1. Introduction
Archaea drives a series of global biogeochemical cycling of carbon and nitrogen (Baker et al. 2020; Bates et al. 2011; Offre et al. 2013).Bathyarchaeia belongs to the kingdom archaea, which was initially discovered in hot springs. They were previously placed in theMiscellaneous Crenarchaeotal Group (MCG) (Barns et al. 1996; Inagaki et al. 2003). Bathyarchaeia has been found in various other environments, including sediments, volcanic mud, termite guts, bioreactors, and soils (Calusinska et al. 2018; Loh et al. 2020; Pan et al. 2019; Xiang et al. 2017; Yu et al. 2017; Zou et al. 2020).Bathyarchaeia is highly abundant in marine sediments, making them one of the most abundant groups of microorganisms on the earth (He et al. 2016; Zhou et al. 2018; Zou et al. 2020). However, previous studies on Bathyarchaeia have mainly focused on sediments, whereas the distribution ofBathyarchaeia in arable soils is not much studied.
To date, pure cultures of Bathyarchaeia have not been successfully isolated. However, cultivation-independent studies suggest that this group of organisms possesses high physiological and metabolic diversity (Lewis et al. 2021). Members of Bathyarchaeia can grow on different substrates, such as detrital proteins, polymeric carbohydrates, fatty acids, methane, and other organic matter (Evans et al. 2015; Lazar et al. 2016; Pan et al. 2020). Four genomes ofBathyarchaeia were reconstructed from White Oak River sediments. They contained genes encoding enzymes involved in acetogenesis using the reductive acetyl-CoA pathway, indicating an anaerobic lifestyle (Lazar et al. 2016). Furthermore, some Bathyarchaeia members are likely to perform dissimilatory nitrite reduction to ammonium (Lazar et al. 2016), and a possible role in methane metabolism has also been suggested (Evans et al. 2015). A previous study reported that supplementing rice paddy soil with fulvic acid significantly increased the relative abundance of Bathyarchaeia (Yi et al. 2019). Therefore,Bathyarchaeia may play a role in the biodegradation of humus, which is abundantly present in paddy soils due to the slow microbial decomposition of plant and animal residues under flooding conditions. Paddy soil is an active zone of global carbon and nitrogen cycling. Therefore, studying the distribution and activity ofBathyarchaeia can be important for food production and climate change regulation.
Previous phylogenetic studies have classified Bathyarchaeia into 25 subgroups (Rinke et al. 2021; Zhou et al. 2018), and different subgroups exhibit different ecological functions and distribution. Therefore, elucidating the mechanisms underlyingBathyarchaeia biogeography and community assembly in paddy soils can help predict corresponding ecological processes. Generally, the microbial community assembly can be described using the Niche-based theory or Neutral-based theory (Hanson et al. 2012; Zhou & Ning 2017). Niche-based approaches consider that the community structure is influenced primarily by deterministic processes such as environmental filtering and species interactions (Chase and Myers 2011; Jiao et al. 2019). For instance, previous studies have revealed that the specific Bathyarchaeia subgroups show niche differentiation and exhibit different habitat preferences. Members of Bathy-6 grow in suboxic zones and sulfide-depleted shallow layers of sediments, whereas members of Bathy-8 prefer deeper and anoxic layers (Lazar et al. 2015). Furthermore, Bathy-8 is considered an indicator of saline environments (Lazar et al. 2015), whereas Bathy-11 and Bathy-5 are indicators of freshwater environments (Fillol et al. 2016). Moreover, salinity and total organic matter (TOC) are crucial factors affecting the abundance and composition of the Bathyarchaeia community (Pan et al. 2019; Yu et al. 2017; Zou et al. 2020). The neutral theory hypothesizes that all individuals are ecologically identical, and the community structure is primarily influenced by stochastic processes such as random death and dispersal (Hubbell 2004; Tilman 2004). Stochastic processes play crucial roles in influencing microbial community structures in various environments (Chen et al. 2019; Zhou & Ning 2017). However, the assembly processes of theBathyarchaeia community have garnered less attention in arable soils.
A recent global meta-analysis reported that Bathyarchaeia is globally distributed in paddy soils with high abundance, and the predominant subgroup is Bathy-6 (Xue et al. 2023). The meta-analysis showed that the mean annual precipitation and the mean annual temperature could be associated with the relative abundance of Bathyarchaeia and Bathyarchaeial community structure, respectively (Xue et al. 2023). However, this meta-analysis had some limitations, such as the limited availability of soil physicochemical parameters data and distribution. Therefore, studying niche differentiation governed by soil type-related factors was difficult. Furthermore, it is important to note that this meta-analysis could potentially be affected by various additional factors associated with soil management practices, including irrigation, anthropogenic interventions like flooding, the specific growth stages of rice, and the absence of uniform approaches for soil sampling procedures (e.g., sampling depth), DNA extraction techniques, and primer selection for sequencing. Such disparities can introduce potential biases into the results. Consequently, our approach involved the sampling of paddy soils from contrasting pedoclimatic regions across eastern China, all at the same stage of rice growth. We then conducted an examination of their taxonomic composition through Illumina sequencing of the 16S rRNA genes. The primary objectives of this study encompassed characterizing the composition and diversity of Bathyarchaeia in paddy soils across eastern China, exploring the mechanisms governing the assembly ofBathyarchaeia communities in paddy soil, and delving into the differentiation of ecological niches and potential ecological functions of Bathyarchaeia within paddy soils.