3.1. Archaeal community composition and diversity
Archaeal α-diversity (Shannon and Chao1 indices) varied among different
soil types (Fig. S1, p < 0.05). Generally, soils with
medium pH (6.0 < pH < 7.0) showed higher archaeal
α-diversity than soils with pH over 7.5. Archaeal community composition
also differed between the different sites (Fig. S1).Crenarchaeota was the most abundant in most samples at the phylum
level, accounting for 20% to 70% of total archaea, followed byHalobacterota (1% to 70%) as the second most abundant phylum
(Fig. S2). The relative abundance of Euryarchaeota andThermoplasmatota was 2%–33% and 5%–20%, respectively.Asgardarchaeota and Micrarchaeota were also detected in
some samples with lower relative abundance. Bathyarchaiea andNitrososphaeria were the two most dominant classes in most
samples at the class level (Fig. 2a). However, the relative abundance ofBathyarchaeia differed drastically among different sites, ranging
from 3% to 68% of total archaea. Methanosarcinia andMethanobacteria were also detected at relatively high abundance
in most samples, which belong to Halobacterota andEuryarchaeota , respectively.
3.2. Distribution and diversity
ofBathyarchaeia
in paddy soils
The α-diversity of Bathyarchaeia in various paddy soils exhibited
significant differences among distinct paddy soils, with the Shannon
index ranging from 2.16 to 5.63 (refer to Fig. S3, p <
0.05). Notably, soils characterized by a pH > 7.5 displayed
a reduced Bathyarchaeial α-diversity when compared to soils with a pH
< 7.5. Furthermore, the NMDS analysis indicated thatBathyarchaeia within paddy soils clustered distinctly based on
the sampling sites and pH (see Fig. S3).
In the aggregate, five subgroups (Bathy-6 , Bathy-11 ,Bathy-15 , Bathy-17, and Bathy-5bb ) were identified
within all the paddy soils (Fig. 2b). Bathy-6 constituted the
predominant subgroup across most samples, accounting for 70% to 80% of
the total Bathyarchaeia (as depicted in Fig. 2c). Conversely,Bathy-11 , Bathy-17, and Bathy-5bb were detected as
less prevalent groups in numerous samples. It is noteworthy that paddy
soils in Southeast China exhibited a higher relative abundance ofBathy-6 in comparison to their counterparts in Northwest China
(Fig. S4).
The heatmap, based on the 40 most abundant Bathyarchaeial ASVs, was
generated with a focus on soil pH
(as
demonstrated in Fig. 2d). Out of the 40 most abundant Bathyarchaeial
ASVs, 36 ASVs were affiliated with Bathy-6 , while three
ASVs
were associated with Bathy-15 , and one ASV was linked toBathy-17 . Furthermore, soil pH had a substantial impact on the
distribution of these dominant ASVs (see Fig. 2d). Notably, two ASVs
(ASV1970 and ASV1998) affiliated with Bathy-6 were present at
elevated levels in all the samples. Nevertheless, most other ASVs were
solely detected in samples with acidic soil conditions (pH <
7.0).
3. 3.
Bathyarchaeial community assembly in paddy soils
The NCM results at ASV levels indicated that stochastic processes were
dominant in archaea community assembly, with an R2value of 0.613 (Fig. 3a). We found that 86.2%
of archaeal ASVs and 87.0% of
Bathyarchaeial ASVs fitted to the neutral model, indicating that a
majority of archaeal ASVs assembled
in paddy soils following stochastic processes. However, the neutral
model fitted ASVs accounted for only 40.9% and 47.0% relative
abundance of total archaeal and Bathyarchaeial community, respectively.
Approximately 12.6% of Bathyarchaeial ASVs deviated from the neutral
expectation, accounting for more than 45.0% relative abundance. These
results indicate that most low-abundance Bathyarchaeia assembled
following stochastic processes, whereas high-abundanceBathyarchaeia mainly assembled following deterministic processes.
This phenomenon can be further supported by the assembly process of the
highest abundant Bathy-6 (Fig. 2), exhibiting a higher percentage
of the deterministic process (about 38.5%) than total archaea (13.8%)
and total Bathyarchaeia (13%, Fig. 3b).
Among the 13% of Bathyarchaeial ASVs that diverged from neutral
expectations, 12.6% were more frequently observed than anticipated by
the NCM prediction, indicating that they exceeded the neutral
prediction. ASVs exceeding the prediction are believed to possess
greater migratory capabilities and a heightened ability to relocate to
new habitats. Notably, Bathy-6 , as previously mentioned, was the
most prevalent Bathyarchaeial subgroup and exhibited a higher proportion
of ASVs surpassing the NCM prediction compared to other archaea andBathyarchaeia . This suggests that Bathy-6 may have more
robust migratory abilities and experience less constraint on dispersal
than other subgroups. The breadth of ecological niches at the class
level, as determined by the null model, was computed to assess the
diversity of resource utilization among Bathyarchaeia . The
outcomes demonstrated that the niche width of Bathyarchaeia in
paddy soils surpassed that of other archaea, indicating a greater
diversity in resource utilization among Bathyarchaeia in paddy soils (as
visualized in Fig. 3c).