Diverse Bathyarchaeotal Lineages Dominate Archaeal Communities in the Acidic Dajiuhu Peatland, Central China

Xiao, Xiang; Xiang, Xing; Man, Baiying; Xu, Ying; Gong, Li; Yang, Huan

doi:10.1007/s00248-022-01990-1

Cited by 5 publications

(6 citation statements)

References 80 publications

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“…2 ), respectively. These results suggest that Bathyarchaeota was also dominant in aerobic paddy soil, and broadened previous prescription that Bathyarchaeota are generalists in anaerobic environments such as sediments ( 5 ), peatland ( 59 ), and anaerobic digestion system ( 9 ), which will expand our understanding of Bathyarchaeota.…”

Section: Discussionsupporting

confidence: 75%

“…In addition, Bathy-15 and Bathy-5bb were two other abundant subgroups in paddy soils with average relative abundance more than 1% ( Fig. 5B ), while their abundance was much lower compared to those detected in freshwater sediments ( 5 , 59 ). However, Bathy-1 and Bathy-8, which are Bathyarchaeota indicator lineages of marine sediments ( 20 ), were almost undetected in paddy soils analyzed in this study.…”

Section: Discussionmentioning

confidence: 90%

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Global biogeographic distribution of Bathyarchaeota in paddy soils

Xue

Cui

et al. 2023

mSystems

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Bathyarchaeota, known as key participants of global elements cycling, is highly abundant and diverse in the sedimentary environments. Bathyarchaeota has been the research spotlight on sedimentary microbiology; however, its distribution in arable soils is far from understanding. Paddy soil is a habitat similar to freshwater sediments, while the distribution and composition of Bathyarchaeota in paddy soils have largely been overlooked. In this study, we collected 342 in situ paddy soil sequencing data worldwide to illuminate the distribution patterns of Bathyarchaeota and explore their potential ecological functions in paddy soils. The results showed that Bathyarchaeota is the dominant archaeal lineage, and Bathy-6 is the most predominant subgroup in paddy soils. Based on random forest analysis and construction of a multivariate regression tree, the mean annual precipitation and mean annual temperature are identified as the factors significantly influencing the abundance and composition of Bathyarchaeota in paddy soils. Bathy-6 was abundant in temperate environments, while other subgroups were more abundant in sites with higher rainfall. There are highly frequent associations between Bathyarchaeota and methanogens and ammonia-oxidizing archaea. The interactions between Bathyarchaeota and microorganisms involved in carbon and nitrogen metabolism imply a potential syntrophy between these microorganisms, suggesting that members of Bathyarchaeota could be important participants of geochemical cycle in paddy soils. These results shed light on the ecological lifestyle of Bathyarchaeota in paddy soils, and provide some baseline for further understanding Bathyarchaeota in arable soils. IMPORTANCE Bathyarchaeota, the dominant archaeal lineage in sedimentary environments, has been the spotlight of microbial research due to its vital role in carbon cycling. Although Bathyarchaeota has been also detected in paddy soils worldwide, its distribution in this environment has not yet been investigated. In this study, we conducted a global scale meta-analysis and found that Bathyarchaeota is also the dominant archaeal lineage in paddy soils with significant regional abundance differences. Bathy-6 is the most predominant subgroup in paddy soils, which differs from sediments. Furthermore, Bathyarchaeota are highly associated with methanogens and ammonia-oxidizing archaea, suggesting that they may be involved in the carbon and nitrogen cycle in paddy soil. These interactions provide insight into the ecological functions of Bathyarchaeota in paddy soils, which will be the foundation of future studies regarding the geochemical cycle in arable soils and global climate change.

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Section: Discussionsupporting

confidence: 75%

Section: Discussionmentioning

confidence: 90%

Global biogeographic distribution of Bathyarchaeota in paddy soils

Xue

Cui

et al. 2023

mSystems

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“…We found that the degree distribution of the mycobiomes' co-occurrence networks of weathered rocks and sediments in Luohandu cave followed a power law, as usually observed for peat sediment and soil microbial interaction networks [29,45]. The power law distribution was evidenced by analyzing competition, habitat filtering, evolution history and neutral process [46].…”

Section: Ascomycota Dominate the Mycobiome Networksupporting

confidence: 66%

“…To optimize the networks’ specificity and sensitivity, the ASVs were filtered based on abundance (>0.05%) and frequency (>20% of samples); the remaining ASVs (219 vs. 107) were used to calculate the Spearman rank correlations (rho). Significant relations with rho > 0.663 (sediments) and >0.641 (weathered rocks), with p < 0.01, which were determined by the random matrix theory-based approach using the RMThreshold (version:1.1) package [ 29 ], were selected to construct co-occurrence and mutual-exclusion networks using the meconetcomp (version: 0.4.1) package [ 30 ] and visualized by Gephi software (version: 0.9.2). In the co-occurrence networks, the nodes represent the mycobiome ASVs, and the edges reflect significant correlations between them.…”

Section: Methodsmentioning

confidence: 99%

Deconstructing the Dimensions of Mycobiome Fingerprints in Luohandu Cave, Guilin, Southern China

Man,

Xiang,

Cheng

et al. 2024

Microorganisms

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Subterranean karst caves are windows into the terrestrial subsurface to deconstruct the dimensions of mycobiome fingerprints. However, impeded by the constraints of remote locations, the inaccessibility of specimens and technical limitations, the mycobiome of subterranean karst caves has remained largely unknown. Weathered rock and sediment samples were collected from Luohandu cave (Guilin, Southern China) and subjected to Illumina Hiseq sequencing of ITS1 genes. A total of 267 known genera and 90 known orders in 15 phyla were revealed in the mycobiomes. Ascomycota dominated all samples, followed by Basidiomycota and Mortierellomycota. The sediments possessed the relatively highest alpha diversity and were significantly different from weathered rocks according to the diversity indices and richness metrics. Fifteen families and eight genera with significant differences were detected in the sediment samples. The Ca/Mg ratio appeared to significantly affect the structure of the mycobiome communities. Ascomycota appeared to exert a controlling influence on the mycobiome co-occurrence network of the sediments, while Ascomycota and Basidiomycota were found to be the main phyla in the mycobiome co-occurrence network of weathered rocks. Our results provide a more comprehensive dimension to the mycobiome fingerprints of Luohandu cave and a new window into the mycobiome communities and the ecology of subterranean karst cave ecosystems.

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“…The relative abundance of Woesearchaeia and Aenigmarchaeales negatively correlated to TOC ( Figure 3A ), which dominated in DW samples with a relative abundance of 1.31 ± 1.09% and 0.31 ± 0.33%, respectively ( Supplementary Table 2 ). These anaerobes might be brought into the cave by drip water from the anoxic overlying rocks, which performed nutrient complementation with other microbes due to their prominent metabolic shortages ( Castelle et al, 2015 ; Liu et al, 2018 ; Vigneron et al, 2022 ; Xiang et al, 2022 ). NH 4 + concentration significantly impacted on the relative abundances of many archaeal and bacterial groups in the Heshang Cave ( Figures 3A , B ), such as the important taxa of Thermoplasmata , Nitrosopumilaceae , Aenigmarchaeales , Crossiella , Acidothermus , and Solirubrobacter , indicating the significance of NH 4 + in cave ecosystems.…”

Section: Discussionmentioning

confidence: 99%

Archaea and their interactions with bacteria in a karst ecosystem

et al. 2023

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Karst ecosystems are widely distributed around the world, accounting for 15–20% of the global land area. However, knowledge on microbial ecology of these systems does not match with their global importance. To close this knowledge gap, we sampled three niches including weathered rock, sediment, and drip water inside the Heshang Cave and three types of soils overlying the cave (forest soil, farmland soil, and pristine karst soil). All these samples were subjected to high-throughput sequencing of V4-V5 region of 16S rRNA gene and analyzed with multivariate statistical analysis. Overall, archaeal communities were dominated by Thaumarchaeota, whereas Actinobacteria dominated bacterial communities. Thermoplasmata, Nitrosopumilaceae, Aenigmarchaeales, Crossiella, Acidothermus, and Solirubrobacter were the important predictor groups inside the Heshang Cave, which were correlated to NH4+ availability. In contrast, Candidatus Nitrososphaera, Candidatus Nitrocosmicus, Thaumarchaeota Group 1.1c, and Pseudonocardiaceae were the predictors outside the cave, whose distribution was correlated with pH, Ca2+, and NO2−. Tighter network structures were found in archaeal communities than those of bacteria, whereas the topological properties of bacterial networks were more similar to those of total prokaryotic networks. Both chemolithoautotrophic archaea (Candidatus Methanoperedens and Nitrosopumilaceae) and bacteria (subgroup 7 of Acidobacteria and Rokubacteriales) were the dominant keystone taxa within the co-occurrence networks, potentially playing fundamental roles in obtaining energy under oligotrophic conditions and thus maintaining the stability of the cave ecosystem. To be noted, all the keystone taxa of karst ecosystems were related to nitrogen cycling, which needs further investigation, particularly the role of archaea. The predicted ecological functions in karst soils mainly related to carbohydrate metabolism, biotin metabolism, and synthesis of fatty acid. Our results offer new insights into archaeal ecology, their potential functions, and archaeal interactions with bacteria, which enhance our understanding about the microbial dark matter in the subsurface karst ecosystems.

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Diverse Bathyarchaeotal Lineages Dominate Archaeal Communities in the Acidic Dajiuhu Peatland, Central China

Cited by 5 publications

References 80 publications

Global biogeographic distribution of Bathyarchaeota in paddy soils

Global biogeographic distribution of Bathyarchaeota in paddy soils

Deconstructing the Dimensions of Mycobiome Fingerprints in Luohandu Cave, Guilin, Southern China

Archaea and their interactions with bacteria in a karst ecosystem

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