Cultivation and metabolic versatility of novel and ubiquitous chemolithoautotrophic Campylobacteria from mangrove sediments

Abstract

Chemolithoautotrophic members from the Campylobacteria class are dominant key players in sulfidic habitats, where they make up a stable portion of sulfide-oxidizing bacterial communities. Nevertheless, few isolates have so far been cultivated and studied in situ, and most are derived from chemosynthetic ecosystems, limiting our understanding of their physiological and metabolic features as well as ecological roles in the global marine environments. In this study, seven potentially new species were successfully isolated from mangrove sediments and further diverged into three potentially new genera within the class Campylobacteria. These isolates were obligate chemolithoautotrophs that could grow through hydrogen oxidation as well as sulfur oxidation, reduction, and disproportionation. Metabolic reconstructions revealed that these isolates contained diverse sulfide:quinone oxidoreductase and flavocytochrome c sulfide dehydrogenase for sulfide oxidation, distinct Sox gene cluster for sulfur oxidation, as well as group I, II, and IV hydrogenases for hydrogen consumption and production. Notably, these strains lacked the complete denitrification pathway, instead having all genes for nitrogen fixation, which might facilitate their survival in the nitrogen-limited mangrove sediments. Moreover, they also demonstrated the ability to adapt to low O₂ conditions, such as a more efficient 2-oxoglutarate:ferredoxin oxidoreductase complex for CO₂ fixation and diverse terminal oxidases including Cco, Cox, and Cyd. Metatranscriptomic analysis further confirmed their activity and different adaptation mechanisms in in situ mangrove sediments. Assessing their occurrences indicated that these lineages were globally distributed in hypoxic and anoxic environments and dominant members of marine and mangrove sediments. Overall, these results indicate that these new Campylobacteria members are metabolically versatile and play an underappreciated role in the biogeochemical cycling of carbon-rich mangrove sediments.IMPORTANCEChemolithoautotrophic Campylobacteria spp. are generally associated with sulfide-rich environments, where they play a key role in the cycling of carbon, nitrogen, and sulfur. Yet, only a limited number of cultured isolates are currently available. In this study, we isolated seven potentially new species belonging to three new genera from mangrove sediments, which significantly expanded our understanding of the species diversity within the class Campylobacteria. These isolates demonstrated diverse and unique metabolic potentials for CO₂ fixation, sulfur oxidation, hydrogen oxidation, nitrogen metabolism, and oxygen respiration, making them well adapted to the sulfur-rich, nitrogen-limited, and low-oxygen habitats they inhabit. The frequent detection of these novel species in marine and mangrove sediments, as revealed by 16S rRNA gene sequences in public databases, indicates a potential preference for oxygen-limited environments. Overall, this study promotes our understanding of the in situ function and ecological role of Campylobacteria, especially in previously overlooked carbon-rich sediment ecosystems.

Keywords: Campylobacteria; biogeochemical cycles; chemolithoautotrophic; in situ; mangrove sediments; metatranscriptomic.