Subtropical coastal microbiome variations due to massive river runoff after a cyclonic event

Type Article
Date 2024-01
Language English
Author(s) Meyneng Mathisse1, Lemonnier HuguesORCID2, Le Gendre RomainORCID2, Antypas Florence2, Ansquer Dominique2, Serghine Joelle1, Schmitt Sophie1, Siano Raffaele1
Affiliation(s) 1 : IFREMER, DYNECO, BP70, Plouzané, France
2 : French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
Source Environmental Microbiome (2524-6372) (BMC), 2024-01 , Vol. 19 , N. 1 , P. 10 (24p.)
DOI 10.1186/s40793-024-00554-9
Keyword(s) Microbial dynamics, Environmental DNA, Extreme events, River runoff, Land-sea continuum, New Caledonia


Coastal ecosystem variability at tropical latitudes is dependent on climatic conditions. During the wet, rainy season, extreme climatic events such as cyclones, precipitation, and winds can be intense over a short period and may have a significant impact on the entire land‒sea continuum. This study focused on the effect of river runoff across the southwest coral lagoon ecosystem of Grand Terre Island of New Caledonia (South Pacific) after a cyclonic event, which is considered a pulse disturbance at our study site. The variability of coastal microbiomes, studied by the metabarcoding of V4 18S (protists) and V4–V5 16S (bacteria) rDNA genes, after the cyclone passage was associated with key environmental parameters describing the runoff impact (salinity, organic matter proxies, terrestrial rock origin metals) and compared to community structures observed during the dry season.


Microbiome biodiversity patterns of the dry season were destructured because of the runoff impact, and land-origin taxa were observed in the coastal areas. After the rainy event, different daily community dynamics were observed locally, with specific microbial taxa explaining these variabilities. Plume dispersal modeling revealed the extent of low salinity areas up to the coral reef area (16 km offshore), but a rapid (< 6 days) recovery to typical steady conditions of the lagoon's hydrology was observed. Conversely, during the same time, some biological components (microbial communities, Chl a) and biogeochemical components (particulate nickel, terrigenous organic matter) of the ecosystem did not recover to values observed during the dry season conditions.


The ecosystem resilience of subtropical ecosystems must be evaluated from a multidisciplinary, holistic perspective and over the long term. This allows evaluating the risk associated with a potential continued and long-term disequilibrium of the ecosystem, triggered by the change in the frequency and intensity of extreme climatic events in the era of planetary climatic changes.

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Publisher's official version 24 8 MB Open access
Additional methodological information with more details of the sampling site, laboratory procedures and functional classification of the communities. 7 MB Open access
Supporting information with the description of the ecological descriptors and the detailed spatial gradient illustrated by community composition. Table S1: Details of all sampling stations. Figure ... 3 MB Open access
Dataset including all environmental parameters generated and analyzed in this study. 19 KB Open access
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How to cite 

Meyneng Mathisse, Lemonnier Hugues, Le Gendre Romain, Antypas Florence, Ansquer Dominique, Serghine Joelle, Schmitt Sophie, Siano Raffaele (2024). Subtropical coastal microbiome variations due to massive river runoff after a cyclonic event. Environmental Microbiome, 19(1), 10 (24p.). Publisher's official version : , Open Access version :