1
|
Liu Y, Wang X, Wen Y, Cai H, Song X, Zhang Z. Effects of freeze-thaw cycles on soil greenhouse gas emissions: A systematic review. Environ Res 2024; 248:118386. [PMID: 38316387 DOI: 10.1016/j.envres.2024.118386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/20/2024] [Accepted: 01/30/2024] [Indexed: 02/07/2024]
Abstract
In the context of global warming, increasingly widespread and frequent freezing and thawing cycles (FTCs) will have profound effects on the biogeochemical cycling of soil carbon and nitrogen. FTCs can increase soil greenhouse gas (GHG) emissions by reducing the stability of soil aggregates, promoting the release of dissolved organic carbon, decreasing the number of microorganisms, inducing cell rupture, and releasing carbon and nitrogen nutrients for use by surviving microorganisms. However, the similarity and disparity of the mechanisms potentially contributing to changes in GHGs have not been systematically evaluated. The present study consolidates the most recent findings on the dynamics of soil carbon and nitrogen, as well as GHGs, in relation to FTCs. Additionally, it analyzes the impact of FTCs on soil GHGs in a systematic manner. In this study, particular emphasis is given to the following: (i) the reaction mechanism involved; (ii) variations in soil composition in different types of land (e.g., forest, peatland, farmland, and grassland); (iii) changes in soil structure in response to cycles of freezing temperatures; (iv) alterations in microbial biomass and community structure that may provide further insight into the fluctuations in GHGs after FTCs. The challenges identified included the extension of laboratory-scale research to ecosystem scales, the performance of in-depth investigation of the coupled effects of carbon, nitrogen, and water in the freeze-thaw process, and analysis of the effects of FTCs through the use of integrated research tools. The results of this study can provide a valuable point of reference for future experimental designs and scientific investigations and can also assist in the analysis of the attributes of GHG emissions from soil and the ecological consequences of the factors that influence these emissions in the context of global permafrost warming.
Collapse
Affiliation(s)
- Yuqing Liu
- Key Laboratory of Regional Environment and Eco-restoration, Ministry of Education, Shenyang University, Shenyang, 110044, China
| | - Xiaochu Wang
- Key Laboratory of Regional Environment and Eco-restoration, Ministry of Education, Shenyang University, Shenyang, 110044, China
| | - Yujuan Wen
- Key Laboratory of Regional Environment and Eco-restoration, Ministry of Education, Shenyang University, Shenyang, 110044, China; Northeast Geological S&T Innovation Center of China Geological Survey, Shenyang, 110000, China; Key Laboratory of Black Soil Evolution and Ecological Effect, Ministry of Natural Resources, Shenyang, 110000, China.
| | - Haoxuan Cai
- Key Laboratory of Regional Environment and Eco-restoration, Ministry of Education, Shenyang University, Shenyang, 110044, China
| | - Xiaoming Song
- Key Laboratory of Regional Environment and Eco-restoration, Ministry of Education, Shenyang University, Shenyang, 110044, China
| | - Zhipeng Zhang
- Sichuan Geological Environment Survey and Research Center, Sichuan, 610000, China.
| |
Collapse
|
2
|
Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi M, Iwayama K, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H. Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics. Microbiome 2023; 11:63. [PMID: 36978146 PMCID: PMC10052866 DOI: 10.1186/s40168-023-01474-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Microbiome dynamics are both crucial indicators and potential drivers of human health, agricultural output, and industrial bio-applications. However, predicting microbiome dynamics is notoriously difficult because communities often show abrupt structural changes, such as "dysbiosis" in human microbiomes. METHODS We integrated theoretical frameworks and empirical analyses with the aim of anticipating drastic shifts of microbial communities. We monitored 48 experimental microbiomes for 110 days and observed that various community-level events, including collapse and gradual compositional changes, occurred according to a defined set of environmental conditions. We analyzed the time-series data based on statistical physics and non-linear mechanics to describe the characteristics of the microbiome dynamics and to examine the predictability of major shifts in microbial community structure. RESULTS We confirmed that the abrupt community changes observed through the time-series could be described as shifts between "alternative stable states" or dynamics around complex attractors. Furthermore, collapses of microbiome structure were successfully anticipated by means of the diagnostic threshold defined with the "energy landscape" analysis of statistical physics or that of a stability index of nonlinear mechanics. CONCLUSIONS The results indicate that abrupt microbiome events in complex microbial communities can be forecasted by extending classic ecological concepts to the scale of species-rich microbial systems. Video Abstract.
Collapse
Affiliation(s)
- Hiroaki Fujita
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan.
| | - Masayuki Ushio
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Kenta Suzuki
- Integrated Bioresource Information Division, BioResource Research Center, RIKEN, Tsukuba, Ibaraki, 305-0074, Japan
| | - Masato S Abe
- Faculty of Culture and Information Science, Doshisha University, Kyotanabe, Kyoto, 610-0321, Japan
| | - Masato Yamamichi
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Koji Iwayama
- Faculty of Data Science, Shiga University, Hikone, 522-8522, Japan
| | - Alberto Canarini
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan
| | - Ibuki Hayashi
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan
| | - Keitaro Fukushima
- Faculty of Food and Agricultural Sciences, Fukushima University, Kanayagawa 1, Fukushima, Fukushima, 960-1296, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, 210-0821, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - E Toby Kiers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan.
| |
Collapse
|
3
|
Yajima D, Fujita H, Hayashi I, Shima G, Suzuki K, Toju H. Core species and interactions prominent in fish-associated microbiome dynamics. Microbiome 2023; 11:53. [PMID: 36941627 PMCID: PMC10026521 DOI: 10.1186/s40168-023-01498-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND In aquatic ecosystems, the health and performance of fish depend greatly on the dynamics of microbial community structure in the background environment. Nonetheless, finding microbes with profound impacts on fish's performance out of thousands of candidate species remains a major challenge. METHODS We examined whether time-series analyses of microbial population dynamics could illuminate core components and structure of fish-associated microbiomes in the background (environmental) water. By targeting eel-aquaculture-tank microbiomes as model systems, we reconstructed the population dynamics of the 9605 bacterial and 303 archaeal species/strains across 128 days. RESULTS Due to the remarkable increase/decrease of constituent microbial population densities, the taxonomic compositions of the microbiome changed drastically through time. We then found that some specific microbial taxa showed a positive relationship with eels' activity levels even after excluding confounding effects of environmental parameters (pH and dissolved oxygen level) on population dynamics. In particular, a vitamin-B12-producing bacteria, Cetobacterium somerae, consistently showed strong positive associations with eels' activity levels across the replicate time series of the five aquaculture tanks analyzed. Network theoretical and metabolic modeling analyses further suggested that the highlighted bacterium and some other closely-associated bacteria formed "core microbiomes" with potentially positive impacts on eels. CONCLUSIONS Overall, these results suggest that the integration of microbiology, ecological theory, and network science allows us to explore core species and interactions embedded within complex dynamics of fish-associated microbiomes. Video Abstract.
Collapse
Affiliation(s)
- Daii Yajima
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan
| | - Hiroaki Fujita
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan
| | - Ibuki Hayashi
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan
| | - Genta Shima
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan
| | - Kenta Suzuki
- Integrated Bioresource Information Division, BioResource Research Center, RIKEN, Tsukuba, Ibaraki, 305-0074, Japan
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan.
| |
Collapse
|
4
|
Buckley HL, Day NJ, Lear G, Case BS. Changes in the analysis of temporal community dynamics data: a 29-year literature review. PeerJ 2021; 9:e11250. [PMID: 33889452 PMCID: PMC8038643 DOI: 10.7717/peerj.11250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/18/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Understanding how biological communities change over time is of increasing importance as Earth moves into the Anthropocene. A wide variety of methods are used for multivariate community analysis and are variously applied to research that aims to characterise temporal dynamics in community composition. Understanding these methods and how they are applied is useful for determining best practice in community ecology. METHODOLOGY We reviewed the ecological literature from 1990 to 2018 that used multivariate methods to address questions of temporal community dynamics. For each paper that fulfilled our search criteria, we recorded the types of multivariate analysis used to characterise temporal community dynamics in addition to the research aim, habitat type, location, taxon and the experimental design. RESULTS Most studies had relatively few temporal replicates; the median number was seven time points. Nearly 70% of studies applied more than one analysis method; descriptive methods such as bar graphs and ordination were the most commonly applied methods. Surprisingly, the types of analyses used were only related to the number of temporal replicates, but not to research aim or any other aspects of experimental design such as taxon, or habitat or year of study. CONCLUSIONS This review reveals that most studies interested in understanding community dynamics use relatively short time series meaning that several, more sophisticated, temporal analyses are not widely applicable. However, newer methods using multivariate dissimilarities are growing in popularity and many can be applied to time series of any length.
Collapse
Affiliation(s)
- Hannah L. Buckley
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Nicola J. Day
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Bradley S. Case
- School of Science, Auckland University of Technology, Auckland, New Zealand
| |
Collapse
|
5
|
Staentzel C, Kondolf GM, Schmitt L, Combroux I, Barillier A, Beisel JN. Restoring fluvial forms and processes by gravel augmentation or bank erosion below dams: A systematic review of ecological responses. Sci Total Environ 2020; 706:135743. [PMID: 31841838 DOI: 10.1016/j.scitotenv.2019.135743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/22/2019] [Accepted: 11/23/2019] [Indexed: 06/10/2023]
Abstract
Aquatic biological communities have directly undergone human-induced changes. Altered hydrological and morphological processes in running waters have caused the degradation of main habitats for biotas and have disturbed ecosystem functionality. The latest advances in river restoration concerned the rise in far-reaching hydromorphological restoration actions that have been implemented below dams to reverse well-known negative impacts of anthropogenic pressures. Some authors emphasized the enhancement of sediment supply and habitat diversity using gravel augmentation or bank erosion to restore morphodynamics, and thus improve biodiversity. We explored the Web of Science database for empirical research papers that specifically addressed such hydromorphological river restoration actions. Articles were examined using a text-content analysis tool to determine the major concepts or ideas they deal with. It has also been proved as useful in defining interrelationships and degree of interdisciplinary. Results showed that a low number of published scientific articles exist about such projects, mainly condensed in the North hemisphere. Divergent ecological issues were highlighted by the word co-occurrence networks: (i) gravel augmentation was used to improve spawning habitats for fish of economic interest whereas (ii) erodible corridor was designed to safeguard natural riparian systems, approaching morphological goals of channel widening. Overall, ecological responses were consistent with those expected, leading however rather to functional shifts than richness increase. Gravel augmentation or bank erosion were not usually combined with in-channel structure management. However, this might be an option to consider since the biological communities seem to be sensitive during first restorations with such combination. This review demonstrates the value of word co-occurrence networks in exploring a high number of previous publications, keys for formulating guidance to manage gravel augmentation or bank erosion along ecological purposes.
Collapse
Affiliation(s)
- Cybill Staentzel
- Laboratoire Image, Ville, Environnement, UMR 7362 LIVE CNRS, Université de Strasbourg, F-67000 Strasbourg, France; Ecole Nationale du Génie de l'Eau et de l'Environnement (ENGEES), F-67000 Strasbourg, France.
| | - G Mathias Kondolf
- Department of Landscape Architecture & Environmental Planning, University of California Berkeley, Berkeley, CA 94720, USA
| | - Laurent Schmitt
- Laboratoire Image, Ville, Environnement, UMR 7362 LIVE CNRS, Université de Strasbourg, F-67000 Strasbourg, France
| | - Isabelle Combroux
- Laboratoire Image, Ville, Environnement, UMR 7362 LIVE CNRS, Université de Strasbourg, F-67000 Strasbourg, France
| | - Agnès Barillier
- Centre d'ingénierie hydraulique (CIH), Electricité de France (EDF), F-73374 Le Bourget du Lac, France
| | - Jean-Nicolas Beisel
- Laboratoire Image, Ville, Environnement, UMR 7362 LIVE CNRS, Université de Strasbourg, F-67000 Strasbourg, France; Ecole Nationale du Génie de l'Eau et de l'Environnement (ENGEES), F-67000 Strasbourg, France
| |
Collapse
|
6
|
Lopes CL, Bastos L, Caetano M, Martins I, Santos MM, Iglesias I. Development of physical modelling tools in support of risk scenarios: A new framework focused on deep-sea mining. Sci Total Environ 2019; 650:2294-2306. [PMID: 30292122 DOI: 10.1016/j.scitotenv.2018.09.351] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/28/2018] [Accepted: 09/29/2018] [Indexed: 06/08/2023]
Abstract
Deep-sea mining has gained international interest to provide materials for the worldwide industry. European oceans and, particularly, the Portuguese Exclusive Economic Zone present a recognized number of areas with polymetallic sulphides rich in metals used in high technology developments. A large part of these resources are in the vicinity of sensitive ecosystems, where the mineral extraction can potentially damage deep-ocean life services. In this context, technological research must be intensified, towards the implementation of environmental friendly solutions that mitigate the associated impacts. To reproduce deep-sea dynamics and evaluate the effects of the mining activities, reliable numerical modelling tools should be developed. The present work highlights the usefulness of a new framework for risk and impact assessment based on oceanographic numerical models to support the adoption of good management practices for deep-sea sustainable exploitation. This tool integrates the oceanic circulation model ROMS-Agrif with the semi-Lagrangian model ICHTHYOP, allowing the representation of deep-sea dynamics and particles trajectories considering the sediments physical properties. Numerical simulations for the North Mid-Atlantic Ridge region, revealed the ability of ROMS-Agrif to simulate real deep-sea dynamics through validation with in situ data. Results showed a strong diversity in the particle residence time, with a dependency on their density and size but also on local ocean conditions and bottom topography. The highest distances are obtained for the smaller and less dense particles, although they tend to be confined by bathymetric constrains and deposited in deepest regions. This work highlights the potential of this modelling tool to forecast laden plume trajectories, allowing the definition of risk assessment scenarios for deep-sea mining activities and the implementation of sustainable exploitation plans. Furthermore, the coupling of this numerical solution with models of biota inhabiting deep-sea vent fields into ecosystem models is discussed and outlined as cost-effective tools for the management of these remote ecosystems.
Collapse
Affiliation(s)
- Carina L Lopes
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto (U.Porto), Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; Centre for Environmental and Marine Studies (CESAM), University of Aveiro, 3810-193, Aveiro, Portugal; Marine and Environmental Sciences Centre (MARE), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal.
| | - Luísa Bastos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto (U.Porto), Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; Faculty of Sciences (FCUP), University of Porto (U.Porto), Department of Geosciences Environment and Spatial Planning, Rua do Campo Alegre, 4169-007 Porto, Portugal.
| | - Miguel Caetano
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto (U.Porto), Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; IPMA, Portuguese Institute for Sea and Atmosphere, Rua Alfredo Magalhães Ramalho, 6, 1495-006 Lisbon, Portugal.
| | - Irene Martins
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto (U.Porto), Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
| | - Miguel M Santos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto (U.Porto), Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; Faculty of Sciences (FCUP), University of Porto (U.Porto), Department of Biology, Rua do Campo Alegre, 4169-007 Porto, Portugal.
| | - Isabel Iglesias
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto (U.Porto), Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
| |
Collapse
|