Advanced Search

Indexed by SCI、CA、РЖ、PA、CSA、ZR、etc .

Volume 34 Issue 1
Feb 2023
Turn off MathJax
Article Contents
Journal of Earth Science  > 2023  >  34(1): 145-155.
Jiyu Chen, Qiang Li, Qiufang He, Heinz C. Schröder, Zujun Lu, Daoxian Yuan. Influence of CO2/HCO3- on Microbial Communities in Two Karst Caves with High CO2. Journal of Earth Science, 2023, 34(1): 145-155. doi: 10.1007/s12583-020-1368-9
Citation: Jiyu Chen, Qiang Li, Qiufang He, Heinz C. Schröder, Zujun Lu, Daoxian Yuan. Influence of CO2/HCO3- on Microbial Communities in Two Karst Caves with High CO2. Journal of Earth Science, 2023, 34(1): 145-155. doi: 10.1007/s12583-020-1368-9
shu

Influence of CO2/HCO3- on Microbial Communities in Two Karst Caves with High CO2

doi: 10.1007/s12583-020-1368-9
  • 1.

    Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China

  • 2.

    International Research Center on Karst under the Auspices of UNESCO, Guilin 541004, China

  • 3.

    College of Life Science, Guangxi Normal University, Guilin 541006, China

  • 4.

    Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guilin 541004, China

  • 5.

    School of Geographical Sciences, Southwest University, Chongqing 400715, China

  • 6.

    Institute for Physiological Chemistry, University Medical Center of Johannes Gutenberg University, Mainz 55128, Germany

More Information
    Abstract

  • There is limited knowledge about microbial communities and their ecological functions in karst caves with high CO2 concentrations. Here, we studied the microbial community compositions and functions in Shuiming Cave ("SMC", CO2 concentration 3 303 ppm) and Xueyu Cave ("XYC", CO2 concentration 8 753 ppm) using Illumina MiSeq high-throughput sequencing in combination with BIOLOG test. The results showed that Proteobacteria, Actinobacteria and Bacteroidetes were dominant phyla in these two caves, and Thaumarchaeota was the most abundant in the rock wall samples of SMC. The microbial diversity in the water samples decreased with increasing HCO3- concentration, and it was higher in XYC than that in SMC. The microbial community structures in the sediment and rock wall samples were quite different between the two caves. High concentrations of CO2 can reduce the microbial diversity on the rock walls in karst caves, probably through changing microbial preference for different types of carbon sources and decreasing the microbial utilization rate of carbon sources. These results expanded our understanding of microbial community and its response to environments in karst caves with high CO2.

     

    • Electronic Supplementary Materials: Supplementary materials (Tables S1–S3, Figs. S1–S6) are available in the online version of this article at https://doi.org/10.1007/s12583-020-1368-9.
    FullText(HTML)
  • loading
    • References(61)
  • Anderson, M. J., Willis, T. J., 2003. Canonical Analysis of Principal Coordinates: A Useful Method of Constrained Ordination for Ecology. Ecology, 84(2): 511–525. https://doi.org/10.1890/0012-9658(2003)084[0511:caopca]2.0.co;2
    Baldini, J. U. L., Mcdermott, F., Hoffmann, D. L., et al., 2008. Very High-Frequency and Seasonal Cave Atmosphere PCO2 Variability: Implications for Stalagmite Growth and Oxygen Isotope-Based Paleoclimate Records. Earth and Planetary Science Letters, 272(1/2): 118–129. https://doi.org/10.1016/j.epsl.2008.04.031
    Barton, H. A., Taylor, M. R., Pace, N. R., 2004. Molecular Phylogenetic Analysis of a Bacterial Community in an Oligotrophic Cave Environment. Geomicrobiology Journal, 21(1): 11–20. https://doi.org/10.1080/01490450490253428
    Barton, H. A., Taylor, N. M., Kreate, M. P., et al., 2007. The Impact of Host Rock Geochemistry on Bacterial Community Structure in Oligotrophic Cave Environments. International Journal of Speleology, 36(2): 93–104. https://doi.org/10.5038/1827-806X.36.2.5
    Bauermeister, J., Ramette, A., Dattagupta, S., 2012. Repeatedly Evolved Host-Specific Ectosymbioses between Sulfur-Oxidizing Bacteria and Amphipods Living in a Cave Ecosystem. PLoS One, 7(11): e50254. https://doi.org/10.1371/journal.pone.0050254
    Bremner, J. M., 1960. Determination of Nitrogen in Soil by the Kjeldahl Method. The Journal of Agricultural Science, 55(1): 11–33. https://doi.org/10.1017/s0021859600021572
    Caporaso, J. G., Lauber, C. L., Walters, W. A., et al., 2012. Ultra-High-Throughput Microbial Community Analysis on the Illumina HiSeq and MiSeq Platforms. The ISME Journal, 6(8): 1621–1624. https://doi.org/10.1038/ismej.2012.8
    Chelius, M. K., Beresford, G., Horton, H., et al., 2009. Impacts of Alterations of Organic Inputs on the Bacterial Community within the Sediments of Wind Cave, South Dakota, USA. International Journal of Speleology, 38(1): 1–10. https://doi.org/10.5038/1827-806x.38.1.1
    Chen, F. H., Jia, J., Chen, J. H., et al., 2016. A Persistent Holocene Wetting Trend in Arid Central Asia, with Wettest Conditions in the Late Holocene, Revealed by Multi-Proxy Analyses of Loess-Paleosol Sequences in Xinjiang, China. Quaternary Science Reviews, 146: 134–146. https://doi.org/10.1016/j.quascirev.2016.06.002
    Chen, J. Y., Lu, Z. J., He, Q. F., et al., 2020. Characteristics of Culturable Bacterial Communities in Karst Caves with Different CO2 Concentrations―An Example from Xueyu Cave and Shuiming Cave in Chongqing. Carsologica Sinica, 39(2): 264–274. https://doi.org/10.11932/karst2020y20 (in Chinese with English Abstract)
    de Mandal, S., Chatterjee, R., Kumar, N. S., 2017. Dominant Bacterial Phyla in Caves and Their Predicted Functional Roles in C and N Cycle. BMC Microbiology, 17(1): 90. https://doi.org/10.1186/s12866-017-1002-x
    Deininger, M., Lippold, J., Abele, F., et al., 2016. Comparison of a Spatio-Temporal Speleothem-Based Reconstruction of Late Holocene Climate Variability to the Timing of Cultural Developments. EGU General Assembly Conference Abstracts
    Deng, S. L., Liu, F. R., Zhang, Y. M., 2016. Effects of Elevated Temperature and Doubling of CO2 Concentration on the Soil Microbial Community Structure in the Subalpine Coniferous Forest of Western Sichuan, China. Chinese Journal of Applied and Environmental Biology, 22(1): 20–26 https://doi.org/10.3724/SP.J.1145.2015.06021 (in Chinese with English Abstract)
    Dubbs, L. L., Whalen, S. C., 2010. Reduced Net Atmospheric CH4 Consumption is a Sustained Response to Elevated CO2 in a Temperate Forest. Biology and Fertility of Soils, 46(6): 597–606. https://doi.org/10.1007/s00374-010-0467-7
    Ebersberger, D., Niklaus, P. A., Kandeler, E., 2003. Long Term CO2 Enrichment Stimulates N-Mineralisation and Enzyme Activities in Calcareous Grassland. Soil Biology and Biochemistry, 35(7): 965–972. https://doi.org/10.1016/S0038-0717(03)00156-1
    Edgar, R. C., 2013. UPARSE: Highly Accurate OTU Sequences from Microbial Amplicon Reads. Nature Methods, 10(10): 996–998. https://doi.org/10.1038/nmeth.2604
    Edgar, R. C., Haas, B. J., Clemente, J. C., et al., 2011. UCHIME Improves Sensitivity and Speed of Chimera Detection. Bioinformatics, 27(16): 2194–2200. https://doi.org/10.1093/bioinformatics/btr381
    Fu, G., Zhang, H. R., Li, S. W., et al., 2019. A Meta-Analysis of the Effects of Warming and Elevated CO2 on Soil Microbes. Journal of Resources and Ecology, 10(1): 69–76. https://doi.org/10.5814/j.issn.1674-764x.2019.01.009
    Fuhrman, J. A., 2009. Microbial Community Structure and Its Functional Implications. Nature, 459(7244): 193–199. https://doi.org/10.1038/nature08058
    Gao, K. S., Yu, A. J., 2000. Influence of CO2, Light and Watering on Growth of Nostoc Flagelliforme Mats. Journal of Applied Phycology, 12(2): 185–189. https://doi.org/10.1023/A:1008123203409
    Garrity, G. M., Holt, J. G., Castenholz, R. W., et al., 2001. Phylum BVI. Chloroflexi Phy. Nov. . In: Boone, D. R., Castenholz, R. W., Garrity, G. M., eds., Bergey's Manual® of Systematic Bacteriology. Springer, New York. 427–446. https://doi.org/10.1007/978-0-387-21609-6_23
    Goldfarb, K. C., Karaoz, U., Hanson, C. A., et al., 2011. Differential Growth Responses of Soil Bacterial Taxa to Carbon Substrates of Varying Chemical Recalcitrance. Frontiers in Microbiology, 2: 94. https://doi.org/10.3389/fmicb.2011.00094
    Groth, I., Vettermann, R., Schuetze, B., et al., 1999. Actinomycetes in Karstic Caves of Northern Spain (Altamira and Tito Bustillo). Journal of Microbiological Methods, 36(1/2): 115–122. https://doi.org/10.1016/S0167-7012(99)00016-0
    He, M., Mei, C. F., Sun, G. P., et al., 2016. The Effects of Molecular Properties on Ready Biodegradation of Aromatic Compounds in the OECD 301B CO2 Evolution Test. Archives of Environmental Contamination and Toxicology, 71(1): 133–145. https://doi.org/10.1007/s00244-015-0236-6
    Hiraishi, A., Hoshino, Y., Satoh, T., 1991. Rhodoferax Fermentans Gen. Nov., Sp. Nov., a Phototrophic Purple Nonsulfur Bacterium Previously Referred to as the "Rhodocyclus Gelatinosus-Like" Group. Archives of Microbiology, 155(4): 330–336. https://doi.org/10.1007/BF00243451
    Hutchens, E., Radajewski, S., Dumont, M. G., et al., 2004. Analysis of Methanotrophic Bacteria in Movile Cave by Stable Isotope Probing. Environmental Microbiology, 6(2): 111–120. https://doi.org/10.1046/j.1462-2920.2003.00543.x
    Jeong, S. Y., Kim, T. G., 2019. Development of a Novel Methanotrophic Process with the Helper Micro-Organism Hyphomicrobium Sp. NM3. Journal of Applied Microbiology, 126(2): 534–544. https://doi.org/10.1111/jam.14140
    Jiang, H. C., Dong, H. L., Zhang, G. X., et al., 2006. Microbial Diversity in Water and Sediment of Lake Chaka, an Athalassohaline Lake in Northwestern China. Applied and Environmental Microbiology, 72(6): 3832–3845. https://doi.org/10.1128/AEM.02869-05
    Könneke, M., Bernhard, A. E., de la Torre, J. R., et al., 2005. Isolation of an Autotrophic Ammonia-Oxidizing Marine Archaeon. Nature, 437(7058): 543–546. https://doi.org/10.1038/nature03911
    Kramer, C., Gleixner, G., 2008. Soil Organic Matter in Soil Depth Profiles: Distinct Carbon Preferences of Microbial Groups during Carbon Transformation. Soil Biology and Biochemistry, 40(2): 425–433. https://doi.org/10.1016/j.soilbio.2007.09.016
    Li, Q., Song, A., Peng, W. J., et al., 2017. Contribution of Aerobic Anoxygenic Phototrophic Bacteria to Total Organic Carbon Pool in Aquatic System of Subtropical Karst Catchments, Southwest China: Evidence from Hydrochemical and Microbiological Study. FEMS Microbiology Ecology, 93(6): fix065. https://doi.org/10.1093/femsec/fix065
    Liu, X. H., Song, X. S., Wang, Y., et al., 2015. Effects of drought and double CO2 in atmosphere on soil microbial biomass and activities. Jiangsu Agricultural Sciences, 43(12): 336–338. https://doi.org/10.15889/j.issn.1002-1302.2015.12.106 (in Chinese with English Abstract)
    Liu, Y. C., Whitman, W. B., 2008. Metabolic, Phylogenetic, and Ecological Diversity of the Methanogenic Archaea. Annals of the New York Academy of Sciences, 1125(1): 171–189. https://doi.org/10.1196/annals.1419.019
    Louca, S., Parfrey, L. W., Doebeli, M., 2016. Decoupling Function and Taxonomy in the Global Ocean Microbiome. Science, 353(6305): 1272–1277. https://doi.org/10.1126/science.aaf4507
    Lü, X. F., He, Q. F., Wang, Z. J., et al., 2019. Calcium Carbonate Precipitation Mediated by Bacterial Carbonic Anhydrase in a Karst Cave: Crystal Morphology and Stable Isotopic Fractionation. Chemical Geology, 530: 119331. https://doi.org/10.1016/j.chemgeo.2019.119331
    Luo, W. Q., 2009. Analysing Ecological Data. Journal of Applied Statistics, 36(2): 233–234. https://doi.org/10.1080/02664760802340267
    Magoč, T., Salzberg, S. L., 2011. FLASH: Fast Length Adjustment of Short Reads to Improve Genome Assemblies. Bioinformatics, 27(21): 2957–2963. https://doi.org/10.1093/bioinformatics/btr507
    McCann, K. S., 2000. The Diversity–Stability Debate. Nature, 405(6783): 228–233. https://doi.org/10.1038/35012234
    McDonough, L. K., Iverach, C. P., Beckmann, S., et al., 2016. Spatial Variability of Cave-Air Carbon Dioxide and Methane Concentrations and Isotopic Compositions in a Semi-Arid Karst Environment. Environmental Earth Sciences, 75(8): 700. https://doi.org/10.1007/s12665-016-5497-5
    Paerl, H. W., Gardner, W. S., Havens, K. E., et al., 2016. Mitigating Cyanobacterial Harmful Algal Blooms in Aquatic Ecosystems Impacted by Climate Change and Anthropogenic Nutrients. Harmful Algae, 54: 213–222. https://doi.org/10.1016/j.hal.2015.09.009
    Palmer, A. N., 2017. Geology of Mammoth Cave. In: Hobbs, H. III, Olson, R., Winkler, E., et al., eds., Mammoth Cave: Cave and Karst Systems of the World. Springer. https://doi.org/10.1007/978-3-319-53718-4_6
    Pearson, A., McNichol, A. P., Benitez-Nelson, B. C., et al., 2001. Origins of Lipid Biomarkers in Santa Monica Basin Surface Sediment: A Case Study Using Compound-Specific δ14C Analysis. Geochimica et Cosmochimica Acta, 65(18): 3123–3137. https://doi.org/10.1016/S0016-7037(01)00657-3
    Pedersen, K., 2000. Exploration of Deep Intraterrestrial Microbial Life: Current Perspectives. FEMS Microbiology Letters, 185(1): 9–16. https://doi.org/10.1016/S0378-1097(00)00061-6
    Pierce, S., Sjögersten, S., 2009. Effects of below Ground CO2 Emissions on Plant and Microbial Communities. Plant and Soil, 325(1): 197. https://doi.org/10.1007/s11104-009-9969-1
    Rothschild, L. J., Mancinelli, R. L., 2001. Life in Extreme Environments. Nature, 409(6823): 1092–1101. https://doi.org/10.1038/35059215
    Team, R. D. C., 2009. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. Computing, 14: 12–21. https://doi.org/10.1890/0012-9658(2002)083[3097:CFHIWS]2.0.CO;2.
    Tian, C. Q., Shao, K., 2013. Determination of Total Phosphorus in Soils and Stream Sediments by Microwave Digestion-Phosphorus Molybdenum Blue Spectrophotometry. Metallurgical Analysis, 33(12): 52–56. https://doi.org/10.13228/j.issn.1000-7571.2013.12.010 (in Chinese with English Abstract)
    Vanfossen, A. L., Verhaart, M. R. A., Kengen, S. M. W., et al., 2009. Carbohydrate Utilization Patterns for the Extremely Thermophilic Bacterium Caldicellulosiruptor Saccharolyticus Reveal Broad Growth Substrate Preferences. Applied and Environmental Microbiology, 75(24): 7718–7724. https://doi.org/10.1128/AEM.01959-09
    Wang, F. X., Cao, J. H., Huang, J. F., 1998. Biokarst in Cave Twilight Zones. Carsologica Sinica, 17(1): 41–48.https://doi.org/CNKI:SUN:ZGYR.0.1998-01-005 (in Chinese with English Abstract)
    Wang, J. F., Wang, Y. H., Song, X. S., et al., 2017. Elevated Atmospheric CO2 and Drought Affect Soil Microbial Community and Functional Diversity Associated with Glycine Max. Revista Brasileira De Ciência Do Solo, 41: e0160460. https://doi.org/10.1590/18069657rbcs20160460
    Willis, K. J., MacDonald, G. M., 2011. Long-Term Ecological Records and Their Relevance to Climate Change Predictions for a Warmer World. Annual Review of Ecology, Evolution, and Systematics, 42(1): 267–287. https://doi.org/10.1146/annurev-ecolsys-102209-144704
    Wong, C. I., Breecker, D. O., 2015. Advancements in the Use of Speleothems as Climate Archives. Quaternary Science Reviews, 127: 1–18. https://doi.org/10.1016/j.quascirev.2015.07.019
    Wuchter, C., Schouten, S., Boschker, H. T. S., et al., 2003. Bicarbonate Uptake by Marine Crenarchaeota. FEMS Microbiology Letters, 219(2): 203–207. https://doi.org/10.1016/S0378-1097(03)00060-0
    Xie, S. C., Wang, F. P., Yan, J. X., et al., 2016. Geobiological Processes during Critical Environmental Transitions in Earth History. Science & Technology Information, 14(21): 176–177. https://doi.org/10.3969/j.issn.1672-3791.2016.21.107 (in Chinese with English Abstract)
    Yang, S. H., Zheng, Q. S., Yuan, M. T., et al., 2019. Long-Term Elevated CO2 Shifts Composition of Soil Microbial Communities in a Californian Annual Grassland, Reducing Growth and N Utilization Potentials. Science of the Total Environment, 652: 1474–1481. https://doi.org/10.1016/j.scitotenv.2018.10.353
    Yun, Y., Cheng, X. Y., Wang, W. Q., et al., 2018. Seasonal Variation of Bacterial Community and Their Functional Diversity in Drip Water from a Karst Cave. Chinese Science Bulletin, 63(36): 3932–3944, 3932. https://doi.org/10.1360/N972018-00627 (in Chinese with English Abstract)
    Zhang, J., Gu, T., Zhou, Y., et al., 2012. Terrimonas Rubra Sp. Nov., Isolated from a Polluted Farmland Soil and Emended Description of the Genus Terrimonas. International Journal of Systematic and Evolutionary Microbiology, 62(Pt_11): 2593–2597. https://doi.org/10.1099/ijs.0.036079-0
    Zhang, L. M., He, J. Z., 2012. A Novel Archaeal Phylum: Thaumarchaeota—A Review. Acta Microbiologica Sinica, 52(4): 411–421. https://doi. org/http://ir.rcees.ac.cn/handle/311016/8332.
    Zhang, Z. H., Li, X. N., Peng T., et al., 2004. New Records of Luminous Liverworts from the Karst Caves of Guangxi Province, P. R. China: Cyathodium Cavernarum Kunze and C. Smaragdium Schiffin ex Keissler (Cyathodiaceae, Hepaticae). Carsologica Sinica, 23(2): 154–157. https://doi.org/10.3969/j.issn.1001-4810.2004.02.011 (in Chinese with English Abstract)
    Zhao, H. B., Xu, B. Q., Yao, T. D., et al., 2012. Deuterium Excess Record in a Southern Tibetan Ice Core and Its Potential Climatic Implications. Climate Dynamics, 38(9): 1791–1803. https://doi.org/10.1007/s00382-011-1161-7
    Zhao, J., Lu, W., Zhang, F. J., et al., 2014. Evaluation of CO2 Solubility-Trapping and Mineral-Trapping in Microbial-Mediated CO2-Brine-Sandstone Interaction. Marine Pollution Bulletin, 85(1): 78–85. https://doi.org/10.1016/j.marpolbul.2014.06.019
    • Relative Articles
    • Supplements(0)
    • Cited By
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Figures(6)  / Tables(2)

    Get Citation
    PDF
    XML

    Article Metrics

    Article views(187) PDF downloads(98) Cited by()
    Proportional views
    Related

    Copyright © 2013-2020 Journal of Earth Science 鄂ICP备15021562号-2

    Tel: +86-27-67885075 Fax: +86-27-67885075 E-mail: xbb@cug.edu.cn

    Address: Editorial Office of Journal, China University of Geosciences, Yujiashan, Wuhan, Hubei 430074, P. R. China

    Supported by: Beijing Renhe Information Technology Co. Ltd  E-mail: info@rhhz.net  

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return