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Gao D, Xu A, Zhang Y, Liu F, Li H, Liang H. Metagenomic insights into carbon and nitrogen cycling in the water-land transition zone of inland alkaline wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170856. [PMID: 38340836 DOI: 10.1016/j.scitotenv.2024.170856] [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: 11/28/2023] [Revised: 01/16/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Inland alkaline wetlands play a crucial role in maintaining ecological functions. However, these wetlands are becoming more vulnerable to the effects of water level fluctuations caused by global climate change, especially concerning carbon (C) and nitrogen (N) cycling. Here, metagenomics sequencing was used to investigate microorganism diversity, C and N cycling gene abundance at three water level types (D (dry), MF (middle flooded), HF (high flooded)) along an inland alkaline wetland. Our findings reveal that water level was the most important factor in regulating the microbial communities. Distinct shifts in community composition were found along the water level increases, without fundamentally altering their composition. With the increase of water level, the relative abundance of pmoA decreased from 2.5 × 10-5 to 5.1 × 10-6. The C cycling processes shift from predominantly CO2-generated processes under low water levels to CO2 and CH4 co-generated processes under high water levels. The relative abundance of nosZ reached 4.9 × 10-5 in HF, while in D and MF, it is recorded at 4.5 × 10-5 and 3.4 × 10-5, respectively. Water levels accelerate N cycling and generating N2O intermediates. Furthermore, our study highlights the dynamic competition and cooperation between C and N cycling processes. This research provides a comprehensive biological understanding of the influence of varying water levels on soil C and N cycling processes in wetland.
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Affiliation(s)
- Dawen Gao
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing 100044, China; Collaborative Innovation Center of Energy Conservation & Emission Reduction and Sustainable Urban-Rural Development in Beijing, Beijing University of Civil Engineering and Architecture, Beijing 100044, China.
| | - Ao Xu
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing 100044, China; Collaborative Innovation Center of Energy Conservation & Emission Reduction and Sustainable Urban-Rural Development in Beijing, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
| | - Yupeng Zhang
- College of Resources and Environmental Sciences, Henan Agricultural University, No.63 Agricultural Road, Zhengzhou 450002, China
| | - Fengqin Liu
- College of Life Sciences, Henan Agricultural University, No.63 Agricultural Road, Zhengzhou 450002, China
| | - Huiju Li
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing 100044, China; Collaborative Innovation Center of Energy Conservation & Emission Reduction and Sustainable Urban-Rural Development in Beijing, Beijing University of Civil Engineering and Architecture, Beijing 100044, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Liang
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing 100044, China; Collaborative Innovation Center of Energy Conservation & Emission Reduction and Sustainable Urban-Rural Development in Beijing, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
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Kenya E, Kinyanjui G, Kipnyargis A, Kinyua F, Mwangi M, Khamis F, Mwirichia R. Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya. Heliyon 2022; 8:e11577. [PMID: 36411924 PMCID: PMC9674510 DOI: 10.1016/j.heliyon.2022.e11577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/14/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
Forest soils provide a multitude of habitats for diverse communities of bacteria. In this study, we selected three tropical forests in Kenya to determine the diversity and community structure of soil bacteria inhabiting these regions. Kakamega and Irangi are rainforests, whereas Gazi Bay harbors mangrove forests. The three natural forests occupy different altitudinal zones and differ in their environmental characteristics. Soil samples were collected from a total of 12 sites and soil physicochemical parameters for each sampling site were analyzed. We used an amplicon-based Illumina high-throughput sequencing approach. Total community DNA was extracted from individual samples using the phenol-chloroform method. The 16S ribosomal RNA gene segment spanning the V4 region was amplified using the Illumina MiSeq platform. Diversity indices, rarefaction curves, hierarchical clustering, principal component analysis (PCA), and non-metric multidimensional scaling (NMDS) analyses were performed in R software. A total of 13,410 OTUs were observed at 97% sequence similarity. Bacterial communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria in both rainforest and mangrove sampling sites. Alpha diversity indices and species richness were higher in Kakamega and Irangi rainforests compared to mangroves in Gazi Bay. The composition of bacterial communities within and between the three forests was also significantly differentiated (R = 0.559, p = 0.007). Clustering in both PCA and NMDS plots showed that each sampling site had a distinct bacterial community profile. The NMDS analysis also indicated that soil EC, sodium, sulfur, magnesium, boron, and manganese contributed significantly to the observed variation in the bacterial community structure. Overall, this study demonstrated the presence of diverse taxa and heterogeneous community structures of soil bacteria inhabiting three tropical forests of Kenya. Our results also indicated that variation in soil chemical parameters was the major driver of the observed bacterial diversity and community structure in these forests.
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Affiliation(s)
- Eucharia Kenya
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Grace Kinyanjui
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Alex Kipnyargis
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Franklin Kinyua
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Mary Mwangi
- Department of Biochemistry and Biotechnology, Kenyatta University, P. O. Box 43844-00100, Nairobi, Kenya
| | - Fathiya Khamis
- International Centre of Insect Physiology and Ecology (ICIPE), P. O. Box 30772-00100, Nairobi, Kenya
| | - Romano Mwirichia
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
- Corresponding author.
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Woolet J, Whitman E, Parisien MA, Thompson DK, Flannigan MD, Whitman T. Effects of short-interval reburns in the boreal forest on soil bacterial communities compared to long-interval reburns. FEMS Microbiol Ecol 2022; 98:6603815. [PMID: 35671126 PMCID: PMC9303391 DOI: 10.1093/femsec/fiac069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/23/2022] [Accepted: 06/03/2022] [Indexed: 11/14/2022] Open
Abstract
Increasing fire frequency in some biomes is leading to fires burning in close succession, triggering rapid vegetation change and altering soil properties. We studied the effects of short-interval (SI) reburns on soil bacterial communities of the boreal forest of northwestern Canada using paired sites (n = 44). Both sites in each pair had burned in a recent fire; one site had burned within the previous 20 years before the recent fire (SI reburn) and the other had not. Paired sites were closely matched in prefire ecosite characteristics, prefire tree species composition, and stand structure. We hypothesized that there would be a significant effect of short vs. long fire-free intervals on community composition and that richness would not be consistently different between paired sites. We found that Blastococcus sp. was consistently enriched in SI reburns, indicating its role as a strongly ‘pyrophilous’ bacterium. Caballeronia sordidicola was consistently depleted in SI reburns. The depletion of this endophytic diazotroph raises questions about whether this is contributing to—or merely reflects—poor conifer seedling recolonization post-fire at SI reburns. While SI reburns had no significant effect on richness, dissimilarity between short- and long-interval pairs was significantly correlated with difference in soil pH, and there were small significant changes in overall community composition.
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Affiliation(s)
- Jamie Woolet
- Department of Soil Science, University of Wisconsin-Madison , 1525 Observatory Dr., Madison, WI, 53706 , USA
- Department of Forest and Rangeland Stewardship, Colorado State University , 1001 Amy VanDyken Way, Fort Collins, CO, 80521 , USA
| | - Ellen Whitman
- Northern Forestry Centre , Canadian Forest Service, Natural Resources Canada, 5320 122Street, Edmonton, AB, T6H 3S5 , Canada
- Great Lakes Forestry Centre , Canadian Forest Service, Natural Resources Canada, 1219 Queen St. E., Sault Ste. Marie, ON, P6A 2E5 , Canada
| | - Marc-André Parisien
- Northern Forestry Centre , Canadian Forest Service, Natural Resources Canada, 5320 122Street, Edmonton, AB, T6H 3S5 , Canada
| | - Dan K Thompson
- Northern Forestry Centre , Canadian Forest Service, Natural Resources Canada, 5320 122Street, Edmonton, AB, T6H 3S5 , Canada
- Great Lakes Forestry Centre , Canadian Forest Service, Natural Resources Canada, 1219 Queen St. E., Sault Ste. Marie, ON, P6A 2E5 , Canada
| | - Mike D Flannigan
- Department of Renewable Resources, University of Alberta , 751 General Services Building, Edmonton, AB, T6G 2H1 , Canada
- Faculty of Science, Thompson Rivers University , 805 TRU Way, Kamloops, BC, V2C 0C8 , Canada
| | - Thea Whitman
- Department of Soil Science, University of Wisconsin-Madison , 1525 Observatory Dr., Madison, WI, 53706 , USA
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Fernández LD, Seppey CVW, Singer D, Fournier B, Tatti D, Mitchell EAD, Lara E. Niche Conservatism Drives the Elevational Diversity Gradient in Major Groups of Free-Living Soil Unicellular Eukaryotes. MICROBIAL ECOLOGY 2022; 83:459-469. [PMID: 34052880 DOI: 10.1007/s00248-021-01771-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
Ancestral adaptations to tropical-like climates drive most multicellular biogeography and macroecology. Observational studies suggest that this niche conservatism could also be shaping unicellular biogeography and macroecology, although evidence is limited to Acidobacteria and testate amoebae. We tracked the phylogenetic signal of this niche conservatism in far related and functionally contrasted groups of common soil protists (Bacillariophyta, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida) along a humid but increasingly cold elevational gradient in Switzerland. Protist diversity decreased, and the size of the geographic ranges of taxa increased with elevation and associated decreasing temperature (climate), which is consistent with a macroecological pattern known as the Rapoport effect. Bacillariophyta exhibited phylogenetically overdispersed communities assembled by competitive exclusion of closely related taxa with shared (conserved) niches. By contrast, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida exhibited phylogenetically clustered communities assembled by habitat filtering, revealing the coexistence of closely related taxa with shared (conserved) adaptations to cope with the humid but temperate to cold climate of the study site. Phylobetadiversity revealed that soil protists exhibit a strong phylogenetic turnover among elevational sites, suggesting that most taxa have evolutionary constraints that prevent them from colonizing the colder and higher sites of the elevation gradient. Our results suggest that evolutionary constraints determine how soil protists colonize climates departing from warm and humid conditions. We posit that these evolutionary constraints are linked to an ancestral adaptation to tropical-like climates, which limits their survival in exceedingly cold sites. This niche conservatism possibly drives their biogeography and macroecology along latitudinal and altitudinal climatic gradients.
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Affiliation(s)
- Leonardo D Fernández
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O'Higgins, Avenida Viel 1497, Santiago, Chile.
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000, Neuchâtel, Switzerland.
| | - Christophe V W Seppey
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000, Neuchâtel, Switzerland
- Institute of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019, Tromsø, Norway
- Institute of Environmental Sciences and Geography, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - David Singer
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000, Neuchâtel, Switzerland
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, 05508-090, Brazil
- UMR CNRS 6112 LPG-BIAF, Université D'Angers, Cedex 1, Angers, France
| | - Bertrand Fournier
- Institute of Environmental Sciences and Geography, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Dylan Tatti
- Division Agronomie, Soil Protection and Use Group, School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences BFH, Länggasse 85, 3052, Zollikofen, Switzerland
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000, Neuchâtel, Switzerland
- Botanical Garden of Neuchâtel, Chemin du Pertuis-du-Sault 58, CH-2000, Neuchâtel, Switzerland
| | - Enrique Lara
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000, Neuchâtel, Switzerland
- Department of Mycology, Real Jardín Botánico de Madrid, CSIC, Plaza de Murillo 2, 28014, Madrid, Spain
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Velmurugan A, Swarnam TP, Jaisankar I, Swain S, Subramani T. Vegetation–soil–microbial diversity influences ecosystem multifunctionality across different tropical coastal ecosystem types. Trop Ecol 2021. [DOI: 10.1007/s42965-021-00209-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Lantana camara and Ageratina adenophora invasion alter the understory species composition and diversity of chir pine forest in central Himalaya, India. ACTA OECOLOGICA 2020. [DOI: 10.1016/j.actao.2020.103642] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Liu F, Zhang Y, Liang H, Gao D. Long-term harvesting of reeds affects greenhouse gas emissions and microbial functional genes in alkaline wetlands. WATER RESEARCH 2019; 164:114936. [PMID: 31382148 DOI: 10.1016/j.watres.2019.114936] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/28/2019] [Accepted: 07/30/2019] [Indexed: 06/10/2023]
Abstract
Reed (Phragmites australis) is dominant vegetation in alkaline wetlands that is harvested annually due to its economic value. To reveal the effects of harvesting reeds on the emission of greenhouse gases (GHG), the annual soil physicochemical characteristics and flux of GHGs in a reed wetland without harvesting (NHRW) and with harvesting (HRW) were measured. The results showed that after the harvesting of reeds, the total organic carbon (TOC) and total nitrogen (TN) significantly decreased, and soil temperature significantly increased. The annual cumulative N2O emissions decreased from 0.73 ± 0.20 kg ha-1 to -0.57 ± 0.49 kg ha-1 with the harvesting of reeds. The annual cumulative CH4 emissions also decreased from 561.88 ± 18.61 kg ha-1 to 183.13 ± 18.77 kg ha-1 with the harvesting of reeds. However, harvesting of reeds had only a limited influence on the annual cumulative CO2 emissions. A Pearson correlation analysis revealed that the CO2 and N2O emissions were more sensitive to temperature than the CH4 emissions. Both structural equation modeling (SEM) analysis and slurry incubation confirmed that higher temperatures offset the reduction of CO2 emissions after reed harvesting. Metagenomics showed that the abundance of functional genes involved in both GHG sink and source decreased with reed harvesting. This study presents a comprehensive view of reed harvesting on GHG emissions in alkaline wetlands, yielding new insight into the microbial response and offering a novel perspective on the potential impacts of wetland management.
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Affiliation(s)
- Fengqin Liu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Yupeng Zhang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Hong Liang
- School of Environment, Harbin Institute of Technology, Harbin, China.
| | - Dawen Gao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China; School of Environment, Harbin Institute of Technology, Harbin, China.
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The Influence of Soil Physico-Chemical Properties and Enzyme Activities on Soil Quality of Saline-Alkali Agroecosystems in Western Jilin Province, China. SUSTAINABILITY 2018. [DOI: 10.3390/su10051529] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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