Nitrogen fixation in the widely distributed marine gammaproteobacteria diazotroph Candidatus Thalassolituus haligoni

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Abstract

The high diversity and global distribution of heterotrophic bacterial diazotrophs (HBDs) in the ocean has recently become apparent. However, understanding the role these largely uncultured microorganisms play in marine N2 fixation poses a challenge due to their undefined growth requirements and the complex regulation of the nitrogenase enzyme. We isolated and characterized Candidatus Thalassolituus haligoni, a member of a widely distributed clade of HBD belonging to the Oceanospirillales. Analysis of its nifH gene via amplicon sequencing revealed the extensive distribution of Cand. T. haligoni across the Pacific, Atlantic, and Arctic Oceans. Pangenome analysis indicates that the isolate shares >99% identity with an uncultured metagenome-assembled genome called Arc-Gamma-03, recently recovered from the Arctic Ocean. Through combined genomic, proteomic, and physiological approaches, we confirmed that the isolate fixes N2 gas. However, the mechanisms governing nitrogenase regulation in Cand. T. haligoni remain unclear. We propose Cand. T. haligoni as a globally distributed, cultured HBD model species within this understudied clade of Oceanospirillales.

Figure

Fig. 1. Scanning electron microscopy and genomic, proteomic, and genome-assisted metabolic models of Cand. T. haligoni.
(A) (A) cell morphology of the isolate under n2- fixing conditions using scanning electron microscopy (SeM; top) and transmission electron microscopy (teM; bottom). SeM magnification = 17.71 × 103. Arrows indicate flagella (F) and PhB granules (PhB).
(B) CProteome-genome circular map under nO3− depleted conditions. Starting from the innermost ring: Gc content (gray), Gc skew for forward (green) and reverse strands (magenta), leading and lagging strand cdSs (light purple), and detected proteins (blue). Arrows in the genome indicate genes of interest [nif clusters, n2 fixation–related genes are molybdate uptake and transformation genes (mod factors), tRAP-c4 uptake, and glutamine synthesis] and have corresponding detected proteins highlighted in respective colors. White spaces in the proteome indicate regions not detected.
(C) Nif clusters (red, blue, and orange) and associated n2 fixation genes (gray). n2 fixation–associated genes include glycogen phosphorylase and glycogen uptake genes. numbers along the line indicate base-pair locations within the genome. A nucleotide break in the center of the diagram from 3,598,007 nt to 3,737,467 nt is represented by the zig-zag line in red (concatenated). Clusters are color-coded to the associated nif clusters, with accessory genes to that cluster indicated by respective color hues.
(D) Simplified metabolic schematic of the isolate based on the genome annotation. the schematic was created using the RASt server and BioRender.

 

Reference

Sonja A. Rose, Brent M. Robicheau, Jennifer Tolman, Debany Fonseca-Batista, Elden Rowland, Dhwani Desai, Jenni-Marie Ratten, Ella Joy H. Kantor, André M. Comeau, Morgan G.I. Langille, Jon Jerlström-Hultqvist, Emmanuel Devred, Géraldine Sarthou, Erin M. Bertrand and Julie La Roche. “Nitrogen fixation in the widely distributed marine γ-proteobacterial diazotroph Candidatus Thalassolituus haligoni“. Science Advances Volume 10, Issue 31 (Aug 2024)

https://www.science.org/doi/epdf/10.1126/sciadv.adn1476

Deciphering environmental forcings in the distribution of meiofauna and nematodes in mangroves of the Atlantic-Caribbean-East Pacific and Indo-West Pacific regions

Abstract

Mangroves develop under environmental conditions and anthropogenic pressures whose impact on benthic meiofauna remains poorly understood. It is unclear how meiofauna communities are structured according to local sedimentary conditions. This study was designed to characterize the community structure of meiofauna and nematodes (dominant taxa) and the associated environmental forcings in intertidal mangrove sediments from Mayotte (Indo-West-Pacific), Martinique and Guadeloupe (Caribbean). Sediment cores were sampled at the end of the dry season at low tide on adult mangrove stands with similar immersion time. In each sediment layer, we analyzed redox potential, pH, porewater salinity, grain size, organic matter, metals, organic contaminants, prokaryotes and meiofauna. Our results show that sediments far from cities and agricultural fields trapped site-specific contaminants due to local water transport processes. Some metals, PAHs or pesticides exceeded toxicity thresholds in most of the studied stations, thus being harmful to benthic fauna. The sedimentary environment acts as a filter selecting specific meiofauna communities at station scale only in the Caribbean. In Mayotte, horizontal homogeneity contrasts with vertical heterogeneity of the sedimentary environment and the meiofauna. Nematode genera showed particular distribution patterns horizontally and vertically, suggesting the presence of sediment patches suitable for a restricted pool of genera on each island. Results in the Caribbean are consistent with nested diversity patterns due to environmental filtering. Conversely, horizontal homogeneity at Mayotte would reflect greater dispersal between stations or more spatially homogeneous anthropogenic pressures. The nematode genera present at depth may not be the most specialized, but the most versatile, capable of thriving in different conditions. Terschellingia and Daptonema showed contrasted responses to environmental forcing, likely due to their versatility, while Desmodora showed uniform responses between study areas, except when toxicity thresholds were exceeded. Our results emphasize that a given genus of nematode may respond differently to sedimentary conditions depending on sites.

 

Graphical abstract

 

Highlights

  • Metals, PCBs, PAHs or pesticides exceed toxicity thresholds on each island.

  • Meiofauna and nematode density significantly decreased over depth.

  • The nematode community is structured at the scale of the station in all islands.

  • Nematode communities form local patches with highly different genus composition.
  • Site-specific variability of nematode response to multiple stressors

 

Référence

Spedicato, Adriana, Daniela Zeppilli, Gerard Thouzeau, Philippe Cuny, Cecile Militon, Cedric Hubas, Lea Sylvi, et al. « Deciphering Environmental Forcings in the Distribution of Meiofauna and Nematodes in Mangroves of the Atlantic-Caribbean-East Pacific and Indo-West Pacific Regions ». SCIENCE OF THE TOTAL ENVIRONMENT 930 (20 juin 2024): 172612. https://doi.org/10.1016/j.scitotenv.2024.172612.

French coastal network for carbonate system monitoring: the CocoriCO2 dataset

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Abstract

Since the beginning of the industrial revolution, atmospheric carbon dioxide (CO2) concentrations have risen steadily and have induced a decrease of the averaged surface ocean pH by 0.1 units, corresponding to an increase in ocean acidity of about 30 %. In addition to ocean warming, ocean acidification poses a tremendous challenge to some marine organisms, especially calcifiers. The need for long-term oceanic observations of pH and temperature is a key element to assess the vulnerability of marine communities and ecosystems to these pressures. Nearshore productive environments, where a large majority of shellfish farming activities are conducted, are known to present pH levels as well as amplitudes of daily and seasonal variations that are much larger than those observed in the open ocean. Yet, to date, there are very few coastal observation sites where these parameters are measured simultaneously and at high frequency.

To bridge this gap, an observation network was initiated in 2021 in the framework of the CocoriCO2 project. Six sites were selected along the French Atlantic and Mediterranean coastlines based on their importance in terms of shellfish production and the presence of high- and low-frequency monitoring activities. At each site, autonomous pH sensors were deployed, both inside and outside shellfish production areas, next to high-frequency CTD (conductivity–temperature–depth) probes operated through two operating monitoring networks. pH sensors were set to an acquisition rate of 15 min, and discrete seawater samples were collected biweekly in order to control the quality of pH data (laboratory spectrophotometric measurements) as well as to measure total alkalinity and dissolved inorganic carbon concentrations for full characterization of the carbonate system. While this network has been up and running for more than 2 years, the acquired dataset has already revealed important differences in terms of pH variations between monitored sites related to the influence of diverse processes (freshwater inputs, tides, temperature, biological processes). Data are available at https://doi.org/10.17882/96982 (Petton et al., 2023a).

 

Figure 1

Location of the high-frequency monitoring sites (blue dots) from the CocoriCO2 network. The pink and green dots indicate SOMLIT and REPHY low-frequency stations, respectively, from which nutrient data were acquired.

 

Conclusion and present status of the network

The network initiated in 2021 along the French coast area has provided essential data for the assessment of carbonate chemistry dynamics at various temporal scales and in contrasted coastal sites (shellfish farms located close to the shore vs. sites with no shellfish farming more subjected to oceanic conditions). The large number of sites and geographical coverage of the network has already allowed us to evaluate the influence of diverse physical, chemical, and biological processes (freshwater inputs, tides, temperature, biological processes), which we briefly presented in the present paper. The acquired dataset will undoubtedly be of great interest to the public and scientific communities in the future as our choice to base our network on existing monitoring activities not only allowed for providing reliable data at a very high acquisition rate and at a lower financial cost, but also allows for the possibility to rely on existing low-frequency datasets (chlorophyll, nutrients, organic matter concentrations, etc.) for assessing the interplay between biology and the chemical environment. However, autonomous time-series acquisition close to shellfish farming involves a number of challenges mostly related to intense biofouling pressure. It explained most invalidated data even when employing fortnightly manual cleaning protocols, which will require in the future the development of active and efficient antifouling solutions that are currently in development (localized chlorination, adapted wiper) in the framework of our project. Furthermore, the SeaFET technology is relatively novel when compared to more conventional temperature or conductivity sensors. We encountered disparities within the whole set of probes acquired with specific electrodes malfunctioning within just a few months of deployment, despite the manufacturer Sea-Bird indicating a minimum of 1-year service life. Adding complexity, a further issue emerged from June 2022 onwards: the SeaFET maintenance service has been suspended due to a lack of the DuraFET component. While the service will apparently resume by late 2023, this disruption has already resulted in temporal gaps within the time-series data. Additionally, evaluation of new sensors is underway with the objective of obtaining the reliability and accuracy of the already collected data.

 

Reference

Petton, S., Pernet, F., Le Roy, V., Huber, M., Martin, S., Macé, É., Bozec, Y., Loisel, S., Rimmelin-Maury, P., Grossteffan, É., Repecaud, M., Quemener, L., Retho, M., Manac’h, S., Papin, M., Pineau, P., Lacoue-Labarthe, T., Deborde, J., Costes, L., Polsenaere, P., Rigouin, L., Benhamou, J., Gouriou, L., Lequeux, J., Labourdette, N., Savoye, N., Messiaen, G., Foucault, E., Ouisse, V., Richard, M., Lagarde, F., Voron, F., Kempf, V., Mas, S., Giannecchini, L., Vidussi, F., Mostajir, B., Leredde, Y., Alliouane, S., Gattuso, J.-P., and Gazeau, F.: French coastal network for carbonate system monitoring: the CocoriCO2 dataset, Earth Syst. Sci. Data, 16, 1667–1688

https://doi.org/10.5194/essd-16-1667-2024, 2024.

Pearl Farming Micro-Nanoplastics Affect Oyster Physiology and Pearl Quality

Abstract

Pearl farming is crucial for the economy of French Polynesia. However, rearing structures contribute significantly to plastic waste, and the widespread contamination of pearl farming lagoons by microplastics has raised concerns about risks to the pearl industry. This study aimed to evaluate the effects of micro-nanoplastics (MNPs, 0.4–200 μm) on the pearl oyster (Pinctada margaritifera) over a 5-month pearl production cycle by closely mimicking ecological scenarios. MNPs were produced from weathered plastic pearl farming gear and tested at environmentally relevant concentrations (0.025 and 1 μg L–1) to decipher biological and functional responses through integrative approaches. The significant findings highlighted the impacts of MNPs on oyster physiology and pearl quality, even at remarkably low concentrations. Exposure to MNPs induced changes in energy metabolism, predominantly driven by reduced assimilation efficiency of microalgae, leading to an alteration in gene expression patterns. A distinct gene expression module exhibited a strong correlation with physiological parameters affected by MNP conditions, identifying key genes as potential environmental indicators of nutritional-MNP stress in cultured oysters. The alteration in pearl biomineralization, evidenced by thinner aragonite crystals and the presence of abnormal biomineral concretions, known as keshi pearls, raises concerns about the potential long-term impact on the Polynesian pearl industry.

 

Graphical abstract


 

Keywords
Pearl ; oyster ; micro-nanoplastic exposure ; environmental scenarios ; ecophysiology ; energy metabolism ; functional genomics ; pearl cycle

Reference
Gardon, Tony, Jeremy Le Luyer, Gilles Le Moullac, Claude Soyez, Fabienne Lagarde, Alexandre Dehaut, Ika Paul-Pont, et Arnaud Huvet. « Pearl Farming Micro-Nanoplastics Affect Oyster Physiology and Pearl Quality ». ENVIRONMENTAL SCIENCE & TECHNOLOGY 58, no 1 (9 janvier 2024): 207‑18. https://doi.org/10.1021/acs.est.3c06684.

A critical review on the evaluation of toxicity and ecological risk assessment of plastics in the marine environment

Abstract

The increasing production of plastics together with the insufficient waste management has led to massive pollution by plastic debris in the marine environment. Contrary to other known pollutants, plastic has the potential to induce three types of toxic effects: physical (e.g intestinal injuries), chemical (e.g leaching of toxic additives) and biological (e.g transfer of pathogenic microorganisms). This critical review questions our capability to give an effective ecological risk assessment, based on an ever-growing number of scientific articles in the last two decades acknowledging toxic effects at all levels of biological integration, from the molecular to the population level. Numerous biases in terms of concentration, size, shape, composition and microbial colonization revealed how toxicity and ecotoxicity tests are still not adapted to this peculiar pollutant. Suggestions to improve the relevance of plastic toxicity studies and standards are disclosed with a view to support future appropriate legislation.

 

Graphical Abstract



Highlignts

  • Recurrent toxic effects of plastic debris seen from molecular to population levels.
  • Tested conditions (concentration, type, size, shape) lack environmental relevancy.
  • Environmental studies on plastic debris are scarce.
  • Actual toxicity standards are not adapted to plastic.

Reference

David Leistenschneider, Adèle Wolinski, Jingguang Cheng, Alexandra ter Halle, Guillaume Duflos, Arnaud Huvet, Ika Paul-Pont, Franck Lartaud, François Galgani, Édouard Lavergne, Anne-Leila Meistertzheim, Jean-François Ghiglione, A critical review on the evaluation of toxicity and ecological risk assessment of plastics in the marine environment, Science of The Total Environment, Vol 896, 2023

Read the paper, published in Open Access
https://doi.org/10.1016/j.scitotenv.2023.164955