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

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.

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

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.

Niche differentiation of atmospheric methane-oxidizing bacteria and their community assembly in subsurface karst caves.

Karst caves are recently proposed as atmospheric methane sinks in terrestrial ecosystems. Despite of the detection of atmospheric methane-oxidizing bacteria (atmMOB) in caves, we still know little about their ecology and potential ability of methane oxidation in this ecosystem. To understand atmMOB ecology and their potential in methane consumption, we collected weathered rocks and sediments from three different caves in southwestern China. We determined the potential methane oxidization rates in the range of 1.25 ± 0.08 to 1.87 ± 0.41 ng CH4  g-1 DW h-1 , which are comparable to those reported in forest and grassland soils. Results showed that alkaline oligotrophic caves harbour high numbers of atmMOB, particularly upland soil cluster (USC), which significantly correlated with temperature, CH4 and CO2 concentrations. The absolute abundance of USCγ was higher than that of USCα. USCγ-OPS (open patch soil) and USCγ-SS (subsurface soil) dominated in most samples, whereas USCα-BFS (boreal forest soil) only predominated in the sediments near cave entrances, indicating niche differentiation of atmMOB in caves. Overwhelming dominance of homogenous selection in community assembly resulted in convergence of atmMOB communities. Collectively, our results demonstrated the niche differentiation of USC in subsurface alkaline caves and their non-negligible methane-oxidizing potential, providing brand-new knowledge about atmMOB ecology in subsurface biosphere.

USCγ Dominated Community Composition and Cooccurrence Network of Methanotrophs and Bacteria in Subterranean Karst Caves.

Karst caves have recently been demonstrated to act as a sink for atmospheric methane, due in part to consumption by microbes residing in caves that can oxidize methane at atmospheric levels. However, our knowledge about the responsible atmospheric methane-oxidizing bacteria (atmMOB) in this vast habitat remains limited to date. To address this issue, weathered rock samples from three karst caves were collected in Guilin City and subjected to high-throughput sequencing of pmoA and 16S rRNA genes. The results showed that members of the high-affinity upland soil cluster (USC), especially upland soil cluster gamma (USCγ), with absolute abundances of 104 to 109 copies · g-1 dry sample, dominated the atmMOB communities, while Proteobacteria and Actinobacteria dominated the overall bacterial communities. Moreover, USCγ was a keystone taxon in cooccurrence networks of both the atmMOB and the total bacterial community, whereas keystone taxa in the bacterial network also included Gaiella and Aciditerrimonas. Positive links overwhelmingly dominated the cooccurrence networks of both atmMOB and the total bacterial community, indicating a consistent response to environmental disturbances. Our study shed new insights on the diversity and abundances underlining atmMOB and total bacterial communities and on microbial interactions in subterranean karst caves, which increased our understanding about USC and supported karst caves as a methane sink. IMPORTANCE Karst caves have recently been demonstrated to be a potential atmospheric methane sink, presumably due to consumption by methane-oxidizing bacteria. However, the sparse knowledge about the diversity, distribution, and community interactions of methanotrophs requires us to seek further understanding of the ecological significance of methane oxidation in these ecosystems. Our pmoA high-throughput results from weathered rock samples from three karst caves in Guilin City confirm the wide occurrence of atmospheric methane-oxidizing bacteria in this habitat, especially those affiliated with the upland soil cluster, with a gene copy number of 104 to 109 copies per gram dry sample. Methanotrophs and the total bacterial communities had more positive than negative interactions with each other as indicated by the cooccurrence network, suggesting their consistent response to environmental disturbance. Our results solidly support caves as an atmospheric methane sink, and they contribute to a comprehensive understanding of the diversity, distribution, and interactions of microbial communities in subsurface karst caves.

Characteristics and influencing factors of hydrochemistry and dissolved organic matter in typical karst water system.

The unique hydrogeological conditions of karst area make the groundwater react rapidly to rainfall events, which makes the groundwater more susceptible to anthropogenic pollutions. The current study based on a combined excitation-emission matrix fluorescence spectroscopy and parallel factor analysis (EEM-PARAFAC) and geochemical-statistical investigation of water samples from the karst water system in Xintian County, Hunan Province, China, gives crucial information about the principal factors influencing karst water hydrochemistry and dissolved organic matter (DOM). The analyzed data revealed that both surface water and descending spring samples were within the Ca-Mg-HCO3 water type and dominated by humic-like fluorophore, and well water samples were within both the Ca-Mg-HCO3 and Na-HCO3 water types and controlled by protein-like fluorophore. The chemical compositions of surface water and descending springs were mainly influenced by the weathering of silicate, carbonate, and evaporate rocks and precipitation. In addition to be affected by the weathering of silicate, carbonate, and evaporate rocks and precipitation, the well water was also impacted by ion exchange and other activities like anthropogenic. The DOM in the karst water system was affected by allochthonous and autochthonous inputs as well as the chemical compositions of the water.

Impact of sulfuric and nitric acids on carbonate dissolution, and the associated deficit of CO2 uptake in the upper-middle reaches of the Wujiang River, China.

Carbonate weathering and the CO2 consumption in karstic area are extensive affected by anthropogenic activities, especially sulfuric and nitric acids usage in the upper-middle reaches of Wujiang River, China. The carbonic acid would be substituted by protons from sulfuric and nitric acids which can be reduce CO2 absorption. Therefore, The goal of this study was to highlight the impacts of sulfuric and nitric acids on carbonate dissolution and the associated deficit of CO2 uptaking during carbonate weathering. The hydrochemistries and carbon isotopic signatures of dissolved inorganic carbon from groundwater were measured during the rainy season (July; 41 samples) and post-rainy season (October; 26 samples). Our results show that Ca2+ and Mg2+ were the dominant cations (55.87-98.52%), and HCO3- was the dominant anion (63.63-92.87%). The combined concentrations of Ca2+ and Mg2+ commonly exceeded the equivalent concentration of HCO3-, with calculated [Ca2++Mg2+]/[HCO3-] equivalent ratios of 1.09-2.12. The mean measured groundwater δ13CDIC value (-11.38‰) was higher than that expected for carbonate dissolution mediated solely by carbonic acid (-11.5‰), and the strong positive correlation of these values with [SO42-+NO3-]/HCO3- showed that additional SO42- and NO3- were required to compensate for this cation excess. Nitric and sulfuric acids are, therefore, suggested to have acted as the additional proton-promoted weathering agents of carbonate in the region, alongside carbonic acid. The mean contribution of atmospheric/pedospheric CO2 to the total aquatic HCO3- decreased by 15.67% (rainy season) and 14.17% (post-rainy season) due to the contributions made by these acids. The annual mean deficit of soil CO2 uptake by carbonate weathering across the study area was 14.92%, which suggests that previous workers may have overestimated the absorption of CO2 by carbonate weathering in other karstic areas worldwide.

[Major Ionic Features and Their Controlling Factors in the Upper-Middle Reaches of Wujiang River].

The Wujing River, the largest river in Guizhou Province, is one of the most important water resources for social and economical development. Recently, with the fast population proliferation and rapid economic growth, the drainage basin is intensively interfered by anthropogenic activities. The hydrochemistry of surface water was analyzed from the upper-middle reaches of Wujiang River for investigating the hydrochemical characteristics and their main influencing factors. The results showed that the major cations of the four rivers were Ca²âº and Mg²âº, accounting for more than 70%, and the main anions were HCO3⁻ and SO4²â», occupying more than 85%. The hydrochemical characteristics in the four rivers were found to be of HCO3-Ca type, and mainly determined by the carbonate rock dissolution, while only a small proportion of them were of HCO3 · SO4-Ca type, reflecting the influence of SO4²â» from anthropogenic activities. Compared to hydrochemical data in 1999, there was an obvious increase in cations and anions concentrations, majorly in NO3⁻, SO2- ion concentrations, which were significantly affected by human activities. The Na⁺, K⁺ , Cl⁻ in the river mainly came from atmospheric precipitation, and Ca²âº, HCO3⁻, Mg²âº, mainly came from carbonate rocks dissolution, while NO3⁻ and SO4²â» mainly came from human activities. According to principal component analysis and correlation analysis, hydrochemical composition of Liuchong River was affected by human activity, and that in the upstream of Sancha River was controlled by atmospheric precipitation and the dissolution of carbonate rocks, that to the downstream was enhanced by human activities. The main ion of Maotiao River was controlled by atmospheric precipitation and carbonate rocks dissolution, and also affected by human activity. The Nanming River, the Qingshui river's tributary, was mainly affected by human activity, while the middle and lower reaches of Qingshui River were affected by both the atmospheric precipitation and human activity.

[Influence of Sulfuric Acid to Karst Hydrochemical and δ13CDIC in the Upper and Middle Reaches of the Wujiang River].

Groundwater and surface water from the Upper and Middle Reaches of the Wujiang River were sampled and analyzed for the hydrochemistry and Carbon isotope in DIC. Then hydrochemical characteristics and the main influencing factors were investigated, and the contributions of carbonate dissolution by sulphuric acid to total(Ca2+ + Mg2+) and HCO3 were calculated using the stoichiometry method. The results showed that the advantage cations of groundwater and surface water is Ca2+, which accounted for more than 50% and the advantage anions is HCO3- and SO(4)2-, which accounted for more than 85%. The hydrochemical characteristics of most samples were of Ca-HCO3 type, and a small part of HCO3.SO4-Ca, reflecting a few samples affected by SO(4)2- from human source. The δ13CDIC of groundwater and surface water, varying from -12. 98%o to -6. 36%o with a changeable molar ratio between (Ca2+ + Mg2+) and HCO3- of 1. 11 to 1. 90, indicated that sulfuric acid has an important influence on hydrochemistry and δ3CDIC. The contributions of carbonate dissolution by sulphuric acid to total (Ca2+ + Mg2+) and HCO3 in groundwater ranged from 20. 59% to 92. 87% (average 51. 50%), and from 11. 47% to 86. 69% (average 36. 90%). While the contributions of carbonate dissolution by sulphuric acid to total (Ca2+ + Mg2+) and HCO3- in surface water ranged from 56. 14% to 94. 55% (with an average of 76. 89%), and 39. 02% to 89. 66% (with an average of 64.24%), respectively, demonstrated that sulphuric acid is an important agent of carbon rock weathering. The results of this study have a great significance for the protection and development and utilization of water resources in the Wujiang River basin and for karst carbon cycle research.