Long-term patterns of an interconnected core marine microbiota

24 pages, 5 figures, 6 tables, supplementary information https://doi.org/10.1186/s40793-022-00417-1

Background: Ocean microbes constitute ~ 70% of the marine biomass, are responsible for ~ 50% of the Earth’s primary production and are crucial for global biogeochemical cycles. Marine microbiotas include core taxa that are usually key for ecosystem function. Despite their importance, core marine microbes are relatively unknown, which reflects the lack of consensus on how to identify them. So far, most core microbiotas have been defined based on species occurrence and abundance. Yet, species interactions are also important to identify core microbes, as communities include interacting species. Here, we investigate interconnected bacteria and small protists of the core pelagic microbiota populating a long-term marine-coastal observatory in the Mediterranean Sea over a decade. Results: Core microbes were defined as those present in > 30% of the monthly samples over 10 years, with the strongest associations. The core microbiota included 259 Operational Taxonomic Units (OTUs) including 182 bacteria, 77 protists, and 1411 strong and mostly positive (~ 95%) associations. Core bacteria tended to be associated with other bacteria, while core protists tended to be associated with bacteria. The richness and abundance of core OTUs varied annually, decreasing in stratified warmers waters and increasing in colder mixed waters. Most core OTUs had a preference for one season, mostly winter, which featured subnetworks with the highest connectivity. Groups of highly associated taxa tended to include protists and bacteria with predominance in the same season, particularly winter. A group of 13 highly-connected hub-OTUs, with potentially important ecological roles dominated in winter and spring. Similarly, 18 connector OTUs with a low degree but high centrality were mostly associated with summer or autumn and may represent transitions between seasonal communities. Conclusions: We found a relatively small and dynamic interconnected core microbiota in a model temperate marine-coastal site, with potential interactions being more deterministic in winter than in other seasons. These core microbes would be essential for the functioning of this ecosystem over the year. Other non-core taxa may also carry out important functions but would be redundant and non-essential. Our work contributes to the understanding of the dynamics and potential interactions of core microbes possibly sustaining ocean ecosystem function.

RL was supported by a Ramón y Cajal fellowship (RYC-2013-12554, MINECO, Spain). IMD was supported by an ITN-SINGEK fellowship (ESR2-EU-H2020-MSCA-ITN-2015, Grant Agreement 675752 [ESR2] to RL). This work was supported by the projects INTERACTOMICS (CTM2015-69936-P, MINECO, Spain to RL), MicroEcoSystems (240904, RCN, Norway to RL), MINIME (PID2019-105775RB-I00, AEI, Spain, to RL), ALLFLAGS (CTM2016-75083-R, MINECO to RM), MIAU (RTI2018-101025-B-I00, to JMG) and DEVOTES (grant agreement n° 308392, European Union to EG). It was further supported by Grup Consolidat de Recerca 2017SGR/1568 (Generalitat de Catalunya). [...] With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)