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.