Habitat specificity and co-occurrence network of bacterial communities in the Xincuntun Cave, Guilin, Guangxi

Cheng, Xiaoyu; Zeng, Zhilin; Yang, Ziyin; Liu, Xiaoyan; Wang, Hongmei; Ma, Liang; Lu, Xiaolu; Su, Chuntian; Qibo, Huang

doi:10.1360/tb-2021-0021

Cited by 5 publications

(5 citation statements)

References 40 publications

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“…The alpha diversity of bacterial communities was higher in sediments than in the weathered rocks in the Chang Cave, consistent with observations in other caves (Ma et al, 2021;Ai et al, 2022). Moreover, our observation of the difference in the beta diversity between weathered rocks and sediments was also reported in other caves in Guilin city (Cao et al, 2021;Yang et al, 2021). These differences in bacterial diversities are likely results from the nitrate impact.…”

Section: Nitrate Impact Differently On Bacterial Communities In Weath...supporting

confidence: 91%

“…Consistent with previous studies (Cao et al, 2021;Ma et al, 2021;Yang et al, 2021), nodes in the co-occurrence network of weathered rocks and sediments were mostly positively linked (88.9% and 84.64%, respectively; Figures 5A-D), which suggested a prevalence of collaboration rather than competition to overcome nutrient limitation in oligotrophic caves. The higher modularity of Co-NW indicated that bacterial populations form closer collective structures, in which they mainly cooperated and established mutualistic relationships to maintain the stability of the ecosystem.…”

Section: Bacterial Interactions and Functionssupporting

confidence: 91%

“…For example, microbial communities therein show a high habitat specialization and respond differently to environmental variables ( Yang et al, 2021 ). TOC and pH have been reported to modulate bacterial communities in the Heshang Cave and the Xincuntun Cave across different habitats ( Yun et al, 2016a ; Cao et al, 2021 ). In the Luohandu Cave, for example, electrical conductivity and dissolved oxygen appear to influence microbial communities in dripping water and pool water, and those in sediments and weathered rocks are shaped by temperature, Ca/Mg, and sulfate ( Yang et al, 2021 ), but these variables give little insight into understanding the underlying microbial biology.…”

Section: Introductionmentioning

confidence: 99%

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Nitrate determines the bacterial habitat specialization and impacts microbial functions in a subsurface karst cave

Liu

Wang²,

Wang³

et al. 2023

Front. Microbiol.

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Karst caves are usually considered as natural laboratories to study pristine microbiomes in subsurface biosphere. However, effects of the increasingly detected nitrate in underground karst ecosystem due to the acid rain impact on microbiota and their functions in subsurface karst caves have remained largely unknown. In this study, samples of weathered rocks and sediments were collected from the Chang Cave, Hubei province and subjected to high-throughput sequencing of 16S rRNA genes. The results showed that nitrate significantly impacted bacterial compositions, interactions, and functions in different habitats. Bacterial communities clustered according to their habitats with distinguished indicator groups identified for each individual habitat. Nitrate shaped the overall bacterial communities across two habitats with a contribution of 27.2%, whereas the pH and TOC, respectively, structured bacterial communities in weathered rocks and sediments. Alpha and beta diversities of bacterial communities increased with nitrate concentration in both habitats, with nitrate directly affecting alpha diversity in sediments, but indirectly on weathered rocks by lowering pH. Nitrate impacted more on bacterial communities in weathered rocks at the genus level than in sediments because more genera significantly correlated with nitrate concentration in weathered rocks. Diverse keystone taxa involved in nitrogen cycling were identified in the co-occurrence networks such as nitrate reducers, ammonium-oxidizers, and N2-fixers. Tax4Fun2 analysis further confirmed the dominance of genes involved in nitrogen cycling. Genes of methane metabolism and carbon fixation were also dominant. The dominance of dissimilatory and assimilatory nitrate reduction in nitrogen cycling substantiated nitrate impact on bacterial functions. Our results for the first time revealed the impact of nitrate on subsurface karst ecosystem in terms of bacterial compositions, interactions, and functions, providing an important reference for further deciphering the disturbance of human activities on the subsurface biosphere.

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Section: Nitrate Impact Differently On Bacterial Communities In Weath...supporting

confidence: 91%

Section: Bacterial Interactions and Functionssupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

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Nitrate determines the bacterial habitat specialization and impacts microbial functions in a subsurface karst cave

Liu

Wang²,

Wang³

et al. 2023

Front. Microbiol.

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“…Karst caves are known as subsurface extreme ecosystems with twilight or dark conditions, nutrient deprivation and isolation from the surficial environments, which harbor numerous chemoautotrophic microorganisms ( Marques et al, 2019 ). Currently, progresses have been made on microbial communities, niche differentiation, community assembly and their correlation with environmental variables ( Yun et al, 2016 ; Zhao et al, 2017 ; Cheng et al, 2019 , 2021 , 2022 ; Cao et al, 2021 ). Bacteria, microalgae, and fungi are found to be involved in the elemental cycles of carbon, nitrogen, sulfur, manganese, and iron, as well as in the dissolution and precipitation of limestone ( Grobbelaar, 2000 ; Mulec, 2008 ; Sebela et al, 2015 ; Jones and Northup, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

“…Ecological guilds exhibit different community structures due to different responses to environmental selection ( Zhao et al, 2019b ). Studies have clearly demonstrated the strong niche specificity of bacterial communities in loose sediments and those living on weathered rocks ( Cao et al, 2021 ; Liu X. Y. et al, 2023 ) as well as for methanotrophs ( Cheng et al, 2022 ), which may be also true in microbial functional groups involved in nitrification. If it is the case, what ecological processes contribute to the differences in ammonia-oxidizing communities in different niches in karst caves?…”

Section: Introductionmentioning

confidence: 99%

Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts

Li,

Cheng,

Liu

et al. 2024

Front. Microbiol.

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Subsurface karst caves provide unique opportunities to study the deep biosphere, shedding light on microbial contribution to elemental cycling. Although ammonia oxidation driven by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is well explored in soil and marine environments, our understanding in the subsurface biosphere still remained limited to date. To address this gap, weathered rock and sediment samples were collected from the Xincuntun Cave in Guilin City, an alkaline karst cave, and subjected to high-throughput sequencing and quantification of bacterial and archaeal amoA, along with determination of the potential nitrification rates (PNR). Results revealed that AOA dominated in ammonia oxidation, contributing 48–100% to the PNR, and AOA amoA gene copies outnumbered AOB by 2 to 6 orders. Nitrososphaera dominated in AOA communities, while Nitrosopira dominated AOB communities. AOA demonstrated significantly larger niche breadth than AOB. The development of AOA communities was influenced by deterministic processes (50.71%), while AOB communities were predominantly influenced by stochastic processes. TOC, NH4+, and Cl− played crucial roles in shaping the compositions of ammonia oxidizers at the OTU level. Cross-domain co-occurrence networks highlighted the dominance of AOA nodes in the networks and positive associations between AOA and AOB, especially in the inner zone, suggesting collaborative effort to thrive in extreme environments. Their high gene copies, dominance in the interaction with ammonia oxidizing bacteria, expansive niche breadth and substantial contribution to PNR collectively confirmed that AOA better adapted to alkaline, oligotrophic karst caves environments, and thus play a fundamental role in nitrogen cycling in subsurface biosphere.

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Water quality determines protist taxonomic and functional group composition in a high-altitude wetland of international importance

Liu

Pan

et al. 2023

Science of The Total Environment

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Habitat specificity and co-occurrence network of bacterial communities in the Xincuntun Cave, Guilin, Guangxi

Cited by 5 publications

References 40 publications

Nitrate determines the bacterial habitat specialization and impacts microbial functions in a subsurface karst cave

Nitrate determines the bacterial habitat specialization and impacts microbial functions in a subsurface karst cave

Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts

Water quality determines protist taxonomic and functional group composition in a high-altitude wetland of international importance

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