrasting results were observed, depending on the metal tested. While Cd inhibited net N2O production from PV-4 (Pizarro et al., 2023), Cu appears to promote net N2O production in the same strain.
4) Preliminary results suggest that Cu delays N2O reduction in PB8B, inhibiting the capacity to fully reduce N2O, when compared to controls without the metal.
5) Relative expression of genes involved in N2O production or reduction has generally contributed to explain the results observed in net N2O production rates.

Part of the results obtained so far were published in an open access peer-reviewed publication (Pizarro et al., 2023) and three more publications are currently being prepared. Results from this project were also presented in two oral and two poster communications in international conferences as well as in three outreach activities to the general public. The researcher has also participated in three international working groups aiming at providing expert advice to the policy-makers involved in the development of future regulations for deep-sea exploration and exploitation.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

This project generated the first results of Cd exposure impacts on deep-sea bacterial isolates (Pizarro et al., 2023). Moreover, the data generated from all the experiments (still to be analysed) will generate the first results on Cd and Cu effects on N2O metabolism, gene expression and overall transcriptome, as well as on genetic and functional diversity of deep-sea sediments.

This research presents significant scientific and societal impacts. Regarding the scientific impacts the following can be highlighted:
- Even though several studies have quantified the toxicity of metals to organisms from all domains of life in different environments, very few studies have quantified this toxicity in deep-sea substrates or under deep-sea conditions. By performing shipboard exposure experiments with freshly collected deep-sea samples and by replicating deep-sea conditions using high-pressure bioreactors , this project represents a novel approach towards understanding metal toxicity in the deep ocean.
- Besides evaluating the metal exposure impacts on overall microbial diversity, the MIDFun project is investigating the impacts on specific functional diversity (e.g. N cycling transformations, biosynthetic gene clusters, etc.), which has implications for diverse scientific fields, from biogeochemistry to marine biotechnology. Moreover, this project will evaluate the effects of increased metal exposure on a process with global impacts on the climate: microbial production of N2O, an important greenhouse gas and a major disruptor of the ozone layer.Despite microbial in nature, the scientific impacts of our findings will be “macroscopic”, due to the environmental importance of the studied phenomena and the magnitude of the deep ocean.
- The methodological approach used combines the application of pure cultures and complex communities, which is not commonly performed in environmental microbiology studies. This approach will allow the project to explore mechanistic subcellular processes as well as evaluate their contribution to the overall outcomes from more realistic communities. The metagenomic and transcriptomic analyses will also target diverse metabolic pathways, including metal resistance and nitrogen metabolism. This approach will generate information about the cellular mechanisms responsible for a potential metal effect on the functional genetic capacity of the microbial models.

Besides the scientific impacts, this research project also presents significant societal impacts:
- This research will contribute to improve understanding of the multiple roles that deep-sea microbial communities play in the in ocean as well to investigate potential impacts of mining on microbial diversity and ecosystem services, thus contributing to better inform future decisions regarding deep seabed management.
- The findings from this project will also be particularly timely, with the recently completed UN’s High-Seas Treaty and the ongoing negotiations at the International Seabed Authority (ISA) for the first regulations of commercial mining in international waters. Our specific societal audience are the members of the ISA’s Intersession Expert Groups as well as ISA’s Legal and Technical Commission, tasked with developing binding environmental thresholds for suggested standards and guidelines for the mining activities.

Summary poster