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Zeng G, Lu W, Wang Y, Peng H, Chen P, Weng X, Chen J, Zhang L, Du H, Luo W, Wang S. Methane sink of subterranean space in an integrated atmosphere-soil-cave system. ENVIRONMENTAL RESEARCH 2024; 252:118904. [PMID: 38614203 DOI: 10.1016/j.envres.2024.118904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/12/2024] [Accepted: 04/08/2024] [Indexed: 04/15/2024]
Abstract
CH4 serves as an important greenhouse gas, yet limited knowledge is available in global and regional CH4 cycling, particularly in widely distributed karst terrain. In this study, we investigated an upland in Puding Karst Ecosystem Research Station, and explored CH4 concentration and/or flux in atmosphere, soil and cave using a closed static chamber method and an eddy covariance system. Meanwhile, we monitored atmospheric temperature, precipitation, temperature and wind velocity in the cave entrance. The results demonstrated that atmospheric CH4 and actual soil CH4 fluxes in the source area of eddy covariance system were -0.19 ± 8.64 nmols-1m-2 and -0.16 nmols-1m-2 respectively. The CH4 concentrations in Shawan Cave exhibited 10 ∼ 100-fold lower than that of the external atmosphere. CH4 oxidation rate dominated by methane-oxidizing bacteria was 1.98 nmols-1m-2 in Shawan Cave when it combined with temperature difference between cave and external atmosphere. Therefore, CH4 sink in global karst subterranean spaces was estimated at 106.2 Tg CH4 yr-1. We supplemented an understanding of CH4 cycling paths and fluxes in karst terrain, as well as CH4 sinks in karst subterranean space. Further works require to establish a karst ecosystem observation network to conduct long-term integrated studies on CH4 fluxes regarding atmosphere, soils, plants and caves.
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Affiliation(s)
- Guangneng Zeng
- College of Eco-Environmental Engineering, Guizhou Minzu University, Guiyang, 550025, China; Puding Karst Ecosystem Research Station, Chinese Academy of Sciences, Puding, 562100, China
| | - Wangbiao Lu
- College of Eco-Environmental Engineering, Guizhou Minzu University, Guiyang, 550025, China
| | - Yanwei Wang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China; Puding Karst Ecosystem Research Station, Chinese Academy of Sciences, Puding, 562100, China
| | - Haijun Peng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| | - Ping Chen
- Guizhou Provincial Environmental Science Research and Design Institute, Guiyang, 550008, China
| | - Xu Weng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China; Puding Karst Ecosystem Research Station, Chinese Academy of Sciences, Puding, 562100, China
| | - Jia Chen
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China; Puding Karst Ecosystem Research Station, Chinese Academy of Sciences, Puding, 562100, China
| | - Lin Zhang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China; Puding Karst Ecosystem Research Station, Chinese Academy of Sciences, Puding, 562100, China
| | - Haijun Du
- School of Chemical Engineering, Guizhou Minzu University, Guiyang, 550025, China
| | - Weijun Luo
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China; Puding Karst Ecosystem Research Station, Chinese Academy of Sciences, Puding, 562100, China.
| | - Shijie Wang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China; Puding Karst Ecosystem Research Station, Chinese Academy of Sciences, Puding, 562100, China
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Martin-Pozas T, Cuezva S, Fernandez-Cortes A, Benavente D, Saiz-Jimenez C, Sanchez-Moral S. Prokaryotic communities inhabiting a high-radon subterranean ecosystem (Castañar Cave, Spain): Environmental and substrate-driven controls. Microbiol Res 2023; 277:127511. [PMID: 37852679 DOI: 10.1016/j.micres.2023.127511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023]
Abstract
Castañar Cave (Caceres, Spain) is a unique show cave known for its high natural radiation levels. This study presents a comprehensive analysis of its prokaryotic diversity, specifically focusing on investigating the influence of environmental conditions and substrate characteristics on the prokaryotic community structure in the cave sediments. Additionally, the research aims to evaluate the potential impact of human activities on the cave ecosystem. The identification of distinct bioclimatic zones within the cave was made possible through a combination of environmental and microbial monitoring (ATP assays). The results reveal sediment texture as a significant factor, notably affecting the structure, diversity, and phylogenetic variability of the microbial community, including both Bacteria and Archaea. The proportion of clay minerals in sediments plays a crucial role in regulating moisture levels and nutrient availability. These substrate properties collectively exert a significant selective pressure on the structure of prokaryotic communities within cave sediments. The molecular approach shows that heterotrophic bacteria, including those with chitinolytic enzymes, primarily inhabit the cave. Furthermore, chemoautotrophic nitrifiers such as the archaea Nitrososphaeria and the genus Nitrospira, as well as methanotrophic bacteria from the phyla Methylomirabilota, Pseudomonadota, and Verrucomicrobiota, are also present. Remarkably, despite being a show cave, the cave microbiota displays minimal impacts from human activities and the surface ecosystem. Prokaryotic populations exhibit stability in the innermost areas, while the tourist trail area experiences slightly higher biomass increases due to visitor traffic. This suggests that conservation efforts have successfully limited the entry of external nutrients into the innermost cave areas. Additionally, the results suggest that integrating biomarkers like ATP into environmental monitoring can significantly enhance the methods used to study the negative impacts of tourism on cave ecosystems.
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Affiliation(s)
- Tamara Martin-Pozas
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | - Soledad Cuezva
- Department of Geology, Geography and Environment, University of Alcala, 28805 Madrid, Spain.
| | | | - David Benavente
- Department of Environmental and Earth Sciences, University of Alicante, Campus San Vicente del Raspeig, 03690 Alicante, Spain.
| | - Cesareo Saiz-Jimenez
- Department of Agrochemistry, Environmental Microbiology and Soil and Water Protection, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Sergio Sanchez-Moral
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
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Hallsworth JE, Udaondo Z, Pedrós‐Alió C, Höfer J, Benison KC, Lloyd KG, Cordero RJB, de Campos CBL, Yakimov MM, Amils R. Scientific novelty beyond the experiment. Microb Biotechnol 2023; 16:1131-1173. [PMID: 36786388 PMCID: PMC10221578 DOI: 10.1111/1751-7915.14222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 02/15/2023] Open
Abstract
Practical experiments drive important scientific discoveries in biology, but theory-based research studies also contribute novel-sometimes paradigm-changing-findings. Here, we appraise the roles of theory-based approaches focusing on the experiment-dominated wet-biology research areas of microbial growth and survival, cell physiology, host-pathogen interactions, and competitive or symbiotic interactions. Additional examples relate to analyses of genome-sequence data, climate change and planetary health, habitability, and astrobiology. We assess the importance of thought at each step of the research process; the roles of natural philosophy, and inconsistencies in logic and language, as drivers of scientific progress; the value of thought experiments; the use and limitations of artificial intelligence technologies, including their potential for interdisciplinary and transdisciplinary research; and other instances when theory is the most-direct and most-scientifically robust route to scientific novelty including the development of techniques for practical experimentation or fieldwork. We highlight the intrinsic need for human engagement in scientific innovation, an issue pertinent to the ongoing controversy over papers authored using/authored by artificial intelligence (such as the large language model/chatbot ChatGPT). Other issues discussed are the way in which aspects of language can bias thinking towards the spatial rather than the temporal (and how this biased thinking can lead to skewed scientific terminology); receptivity to research that is non-mainstream; and the importance of theory-based science in education and epistemology. Whereas we briefly highlight classic works (those by Oakes Ames, Francis H.C. Crick and James D. Watson, Charles R. Darwin, Albert Einstein, James E. Lovelock, Lynn Margulis, Gilbert Ryle, Erwin R.J.A. Schrödinger, Alan M. Turing, and others), the focus is on microbiology studies that are more-recent, discussing these in the context of the scientific process and the types of scientific novelty that they represent. These include several studies carried out during the 2020 to 2022 lockdowns of the COVID-19 pandemic when access to research laboratories was disallowed (or limited). We interviewed the authors of some of the featured microbiology-related papers and-although we ourselves are involved in laboratory experiments and practical fieldwork-also drew from our own research experiences showing that such studies can not only produce new scientific findings but can also transcend barriers between disciplines, act counter to scientific reductionism, integrate biological data across different timescales and levels of complexity, and circumvent constraints imposed by practical techniques. In relation to urgent research needs, we believe that climate change and other global challenges may require approaches beyond the experiment.
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Affiliation(s)
- John E. Hallsworth
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
| | - Zulema Udaondo
- Department of Biomedical InformaticsUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Carlos Pedrós‐Alió
- Department of Systems BiologyCentro Nacional de Biotecnología (CSIC)MadridSpain
| | - Juan Höfer
- Escuela de Ciencias del MarPontificia Universidad Católica de ValparaísoValparaísoChile
| | - Kathleen C. Benison
- Department of Geology and GeographyWest Virginia UniversityMorgantownWest VirginiaUSA
| | - Karen G. Lloyd
- Microbiology DepartmentUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Radamés J. B. Cordero
- Department of Molecular Microbiology and ImmunologyJohns Hopkins Bloomberg School of Public HealthBaltimoreMarylandUSA
| | - Claudia B. L. de Campos
- Institute of Science and TechnologyUniversidade Federal de Sao Paulo (UNIFESP)São José dos CamposSPBrazil
| | | | - Ricardo Amils
- Department of Molecular Biology, Centro de Biología Molecular Severo Ochoa (CSIC‐UAM)Nicolás Cabrera n° 1, Universidad Autónoma de MadridMadridSpain
- Department of Planetology and HabitabilityCentro de Astrobiología (INTA‐CSIC)Torrejón de ArdozSpain
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Zhu HZ, Jiang CY, Liu SJ. Microbial roles in cave biogeochemical cycling. Front Microbiol 2022; 13:950005. [PMID: 36246268 PMCID: PMC9554484 DOI: 10.3389/fmicb.2022.950005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 09/14/2022] [Indexed: 11/23/2022] Open
Abstract
Among fundamental research questions in subterranean biology, the role of subterranean microbiomes playing in key elements cycling is a top-priority one. Karst caves are widely distributed subsurface ecosystems, and cave microbes get more and more attention as they could drive cave evolution and biogeochemical cycling. Research have demonstrated the existence of diverse microbes and their participance in biogeochemical cycling of elements in cave environments. However, there are still gaps in how these microbes sustain in caves with limited nutrients and interact with cave environment. Cultivation of novel cave bacteria with certain functions is still a challenging assignment. This review summarized the role of microbes in cave evolution and mineral deposition, and intended to inspire further exploration of microbial performances on C/N/S biogeocycles.
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Affiliation(s)
- Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- *Correspondence: Shuang-Jiang Liu,
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Diversity and Composition of Methanotroph Communities in Caves. Microbiol Spectr 2022; 10:e0156621. [PMID: 35943259 PMCID: PMC9430973 DOI: 10.1128/spectrum.01566-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Methane oxidizing microorganisms (methanotrophs) are ubiquitous in the environment and represent a major sink for the greenhouse gas methane (CH4). Recent studies have demonstrated methanotrophs are abundant and contribute to CH4 dynamics in caves. However, very little is known about what controls the distribution and abundance of methanotrophs in subterranean ecosystems. Here, we report a survey of soils collected from > 20 caves in North America to elucidate the factors shaping cave methanotroph communities. Using 16S rRNA sequencing, we recovered methanotrophs from nearly all (98%) of the samples, including cave sites where CH4 concentrations were at or below detection limits (≤0.3 ppmv). We identified a core methanotroph community among caves comprised of high-affinity methanotrophs. Although associated with local-scale mineralogy, methanotroph composition did not systematically vary between the entrances and interior of caves, where CH4 concentrations varied. We also observed methanotrophs are able to disperse readily between cave systems showing these organisms have low barriers to dispersal. Lastly, the relative abundance of methanotrophs was positively correlated with cave-air CH4 concentrations, suggesting these microorganisms contribute to CH4 flux in subterranean ecosystems. IMPORTANCE Recent observations have shown the atmospheric greenhouse gas methane (CH4) is consumed by microorganisms (methanotrophs) in caves at rates comparable to CH4 oxidation in surface soils. Caves are abundant in karst landscapes that comprise 14% of Earth’s land surface area, and therefore may represent a potentially important, but overlooked, CH4 sink. We sampled cave soils to gain a better understand the community composition and structure of cave methanotrophs. Our results show the members of the USC-γ clade are dominant in cave communities and can easily disperse through the environment, methanotroph relative abundance was correlated with local scale mineralogy of soils, and the relative abundance of methanotrophs was positively correlated with CH4 concentrations in cave air.
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Martin-Pozas T, Cuezva S, Fernandez-Cortes A, Cañaveras JC, Benavente D, Jurado V, Saiz-Jimenez C, Janssens I, Seijas N, Sanchez-Moral S. Role of subterranean microbiota in the carbon cycle and greenhouse gas dynamics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 831:154921. [PMID: 35364174 DOI: 10.1016/j.scitotenv.2022.154921] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/15/2022] [Accepted: 03/26/2022] [Indexed: 06/14/2023]
Abstract
Subterranean ecosystems play an active role in the global carbon cycle, yet only a few studies using indirect methods have focused on the role of the cave microbiota in this critical cycle. Here we present pioneering research based on in situ real-time monitoring of CO2 and CH4 diffusive fluxes and concurrent δ13C geochemical tracing in caves, combined with 16S microbiome analysis. Our findings show that cave sediments are promoting continuous CH4 consumption from cave atmosphere, resulting in a significant removal of 65% to 90%. This research reveals the most effective taxa and metabolic pathways in consumption and uptake of greenhouse gases. Methanotrophic bacteria were the most effective group involved in CH4 consumption, namely within the families Methylomonaceae, Methylomirabilaceae and Methylacidiphilaceae. In addition, Crossiella and Nitrosococcaceae wb1-P19 could be one of the main responsible of CO2 uptake, which occurs via the Calvin-Benson-Bassham cycle and reversible hydration of CO2. Thus, syntrophic relationships exist between Crossiella and nitrifying bacteria that capture CO2, consume inorganic N produced by heterotrophic ammonification in the surface of sediments, and induce moonmilk formation. Moonmilk is found as the most evolved phase of the microbial processes in cave sediments that fixes CO2 as calcite and intensifies CH4 oxidation. From an ecological perspective, cave sediments act qualitatively as soils, providing fundamental ecosystem services (e.g. nutrient cycling and carbon sequestration) with direct influence on greenhouse gas emissions.
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Affiliation(s)
- Tamara Martin-Pozas
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | - Soledad Cuezva
- Department of Geology, Geography and Environment, University of Alcalá, Scientific Technological Campus, 28802 Alcalá de Henares, Spain; Plants and Ecosystems, Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium.
| | | | - Juan Carlos Cañaveras
- Department of Environmental and Earth Sciences, University of Alicante, San Vicente del Raspeig Campus, 03690 Alicante, Spain.
| | - David Benavente
- Department of Environmental and Earth Sciences, University of Alicante, San Vicente del Raspeig Campus, 03690 Alicante, Spain.
| | - Valme Jurado
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Cesareo Saiz-Jimenez
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Ivan Janssens
- Plants and Ecosystems, Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Naomi Seijas
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | - Sergio Sanchez-Moral
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
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A Qualitative Assessment of the Trends, Distribution and Sources of Methane in South Africa. SUSTAINABILITY 2022. [DOI: 10.3390/su14063528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Methane (CH4) is the second most important greenhouse gas (GHG) in terms of its concentration and impact on the climate. In the present study, we investigate the trends, sources and distribution of CH4 in South Africa. The study uses satellite datasets from Sentinel-5P and the Atmospheric Infrared Sounder (AIRS). The study also uses credible datasets from the World Bank, Statistics South Africa and the Global Methane Initiative (GMI). The results show an increasing trend of CH4 from 1970–1989. A turning point is observed in 1989, where a decreasing trend is observed from 1989–2001. An increasing trend is then observed from 2001 to 2021. A high concentration of CH4 is observed in the northern and interior parts of South Africa. The results also show that CH4 concentration is influenced by seasonal variations. The September–October–November (SON) season has the highest CH4 concentration distribution in South Africa. The World Bank, Statistics South Africa and the GMI CH4 indictors show that agricultural activities, i.e., involving livestock, are the greatest emitters of CH4 in South Africa, followed by landfill sites. From the livestock data, sheep are the highest emitters of CH4. The increasing CH4 trend is a concern and efforts need to be made to drastically reduce emissions, if South Africa is to meet the 1997 Kyoto Protocol, 2015 Paris Agreement, sustainable development goal 13 (SDG 13) and the COP26 outcome agreements.
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Cheng XY, Liu XY, Wang HM, Su CT, Zhao R, Bodelier PLE, Wang WQ, Ma LY, Lu XL. USC γ Dominated Community Composition and Cooccurrence Network of Methanotrophs and Bacteria in Subterranean Karst Caves. Microbiol Spectr 2021; 9:e0082021. [PMID: 34406837 PMCID: PMC8552738 DOI: 10.1128/spectrum.00820-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 07/13/2021] [Indexed: 12/20/2022] Open
Abstract
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.
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Affiliation(s)
- Xiao-Yu Cheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiao-Yan Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Hong-Mei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Chun-Tian Su
- Institute of Karst Geology, CAGS/Key Laboratory of Karst Dynamics, MNR & GZAR, Guilin, China
| | - Rui Zhao
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Wei-Qi Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Li-Yuan Ma
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiao-Lu Lu
- School of Environmental Studies, China University of Geosciences, Wuhan, China
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9
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Sanchez-Moral S, Jurado V, Fernandez-Cortes A, Cuezva S, Martin-Pozas T, Gonzalez-Pimentel JL, Ontañon R, Saiz-Jimenez C. Environment-driven control of fungi in subterranean ecosystems: the case of La Garma Cave (northern Spain). Int Microbiol 2021; 24:573-591. [PMID: 34292448 PMCID: PMC8616876 DOI: 10.1007/s10123-021-00193-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/02/2021] [Accepted: 07/01/2021] [Indexed: 11/24/2022]
Abstract
Airborne microorganisms can cause important conservation problems in caves with Paleolithic art and therefore the knowledge of cave aerodynamic is essential. La Garma Cave (Cantabria, Spain), an exceptional archaeological site with several levels of galleries interconnected and two entrances, presents a complex atmospheric dynamics. An approach including aerobiological sampling together with microclimate monitoring was applied to assess the factors controlling the origin of airborne fungi. Here we show that winter ventilation is critical for the increasing of Basidiomycota spores in the cave air and the highest concentrations were found in the most ventilated areas. On the contrary, Ascomycota spores prevailed in absence of ventilation. Besides, most Ascomycota were linked to insects and bats that visit or inhabit the cave. The combination of aerobiological and microclimate data constitutes a good approach to evaluate the influence of external climatic conditions and design the most suitable strategies for the conservation of cultural heritage in the cave environment.
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Affiliation(s)
| | - Valme Jurado
- Instituto de Recursos Naturales y Agrobiologia (IRNAS-CSIC), 41012, Sevilla, Spain
| | | | - Soledad Cuezva
- Departamento de Geologia, Geografia y Ciencias Ambientales, Universidad de Alcala de Henares, 28805, Madrid, Spain
| | | | | | - Roberto Ontañon
- Museo de Prehistoria y Arqueologia de Cantabria, 39009, Santander, Spain
| | - Cesareo Saiz-Jimenez
- Instituto de Recursos Naturales y Agrobiologia (IRNAS-CSIC), 41012, Sevilla, Spain.
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10
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Gonzalez-Pimentel JL, Martin-Pozas T, Jurado V, Miller AZ, Caldeira AT, Fernandez-Lorenzo O, Sanchez-Moral S, Saiz-Jimenez C. Prokaryotic communities from a lava tube cave in La Palma Island (Spain) are involved in the biogeochemical cycle of major elements. PeerJ 2021; 9:e11386. [PMID: 34026356 PMCID: PMC8121065 DOI: 10.7717/peerj.11386] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/10/2021] [Indexed: 11/21/2022] Open
Abstract
Lava caves differ from karstic caves in their genesis and mineral composition. Subsurface microbiology of lava tube caves in Canary Islands, a volcanic archipelago in the Atlantic Ocean, is largely unknown. We have focused the investigation in a representative lava tube cave, Fuente de la Canaria Cave, in La Palma Island, Spain, which presents different types of speleothems and colored microbial mats. Four samples collected in this cave were studied using DNA next-generation sequencing and field emission scanning electron microscopy for bacterial identification, functional profiling, and morphological characterization. The data showed an almost exclusive dominance of Bacteria over Archaea. The distribution in phyla revealed a majority abundance of Proteobacteria (37-89%), followed by Actinobacteria, Acidobacteria and Candidatus Rokubacteria. These four phyla comprised a total relative abundance of 72-96%. The main ecological functions in the microbial communities were chemoheterotrophy, methanotrophy, sulfur and nitrogen metabolisms, and CO2 fixation; although other ecological functions were outlined. Genome annotations of the especially representative taxon Ga0077536 (about 71% of abundance in moonmilk) predicted the presence of genes involved in CO2 fixation, formaldehyde consumption, sulfur and nitrogen metabolisms, and microbially-induced carbonate precipitation. The detection of several putative lineages associated with C, N, S, Fe and Mn indicates that Fuente de la Canaria Cave basalts are colonized by metabolically diverse prokaryotic communities involved in the biogeochemical cycling of major elements.
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Affiliation(s)
| | | | - Valme Jurado
- Environmental Microbiology, Instituto de Recursos Naturales y Agrobiologia, CSIC, Sevilla, Spain
| | | | | | | | | | - Cesareo Saiz-Jimenez
- Environmental Microbiology, Instituto de Recursos Naturales y Agrobiologia, CSIC, Sevilla, Spain
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11
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Colored Microbial Coatings in Show Caves from the Galapagos Islands (Ecuador): First Microbiological Approach. COATINGS 2020. [DOI: 10.3390/coatings10111134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The Galapagos Islands (Ecuador) have a unique ecosystem on Earth due to their outstanding biodiversity and geological features. This also extends to their subterranean heritage, such as volcanic caves, with plenty of secondary mineral deposits, including coralloid-type speleothems and moonmilk deposits. In this study, the bacterial communities associated with speleothems from two lava tubes of Santa Cruz Island were investigated. Field emission scanning electron microscopy (FESEM) was carried out for the morphological characterization and detection of microbial features associated with moonmilk and coralloid speleothems from Bellavista and Royal Palm Caves. Microbial cells, especially filamentous bacteria in close association with extracellular polymeric substances (EPS), were abundant in both types of speleothems. Furthermore, reticulated filaments and Actinobacteria-like cells were observed by FESEM. The analysis of 16S rDNA revealed the presence of different bacterial phylotypes, many of them associated with the carbon, nitrogen, iron and sulfur cycles, and some others with pollutants. This study gives insights into subsurface microbial diversity of the Galapagos Islands and further shows the interest of the conservation of these subterranean geoheritage sites used as show caves.
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12
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Shakoor A, Ashraf F, Shakoor S, Mustafa A, Rehman A, Altaf MM. Biogeochemical transformation of greenhouse gas emissions from terrestrial to atmospheric environment and potential feedback to climate forcing. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:38513-38536. [PMID: 32770337 DOI: 10.1007/s11356-020-10151-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 07/15/2020] [Indexed: 06/11/2023]
Abstract
Carbon dioxide (CO2) is mainly universal greenhouse gas associated with climate change. However, beyond CO2, some other greenhouse gases (GHGs) like methane (CH4) and nitrous oxide (N2O), being two notable gases, contribute to global warming. Since 1900, the concentrations of CO2 and non-CO2 GHG emissions have been elevating, and due to the effects of the previous industrial revolution which is responsible for climate forcing. Globally, emissions of CO2, CH4, and N2O from agricultural sectors are increasing as around 1% annually. Moreover, deforestation also contributes 12-17% of total global GHGs. Perhaps, the average temperature is likely to increase globally, at least 2 °C by 2100-by mid-century. These circumstances are responsible for climate forcing, which is the source of various human health diseases and environmental risks. From agricultural soils, rhizospheric microbial communities have a significant role in the emissions of greenhouse gases. Every year, microbial communities release approximately 1.5-3 billion tons of carbon into the atmospheric environment. Microbial nitrification, denitrification, and respiration are the essential processes that affect the nitrogen cycle in the terrestrial environment. In the twenty-first century, climate change is the major threat faced by human beings. Climate change adversely influences human health to cause numerous diseases due to their direct association with climate change. This review highlights the different anthropogenic GHG emission sources, the response of microbial communities to climate change, climate forcing potential, and mitigation strategies through different agricultural management approaches and microbial communities.
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Affiliation(s)
- Awais Shakoor
- Department of Environment and Soil Sciences, University of Lleida, Avinguda Alcalde Rovira Roure 191, 25198, Lleida, Spain.
| | - Fatima Ashraf
- Department of Chemistry, Lahore College for Women University, Lahore, Pakistan
| | - Saba Shakoor
- Department of Zoology, The Women University Multan, Multan, Pakistan
| | - Adnan Mustafa
- National Engineering Laboratory for Improving Quality of Arable Land, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Abdul Rehman
- CAS-Key Laboratory of Crust-Mantle Materials and the Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, 230026, People's Republic of China
| | - Muhammad Mohsin Altaf
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Ecology and Environment, Hainan University, Haikou, 570228, People's Republic of China
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Castaño-Vázquez F, Merino S, Cuezva S, Sánchez-Moral S. Nest Gasses as a Potential Attraction Cue for Biting Flying Insects and Other Ectoparasites of Cavity Nesting Birds. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00258] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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14
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Zhao R, Wang H, Cheng X, Yun Y, Qiu X. Upland soil cluster γ dominates the methanotroph communities in the karst Heshang Cave. FEMS Microbiol Ecol 2019; 94:5107866. [PMID: 30265314 DOI: 10.1093/femsec/fiy192] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/26/2018] [Indexed: 11/13/2022] Open
Abstract
Microorganisms are thought to play a critical role in methane (CH4) consumption in karst caves and yet the presence and diversity of methane-oxidizing bacteria (MOB) remain a mystery. In Heshang Cave, CH4 concentration decreases from 1.9 ppm at the entrance to 0.65 ppm inside the cave. To explore the presence and diversity of MOB in this cave, weathered rocks and sediment samples were collected from the cave and subjected to molecular analysis. The abundances of MOB were 107-108 copies g-1 dry sample via quantification of the pmoA gene, which are comparable to or even higher than those reported in other terrestrial environments, and account for up to 20% of the total microbial communities. Phylogenetically, MOB communities were dominated by the 'high-affinity' upland soil cluster γ (USCγ), although the predominance of Type Ia MOB was also detected in the permanently waterlogged stream sediment. The estimated CH4 oxidation potential varied dramatically among samples in the range of 0.6-80 CH4 m-3 d-1. Collectively, this study provides compelling evidence that the high-affinity MOB capable of oxidizing CH4 at the atmospheric level are present in Heshang Cave, which may play an important role in the CH4 consumption, and supports karst caves as important atmospheric CH4 sinks.
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Affiliation(s)
- Rui Zhao
- State Key Laboratory of Biogeology and Environment Geology, China University of Geosciences, Wuhan 430074, P. R. China.,Now at School of Marine Science and Policy, University of Delaware, Lewes 19958, Delaware, USA
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environment Geology, China University of Geosciences, Wuhan 430074, P. R. China.,Laboratory of Basin Hydrology and Wetland Eco-restoration, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Xiaoyu Cheng
- State Key Laboratory of Biogeology and Environment Geology, China University of Geosciences, Wuhan 430074, P. R. China
| | - Yuan Yun
- State Key Laboratory of Biogeology and Environment Geology, China University of Geosciences, Wuhan 430074, P. R. China
| | - Xuan Qiu
- State Key Laboratory of Biogeology and Environment Geology, China University of Geosciences, Wuhan 430074, P. R. China
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Schimmelmann A, Fernandez-Cortes A, Cuezva S, Streil T, Lennon JT. Radiolysis via radioactivity is not responsible for rapid methane oxidation in subterranean air. PLoS One 2018; 13:e0206506. [PMID: 30383783 PMCID: PMC6211692 DOI: 10.1371/journal.pone.0206506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/15/2018] [Indexed: 11/18/2022] Open
Abstract
Atmospheric methane is rapidly lost when it enters humid subterranean critical and vadose zones (e.g., air in soils and caves). Because methane is a source of carbon and energy, it can be consumed by methanotrophic methane-oxidizing bacteria. As an additional subterranean sink, it has been hypothesized that methane is oxidized by natural radioactivity-induced radiolysis that produces energetic ions and radicals, which then trigger abiotic oxidation and consumption of methane within a few hours. Using controlled laboratory experiments, we tested whether radiolysis could rapidly oxidize methane in sealed air with different relative humidities while being exposed to elevated levels of radiation (more than 535 kBq m-3) from radon isotopes 222Rn and 220Rn (i.e., thoron). We found no evidence that radiolysis contributed to methane oxidation. In contrast, we observed the rapid loss of methane when moist soil was added to the same apparatus in the absence of elevated radon abundance. Together, our findings are consistent with the view that methane oxidizing bacteria are responsible for the widespread observations of methane depletion in subterranean environments. Further studies are needed on the ability of microbes to consume trace amounts of methane in poorly ventilated caves, even though the trophic and energetic benefits become marginal at very low partial pressures of methane.
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Affiliation(s)
- Arndt Schimmelmann
- Department of Earth and Atmospheric Sciences, Indiana University, Bloomington, Indiana, United States of America
- * E-mail:
| | - Angel Fernandez-Cortes
- Department of Biology and Geology, University of Almeria, Almeria, Spain
- Department of Earth Sciences, Royal Holloway, University of London, Egham, Surrey, United Kingdom
| | - Soledad Cuezva
- Department of Biology and Geology, University of Almeria, Almeria, Spain
| | | | - Jay T. Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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16
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Yuan J, Yuan Y, Zhu Y, Cao L. Effects of different fertilizers on methane emissions and methanogenic community structures in paddy rhizosphere soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 627:770-781. [PMID: 29426201 DOI: 10.1016/j.scitotenv.2018.01.233] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 01/23/2018] [Accepted: 01/23/2018] [Indexed: 06/08/2023]
Abstract
Paddy soil accounts for 10% of global atmospheric methane (CH4) emissions. Many types of fertilizers may enhance CH4 emissions, especially organic fertilizer. The aim of this study was to explore the effects of different fertilizers on CH4 and methanogen patterns in paddy soil. This experiment involved four treatments: chemical fertilizer (CT), organic fertilizer (OT), mixed with chemical and organic fertilizer (MT), and no fertilizer (ctrl). The three fertilization treatments were applied with total nitrogen at the same rate of 300 kg N ha-1. Paddy CH4, soil physicochemical variables and methanogen communities were quantitatively analyzed. Rhizosphere soil mcrA and pmoA gene copy numbers were determined by qPCR. Methanogenic 16S rRNA genes were identified by MiSeq sequencing. The results indicated CH4 emissions were significantly higher in OT (145.31 kg ha-1) than MT (84.62 kg ha-1), CT (77.88 kg ha-1) or ctrl (32.19 kg ha-1). Soil organic acids were also increased by organic fertilization. CH4 effluxes were significantly and negatively related to mcrA and pmoA gene copy numbers, and positively related to mcrA/pmoA. Above all, hydrogenotrophic Methanocella and acetoclastic Methanosaeta were the predominant methanogenic communities; these communities were strictly associated with soil potassium, oxalate, acetate, and succinate. Application of organic fertilizer promoted the dominant acetoclastic methanogens, but suppressed the dominant hydrogenotrophic methanogens. The transformation in methanogenic community structure and enhanced availability of C substrates may explain the increased CH4 production in OT compared to other treatments. Compared to OT, MT may partially mitigate CH4 emissions while guaranteeing a high rice yield. On this basis, we recommend the local fertilization pattern should change from 300 N kg ha-1 of organic manure to the same level of mixed fertilization. Moreover, we suggest multiple combinations of mixed fertilization merit more investigation in the future.
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Affiliation(s)
- Jing Yuan
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yongkun Yuan
- Irrigation Technology Extension Station of Qingpu, 2 Yuan Road, Shanghai 201707, China
| | - Yihang Zhu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Linkui Cao
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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17
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Dominguez-Moñino I, Diaz-Herraiz M, Jurado V, Laiz L, Miller AZ, Santos JL, Alonso E, Saiz-Jimenez C. Nature and origin of the violet stains on the walls of a Roman tomb. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 598:889-899. [PMID: 28458206 DOI: 10.1016/j.scitotenv.2017.04.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
The Circular Mausoleum tomb (Roman Necropolis of Carmona, Spain) dates back from the first century AD and is characterized by a dense microbial (phototrophic) colonization on the walls and ceiling. However, some walls exhibited an important number of violet stains of unknown origin. The microbial communities of these violet stains are mainly composed of cyanobacteria, streptomycetes and fungi. A strain of Streptomyces parvus, isolated from the walls, produces a violet pigment in culture media. High performance liquid chromatography-mass spectrometry of the culture extracts obtained from this Streptomyces revealed the presence of a few granaticins, pigments with a benzoisochromanequinone structure. When metabolically active in the tomb, S. parvus synthesizes the pigments that diffuse into the mortar. During rain and/or wetting periods, the pigments are solubilized by alkaline waters and elute from the starting position to the surrounding mortar, enlarging the pigmented area and thus contributing to this exceptional biodeterioration phenomenon.
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Affiliation(s)
- Irene Dominguez-Moñino
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
| | - Marta Diaz-Herraiz
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
| | - Valme Jurado
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
| | - Leonila Laiz
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
| | - Ana Z Miller
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
| | - Juan Luis Santos
- Escuela Politecnica Superior, Universidad de Sevilla, Virgen de Africa 7, 41011 Sevilla, Spain
| | - Esteban Alonso
- Escuela Politecnica Superior, Universidad de Sevilla, Virgen de Africa 7, 41011 Sevilla, Spain
| | - Cesareo Saiz-Jimenez
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain.
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18
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Karwautz C, Kus G, Stöckl M, Neu TR, Lueders T. Microbial megacities fueled by methane oxidation in a mineral spring cave. ISME JOURNAL 2017; 12:87-100. [PMID: 28949325 PMCID: PMC5739006 DOI: 10.1038/ismej.2017.146] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/23/2017] [Accepted: 08/01/2017] [Indexed: 12/18/2022]
Abstract
Massive biofilms have been discovered in the cave of an iodine-rich former medicinal spring in southern Germany. The biofilms completely cover the walls and ceilings of the cave, giving rise to speculations about their metabolism. Here we report on first insights into the structure and function of the biofilm microbiota, combining geochemical, imaging and molecular analytics. Stable isotope analysis indicated that thermogenic methane emerging into the cave served as an important driver of biofilm formation. The undisturbed cavern atmosphere contained up to 3000 p.p.m. methane and was microoxic. A high abundance and diversity of aerobic methanotrophs primarily within the Methylococcales (Gammaproteobacteria) and methylotrophic Methylophilaceae (Betaproteobacteria) were found in the biofilms, along with a surprising diversity of associated heterotrophic bacteria. The highest methane oxidation potentials were measured for submerged biofilms on the cavern wall. Highly organized globular structures of the biofilm matrix were revealed by fluorescent lectin staining. We propose that the extracellular matrix served not only as an electron sink for nutrient-limited biofilm methylotrophs but potentially also as a diffusive barrier against volatilized iodine species. Possible links between carbon and iodine cycling in this peculiar habitat are discussed.
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Affiliation(s)
- Clemens Karwautz
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
| | - Günter Kus
- Bavarian Environment Agency (LfU), Department 10: Geological Survey, Hof/Saale, Germany
| | - Michael Stöckl
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
| | - Thomas R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research-UFZ, Magdeburg, Germany
| | - Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
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19
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Waring CL, Hankin SI, Griffith DWT, Kertesz MA, Kobylski V, Wilson NL, Coleman NV, Kettlewell G, Zlot R, Bosse M, Bell G. Seasonal total methane depletion in limestone caves. Sci Rep 2017; 7:8314. [PMID: 28814720 PMCID: PMC5559484 DOI: 10.1038/s41598-017-07769-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/30/2017] [Indexed: 01/08/2023] Open
Abstract
Methane concentration in caves is commonly much lower than the external atmosphere, yet the cave CH4 depletion causal mechanism is contested and dynamic links to external diurnal and seasonal temperature cycles unknown. Here, we report a continuous 3-year record of cave methane and other trace gases in Jenolan Caves, Australia which shows a seasonal cycle of extreme CH4 depletion, from ambient ~1,775 ppb to near zero during summer and to ~800 ppb in winter. Methanotrophic bacteria, some newly-discovered, rapidly consume methane on cave surfaces and in external karst soils with lifetimes in the cave of a few hours. Extreme bacterial selection due to the absence of alternate carbon sources for growth in the cave environment has resulted in an extremely high proportion 2–12% of methanotrophs in the total bacteria present. Unexpected seasonal bias in our cave CH4 depletion record is explained by a three-step process involving methanotrophy in aerobic karst soil above the cave, summer transport of soil-gas into the cave through epikarst, followed by further cave CH4 depletion. Disentangling cause and effect of cave gas variations by tracing sources and sinks has identified seasonal speleothem growth bias, with implied palaeo-climate record bias.
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Affiliation(s)
- Chris L Waring
- ANSTO Environmental Research, New Illawarra Rd., Lucas Heights, NSW 2234, Australia.
| | - Stuart I Hankin
- ANSTO Environmental Research, New Illawarra Rd., Lucas Heights, NSW 2234, Australia
| | - David W T Griffith
- University of Wollongong, Centre for Atmospheric Chemistry, Wollongong, NSW 2522, Australia
| | - Michael A Kertesz
- University of Sydney, Sydney Institute of Agriculture, Sydney, 2006, Australia
| | - Victoria Kobylski
- University of Sydney, Sydney Institute of Agriculture, Sydney, 2006, Australia
| | - Neil L Wilson
- University of Sydney, Sydney Institute of Agriculture, Sydney, 2006, Australia
| | - Nicholas V Coleman
- University of Sydney, School of Life and Environmental Sciences, Sydney, 2006, Australia
| | - Graham Kettlewell
- University of Wollongong, Centre for Atmospheric Chemistry, Wollongong, NSW 2522, Australia
| | - Robert Zlot
- formerly CSIRO, Technology Court, Pullenvale, QLD 4069, Australia
| | - Michael Bosse
- formerly CSIRO, Technology Court, Pullenvale, QLD 4069, Australia
| | - Graham Bell
- formerly CSIRO, Technology Court, Pullenvale, QLD 4069, Australia
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20
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Lennon JT, Nguyễn-Thùy D, Phạm TM, Drobniak A, Tạ PH, Phạm NÐ, Streil T, Webster KD, Schimmelmann A. Microbial contributions to subterranean methane sinks. GEOBIOLOGY 2017; 15:254-258. [PMID: 27671735 DOI: 10.1111/gbi.12214] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/25/2016] [Indexed: 06/06/2023]
Abstract
Sources and sinks of methane (CH4 ) are critical for understanding global biogeochemical cycles and their role in climate change. A growing number of studies have reported that CH4 concentrations in cave ecosystems are depleted, leading to the notion that these subterranean environments may act as sinks for atmospheric CH4 . Recently, it was hypothesized that this CH4 depletion may be caused by radiolysis, an abiotic process whereby CH4 is oxidized via interactions with ionizing radiation derived from radioactive decay. An alternate explanation is that the depletion of CH4 concentrations in caves could be due to biological processes, specifically oxidation by methanotrophic bacteria. We theoretically explored the radiolysis hypothesis and conclude that it is a kinetically constrained process that is unlikely to lead to the rapid loss of CH4 in subterranean environments. We present results from a controlled laboratory experiment to support this claim. We then tested the microbial oxidation hypothesis with a set of mesocosm experiments that were conducted in two Vietnamese caves. Our results reveal that methanotrophic bacteria associated with cave rocks consume CH4 at a rate of 1.3-2.7 mg CH4 · m-2 · d-1 . These CH4 oxidation rates equal or exceed what has been reported in other habitats, including agricultural systems, grasslands, deciduous forests, and Arctic tundra. Together, our results suggest that depleted concentrations of CH4 in caves are most likely due to microbial activity, not radiolysis as has been recently claimed. Microbial methanotrophy has the potential to oxidize CH4 not only in caves, but also in smaller-size open subterranean spaces, such as cracks, fissures, and other pores that are connected to and rapidly exchange with the atmosphere. Future studies are needed to understand how subterranean CH4 oxidation scales up to affect local, regional, and global CH4 cycling.
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Affiliation(s)
- J T Lennon
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - D Nguyễn-Thùy
- Faculty of Geology, Vietnam National University, Hanoi, Vietnam
| | - T M Phạm
- Department of Microbiology, Vietnam National University, Hanoi, Vietnam
| | - A Drobniak
- Indiana Geological Survey, Indiana University, Bloomington, IN, USA
| | - P H Tạ
- Faculty of Geology, Vietnam National University, Hanoi, Vietnam
| | - N Ð Phạm
- Department of Microbiology, Vietnam National University, Hanoi, Vietnam
| | | | - K D Webster
- Department of Geological Sciences, Indiana University, Bloomington, IN, USA
| | - A Schimmelmann
- Department of Geological Sciences, Indiana University, Bloomington, IN, USA
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21
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Leifer I, Melton C, Tratt DM, Buckland KN, Clarisse L, Coheur P, Frash J, Gupta M, Johnson PD, Leen JB, Van Damme M, Whitburn S, Yurganov L. Remote sensing and in situ measurements of methane and ammonia emissions from a megacity dairy complex: Chino, CA. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 221:37-51. [PMID: 27993424 DOI: 10.1016/j.envpol.2016.09.083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 09/23/2016] [Accepted: 09/27/2016] [Indexed: 06/06/2023]
Abstract
Methane (CH4) and ammonia (NH3) directly and indirectly affect the atmospheric radiative balance with the latter leading to aerosol generation. Both have important spectral features in the Thermal InfraRed (TIR) that can be studied by remote sensing, with NH3 allowing discrimination of husbandry from other CH4 sources. Airborne hyperspectral imagery was collected for the Chino Dairy Complex in the Los Angeles Basin as well as in situ CH4, carbon dioxide (CO2) and NH3 data. TIR data showed good spatial agreement with in situ measurements and showed significant emissions heterogeneity between dairies. Airborne remote sensing mapped plume transport for ∼20 km downwind, documenting topographic effects on plume advection. Repeated multiple gas in situ measurements showed that emissions were persistent on half-year timescales. Inversion of one dairy plume found annual emissions of 4.1 × 105 kg CH4, 2.2 × 105 kg NH3, and 2.3 × 107 kg CO2, suggesting 2300, 4000, and 2100 head of cattle, respectively, and Chino Dairy Complex emissions of 42 Gg CH4 and 8.4 Gg NH3 implying ∼200k cows, ∼30% more than Peischl et al. (2013) estimated for June 2010. Far-field data showed chemical conversion and/or deposition of Chino NH3 occurs within the confines of the Los Angeles Basin on a four to six h timescale, faster than most published rates, and likely from higher Los Angeles oxidant loads. Satellite observations from 2011 to 2014 confirmed that observed in situ transport patterns were representative and suggests much of the Chino Dairy Complex emissions are driven towards eastern Orange County, with a lesser amount transported to Palm Springs, CA. Given interest in mitigating husbandry health impacts from air pollution emissions, this study highlights how satellite observations can be leveraged to understand exposure and how multiple gas in situ emissions studies can inform on best practices given that emissions reduction of one gas could increase those of others.
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Affiliation(s)
- Ira Leifer
- Bubbleology Research International (BRI), Solvang, CA 93463, United States.
| | - Christopher Melton
- Bubbleology Research International (BRI), Solvang, CA 93463, United States
| | - David M Tratt
- The Aerospace Corporation, 2310 E. El Segundo Blvd., El Segundo, CA 90245, United States
| | - Kerry N Buckland
- The Aerospace Corporation, 2310 E. El Segundo Blvd., El Segundo, CA 90245, United States
| | | | - Pierre Coheur
- Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Jason Frash
- Bubbleology Research International (BRI), Solvang, CA 93463, United States
| | - Manish Gupta
- ABB, 3055 Orchard Drive, San Jose, CA 95134, United States
| | - Patrick D Johnson
- The Aerospace Corporation, 2310 E. El Segundo Blvd., El Segundo, CA 90245, United States
| | - J Brian Leen
- ABB, 3055 Orchard Drive, San Jose, CA 95134, United States
| | | | | | - Leonid Yurganov
- University of Maryland, Baltimore County (UMBC), Baltimore, MD 21250, United States
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22
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Pla C, Cuezva S, Garcia-Anton E, Fernandez-Cortes A, Cañaveras JC, Sanchez-Moral S, Benavente D. Changes in the CO2 dynamics in near-surface cavities under a future warming scenario: Factors and evidence from the field and experimental findings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 565:1151-1164. [PMID: 27261423 DOI: 10.1016/j.scitotenv.2016.05.160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/16/2016] [Accepted: 05/22/2016] [Indexed: 06/05/2023]
Affiliation(s)
- C Pla
- Departamento de Ciencias de la Tierra y del Medio Ambiente, Universidad de Alicante, San Vicente del Raspeig, 03690 Alicante, Spain.
| | - S Cuezva
- Museo Nacional de Ciencias Naturales (CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain; Geomnia Natural Resources SLNE, 28006 Madrid, Spain
| | - E Garcia-Anton
- Museo Nacional de Ciencias Naturales (CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - A Fernandez-Cortes
- Museo Nacional de Ciencias Naturales (CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain; Department of Earth Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - J C Cañaveras
- Departamento de Ciencias de la Tierra y del Medio Ambiente, Universidad de Alicante, San Vicente del Raspeig, 03690 Alicante, Spain
| | - S Sanchez-Moral
- Museo Nacional de Ciencias Naturales (CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - D Benavente
- Departamento de Ciencias de la Tierra y del Medio Ambiente, Universidad de Alicante, San Vicente del Raspeig, 03690 Alicante, Spain
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