Halophilic archaea within the class Halobacteria (phylum Halobacteriota, domain Archaea) are extremophilic microorganisms relying on hypersaline environments for growth and they usually require a salt concentration of at least 15% (2.5 mol/L) for optimal growth (Cui and Dyall-Smith, 2021). These archaea were mostly found in salt lakes, salt ponds, salt marshes, and extremely salt lagoons (Martínez-Espinosa, 2024; Oren, 2024). They survive in hypersaline environments by employing adaptive strategies such as combining the “salt-in” strategy and the “compatible-solute” strategy to cope with the osmotic stress (Oren, 1999). Beyond this core osmoregulatory capacity, many strains further possess diverse metabolic functions that remain operational under such extreme conditions. For instance, some halophilic archaeal strains can decompose compounds (such as phenols, mercury, uranium) that are highly toxic to most living organisms (Martínez-Espinosa, 2024). Their extracellular polymers, such as extracellular polysaccharides, solubilize hydrophobic organic compounds employing emulsification activity (Vandana et al., 2023), and destroy phenols through ortho-cleavage route, thus playing an important role in degrading pollutants in high-salt industrial wastewater (Liu et al., 2022a). Therefore, halophilic archaea are not only ideal models for the study of adaptation mechanism to extreme environments, but also provide promising biological resources for the treatment of high-salinity pollutants and for applications in green biomanufacturing. However, advancing in both basic and applied research is contingent upon a robust and expanding taxonomic framework. Hence, taxonomic studies aimed at discovering and characterizing novel halophilic archaea remain crucial.

The family Haladaptataceae was proposed in 2023 and currently consists of 3 genera, Haladaptatus, Halomicrococcus, and Halorussus (Cui et al., 2023). The genera Haladaptatus and Halomicrococcus of Haladaptataceae were described for the first time in 2007 and 2020, respectively (Chen et al., 2020; Savage et al., 2007). They currently contain seven and two species with validly published names, respectively (https://lpsn.dsmz.de/family/Haladaptataceae). The current species of the genus Haladaptatus are spherical in cell morphology, forming red, pink or white colonies on agar plates, and capable of growing at a wide range of temperatures (15–55 °C), NaCl concentrations (0.8 M to saturated), and pH (5.0–9.5). The main polar lipids are phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulfate (PGS), sulfated mannosyl glucosyl diether (S-DGD-1), and one to three unidentified glycolipids. The genome sizes of current species range from 3.93 Mbp to 7.28 Mbp, with GC content of 56.1–62.1% (Li et al., 2024; Roh et al., 2010; Savage et al., 2007; Xin et al., 2022; Cui et al., 2010b). Strains of the genus Halomicrococcus are cocci, forming pale pink colonies on agar plates, and can grow across a wide range of temperatures (20–55 °C), NaCl concentrations (1.4–5.1 M), and pH (5.5–9.0). The main polar lipids are phosphatidic acid (PA), PG, PGP-Me, S-DGD-1, sulfated galactosyl mannosyl glucosyl diether (S-TGD-1), and galactosyl mannosyl glucosyl diether (TGD-2). The genome sizes of currently described species range from 3.72 Mbp to 5.61 Mbp, and the GC content is 63.0–67.9% (Chen et al., 2020; Hu et al., 2024).

In this study, metagenome and amplicon sequencing analyses were integrated to reveal the halophilic archaeal diversity of sediment samples from Dafeng tidal flat, Nangang tidal flat, Honghaitan tidal flat, and Shengang tidal flat. Based on phenotypic characteristics, phylogenetic analysis, genomic taxonomy, and comparative genomics, strains DFWS20T, NG-SE-30T, NG-WS-4T, and HHT-WS-8 were proposed as novel species of the genus Haladaptatus, while strains NG-SE-24T and SG-WS-1 as a novel species of the genus Halomicrococcus.