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Huang L, Bao W, Kuzyakov Y, Hu H, Zhang H, Li F. Enzyme stoichiometry reveals microbial nitrogen limitation in stony soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174124. [PMID: 38909790 DOI: 10.1016/j.scitotenv.2024.174124] [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: 11/27/2023] [Revised: 04/19/2024] [Accepted: 06/16/2024] [Indexed: 06/25/2024]
Abstract
Resource limitation for soil microorganisms is the crucial factor in nutrient cycling and vegetation development, which are especially important in arid climate. Given that rock fragments strongly impact hydrologic and geochemical processes in arid areas, we hypothesized that microbial resource (C and N) limitation will increase along the rock fragment content (RFC) gradient. We conducted a field experiment in Minjiang river arid valleys with four RFC content (0 %, 25 %, 50 %, and 75 %, V V-1) and four vegetation types (Artemisia vestita, Bauhinia brachycarpa, Sophora davidii, and the soil without plants). Activities of C (β-1,4-glucosidase, BG), N (β-1,4-N-acetyl-glucosaminidase, NAG; L-leucine aminopeptidase, LAP), and P (acid phosphatase, ACP) acquiring enzymes were investigated to assess the limitations by C, N or P. In unplanted soil, the C acquiring enzyme activity decreased by 43 %, but N acquiring enzyme activity increased by 72 % in 75 % RFC than those in rock-free soils (0 % RFC). Increasing RFC reduced C:N and C:P enzymatic ratios, as well as vector length and vector angle (< 45°). Plants increased the activities of C and N acquiring enzymes in soils, as well as C:P and N:P enzyme activities, as well as vector length (by 5.6 %-25 %), but decreased vector angle (by 13 %-21 %). Enzyme stoichiometry was dependent on biotic and abiotic factors, such as soil water content, soil C:N, and total content of phospholipid fatty acids, reflecting microbial biomass content. Increased RFC shifted enzymatic stoichiometry toward lower C but stronger N limitation for microorganisms. Vegetation increased microbial C and N limitation, and impacted the enzymatic activities and stoichiometry depending on shrub functional groups. Consequently, the direct effects of vegetation, nutrient availability and microbial biomass content, as well as indirect effects of soil properties collectively increased microbial resource limitations along the RFC gradient.
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Affiliation(s)
- Long Huang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization& Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Sichuan, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weikai Bao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization& Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Sichuan, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Goettingen, 37077 Göttingen, Germany; Peoples Friendship University of Russia (RUDN University), 117198 Moscow, Russia; Institute of Environmental Sciences, Kazan Federal University, 420049 Kazan, Russia
| | - Hui Hu
- Henan Key Laboratory of Water Pollution Control and Rehabilitation, Henan University of Urban Construction, Pingdingshan 467000, China
| | - Hanyue Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization& Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Sichuan, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanglan Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization& Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Sichuan, China.
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Deng F, Xie H, Zheng T, Yang Y, Bao X, He H, Zhang X, Liang C. Dynamic responses of soil microbial communities to seasonal freeze-thaw cycles in a temperate agroecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175228. [PMID: 39102954 DOI: 10.1016/j.scitotenv.2024.175228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/22/2024] [Accepted: 07/31/2024] [Indexed: 08/07/2024]
Abstract
Soil freeze-thaw cycles (FTCs) are common in temperate agricultural ecosystems during the non-growing season and are progressively influenced by climate change. The impact of these cycles on soil microbial communities, crucial for ecosystem functioning, varies under different agricultural management practices. Here, we investigated the dynamic changes in soil microbial communities in a Mollisol during seasonal FTCs and examined the effects of stover mulching and nitrogen fertilization. We revealed distinct responses between bacterial and fungal communities. The dominant bacterial phyla reacted differently to FTCs: for example, Proteobacteria responded opportunistically, Actinobacteria, Acidobacteria, Choroflexi and Gemmatimonadetes responded sensitively, and Saccharibacteria exhibited a tolerance response. In contrast, the fungal community composition remained relatively stable during FTCs, except for a decline in Glomeromycota. Certain bacterial OTUs acted as sensitive indicators of FTCs, forming keystone modules in the network that are closely linked to soil carbon, nitrogen content and potential functions. Additionally, neither stover mulching nor nitrogen fertilization significantly influenced microbial richness, diversity and potential functions. However, over time, more indicator species specific to these agricultural practices began to emerge within the networks and gradually occupied the central positions. Furthermore, our findings suggest that farming practices, by introducing keystone microbes and changing interspecies interactions (even without changing microbial richness and diversity), can enhance microbial community stability against FTC disturbances. Specifically, higher nitrogen input with stover removal promotes fungal stability during soil freezing, while lower nitrogen levels increase bacterial stability during soil thawing. Considering the fungal tolerance to FTCs, we recommend reducing nitrogen input for manipulating bacterial interactions, thereby enhancing overall microbial resilience to seasonal FTCs. In summary, our research reveals that microbial responses to seasonal FTCs are reshaped through land management to support ecosystem functions under environmental stress amid climate change.
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Affiliation(s)
- Fangbo Deng
- Key Lab of Conservation Tillage & Ecological Agriculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongtu Xie
- Key Lab of Conservation Tillage & Ecological Agriculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Tiantian Zheng
- Key Lab of Conservation Tillage & Ecological Agriculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Yali Yang
- Key Lab of Conservation Tillage & Ecological Agriculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Xuelian Bao
- Key Lab of Conservation Tillage & Ecological Agriculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Hongbo He
- Key Lab of Conservation Tillage & Ecological Agriculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Xudong Zhang
- Key Lab of Conservation Tillage & Ecological Agriculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Chao Liang
- Key Lab of Conservation Tillage & Ecological Agriculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
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Yin S, Wang C, Abalos D, Guo Y, Pang X, Tan C, Zhou Z. Seasonal response of soil microbial community structure and life history strategies to winter snow cover change in a temperate forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175066. [PMID: 39079633 DOI: 10.1016/j.scitotenv.2024.175066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 06/29/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024]
Abstract
Snow cover provides a thermally stable and humid soil environment and thereby regulates soil microbial communities and biogeochemical cycling. A warmer world with large reductions in snow cover and earlier spring snowmelt may disrupt this stability and associated ecosystem functioning. Yet, little is known about the response of soil microbial communities to decreased snowpack and potential carry-over effects beyond the snow cover period. Herein, we tested this response by conducting a snowpack manipulation experiment (control, addition, and removal) in a temperate forest. Our results showed that fungi were more sensitive to changes in snowpack. Thicker snowpack increased the diversity of fungi, but had weak effects on the diversity of bacteria in winter. Thickening snow cover promoted the ratio of fungi to bacteria abundance across the year, and such relative increase in fungi abundance was largely driven by Basidiomycota phyla (Agaricomycetes class). Increased snowpack decreased soil nitrate concentration, and produced carry-over biogeochemical effects evidenced by increased summer β-1,4-glucosidase and N-acetyl-β-glucosaminidase activities. On a seasonal scale, microbial biomass peaked at both winter and summer; winter microbial community was fungi dominated, while bacteria dominated in summer. The abundances of bacterial phyla had greater seasonal variation than fungal phyla. Specifically, Actinobacteria had greater dominance in winter than in summer, while Acidobacteria, Proteobacteria, and Verrucomicrobia had greater abundance in summer than in winter. Microbial high yield-resource acquisition-stress tolerance life history strategies showed significant seasonal tradeoffs, i.e., resource acquisition and stress tolerance strategies dominated in summer, while high yield strategy dominated in winter. Overall, our findings underline that climate-induced reductions in snow cover can disrupt soil biogeochemical cycling also beyond the snow cover period due to shifts in soil microbial community structure and life history strategies.
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Affiliation(s)
- Shuang Yin
- School of Ecology and Key Laboratory of Sustainable Forest Ecosystem Management, Ministry of Education, Northeast Forestry University, Harbin 150040, China; Northeast Asia Biodiversity Research Center, Northeast Forestry University, Harbin 150040, China
| | - Chuankuan Wang
- School of Ecology and Key Laboratory of Sustainable Forest Ecosystem Management, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Diego Abalos
- Department of Agroecology, iCLIMATE, Aarhus University, Tjele 8830, Denmark
| | - Yu Guo
- School of Ecology and Key Laboratory of Sustainable Forest Ecosystem Management, Ministry of Education, Northeast Forestry University, Harbin 150040, China; Northeast Asia Biodiversity Research Center, Northeast Forestry University, Harbin 150040, China
| | - Xuesen Pang
- School of Ecology and Key Laboratory of Sustainable Forest Ecosystem Management, Ministry of Education, Northeast Forestry University, Harbin 150040, China; Northeast Asia Biodiversity Research Center, Northeast Forestry University, Harbin 150040, China
| | - Chuanqiao Tan
- School of Ecology and Key Laboratory of Sustainable Forest Ecosystem Management, Ministry of Education, Northeast Forestry University, Harbin 150040, China; Northeast Asia Biodiversity Research Center, Northeast Forestry University, Harbin 150040, China
| | - Zhenghu Zhou
- School of Ecology and Key Laboratory of Sustainable Forest Ecosystem Management, Ministry of Education, Northeast Forestry University, Harbin 150040, China; Northeast Asia Biodiversity Research Center, Northeast Forestry University, Harbin 150040, China.
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Erlandson SR, Ewing PM, Osborne SL, Lehman RM. Sterile sentinels and MinION sequencing capture active soil microbial communities that differentiate crop rotations. ENVIRONMENTAL MICROBIOME 2024; 19:30. [PMID: 38715076 PMCID: PMC11077770 DOI: 10.1186/s40793-024-00571-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/21/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Soil microbial communities are difficult to measure and critical to soil processes. The bulk soil microbiome is highly diverse and spatially heterogeneous, which can make it difficult to detect and monitor the responses of microbial communities to differences or changes in management, such as different crop rotations in agricultural research. Sampling a subset of actively growing microbes should promote monitoring how soil microbial communities respond to management by reducing the variation contributed by high microbial spatial and temporal heterogeneity and less active microbes. We tested an in-growth bag method using sterilized soil in root-excluding mesh, "sterile sentinels," for the capacity to differentiate between crop rotations. We assessed the utility of different incubation times and compared colonized sentinels to concurrently sampled bulk soils for the statistical power to differentiate microbial community composition in low and high diversity crop rotations. We paired this method with Oxford Nanopore MinION sequencing to assess sterile sentinels as a standardized, fast turn-around monitoring method. RESULTS Compared to bulk soil, sentinels provided greater statistical power to distinguish between crop rotations for bacterial communities and equivalent power for fungal communities. The incubation time did not affect the statistical power to detect treatment differences in community composition, although longer incubation time increased total biomass. Bulk and sentinel soil samples contained shared and unique microbial taxa that were differentially abundant between crop rotations. CONCLUSIONS Overall, compared to bulk soils, the sentinels captured taxa with copiotrophic or ruderal traits, and plant-associated taxa. The sentinels show promise as a sensitive, scalable method to monitor soil microbial communities and provide information complementary to traditional soil sampling.
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Affiliation(s)
- Sonya R Erlandson
- USDA-ARS-North Central Agricultural Research Laboratory, Brookings, SD, 57006, USA.
| | - Patrick M Ewing
- USDA-ARS-Food Systems Research Unit, Burlington, VT, 57006, USA
| | - Shannon L Osborne
- USDA-ARS-North Central Agricultural Research Laboratory, Brookings, SD, 57006, USA
| | - R Michael Lehman
- USDA-ARS-North Central Agricultural Research Laboratory, Brookings, SD, 57006, USA
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Xiang X, Yao T, Man B, Lin D, Li C. Global hotspots and trends in microbial-mediated grassland carbon cycling: a bibliometric analysis. Front Microbiol 2024; 15:1377338. [PMID: 38741733 PMCID: PMC11090204 DOI: 10.3389/fmicb.2024.1377338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/01/2024] [Indexed: 05/16/2024] Open
Abstract
Grasslands are among the most widespread environments on Earth, yet we still have poor knowledge of their microbial-mediated carbon cycling in the context of human activity and climate change. We conducted a systematic bibliometric analysis of 1,660 literature focusing on microbial-mediated grassland carbon cycling in the Scopus database from 1990 to 2022. We observed a steep increase in the number of multidisciplinary and interdisciplinary studies since the 2000s, with focus areas on the top 10 subject categories, especially in Agricultural and Biological Sciences. Additionally, the USA, Australia, Germany, the United Kingdom, China, and Austria exhibited high levels of productivity. We revealed that the eight papers have been pivotal in shaping future research in this field, and the main research topics concentrate on microbial respiration, interaction relationships, microbial biomass carbon, methane oxidation, and high-throughput sequencing. We further highlight that the new research hotspots in microbial-mediated grassland carbon cycling are mainly focused on the keywords "carbon use efficiency," "enzyme activity," "microbial community," and "high throughput sequencing." Our bibliometric analysis in the past three decades has provided insights into a multidisciplinary and evolving field of microbial-mediated grassland carbon cycling, not merely summarizing the literature but also critically identifying research hotspots and trends, the intellectual base, and interconnections within the existing body of collective knowledge and signposting the path for future research directions.
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Affiliation(s)
- Xing Xiang
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science, Shangrao Normal University, Shangrao, China
- Key Laboratory for Regional Plants Conservation and Ecological Restoration of Northeast Jiangxi, College of Life Science, Shangrao Normal University, Shangrao, China
| | - Tuo Yao
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China
- Key Laboratory of Grassland Ecosystem, Gansu Agricultural University, Ministry of Education, Lanzhou, China
| | - Baiying Man
- College of Life Science, Shangrao Normal University, Shangrao, China
- Key Laboratory for Regional Plants Conservation and Ecological Restoration of Northeast Jiangxi, College of Life Science, Shangrao Normal University, Shangrao, China
| | - Dong Lin
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China
| | - Changning Li
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China
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Fontaine S, Abbadie L, Aubert M, Barot S, Bloor JMG, Derrien D, Duchene O, Gross N, Henneron L, Le Roux X, Loeuille N, Michel J, Recous S, Wipf D, Alvarez G. Plant-soil synchrony in nutrient cycles: Learning from ecosystems to design sustainable agrosystems. GLOBAL CHANGE BIOLOGY 2024; 30:e17034. [PMID: 38273527 DOI: 10.1111/gcb.17034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 10/14/2023] [Indexed: 01/27/2024]
Abstract
Redesigning agrosystems to include more ecological regulations can help feed a growing human population, preserve soils for future productivity, limit dependency on synthetic fertilizers, and reduce agriculture contribution to global changes such as eutrophication and warming. However, guidelines for redesigning cropping systems from natural systems to make them more sustainable remain limited. Synthetizing the knowledge on biogeochemical cycles in natural ecosystems, we outline four ecological systems that synchronize the supply of soluble nutrients by soil biota with the fluctuating nutrient demand of plants. This synchrony limits deficiencies and excesses of soluble nutrients, which usually penalize both production and regulating services of agrosystems such as nutrient retention and soil carbon storage. In the ecological systems outlined, synchrony emerges from plant-soil and plant-plant interactions, eco-physiological processes, soil physicochemical processes, and the dynamics of various nutrient reservoirs, including soil organic matter, soil minerals, atmosphere, and a common market. We discuss the relative importance of these ecological systems in regulating nutrient cycles depending on the pedoclimatic context and on the functional diversity of plants and microbes. We offer ideas about how these systems could be stimulated within agrosystems to improve their sustainability. A review of the latest advances in agronomy shows that some of the practices suggested to promote synchrony (e.g., reduced tillage, rotation with perennial plant cover, crop diversification) have already been tested and shown to be effective in reducing nutrient losses, fertilizer use, and N2 O emissions and/or improving biomass production and soil carbon storage. Our framework also highlights new management strategies and defines the conditions for the success of these nature-based practices allowing for site-specific modifications. This new synthetized knowledge should help practitioners to improve the long-term productivity of agrosystems while reducing the negative impact of agriculture on the environment and the climate.
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Affiliation(s)
- Sébastien Fontaine
- INRAE, VetAgro Sup, Université Clermont Auvergne, UMR Ecosystème Prairial, Clermont-Ferrand, France
| | - Luc Abbadie
- UPEC, CNRS, IRD, INRAE, Institut d'écologie et des sciences de l'environnement, IEES, Sorbonne Université, Paris, France
| | - Michaël Aubert
- UNIROUEN, INRAE, ECODIV-Rouen, Normandie Univ, Rouen, France
| | - Sébastien Barot
- UPEC, CNRS, IRD, INRAE, Institut d'écologie et des sciences de l'environnement, IEES, Sorbonne Université, Paris, France
| | - Juliette M G Bloor
- INRAE, VetAgro Sup, Université Clermont Auvergne, UMR Ecosystème Prairial, Clermont-Ferrand, France
| | | | - Olivier Duchene
- ISARA, Research Unit Agroecology and Environment, Lyon, France
| | - Nicolas Gross
- INRAE, VetAgro Sup, Université Clermont Auvergne, UMR Ecosystème Prairial, Clermont-Ferrand, France
| | | | - Xavier Le Roux
- INRAE UMR 1418, CNRS UMR 5557, VetAgroSup, Microbial Ecology Centre LEM, Université de Lyon, Villeurbanne, France
| | - Nicolas Loeuille
- UPEC, CNRS, IRD, INRAE, Institut d'écologie et des sciences de l'environnement, IEES, Sorbonne Université, Paris, France
| | - Jennifer Michel
- Plant Sciences, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Sylvie Recous
- INRAE, FARE, Université de Reims Champagne-Ardenne, Reims, France
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, CNRS, Université de Bourgogne, INRAE, Université de Bourgogne Franche-Comté, Dijon, France
| | - Gaël Alvarez
- INRAE, VetAgro Sup, Université Clermont Auvergne, UMR Ecosystème Prairial, Clermont-Ferrand, France
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Purcell AM, Dijkstra P, Hungate BA, McMillen K, Schwartz E, van Gestel N. Rapid growth rate responses of terrestrial bacteria to field warming on the Antarctic Peninsula. THE ISME JOURNAL 2023; 17:2290-2302. [PMID: 37872274 PMCID: PMC10689830 DOI: 10.1038/s41396-023-01536-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/25/2023]
Abstract
Ice-free terrestrial environments of the western Antarctic Peninsula are expanding and subject to colonization by new microorganisms and plants, which control biogeochemical cycling. Measuring growth rates of microbial populations and ecosystem carbon flux is critical for understanding how terrestrial ecosystems in Antarctica will respond to future warming. We implemented a field warming experiment in early (bare soil; +2 °C) and late (peat moss-dominated; +1.2 °C) successional glacier forefield sites on the western Antarctica Peninsula. We used quantitative stable isotope probing with H218O using intact cores in situ to determine growth rate responses of bacterial taxa to short-term (1 month) warming. Warming increased the growth rates of bacterial communities at both sites, even doubling the number of taxa exhibiting significant growth at the early site. Growth responses varied among taxa. Despite that warming induced a similar response for bacterial relative growth rates overall, the warming effect on ecosystem carbon fluxes was stronger at the early successional site-likely driven by increased activity of autotrophs which switched the ecosystem from a carbon source to a carbon sink. At the late-successional site, warming caused a significant increase in growth rate of many Alphaproteobacteria, but a weaker and opposite gross ecosystem productivity response that decreased the carbon sink-indicating that the carbon flux rates were driven more strongly by the plant communities. Such changes to bacterial growth and ecosystem carbon cycling suggest that the terrestrial Antarctic Peninsula can respond fast to increases in temperature, which can have repercussions for long-term elemental cycling and carbon storage.
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Affiliation(s)
- Alicia M Purcell
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Kelly McMillen
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Natasja van Gestel
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
- TTU Climate Center, Texas Tech University, Lubbock, TX, USA
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Dou X, Hu T, Köster K, Sun A, Li G, Yue Y, Sun L, Ding Y. Temporal dynamics of soil dissolved organic carbon in temperate forest managed by prescribed burning in Northeast China. ENVIRONMENTAL RESEARCH 2023; 237:117065. [PMID: 37660872 DOI: 10.1016/j.envres.2023.117065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/05/2023]
Abstract
Dissolved organic carbon (DOC) is an important function of soil organic carbon and sensitive to environmental disturbance. Few studies have explored the variations in soil DOC dynamics and effects on soil physicochemical properties following prescribed burnings. In this study, Pinus koraiensis plantation forests in Northeast China were selected and subjected to prescribed burning in early November 2018. Soil DOC and different soil physicochemical and biological properties in the 0-10 cm and 10-20 cm soil layers were sampled six times within two years after a prescribed burning. In this study, some soil physicochemical (SOC, TN, and ST) and microbial biomass properties (MBC) recovered within two years after a prescribed burning. Compared to the unburned control stands, the post-fire soil DOC concentrations in the upper and lower soil layers increased by 16% and 12%, respectively. Soil DOC concentrations varied with sampling time, and peaked one year after the prescribed burning. Our results showed that soil chemical properties (NH4+-N and pH) rather than biological properties (microbial biomass) were the main driving factors for changes in post-fire soil DOC concentrations. Current study provides an important reference for post-fire and seasonal soil C cycling in plantation forests of Northeast China.
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Affiliation(s)
- Xu Dou
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, College of Forestry, Northeast Forestry University, 26 Hexing Road, 150040, Harbin, China
| | - Tongxin Hu
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, College of Forestry, Northeast Forestry University, 26 Hexing Road, 150040, Harbin, China
| | - Kajar Köster
- Department of Environmental and Biological Sciences, University of Eastern Finland, 80101, Joensuu, Finland
| | - Aobo Sun
- Liaoning Academy of Agricultural Sciences, 84 Dongling Road, 110161, Shenyang, China
| | - Guangxin Li
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, College of Forestry, Northeast Forestry University, 26 Hexing Road, 150040, Harbin, China
| | - Yang Yue
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, College of Forestry, Northeast Forestry University, 26 Hexing Road, 150040, Harbin, China
| | - Long Sun
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, College of Forestry, Northeast Forestry University, 26 Hexing Road, 150040, Harbin, China.
| | - Yiyang Ding
- Department of Forest Sciences/ Institute for Atmospheric Sciences and Earth System Research (INAR), Department of Physics, University of Helsinki, 00014 Helsinki, Finland
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Lv Z, Gu Y, Chen S, Chen J, Jia Y. Effects of autumn diurnal freeze–thaw cycles on soil bacteria and greenhouse gases in the permafrost regions. Front Microbiol 2022; 13:1056953. [DOI: 10.3389/fmicb.2022.1056953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/02/2022] [Indexed: 12/05/2022] Open
Abstract
Understanding the impacts of diurnal freeze–thaw cycles (DFTCs) on soil microorganisms and greenhouse gas emissions is crucial for assessing soil carbon and nitrogen cycles in the alpine ecosystems. However, relevant studies in the permafrost regions in the Qinghai-Tibet Plateau (QTP) are still lacking. In this study, we used high-throughput pyrosequencing and static chamber-gas chromatogram to study the changes in topsoil bacteria and fluxes of greenhouse gases, including carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O), during autumn DFTCs in the permafrost regions of the Shule River headwaters on the western part of Qilian Mountains, northeast margin of the QTP. The results showed that the bacterial communities contained a total of 35 phyla, 88 classes, 128 orders, 153 families, 176 genera, and 113 species. The dominant phyla were Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes. Two DFTCs led to a trend of increasing bacterial diversity and significant changes in the relative abundance of 17 known bacteria at the family, genus, and species levels. These were predominantly influenced by soil temperature, water content, and salinity. In addition, CO2 flux significantly increased while CH4 flux distinctly decreased, and N2O flux tended to increase after two DFTCs, with soil bacteria being the primary affecting variable. This study can provide a scientific insight into the impact of climate change on biogeochemical cycles of the QTP.
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Poppeliers SWM, Hefting M, Dorrepaal E, Weedon JT. Functional microbial ecology in arctic soils: the need for a year-round perspective. FEMS Microbiol Ecol 2022; 98:6824434. [PMID: 36368693 PMCID: PMC9701097 DOI: 10.1093/femsec/fiac134] [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] [Received: 03/31/2022] [Revised: 11/01/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022] Open
Abstract
The microbial ecology of arctic and sub-arctic soils is an important aspect of the global carbon cycle, due to the sensitivity of the large soil carbon stocks to ongoing climate warming. These regions are characterized by strong climatic seasonality, but the emphasis of most studies on the short vegetation growing season could potentially limit our ability to predict year-round ecosystem functions. We compiled a database of studies from arctic, subarctic, and boreal environments that include sampling of microbial community and functions outside the growing season. We found that for studies comparing across seasons, in most environments, microbial biomass and community composition vary intra-annually, with the spring thaw period often identified by researchers as the most dynamic time of year. This seasonality of microbial communities will have consequences for predictions of ecosystem function under climate change if it results in: seasonality in process kinetics of microbe-mediated functions; intra-annual variation in the importance of different (a)biotic drivers; and/or potential temporal asynchrony between climate change-related perturbations and their corresponding effects. Future research should focus on (i) sampling throughout the entire year; (ii) linking these multi-season measures of microbial community composition with corresponding functional or physiological measurements to elucidate the temporal dynamics of the links between them; and (iii) identifying dominant biotic and abiotic drivers of intra-annual variation in different ecological contexts.
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Affiliation(s)
- Sanne W M Poppeliers
- Corresponding author: Department of Biology, Utrecht University, 3584 CH, The Netherlands. E-mail:
| | - Mariet Hefting
- Department of Biology, Utrecht University, 3584 CH, The Netherlands
| | - Ellen Dorrepaal
- Climate Impacts Research Centre, Umea University, SE-981 07, Abisko, Sweden
| | - James T Weedon
- Department of Ecological Science, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
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11
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Crevecoeur S, Prairie YT, del Giorgio PA. Tracking the upstream history of aquatic microbes in a boreal lake yields new insights on microbial community assembly. PNAS NEXUS 2022; 1:pgac171. [PMID: 36714827 PMCID: PMC9802056 DOI: 10.1093/pnasnexus/pgac171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/23/2022] [Indexed: 02/01/2023]
Abstract
Bacterial community structure can change rapidly across short spatial and temporal scales as environmental conditions vary, but the mechanisms underlying those changes are still poorly understood. Here, we assessed how a lake microbial community assembles by following its reorganization from the main tributary, which, when flowing into the lake, first traverses an extensive macrophyte-dominated vegetated habitat, before reaching the open water. Environmental conditions in the vegetated habitat changed drastically compared to both river and lake waters and represented a strong environmental gradient for the incoming bacteria. We used amplicon sequencing of the 16S rRNA gene and transcript to reconstruct the shifts in relative abundance of individual taxa and link this to their pattern in activity (here assessed with RNA:DNA ratios). Our results indicate that major shifts in relative abundance were restricted mostly to rare taxa (<0.1% of relative abundance), which seemed more responsive to environmental changes. Dominant taxa (>1% of relative abundance), on the other hand, traversed the gradient mostly unchanged with relatively low and stable RNA:DNA ratios. We also identified a high level of local recruitment and a seedbank of taxa capable of activating/inactivating, but these were almost exclusively associated with the rare biosphere. Our results suggest a scenario where the lake community results from a reshuffling of the rank abundance structure within the incoming rare biosphere, driven by selection and growth, and that numerical dominance is not a synonym of activity, growth rate, or environmental selection, but rather reflect mass effects structuring these freshwater bacterial communities.
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Affiliation(s)
| | - Yves T Prairie
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Université du Québec à Montréal, Montréal, QC H2×1Y4, Canada
| | - Paul A del Giorgio
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Université du Québec à Montréal, Montréal, QC H2×1Y4, Canada
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12
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Kaštovská E, Choma M, Čapek P, Kaňa J, Tahovská K, Kopáček J. Soil warming during winter period enhanced soil N and P availability and leaching in alpine grasslands: A transplant study. PLoS One 2022; 17:e0272143. [PMID: 35917373 PMCID: PMC9345486 DOI: 10.1371/journal.pone.0272143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/13/2022] [Indexed: 11/19/2022] Open
Abstract
Alpine meadows are strongly affected by climate change. Increasing air temperature prolongs the growing season and together with changing precipitation patterns alters soil temperature during winter. To estimate the effect of climate change on soil nutrient cycling, we conducted a field experiment. We transferred undisturbed plant-soil mesocosms from two wind-exposed alpine meadows at ~2100 m a.s.l. to more sheltered plots, situated ~300–400 m lower in the same valleys. The annual mean air temperature was 2°C higher at the lower plots and soils that were normally frozen at the original plots throughout winters were warmed to ~0°C due to the insulation provided by continuous snow cover. After two years of exposure, we analyzed the nutrient content in plants, and changes in soil bacterial community, decomposition, mineralization, and nutrient availability. Leaching of N and P from the soils was continuously measured using ion-exchange resin traps. Warming of soils to ~0°C during the winter allowed the microorganisms to remain active, their metabolic processes were not restricted by soil freezing. This change accelerated nutrient cycling, as evidenced by increased soil N and P availability, their higher levels in plants, and elevated leaching. In addition, root exudation and preferential enzymatic mining of P over C increased. However, any significant changes in microbial biomass, bacterial community composition, decomposition rates, and mineralization during the growing season were not observed, suggesting considerable structural and functional resilience of the microbial community. In summary, our data suggest that changes in soil temperature and snow cover duration during winter periods are critical for altering microbially-mediated processes (even at unchanged soil microbial community and biomass) and may enhance nutrient availability in alpine meadows. Consequently, ongoing climate change, which leads to soil warming and decreasing snow insulation, has a potential to significantly alter nutrient cycling in alpine and subalpine meadows compared to the current situation and increase the year-on-year variability in nutrient availability and leaching.
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Affiliation(s)
- Eva Kaštovská
- Faculty of Science, Department of Ecosystem Biology, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
- * E-mail:
| | - Michal Choma
- Faculty of Science, Department of Ecosystem Biology, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | - Petr Čapek
- Faculty of Science, Department of Ecosystem Biology, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | - Jiří Kaňa
- Faculty of Science, Department of Ecosystem Biology, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
- Biology Centre of the Czech Academy of Sciences, v.v.i., Institute of Hydrobiology, České Budějovice, Czech Republic
| | - Karolina Tahovská
- Faculty of Science, Department of Ecosystem Biology, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | - Jiří Kopáček
- Biology Centre of the Czech Academy of Sciences, v.v.i., Institute of Hydrobiology, České Budějovice, Czech Republic
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13
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Reproducible Propagation of Species-Rich Soil Bacterial Communities Suggests Robust Underlying Deterministic Principles of Community Formation. mSystems 2022; 7:e0016022. [PMID: 35353008 PMCID: PMC9040596 DOI: 10.1128/msystems.00160-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbiomes are typically characterized by high species diversity but it is poorly understood how such system-level complexity can be generated and propagated. Here, we used soil microcosms as a model to study development of bacterial communities as a function of their starting complexity and environmental boundary conditions. Despite inherent stochastic variation in manipulating species-rich communities, both laboratory-mixed medium complexity (21 soil bacterial isolates in equal proportions) and high-diversity natural top-soil communities followed highly reproducible succession paths, maintaining 16S rRNA gene amplicon signatures prominent for known soil communities in general. Development trajectories and compositional states were different for communities propagated in soil microcosms than in liquid suspension. Compositional states were maintained over multiple renewed growth cycles but could be diverged by short-term pollutant exposure. The different but robust trajectories demonstrated that deterministic taxa-inherent characteristics underlie reproducible development and self-organized complexity of soil microbiomes within their environmental boundary conditions. Our findings also have direct implications for potential strategies to achieve controlled restoration of desertified land. IMPORTANCE There is now a great awareness of the high diversity of most environmental (“free-living”) and host-associated microbiomes, but exactly how diverse microbial communities form and maintain is still highly debated. A variety of theories have been put forward, but testing them has been problematic because most studies have been based on synthetic communities that fail to accurately mimic the natural composition (i.e., the species used are typically not found together in the same environment), the diversity (usually too low to be representative), or the environmental system itself (using designs with single carbon sources or solely mixed liquid cultures). In this study, we show how species-diverse soil bacterial communities can reproducibly be generated, propagated, and maintained, either from individual isolates (21 soil bacterial strains) or from natural microbial mixtures washed from top-soil. The high replicate consistency we achieve both in terms of species compositions and developmental trajectories demonstrates the strong inherent deterministic factors driving community formation from their species composition. Generating complex soil microbiomes may provide ways for restoration of damaged soils that are prevalent on our planet.
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Seasonal Dynamics of Organic Carbon and Nitrogen in Biomasses of Microorganisms in Arable Mollisols Affected by Different Tillage Systems. LAND 2022. [DOI: 10.3390/land11040486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Tillage has been reported to induce seasonal changes of organic carbon (Cmicro) and nitrogen (Nmicro) in the biomass of microorganisms. Soil microorganisms execute such ecosystem functions as it is an immediate sink of labile biophil elements; it is an agent of a conversion, catalysis and synthesis of humus substances; it transforms soil contaminants into nonhazardous wastes and it participates in soil aggregation and pedogenesis as a whole. However, the seasonal turnover of microorganisms on arable lands in temperate ecosystems has not been studied at a relevant level. Hence, we are aimed at studying the dynamics of such soil microbial biomass patterns as Cmicro, Nmicro, microbial index (MI = (Cmicro/CTOC)·100%) and CO2-C emissions against the background of 9 years of tillage and 22 years of abandoned (Ab) and fallow (F) usage. Our study was conducted on a long-term experimental site on a Mollisol in Northeast China. The maximum Cmicro and Nmicro contents were recorded at the beginning of the growing season at the 0–10-cm layer and mid-July at the 20–40-cm layer, while the minimum content was during August–October. The Cmicro content ranged from 577.79 to 381.79 mg−1 kg−1 using Ab in the spring to 229.53 to 272.86 mg−1 kg−1 in the autumn using CT (conventional tillage) and F in the 0–10- and 10–20-cm layers, respectively. The amplitude of Nmicro content changes were several times lower as compared with the Cmicro. The smallest quartile range (IQR0.25–0.75) of such changes was shown when using the following treatments: no till (NT) and Ab in the 0–10-, NT and F in the 10–20- and CT in the 20–40-cm layer. The widest Cmicro:Nmicro ratio was recorded at F and CT in the 0–20- and CT and rotational tillage (Rot) in the 20–40-cm layer. The MI dynamics were similar to the trends of Cmicro and Nmicro and changed from 0.72 ± 0.168 to 2.00 ± 0.030%. The highest share of Cmicro in CTOC was at Ab (1.82 ± 1.85%) and NT (1.66 ± 1.52 %) in the 0–10-, Ab (1.23 ± 1.27%) and NT (1.29 ± 1.32%) in the 10–20- and Ab (1.19 ± 1.09%) and F (1.11 ± 1.077%) in the 20–40-cm layer, correspondingly. The Pearson’s correlation coefficient between Cmicro and CTOC increased from the upper 0–10- to the lower 20–40-cm layer; it was “strong” and “high” between Cmicro and CTOC. Different uses of Mollisol affected the amplitude of the Cmicro and Nmicro seasonal changes, but it did not change their trend. Our results suggest the key role of Ab and NT technologies in Cmicro accumulation in the total organic carbon (TOC).
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15
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Eschweiler K, Clayton JB, Moresco A, McKenney EA, Minter LJ, Suhr Van Haute MJ, Gasper W, Hayer SS, Zhu L, Cooper K, Ange-van Heugten K. Host Identity and Geographic Location Significantly Affect Gastrointestinal Microbial Richness and Diversity in Western Lowland Gorillas ( Gorilla gorilla gorilla) under Human Care. Animals (Basel) 2021; 11:3399. [PMID: 34944176 PMCID: PMC8697915 DOI: 10.3390/ani11123399] [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] [Received: 09/19/2021] [Revised: 11/13/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
The last few decades have seen an outpouring of gastrointestinal (GI) microbiome studies across diverse host species. Studies have ranged from assessments of GI microbial richness and diversity to classification of novel microbial lineages. Assessments of the "normal" state of the GI microbiome composition across multiple host species has gained increasing importance for distinguishing healthy versus diseased states. This study aimed to determine baselines and trends over time to establish "typical" patterns of GI microbial richness and diversity, as well as inter-individual variation, in three populations of western lowland gorillas (Gorilla gorilla gorilla) under human care at three zoological institutions in North America. Fecal samples were collected from 19 western lowland gorillas every two weeks for seven months (n = 248). Host identity and host institution significantly affected GI microbiome community composition (p < 0.05), although host identity had the most consistent and significant effect on richness (p = 0.03) and Shannon diversity (p = 0.004) across institutions. Significant changes in microbial abundance over time were observed only at Denver Zoo (p < 0.05). Our results suggest that individuality contributes to most of the observed GI microbiome variation in the study populations. Our results also showed no significant changes in any individual's microbial richness or Shannon diversity during the 7-month study period. While some microbial taxa (Prevotella, Prevotellaceae and Ruminococcaceae) were detected in all gorillas at varying levels, determining individual baselines for microbial composition comparisons may be the most useful diagnostic tool for optimizing non-human primate health under human care.
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Affiliation(s)
- Katrina Eschweiler
- Department of Nutrition, Denver Zoo, Denver, CO 80205, USA;
- Department of Animal Science, NC State University, Raleigh, NC 27695, USA
| | - Jonathan B. Clayton
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA; (J.B.C.); (S.S.H.)
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Primate Microbiome Project, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Anneke Moresco
- Department of Animal Welfare and Research, Denver Zoo, Denver, CO 80205, USA;
- Department of Clinical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NC 27607, USA;
| | - Erin A. McKenney
- Department of Applied Ecology, NC State University, Raleigh, NC 27695, USA;
| | - Larry J. Minter
- Department of Clinical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NC 27607, USA;
- Hanes Veterinary Medical Center, North Carolina Zoo, Asheboro, NC 27205, USA
| | - Mallory J. Suhr Van Haute
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - William Gasper
- College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE 68182, USA;
| | - Shivdeep Singh Hayer
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA; (J.B.C.); (S.S.H.)
| | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (L.Z.); (K.C.)
| | - Kathryn Cooper
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (L.Z.); (K.C.)
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16
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Sequential infection of Daphnia magna by a gut microsporidium followed by a haemolymph yeast decreases transmission of both parasites. Parasitology 2021; 148:1566-1577. [PMID: 35060463 PMCID: PMC8564772 DOI: 10.1017/s0031182021001384] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Over the course of seasonal epidemics, populations of susceptible hosts may encounter a wide variety of parasites. Parasite phenology affects the order in which these species encounter their hosts, leading to sequential infections, with potentially strong effects on within-host growth and host population dynamics. Here, the cladoceran Daphnia magna was exposed sequentially to a haemolymph-infecting yeast (Metschnikowia bicuspidata) and a gut microsporidium (Ordospora colligata), with experimental treatments reflecting two possible scenarios of parasite succession. The effects of single and co-exposure were compared on parasite infectivity, spore production and the overall virulence experienced by the host. We show that neither parasite benefited from coinfection; instead, when hosts encountered Ordospora, followed by Metschnikowia, higher levels of host mortality contributed to an overall decrease in the transmission of both parasites. These results showcase an example of sequential infections generating unilateral priority effects, in which antagonistic interactions between parasites can alleviate the intensity of infection and coincide with maladaptive levels of damage inflicted on the host.
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17
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Ganasamurthy S, Rex D, Samad MS, Richards KG, Lanigan GJ, Grelet GA, Clough TJ, Morales SE. Competition and community succession link N transformation and greenhouse gas emissions in urine patches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146318. [PMID: 34030223 DOI: 10.1016/j.scitotenv.2021.146318] [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: 10/07/2020] [Revised: 01/28/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
Nitrous oxide (N2O) is a strong greenhouse gas produced by biotic/abiotic processes directly linked to both fungal and prokaryotic communities that produce, consume or create conditions leading to its emission. In soils exposed to nitrogen (N) in the form of urea, an ecological succession is triggered resulting in a dynamic turnover of microbial populations. However, knowledge of the mechanisms controlling this succession and the repercussions for N2O emissions remain incomplete. Here, we monitored N2O production and fungal/prokaryotic community changes (via 16S and 18S amplicon sequencing) in soil microcosms exposed to urea. Contributions of microbes to emissions were determined using biological inhibitors. Results confirmed that urea leads to shifts in microbial community assemblages by selecting for certain microbial groups (fast growers) as dictated through life history strategies. Urea reduced overall community diversity by conferring dominance to specific groups at different stages in the succession. The diversity lost under urea was recovered with inhibitor addition through the removal of groups that were actively growing under urea indicating that species replacement is mediated in part by competition. Results also identified fungi as significant contributors to N2O emissions, and demonstrate that dominant fungal populations are consistently replaced at different stages of the succession. These successions were affected by addition of inhibitors which resulted in strong decreases in N2O emissions, suggesting that fungal contributions to N2O emissions are larger than that of prokaryotes.
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Affiliation(s)
- Syaliny Ganasamurthy
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - David Rex
- Department of Soil and Physical Sciences, Lincoln University, Lincoln, New Zealand
| | - Md Sainur Samad
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand; Heinrich von Thünen-Institute, Institute for Biodiversity, Braunschweig, Germany
| | - Karl G Richards
- Teagasc, Environmental Research Centre, Johnstown Castle, Wexford, Ireland
| | - Gary J Lanigan
- Teagasc, Environmental Research Centre, Johnstown Castle, Wexford, Ireland
| | - Gwen-Aëlle Grelet
- Manaaki Whenua- Landcare Research, Land Use & Ecosystems Team, Gerald Street, PO, Box 69040, Lincoln 7640, New Zealand
| | - Timothy J Clough
- Department of Soil and Physical Sciences, Lincoln University, Lincoln, New Zealand.
| | - Sergio E Morales
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand.
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18
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Drivers controlling spatial and temporal variation of microbial properties and dissolved organic forms (DOC and DON) in fen soils with persistently low water tables. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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19
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Ji X, Abakumov E, Chigray S, Saparova S, Polyakov V, Wang W, Wu D, Li C, Huang Y, Xie X. Response of carbon and microbial properties to risk elements pollution in arctic soils. JOURNAL OF HAZARDOUS MATERIALS 2021; 408:124430. [PMID: 33176958 DOI: 10.1016/j.jhazmat.2020.124430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 06/11/2023]
Abstract
A 180-day incubation study was conducted to evaluate the effects of risk elements (REs) on organic carbon use and microbial activities in organic soils in the Arctic during the summer snowmelt period. Soils were artificially spiked with Cd, Pb, Cr, Ni, Cu, As, and a combination of these REs according to the levels measured in Arctic soils from REs-polluted industrial sites. During the incubation period, microbial activities and microbial biomass carbon (MBC) formation were inhibited, and microbial quotient (qCO2) values were relatively high in the spiked soils indicating that more energy was used by microbes for maintenance under REs stress. Meanwhile, microbial metabolism was significantly restrained. Microbial Specific phospholipid fatty acids (PLFAs) were reduced in RE spiked soils relative to the control, especially in the As- and multi-RE-spiked soils. The abundance of both fungi and bacteria was reduced in response to RE amendments by 14-24% and 1-55%, respectively. PLFA biomarkers indicated a shift in soil microbial community structure and activities influenced by REs, consequently having a negative effect on soil organic carbon degradation. This study addresses the knowledge gap regarding the alternation of biochemical reactions in Arctic soils under anthropogenic REs with relevant contamination levels.
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Affiliation(s)
- Xiaowen Ji
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resources Environmental & Chemical Engineering, Nanchang University, Nanchang 330031, PR China; Department of Applied Ecology, Saint Petersburg State University, Saint Petersburg 199178, Russian Federation; School of Environment and Sustainability, University of Saskatchewan, Saskatoon SK, S7N 5B3, Canada
| | - Evgeny Abakumov
- Department of Applied Ecology, Saint Petersburg State University, Saint Petersburg 199178, Russian Federation
| | - Svetlana Chigray
- Department of Applied Ecology, Saint Petersburg State University, Saint Petersburg 199178, Russian Federation
| | - Sheker Saparova
- Department of Applied Ecology, Saint Petersburg State University, Saint Petersburg 199178, Russian Federation
| | - Vyacheslav Polyakov
- Department of Applied Ecology, Saint Petersburg State University, Saint Petersburg 199178, Russian Federation; Arctic and Antarctic Research Institute, Saint Petersburg, 199397, Russian Federation; Department of Soil Science and Agrochemistry, Saint-Petersburg State Agrarian University, Pushkin, Saint Petersburg 19660, Russian Federation
| | - Wenjuan Wang
- Department of Applied Ecology, Saint Petersburg State University, Saint Petersburg 199178, Russian Federation
| | - Daishe Wu
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resources Environmental & Chemical Engineering, Nanchang University, Nanchang 330031, PR China
| | - Chunlan Li
- Institute for Global Innovation and Development, East China Normal University, Shanghai 200062, PR China; School of Urban and Regional Sciences, East China Normal University, Shanghai 200241, PR China
| | - Yu Huang
- Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, PR China
| | - Xianchuan Xie
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Resources Environmental & Chemical Engineering, Nanchang University, Nanchang 330031, PR China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, PR China.
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20
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Broadbent AAD, Snell HSK, Michas A, Pritchard WJ, Newbold L, Cordero I, Goodall T, Schallhart N, Kaufmann R, Griffiths RI, Schloter M, Bahn M, Bardgett RD. Climate change alters temporal dynamics of alpine soil microbial functioning and biogeochemical cycling via earlier snowmelt. ISME JOURNAL 2021; 15:2264-2275. [PMID: 33619353 DOI: 10.1038/s41396-021-00922-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 12/30/2022]
Abstract
Soil microbial communities regulate global biogeochemical cycles and respond rapidly to changing environmental conditions. However, understanding how soil microbial communities respond to climate change, and how this influences biogeochemical cycles, remains a major challenge. This is especially pertinent in alpine regions where climate change is taking place at double the rate of the global average, with large reductions in snow cover and earlier spring snowmelt expected as a consequence. Here, we show that spring snowmelt triggers an abrupt transition in the composition of soil microbial communities of alpine grassland that is closely linked to shifts in soil microbial functioning and biogeochemical pools and fluxes. Further, by experimentally manipulating snow cover we show that this abrupt seasonal transition in wide-ranging microbial and biogeochemical soil properties is advanced by earlier snowmelt. Preceding winter conditions did not change the processes that take place during snowmelt. Our findings emphasise the importance of seasonal dynamics for soil microbial communities and the biogeochemical cycles that they regulate. Moreover, our findings suggest that earlier spring snowmelt due to climate change will have far reaching consequences for microbial communities and nutrient cycling in these globally widespread alpine ecosystems.
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Affiliation(s)
- Arthur A D Broadbent
- Department of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - Helen S K Snell
- Department of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Antonios Michas
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Chair for Soil Science, Technical University of Munich, Emil-Ramann-Str 2, 85354, Freising, Germany
| | - William J Pritchard
- Department of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Lindsay Newbold
- UK Centre for Ecology & Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, UK
| | - Irene Cordero
- Department of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Tim Goodall
- UK Centre for Ecology & Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, UK
| | - Nikolaus Schallhart
- Faculty of Biology, University of Innsbruck, Sternwartestr. 15, Innsbruck, Austria
| | - Ruediger Kaufmann
- Department of Ecology, University of Innsbruck, Technikerstr. 25, Innsbruck, Austria
| | - Robert I Griffiths
- UK Centre for Ecology & Hydrology, Environment Centre Wales, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Chair for Soil Science, Technical University of Munich, Emil-Ramann-Str 2, 85354, Freising, Germany
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, Sternwartestr. 15, Innsbruck, Austria
| | - Richard D Bardgett
- Department of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
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21
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Carfora K, Forgoston E, Billings L, Krumins JA. Seasonal effects on the stoichiometry of microbes, primary production, and nutrient cycling. THEOR ECOL-NETH 2021. [DOI: 10.1007/s12080-020-00500-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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22
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Ma L, Zhang C, Feng J, Liu G, Xu X, Lü Y, He W, Wang R. Retention of early-spring nitrogen in temperate grasslands: The dynamics of ammonium and nitrate nitrogen differ. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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23
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Henneron L, Kardol P, Wardle DA, Cros C, Fontaine S. Rhizosphere control of soil nitrogen cycling: a key component of plant economic strategies. THE NEW PHYTOLOGIST 2020; 228:1269-1282. [PMID: 32562506 DOI: 10.1111/nph.16760] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/11/2020] [Indexed: 06/11/2023]
Abstract
Understanding how plant species influence soil nutrient cycling is a major theme in terrestrial ecosystem ecology. However, the prevailing paradigm has mostly focused on litter decomposition, while rhizosphere effects on soil organic matter (SOM) decomposition have attracted little attention. Using a dual 13 C/15 N labeling approach in a 'common garden' glasshouse experiment, we investigated how the economic strategies of 12 grassland plant species (graminoids, forbs and legumes) drive soil nitrogen (N) cycling via rhizosphere processes, and how this in turn affects plant N acquisition and growth. Acquisitive species with higher photosynthesis, carbon rhizodeposition and N uptake than conservative species induced a stronger acceleration of soil N cycling through rhizosphere priming of SOM decomposition. This allowed them to take up larger amounts of N and allocate it above ground to promote photosynthesis, thereby sustaining their faster growth. The N2 -fixation ability of legumes enhanced rhizosphere priming by promoting photosynthesis and rhizodeposition. Our study demonstrates that the economic strategies of plant species regulate a plant-soil carbon-nitrogen feedback operating through the rhizosphere. These findings provide novel mechanistic insights into how plant species with contrasting economic strategies sustain their nutrition and growth through regulating the cycling of nutrients by soil microbes in their rhizosphere.
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Affiliation(s)
- Ludovic Henneron
- UREP - UMR Ecosystème Prairial, INRAE, VetAgro Sup, Université Clermont Auvergne, Clermont-Ferrand, 63000, France
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, 901 83, Sweden
- ECODIV, Normandie Univ, UNIROUEN, Rouen, 76000, France
| | - Paul Kardol
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, 901 83, Sweden
| | - David A Wardle
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, 901 83, Sweden
- Asian School of the Environment, Nanyang Technological University, Singapore, 639798, Singapore
| | - Camille Cros
- UREP - UMR Ecosystème Prairial, INRAE, VetAgro Sup, Université Clermont Auvergne, Clermont-Ferrand, 63000, France
| | - Sébastien Fontaine
- UREP - UMR Ecosystème Prairial, INRAE, VetAgro Sup, Université Clermont Auvergne, Clermont-Ferrand, 63000, France
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24
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Microbial growth and carbon use efficiency show seasonal responses in a multifactorial climate change experiment. Commun Biol 2020; 3:584. [PMID: 33067550 PMCID: PMC7567817 DOI: 10.1038/s42003-020-01317-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/10/2020] [Indexed: 11/08/2022] Open
Abstract
Microbial growth and carbon use efficiency (CUE) are central to the global carbon cycle, as microbial remains form soil organic matter. We investigated how future global changes may affect soil microbial growth, respiration, and CUE. We aimed to elucidate the soil microbial response to multiple climate change drivers across the growing season and whether effects of multiple global change drivers on soil microbial physiology are additive or interactive. We measured soil microbial growth, CUE, and respiration at three time points in a field experiment combining three levels of temperature and atmospheric CO2, and a summer drought. Here we show that climate change-driven effects on soil microbial physiology are interactive and season-specific, while the coupled response of growth and respiration lead to stable microbial CUE (average CUE = 0.39). These results suggest that future research should focus on microbial growth across different seasons to understand and predict effects of global changes on soil carbon dynamics.
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25
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Qu Z, Liu B, Ma Y, Xu J, Sun H. The response of the soil bacterial community and function to forest succession caused by forest disease. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13665] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhao‐Lei Qu
- Collaborative Innovation Center of Sustainable Forestry in Southern China College of Forestry Nanjing Forestry University Nanjing China
| | - Bing Liu
- Collaborative Innovation Center of Sustainable Forestry in Southern China College of Forestry Nanjing Forestry University Nanjing China
| | - Yang Ma
- Collaborative Innovation Center of Sustainable Forestry in Southern China College of Forestry Nanjing Forestry University Nanjing China
| | - Jie Xu
- Collaborative Innovation Center of Sustainable Forestry in Southern China College of Forestry Nanjing Forestry University Nanjing China
| | - Hui Sun
- Collaborative Innovation Center of Sustainable Forestry in Southern China College of Forestry Nanjing Forestry University Nanjing China
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26
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Chadwick KD, Brodrick PG, Grant K, Goulden T, Henderson A, Falco N, Wainwright H, Williams KH, Bill M, Breckheimer I, Brodie EL, Steltzer H, Williams CFR, Blonder B, Chen J, Dafflon B, Damerow J, Hancher M, Khurram A, Lamb J, Lawrence CR, McCormick M, Musinsky J, Pierce S, Polussa A, Hastings Porro M, Scott A, Singh HW, Sorensen PO, Varadharajan C, Whitney B, Maher K. Integrating airborne remote sensing and field campaigns for ecology and Earth system science. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13463] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K. Dana Chadwick
- Department of Earth System Science Stanford University Stanford CA USA
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Philip G. Brodrick
- Jet Propulsion Laboratory California Institute of Technology Pasadena CA USA
| | - Kathleen Grant
- Department of Earth System Science Stanford University Stanford CA USA
| | | | | | - Nicola Falco
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Haruko Wainwright
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Kenneth H. Williams
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
- Jet Propulsion Laboratory California Institute of Technology Pasadena CA USA
| | - Markus Bill
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | | | - Eoin L. Brodie
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
- Department of Environmental Science, Policy, and Management University of California Berkeley CA USA
| | - Heidi Steltzer
- Environment and Sustainability Department Fort Lewis College Durango CO USA
| | | | - Benjamin Blonder
- Rocky Mountain Biological Laboratory Crested Butte CO USA
- Department of Environmental Science, Policy, and Management University of California Berkeley CA USA
- School of Life Sciences Arizona State University Tempe AZ USA
| | - Jiancong Chen
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Baptiste Dafflon
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Joan Damerow
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | | | - Aizah Khurram
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Jack Lamb
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Corey R. Lawrence
- U.S. Geological Survey, Geosciences and Environmental Change Science Center Denver CO USA
| | - Maeve McCormick
- Department of Earth System Science Stanford University Stanford CA USA
| | - John Musinsky
- National Ecological Observatory Network Boulder CO USA
| | - Samuel Pierce
- SLAC National Accelerator Laboratory Menlo Park CA USA
| | - Alexander Polussa
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | | | - Andea Scott
- Department of Earth System Science Stanford University Stanford CA USA
| | - Hans Wu Singh
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Patrick O. Sorensen
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Charuleka Varadharajan
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Bizuayehu Whitney
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Katharine Maher
- Department of Earth System Science Stanford University Stanford CA USA
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27
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Zhang Y, Zhang N, Yin J, Zhao Y, Yang F, Jiang Z, Tao J, Yan X, Qiu Y, Guo H, Hu S. Simulated warming enhances the responses of microbial N transformations to reactive N input in a Tibetan alpine meadow. ENVIRONMENT INTERNATIONAL 2020; 141:105795. [PMID: 32413623 DOI: 10.1016/j.envint.2020.105795] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/02/2020] [Accepted: 05/02/2020] [Indexed: 06/11/2023]
Abstract
Alpine ecosystems worldwide are characterized with high soil organic carbon (C) and low mineral nitrogen (N). Climate warming has been predicted to stimulate microbial decomposition and N mineralization in these systems. However, experimental results are highly variable, and the underlying mechanisms remain unclear. We examined the effects of warming, N input, and their combination on soil N pools and N-cycling microbes in a field manipulation experiment. Special attention was directed to the ammonia-oxidizing bacteria and archaea, and their mediated N-cycling processes (transformation rates and N2O emissions) in the third plant growing season after the treatments were initiated. Nitrogen input (12 g m-2 y-1) alone significantly increased soil mineral N pools and plant N uptake, and stimulated the growth of AOB and N2O emissions in the late growing season. While warming (by 1.4 °C air temperature) alone did not have significant effects on most parameters, it amplified the effects of N input on soil N concentrations and AOB abundance, eliciting a chain reaction that increased nitrification potential (+83%), soil NO3--N (+200%), and N2O emissions (+412%) across the whole season. Also, N input reduced AOB diversity but increased the dominance of genus Nitrosospira within the AOB community, corresponding to the increased N2O emissions. These results showed that a small temperature increase in soil may significantly enhance N losses through NO3- leaching and N2O emissions when mineral N becomes available. These findings suggest that interactions among global change factors may predominantly affect ammonia-oxidizing microbes and their mediated N-cycling processes in alpine ecosystems under future climate change scenarios.
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Affiliation(s)
- Yi Zhang
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Nan Zhang
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingjing Yin
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yexin Zhao
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fei Yang
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhongquan Jiang
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinjin Tao
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuebin Yan
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunpeng Qiu
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Guo
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuijin Hu
- Ecosystem Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA.
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28
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Hopkins JR, Huffman JM, Platt WJ, Sikes BA. Frequent fire slows microbial decomposition of newly deposited fine fuels in a pyrophilic ecosystem. Oecologia 2020; 193:631-643. [PMID: 32699992 DOI: 10.1007/s00442-020-04699-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 06/25/2020] [Indexed: 11/25/2022]
Abstract
Frequent fires maintain nearly 50% of terrestrial ecosystems, and drive ecosystem changes that govern future fires. Since fires are dependent on available plant or fine fuels, ecosystem processes that alter fine fuel loads like microbial decomposition are particularly important and could modify future fires. We hypothesized that variation in short-term fire history would influence fuel dynamics in such ecosystems. We predicted that frequent fires within a short-time period would slow microbial decomposition of new fine fuels. We expected that fire effects would differ based on dominant substrates and that fire history would also alter soil nutrient availability, indirectly slowing decomposition. We measured decomposition of newly deposited fine fuels in a Longleaf pine savanna, comparing plots that burned 0, 1, 2, or 3 times between 2014 and 2016, and which were located in either close proximity to or away from overstory pines (Longleaf pine, Pinus palustris). Microbial decomposition was slower in plots near longleaf pines and, as the numbers of fires increased, decomposition slowed. We then used structural equation modeling to assess pathways for these effects (number of fires, 2016 fuel/fire characteristics, and soil chemistry). Increased fire frequency was directly associated with decreased microbial decomposition. While increased fires decreased nutrient availability, changes in nutrients were not associated with decomposition. Our findings indicate that increasing numbers of fires over short-time intervals can slow microbial decomposition of newly deposited fine fuels. This could favor fine fuel accumulation and drive positive feedbacks on future fires.
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Affiliation(s)
- Jacob R Hopkins
- Ecology and Evolutionary Biology, University of Kansas, 2101 Constant Avenue Takeru Higuchi Hall, Lawrence, KS, 66047, USA.
| | - Jean M Huffman
- Department of Biological Sciences, Louisiana State University, Baton Rouge, USA
| | - William J Platt
- Department of Biological Sciences, Louisiana State University, Baton Rouge, USA
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29
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Sorensen PO, Beller HR, Bill M, Bouskill NJ, Hubbard SS, Karaoz U, Polussa A, Steltzer H, Wang S, Williams KH, Wu Y, Brodie EL. The Snowmelt Niche Differentiates Three Microbial Life Strategies That Influence Soil Nitrogen Availability During and After Winter. Front Microbiol 2020; 11:871. [PMID: 32477299 PMCID: PMC7242569 DOI: 10.3389/fmicb.2020.00871] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/14/2020] [Indexed: 12/13/2022] Open
Abstract
Soil microbial biomass can reach its annual maximum pool size beneath the winter snowpack and is known to decline abruptly following snowmelt in seasonally snow-covered ecosystems. Observed differences in winter versus summer microbial taxonomic composition also suggests that phylogenetically conserved traits may permit winter- versus summer-adapted microorganisms to occupy distinct niches. In this study, we sought to identify archaea, bacteria, and fungi that are associated with the soil microbial bloom overwinter and the subsequent biomass collapse following snowmelt at a high-altitude watershed in central Colorado, United States. Archaea, bacteria, and fungi were categorized into three life strategies (Winter-Adapted, Snowmelt-Specialist, Spring-Adapted) based upon changes in abundance during winter, the snowmelt period, and after snowmelt in spring. We calculated indices of phylogenetic relatedness (archaea and bacteria) or assigned functional attributes (fungi) to organisms within life strategies to infer whether phylogenetically conserved traits differentiate Winter-Adapted, Snowmelt-Specialist, and Spring-Adapted groups. We observed that the soil microbial bloom was correlated in time with a pulse of snowmelt infiltration, which commenced 65 days prior to soils becoming snow-free. A pulse of nitrogen (N, as nitrate) occurred after snowmelt, along with a collapse in the microbial biomass pool size, and an increased abundance of nitrifying archaea and bacteria (e.g., Thaumarchaeota, Nitrospirae). Winter- and Spring-Adapted archaea and bacteria were phylogenetically clustered, suggesting that phylogenetically conserved traits allow Winter- and Spring-Adapted archaea and bacteria to occupy distinct niches. In contrast, Snowmelt-Specialist archaea and bacteria were phylogenetically overdispersed, suggesting that the key mechanism(s) of the microbial biomass crash are likely to be density-dependent (e.g., trophic interactions, competitive exclusion) and affect organisms across a broad phylogenetic spectrum. Saprotrophic fungi were the dominant functional group across fungal life strategies, however, ectomycorrhizal fungi experienced a large increase in abundance in spring. If well-coupled plant-mycorrhizal phenology currently buffers ecosystem N losses in spring, then changes in snowmelt timing may alter ecosystem N retention potential. Overall, we observed that snowmelt separates three distinct soil niches that are occupied by ecologically distinct groups of microorganisms. This ecological differentiation is of biogeochemical importance, particularly with respect to the mobilization of nitrogen during winter, before and after snowmelt.
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Affiliation(s)
- Patrick O. Sorensen
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Harry R. Beller
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Markus Bill
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nicholas J. Bouskill
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Susan S. Hubbard
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Alexander Polussa
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- School of Forestry and Environmental Studies, Yale University, New Haven, CT, United States
| | - Heidi Steltzer
- Fort Lewis College, Durango, CO, United States
- Rocky Mountain Biological Laboratory, Gothic, CO, United States
| | - Shi Wang
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kenneth H. Williams
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Rocky Mountain Biological Laboratory, Gothic, CO, United States
| | - Yuxin Wu
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Eoin L. Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States
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30
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Murphy AE, Bulseco AN, Ackerman R, Vineis JH, Bowen JL. Sulphide addition favours respiratory ammonification (DNRA) over complete denitrification and alters the active microbial community in salt marsh sediments. Environ Microbiol 2020; 22:2124-2139. [DOI: 10.1111/1462-2920.14969] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 02/14/2020] [Accepted: 02/28/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Anna E. Murphy
- Department of Marine and Environmental Sciences Marine Science Center, Northeastern University Nahant Massachusetts 01908 USA
- INSPIRE Environmental, Inc 513 Broadway Suite 314, Newport Rhode Island 02840 USA
| | - Ashley N. Bulseco
- Department of Marine and Environmental Sciences Marine Science Center, Northeastern University Nahant Massachusetts 01908 USA
- The Ecosystems Center Marine Biological Laboratory Woods Hole Massachusetts 02543 USA
| | - Ross Ackerman
- Biology Department, Bates College Lewiston Maine 04240 USA
| | - Joseph H. Vineis
- Department of Marine and Environmental Sciences Marine Science Center, Northeastern University Nahant Massachusetts 01908 USA
| | - Jennifer L. Bowen
- Department of Marine and Environmental Sciences Marine Science Center, Northeastern University Nahant Massachusetts 01908 USA
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31
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Nishitani S, Ishida A, Nakamura T, Kachi N. Functional differences in seasonally absorbed nitrogen in a winter-green perennial herb. ROYAL SOCIETY OPEN SCIENCE 2020; 7:190034. [PMID: 32218923 PMCID: PMC7029918 DOI: 10.1098/rsos.190034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 12/20/2019] [Indexed: 06/10/2023]
Abstract
Nitrogen (N) uptake in response to its availability and effective N-use are important for determining plant fitness, as N is a major limiting resource and its availability changes both seasonally and annually. Storage organs such as bulbs are considered an adaptive trait with respect to plant N-use strategies. It is well known that N is remobilized from storage organs to satisfy the high demand for new growth that is not completely satisfied by external uptake alone. However, little is known about how this N absorbed during different seasons contributes to plant performance. By manipulating seasonal N availability in potted Lycoris radiata var. radiata (Amaryllidaceae), a winter-green perennial, we found that the N absorbed during different seasons had different effects on leaf growth and leaf N concentrations, effectively increasing the growth and survival of the plants. N absorbed during the summer (leafless period; N was thus stored in the bulb) enhanced plant growth by increasing leaf growth. Compared with the plants supplied with N during autumn (leaf flush period), the leafy plants also showed greater growth per unit leaf area despite the lower area-based photosynthetic capacity of the latter. By contrast, N absorbed during the autumn increased the leaf N concentration and thus the photosynthetic capacity, which was considered to enhance survival and growth of the plant during winter by reducing the potentially fatal risk caused by the absorption of photons under low temperature. Our findings have important implications for estimating plant responses to environmental changes. We predict that changes in seasonal N availability impact the performance of plants, even that of perennials that have large storage organs, via an altered relative investment of N into different functions.
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Affiliation(s)
- Satomi Nishitani
- Department of Biology, Nippon Medical School, Kyonancho 1-7-1, Musashino, Tokyo 180-0023, Japan
- Department of Biological Sciences, Tokyo Metropolitan University, Minami-Osawa 1-1, Hachioji, Tokyo 192-0397, Japan
| | - Atsushi Ishida
- Center for Ecological Research, Kyoto University, Hirano 2, Otsu, Shiga 520-2113, Japan
| | - Toshie Nakamura
- Department of Biological Sciences, Tokyo Metropolitan University, Minami-Osawa 1-1, Hachioji, Tokyo 192-0397, Japan
| | - Naoki Kachi
- Department of Biological Sciences, Tokyo Metropolitan University, Minami-Osawa 1-1, Hachioji, Tokyo 192-0397, Japan
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32
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Soil fungal community changes in response to long-term fire cessation and N fertilization in tallgrass prairie. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.03.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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Khan A, Kong W, Muhammad S, Wang F, Zhang G, Kang S. Contrasting environmental factors drive bacterial and eukaryotic community successions in freshly deglaciated soils. FEMS Microbiol Lett 2019; 366:5628325. [PMID: 31738416 DOI: 10.1093/femsle/fnz229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 11/15/2019] [Indexed: 11/14/2022] Open
Abstract
Glacier retreats expose deglaciated soils to microbial colonization and succession; however, the differences in drivers of bacterial and eukaryotic succession remain largely elusive. We explored soil bacterial and eukaryotic colonization and yearly community succession along a deglaciation chronosequence (10 years) on the Tibetan Plateau using qPCR, terminal restriction fragment length polymorphism (T-RFLP) and sequencing of clone libraries. The results exhibited that bacteria and eukaryotes rapidly colonized the soils in the first year of deglaciation, thereafter slowly increasing from 107 up to 1010 and 1011 gene copies g-1 soil, respectively. Bacterial and eukaryotic community changes were observed to group into distinct stages, including early (0-2 year old), transition (3-5 year old) and late stages (6-10 year old). Bacterial community succession was dominantly driven by soil factors (47.7%), among which soil moisture played a key role by explaining 26.9% of the variation. In contrast, eukaryotic community succession was dominantly driven by deglaciation age (22.2%). The dominant bacterial lineage was Cyanobacteria, which rapidly decreased from the early to the transition stage. Eukaryotes were dominated by glacier-originated Cercozoa in early stage soils, while green algae Chlorophyta substantially increased in late stage soils. Our findings revealed contrasting environmental factors driving bacterial and eukaryotic community successions.
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Affiliation(s)
- Ajmal Khan
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, No. 16 Lincui Road, Chaoyang District, Beijing 100101, China.,College of Resources and Environmnet, University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Weidong Kong
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, No. 16 Lincui Road, Chaoyang District, Beijing 100101, China.,College of Resources and Environmnet, University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Said Muhammad
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, No. 16 Lincui Road, Chaoyang District, Beijing 100101, China
| | - Fei Wang
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, No. 16 Lincui Road, Chaoyang District, Beijing 100101, China.,College of Resources and Environmnet, University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Guoshuai Zhang
- Key Laboratory of Tibetan Environmental Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, No. 16 Lincui Road, Chaoyang District, Beijing 100101, China
| | - Shichang Kang
- State Key Laboratory of Cryospheric Sciences, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Donggang West Road 320, Lanzhou 730000, China
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34
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Semenova-Nelsen TA, Platt WJ, Patterson TR, Huffman J, Sikes BA. Frequent fire reorganizes fungal communities and slows decomposition across a heterogeneous pine savanna landscape. THE NEW PHYTOLOGIST 2019; 224:916-927. [PMID: 31396966 DOI: 10.1111/nph.16096] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/22/2019] [Indexed: 06/10/2023]
Abstract
Pyrogenic savannas with a tree-grassland 'matrix' experience frequent fires (i.e. every 1-3 yr). Aboveground responses to frequent fires have been well studied, but responses of fungal litter decomposers, which directly affect fuels, remain poorly known. We hypothesized that each fire reorganizes belowground communities and slows litter decomposition, thereby influencing savanna fuel dynamics. In a pine savanna, we established patches near and away from pines that were either burned or unburned in that year. Within patches, we assessed fungal communities and microbial decomposition of newly deposited litter. Soil variables and plant communities were also assessed as proximate drivers of fungal communities. Fungal communities, but not soil variables or vegetation, differed substantially between burned and unburned patches. Saprotrophic fungi dominated in unburned patches but decreased in richness and relative abundance after fire. Differences in fungal communities with fire were greater in litter than in soils, but unaffected by pine proximity. Litter decomposed more slowly in burned than in unburned patches. Fires drive shifts between fire-adapted and sensitive fungal taxa in pine savannas. Slower fuel decomposition in accordance with saprotroph declines should enhance fuel accumulation and could impact future fire characteristics. Thus, fire reorganization of fungal communities may enhance persistence of these fire-adapted ecosystems.
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Affiliation(s)
- Tatiana A Semenova-Nelsen
- Kansas Biological Survey, Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66047, USA
| | - William J Platt
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Taylor R Patterson
- Kansas Biological Survey, Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66047, USA
| | - Jean Huffman
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Benjamin A Sikes
- Kansas Biological Survey, Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66047, USA
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Hamard S, Robroek BJM, Allard PM, Signarbieux C, Zhou S, Saesong T, de Baaker F, Buttler A, Chiapusio G, Wolfender JL, Bragazza L, Jassey VEJ. Effects of Sphagnum Leachate on Competitive Sphagnum Microbiome Depend on Species and Time. Front Microbiol 2019; 10:2042. [PMID: 31555245 PMCID: PMC6742715 DOI: 10.3389/fmicb.2019.02042] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 08/20/2019] [Indexed: 12/03/2022] Open
Abstract
Plant specialized metabolites play an important role in soil carbon (C) and nutrient fluxes. Through anti-microbial effects, they can modulate microbial assemblages and associated microbial-driven processes, such as nutrient cycling, so to positively or negatively cascade on plant fitness. As such, plant specialized metabolites can be used as a tool to supplant competitors. These compounds are little studied in bryophytes. This is especially notable in peatlands where Sphagnum mosses can dominate the vegetation and show strong interspecific competition. Sphagnum mosses form carpets where diverse microbial communities live and play a crucial role in Sphagnum fitness by regulating C and nutrient cycling. Here, by means of a microcosm experiment, we assessed to what extent moss metabolites of two Sphagnum species (S. fallax and S. divinum) modulate the competitive Sphagnum microbiome, with particular focus on microbial respiration. Using a reciprocal leachate experiment, we found that interactions between Sphagnum leachates and microbiome are species-specific. We show that both Sphagnum leachates differed in compound richness and compound relative abundance, especially sphagnum acid derivates, and that they include microbial-related metabolites. The addition of S. divinum leachate on the S. fallax microbiome immediately reduced microbial respiration (−95%). Prolonged exposition of S. fallax microbiome to S. divinum leachate destabilized the food web structure due to a modulation of microbial abundance. In particular, leachate addition decreased the biomass of testate amoebae and rotifers but increased that of ciliates. These changes did not influence microbial CO2 respiration, suggesting that the structural plasticity of the food web leads to its functional resistance through the replacement of species that are functionally redundant. In contrast, S. fallax leachate neither affected S. divinum microbial respiration, nor microbial biomass. We, however, found that S. fallax leachate addition stabilized the food web structure associated to S. divinum by changing trophic interactions among species. The differences in allelopathic effects between both Sphagnum leachates might impact their competitiveness and affect species distribution at local scale. Our study further paves the way to better understand the role of moss and microbial specialized metabolites in peatland C dynamics.
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Affiliation(s)
- Samuel Hamard
- ECOLAB, Laboratoire d'Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France.,Laboratory of Ecological Systems (ECOS), Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Lausanne, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Lausanne, Switzerland.,Laboratoire de Géologie, UMR 8538, CNRS-ENS, Ecole Normale Supérieure, Paris, France
| | - Bjorn J M Robroek
- Laboratory of Ecological Systems (ECOS), Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Lausanne, Switzerland.,School of Biological Sciences, University of Southampton, Southampton, United Kingdom.,Aquatic Ecology and Environmental Biology Group, Faculty of Science, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Constant Signarbieux
- Laboratory of Ecological Systems (ECOS), Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Lausanne, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Lausanne, Switzerland
| | - Shuaizhen Zhou
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Tongchai Saesong
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland.,Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmaceutical Sciences and Center of Excellence for Innovation in Chemistry, Naresuan University, Phitsanulok, Thailand
| | - Flore de Baaker
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Alexandre Buttler
- Laboratory of Ecological Systems (ECOS), Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Lausanne, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Lausanne, Switzerland.,Laboratoire Chrono-Environnement, Université Bourgogne Franche Comté, UMR CNRS 6249 USC INRA, Montbéliard, France
| | - Geneviève Chiapusio
- Laboratoire Chrono-Environnement, Université Bourgogne Franche Comté, UMR CNRS 6249 USC INRA, Montbéliard, France.,Laboratoire Carrtel, Université Savoie Mont Blanc INRA 042, Domaine Universitaire Belledonne, Le Bourget-du-Lac, France
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Luca Bragazza
- Laboratory of Ecological Systems (ECOS), Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Lausanne, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Lausanne, Switzerland.,Department of Life Science and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Vincent E J Jassey
- ECOLAB, Laboratoire d'Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France.,Laboratory of Ecological Systems (ECOS), Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Lausanne, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Lausanne, Switzerland
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Shigyo N, Umeki K, Hirao T. Seasonal Dynamics of Soil Fungal and Bacterial Communities in Cool-Temperate Montane Forests. Front Microbiol 2019; 10:1944. [PMID: 31507559 PMCID: PMC6716449 DOI: 10.3389/fmicb.2019.01944] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/07/2019] [Indexed: 02/01/2023] Open
Abstract
Both fungal and bacterial communities in soils play key roles in driving forest ecosystem processes across multiple time scales, but how seasonal changes in environmental factors shape these microbial communities is not well understood. Here, we aimed to evaluate the importance of seasons, elevation, and soil depth in determining soil fungal and bacterial communities, given the influence of climate conditions, soil properties and plant traits. In this study, seasonal patterns of diversity and abundance did not synchronize between fungi and bacteria, where soil fertility explained the diversity and abundance of soil fungi but soil water content explained those of soil bacteria. Model-based clustering showed that seasonal changes in both abundant and rare taxonomic groups were different between soil fungi and bacteria. The cluster represented by ectomycorrhizal genus Lactarius was a dominant group across soil fungal communities and fluctuated seasonally. For soil bacteria, the clusters composed of dominant genera were seasonally stable but varied greatly depending on elevation and soil depth. Seasonally changing clusters of soil bacteria (e.g., Nitrospira and Pelosinus) were not dominant groups and were related to plant phenology. These findings suggest that the contribution of seasonal changes in climate conditions, soil fertility, and plant phenology to microbial communities might be equal to or greater than the effects of spatial heterogeneity of those factors. Our study identifies aboveground-belowground components as key factors explaining how microbial communities change during a year in forest soils at mid-to-high latitudes.
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Affiliation(s)
- Nobuhiko Shigyo
- The University of Tokyo Chichibu Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Chichibu, Japan
| | - Kiyoshi Umeki
- Graduate School of Horticulture, Chiba University, Matsudo, Japan
| | - Toshihide Hirao
- The University of Tokyo Chichibu Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Chichibu, Japan
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Gendron EMS, Darcy JL, Hell K, Schmidt SK. Structure of bacterial and eukaryote communities reflect in situ controls on community assembly in a high-alpine lake. J Microbiol 2019; 57:852-864. [DOI: 10.1007/s12275-019-8668-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 01/16/2023]
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Miller EC, Perron GG, Collins CD. Plant-driven changes in soil microbial communities influence seed germination through negative feedbacks. Ecol Evol 2019; 9:9298-9311. [PMID: 31463022 PMCID: PMC6706191 DOI: 10.1002/ece3.5476] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 06/24/2019] [Accepted: 06/28/2019] [Indexed: 01/25/2023] Open
Abstract
Plant-soil feedbacks (PSFs) drive plant community diversity via interactions between plants and soil microbes. However, we know little about how frequently PSFs affect plants at the seed stage, and the compositional shifts in fungi that accompany PSFs on germination.We conducted a pairwise PSF experiment to test whether seed germination was differentially impacted by conspecific versus heterospecific soils for seven grassland species. We used metagenomics to characterize shifts in fungal community composition in soils conditioned by each plant species. To investigate whether changes in the abundance of certain fungal taxa were associated with multiple PSFs, we assigned taxonomy to soil fungi and identified putative pathogens that were significantly more abundant in soils conditioned by plant species that experienced negative or positive PSFs.We observed negative, positive, and neutral PSFs on seed germination. Although conspecific and heterospecific soils for pairs with significant PSFs contained host-specialized soil fungal communities, soils with specialized microbial communities did not always lead to PSFs. The identity of host-specialized pathogens, that is, taxa uniquely present or significantly more abundant in soils conditioned by plant species experiencing negative PSFs, overlapped among plant species, while putative pathogens within a single host plant species differed depending on the identity of the heterospecific plant partner. Finally, the magnitude of feedback on germination was not related to the degree of fungal community differentiation between species pairs involved in negative PSFs. Synthesis. Our findings reveal the potential importance of PSFs at the seed stage. Although plant species developed specialized fungal communities in rhizosphere soil, pathogens were not strictly host-specific and varied not just between plant species, but according to the identity of plant partner. These results illustrate the complexity of microbe-mediated interactions between plants at different life stages that next-generation sequencing can begin to unravel.
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Cordero I, Snell H, Bardgett RD. High throughput method for measuring urease activity in soil. SOIL BIOLOGY & BIOCHEMISTRY 2019; 134:72-77. [PMID: 31274933 PMCID: PMC6559327 DOI: 10.1016/j.soilbio.2019.03.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/20/2019] [Accepted: 03/13/2019] [Indexed: 05/26/2023]
Abstract
Extracellular enzymes break down soil organic matter into smaller compounds and their measurement has proved to be a powerful tool to evaluate the functionality of soils. Urease is the enzyme that degrades urea and is widely considered to be a good proxy of nitrogen (N) mineralisation. But the methods available to measure this enzyme are time consuming; as such, urease is not commonly included in standard enzyme profiling of soils. We developed a fast, high throughput and reproducible colorimetric microplate technique to evaluate urease activity in soil. The method involves the incubation of soil slurries in 96-deepwell blocks with urea solutions and the measurement, by colorimetric reaction, of ammonium produced. We compared the new method with existing methods, yielding comparable results, and evaluated optimal conditions for urease analysis (soil slurry concentration, substrate concentration, incubation times and extractant salt concentration) in different grassland soils. The method proved to be a faster, higher throughput, and more precise alternative to existing methods for evaluating this important N-related enzyme.
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40
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Figueiredo V, Enrich-Prast A, Rütting T. Evolution of nitrogen cycling in regrowing Amazonian rainforest. Sci Rep 2019; 9:8538. [PMID: 31189968 PMCID: PMC6561906 DOI: 10.1038/s41598-019-43963-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 04/12/2019] [Indexed: 11/16/2022] Open
Abstract
Extensive regions of tropical forests are subjected to high rates of deforestation and forest regrowth and both are strongly affect soil nutrient cycling. Nitrogen (N) dynamics changes during forest regrowth and the recovery of forests and functioning similar to pristine conditions depends on sufficient N availability. We show that, in a chronosequence of Amazonian forests, gross nitrification and, as a result, nitrate-to-ammonium (NO3-: NH4+) ratio were lower in all stages of regrowing forests (10 to 40 years) compared to pristine forest. This indicates the evolution of a more conservative and closed N cycle with reduced risk for N leaking out of the ecosystem in regrowing forests. Furthermore, our results indicate that mineralization and nitrification are decoupled in young regrowing forests (10 years), such as that high gross mineralization is accompanied by low gross nitrification, demonstrating a closed N cycle that at the same time maintains N supply for forest regrowth. We conclude that the status of gross nitrification in disturbed soil is a key process to understand the mechanisms of and time needed for tropical forest recovery.
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Affiliation(s)
- Viviane Figueiredo
- Department of Botany, University Federal of Rio de Janeiro, 21941-971 Avenida Carlos Chagas Filho, Rio de Janeiro, Brazil
- Postgraduate Program in Geochemistry, University Federal Fluminense, 24020-007 Outeiro de São João Batista, Niterói, Brazil
- Postgraduate Program in Biotechnology, University Federal of Rio de Janeiro, 21941-971 Avenida Carlos Chagas Filho, Rio de Janeiro, Brazil
| | - Alex Enrich-Prast
- Department of Botany, University Federal of Rio de Janeiro, 21941-971 Avenida Carlos Chagas Filho, Rio de Janeiro, Brazil.
- Postgraduate Program in Geochemistry, University Federal Fluminense, 24020-007 Outeiro de São João Batista, Niterói, Brazil.
- Postgraduate Program in Biotechnology, University Federal of Rio de Janeiro, 21941-971 Avenida Carlos Chagas Filho, Rio de Janeiro, Brazil.
- Department of Environmental Change, Linköping University, 58183, Linköping, Sweden.
| | - Tobias Rütting
- Department of Earth Sciences, University of Gothenburg, 405 30, Gothenburg, Sweden
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41
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Darrouzet‐Nardi A, Steltzer H, Sullivan PF, Segal A, Koltz AM, Livensperger C, Schimel JP, Weintraub MN. Limited effects of early snowmelt on plants, decomposers, and soil nutrients in Arctic tundra soils. Ecol Evol 2019; 9:1820-1844. [PMID: 30847075 PMCID: PMC6392369 DOI: 10.1002/ece3.4870] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 11/03/2018] [Accepted: 12/04/2018] [Indexed: 11/29/2022] Open
Abstract
In addition to warming temperatures, Arctic ecosystems are responding to climate change with earlier snowmelt and soil thaw. Earlier snowmelt has been examined infrequently in field experiments, and we lack a comprehensive look at belowground responses of the soil biogeochemical system that includes plant roots, decomposers, and soil nutrients. We experimentally advanced the timing of snowmelt in factorial combination with an open-top chamber warming treatment over a 3-year period and evaluated the responses of decomposers and nutrient cycling processes. We tested two alternative hypotheses: (a) Early snowmelt and warming advance the timing of root growth and nutrient uptake, altering the timing of microbial and invertebrate activity and key nutrient cycling events; and (b) loss of insulating snow cover damages plants, leading to reductions in root growth and altered biological activity. During the 3 years of our study (2010-2012), we advanced snowmelt by 4, 15, and 10 days, respectively. Despite advancing aboveground plant phenology, particularly in the year with the warmest early-season temperatures (2012), belowground effects were primarily seen only on the first sampling date of the season or restricted to particular years or soil type. Overall, consistent and substantial responses to early snowmelt were not observed, counter to both of our hypotheses. The data on soil physical conditions, as well interannual comparisons of our results, suggest that this limited response was because of the earlier date of snowmelt that did not coincide with substantially warmer air and soil temperatures as they might in response to a natural climate event. We conclude that the interaction of snowmelt timing with soil temperatures is important to how the ecosystem will respond, but that 1- to 2-week changes in timing of snowmelt alone are not enough to drive season-long changes in soil microbial and nutrient cycling processes.
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Affiliation(s)
- Anthony Darrouzet‐Nardi
- Department of Biological SciencesUniversity of Texas at El PasoEl PasoTexas
- Department of Environmental SciencesUniversity of ToledoToledoOhio
| | | | - Patrick F. Sullivan
- Environment and Natural Resources InstituteUniversity of Alaska AnchorageAnchorageAlaska
| | - Aliza Segal
- Environment and Natural Resources InstituteUniversity of Alaska AnchorageAnchorageAlaska
| | - Amanda M. Koltz
- Department of BiologyWashington University in St. LouisSt. LouisMissouri
| | - Carolyn Livensperger
- Natural Resource Ecology LaboratoryColorado State UniversityFort CollinsColorado
| | - Joshua P. Schimel
- Department of Ecology, Evolution, and Marine BiologyUniversity of California Santa BarbaraSanta BarbaraCalifornia
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Väisänen M, Gavazov K, Krab EJ, Dorrepaal E. The Legacy Effects of Winter Climate on Microbial Functioning After Snowmelt in a Subarctic Tundra. MICROBIAL ECOLOGY 2019; 77:186-190. [PMID: 29948015 DOI: 10.1007/s00248-018-1213-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/28/2018] [Indexed: 06/08/2023]
Abstract
Warming-induced increases in microbial CO2 release in northern tundra may positively feedback to climate change. However, shifts in microbial extracellular enzyme activities (EEAs) may alter the impacts of warming over the longer term. We investigated the in situ effects of 3 years of winter warming in combination with the in vitro effects of a rapid warming (6 days) on microbial CO2 release and EEAs in a subarctic tundra heath after snowmelt in spring. Winter warming did not change microbial CO2 release at ambient (10 °C) or at rapidly increased temperatures, i.e., a warm spell (18 °C) but induced changes (P < 0.1) in the Q10 of microbial respiration and an oxidative EEA. Thus, although warmer winters may induce legacy effects in microbial temperature acclimation, we found no evidence for changes in potential carbon mineralization after spring thaw.
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Affiliation(s)
- Maria Väisänen
- Climate Impacts Research Center, EMG, Umeå University, Vetenskapensväg 38, SE-981 07, Abisko, Sweden.
- Arctic Centre, University of Lapland, P. O. Box 122, FI-96 101, Rovaniemi, Finland.
| | - Konstantin Gavazov
- Climate Impacts Research Center, EMG, Umeå University, Vetenskapensväg 38, SE-981 07, Abisko, Sweden
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Case postale 96, 1015, Lausanne, Switzerland
| | - Eveline J Krab
- Climate Impacts Research Center, EMG, Umeå University, Vetenskapensväg 38, SE-981 07, Abisko, Sweden
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Lennart Hjelms väg 9, SE-750 07, Uppsala, Sweden
| | - Ellen Dorrepaal
- Climate Impacts Research Center, EMG, Umeå University, Vetenskapensväg 38, SE-981 07, Abisko, Sweden
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Chen H, Yang T, Xia Q, Bowman D, Williams D, Walker JT, Shi W. The extent and pathways of nitrogen loss in turfgrass systems: Age impacts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:746-757. [PMID: 29758430 PMCID: PMC6064208 DOI: 10.1016/j.scitotenv.2018.05.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/07/2018] [Accepted: 05/04/2018] [Indexed: 05/25/2023]
Abstract
Nitrogen loss from fertilized turf has been a concern for decades, with most research focused on inorganic (NO3-) leaching. The present work examined both inorganic and organic N species in leachate and soil N2O emissions from intact soil cores of a bermudagrass chronosequence (1, 15, 20, and 109 years old) collected in both winter and summer. Measurements of soil N2O emissions were made daily for 3 weeks, while leachate was sampled once a week. Four treatments were established to examine the impacts of fertilization and temperature: no N, low N at 30 kg N ha-1, and high N at 60 kg N ha-1, plus a combination of high N and temperature (13 °C in winter or 33 °C in summer compared to the standard 23 °C). Total reactive N loss generally showed a "cup" pattern of turf age, being lowest for the 20 years old. Averaged across all intact soil cores sampled in winter and summer, organic N leaching accounted for 51% of total reactive N loss, followed by inorganic N leaching at 41% and N2O-N efflux at 8%. Proportional loss among the fractions varied with grass age, season, and temperature and fertilization treatments. While high temperature enhanced total reactive N loss, it had little influence on the partitioning of loss among dissolved organic N, inorganic N and N2O-N when C availability was expected to be high in summer due to rhizodeposition and root turnover. This effect of temperature was perhaps due to higher microbial turnover in response to increased C availability in summer. However when C availability was low in winter, warming might mainly affect microbial growth efficiency and therefore partitioning of N. This work provides a new insight into the interactive controls of warming and substrate availability on dissolved organic N loss from turfgrass systems.
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Affiliation(s)
- Huaihai Chen
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA; Environmental Sciences Division, National Exposure Research Laboratory, U.S. Environmental Protection Agency, RTP, NC, USA; Air Pollution Prevention and Control Division, National Risk Management Research Laboratory, U.S. Environmental Protection Agency, RTP, NC, USA
| | - Tianyou Yang
- College of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Qing Xia
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Daniel Bowman
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - David Williams
- Environmental Sciences Division, National Exposure Research Laboratory, U.S. Environmental Protection Agency, RTP, NC, USA
| | - John T Walker
- Air Pollution Prevention and Control Division, National Risk Management Research Laboratory, U.S. Environmental Protection Agency, RTP, NC, USA
| | - Wei Shi
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA.
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Guo X, Zhou X, Hale L, Yuan M, Feng J, Ning D, Shi Z, Qin Y, Liu F, Wu L, He Z, Van Nostrand JD, Liu X, Luo Y, Tiedje JM, Zhou J. Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass. Front Microbiol 2018; 9:954. [PMID: 29904372 PMCID: PMC5990867 DOI: 10.3389/fmicb.2018.00954] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/24/2018] [Indexed: 11/13/2022] Open
Abstract
Clipping, removal of aboveground plant biomass, is an important issue in grassland ecology. However, few studies have focused on the effect of clipping on belowground microbial communities. Using integrated metagenomic technologies, we examined the taxonomic and functional responses of soil microbial communities to annual clipping (2010-2014) in a grassland ecosystem of the Great Plains of North America. Our results indicated that clipping significantly (P < 0.05) increased root and microbial respiration rates. Annual temporal variation within the microbial communities was much greater than the significant changes introduced by clipping, but cumulative effects of clipping were still observed in the long-term scale. The abundances of some bacterial and fungal lineages including Actinobacteria and Bacteroidetes were significantly (P < 0.05) changed by clipping. Clipping significantly (P < 0.05) increased the abundances of labile carbon (C) degrading genes. More importantly, the abundances of recalcitrant C degrading genes were consistently and significantly (P < 0.05) increased by clipping in the last 2 years, which could accelerate recalcitrant C degradation and weaken long-term soil carbon stability. Furthermore, genes involved in nutrient-cycling processes including nitrogen cycling and phosphorus utilization were also significantly increased by clipping. The shifts of microbial communities were significantly correlated with soil respiration and plant productivity. Intriguingly, clipping effects on microbial function may be highly regulated by precipitation at the interannual scale. Altogether, our results illustrated the potential of soil microbial communities for increased soil organic matter decomposition under clipping land-use practices.
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Affiliation(s)
- Xue Guo
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Xishu Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Lauren Hale
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Mengting Yuan
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Jiajie Feng
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Daliang Ning
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Zhou Shi
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Yujia Qin
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Feifei Liu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Liyou Wu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Zhili He
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Joy D. Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yiqi Luo
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, United States
- Earth and Environmental Science, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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Liu D, Huang Y, Yan H, Jiang Y, Zhao T, An S. Dynamics of soil nitrogen fractions and their relationship with soil microbial communities in two forest species of northern China. PLoS One 2018; 13:e0196567. [PMID: 29795562 PMCID: PMC5967799 DOI: 10.1371/journal.pone.0196567] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 04/16/2018] [Indexed: 11/19/2022] Open
Abstract
Microbially-mediated soil N mineralization and transformation are crucial to plant growth. However, changes in soil microbial groups and various N components are not clearly understood. To explore the relationship between soil N components and microbial communities, we conducted an in-situ experiment on two typically planted forest species, namely, Sibirica Apricot (SA) and Prunus davidiana Franch (PdF) by using closed-top polyvinyl chloride tubes. Changes in soil inorganic N, organic N (ON) fractions, and levels of microbial phospholipid fatty acids (PLFAs) were measured bimonthly from April 2012 to April 2013. Microbial PLFAs and the concentrations of easily-available microbial biomass N (MBN; ~60 mg kg-1), soluble ON (SON; ~20 mg kg-1), and inorganic N were similar between the two soils whereas the ON (~900 mg kg-1) and its major part total acid-hydrolyzable N (HTN; ~500 mg kg-1), were significantly different (p < 0.05) in most months (5/6 and 4/6; respectively). The canonical correlation analysis of soil N fractions and microbial parameters indicated that the relationship between total PLFAs (total biomass of living cells) and NH4+-N was the most representative. The relative contributions (indicated by the absolute value of canonical coefficient) of NH4+-N were the largest, followed by NO3--N and MBN. For the HTN component, the relative percentage of hydrolyzable amino acid N and ammonium N decreased markedly in the first half of the year. Canonical variation mainly reflected the relationship between ammonium N and bacterial PLFAs, which were the most sensitive indicators related to soil N changes. The relative contributions of HTN components to the link between soil microbial groups and HTN components were ammonium N > amino acid N > amino sugar N. Observations from our study indicate the sensitivity of soil N mineralization indicators in relation to the temporal variation of soil microbial groups and N fractions.
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Affiliation(s)
- Dong Liu
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Resource and Environment Science, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on Loess Plateau, Northwest A&F University, Yangling, China
| | - Yimei Huang
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Resource and Environment Science, Northwest A&F University, Yangling, China
- * E-mail:
| | - Hao Yan
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Resource and Environment Science, Northwest A&F University, Yangling, China
| | - Yueli Jiang
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Resource and Environment Science, Northwest A&F University, Yangling, China
| | - Tong Zhao
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Resource and Environment Science, Northwest A&F University, Yangling, China
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on Loess Plateau, Northwest A&F University, Yangling, China
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Röhl O, Graupner N, Peršoh D, Kemler M, Mittelbach M, Boenigk J, Begerow D. Flooding Duration Affects the Structure of Terrestrial and Aquatic Microbial Eukaryotic Communities. MICROBIAL ECOLOGY 2018; 75:875-887. [PMID: 29026984 DOI: 10.1007/s00248-017-1085-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/29/2017] [Indexed: 05/22/2023]
Abstract
The increasing number and duration of inundations is reported to be a consequence of climate change and may severely compromise non-adapted macroorganisms. The effect of flooding events on terrestrial and aquatic microbial communities is, however, less well understood. They may respond to the changed abiotic properties of their native habitat, and the native community may change due to the introduction of alien species. We designed an experiment to investigate the effect of five different flooding durations on the terrestrial and aquatic communities of eukaryotic microorganism, using the AquaFlow mesocosms. With amplicon sequencing of the small subunit (SSU) and internal transcribed spacer (ITS) rRNA gene regions, we analyzed community compositions directly before and after flooding. Subsequently, they were monitored for another 28 days, to determine the sustainability of community changes. Our results revealed a temporary increase in similarity between terrestrial and aquatic communities according to OTU composition (operational taxonomic unit, serves as a proxy for species). Increased similarity was mainly caused by the transmission of OTUs from water to soil. A minority of these were able to persist in soil until the end of the experiment. By contrast, the vast majority of soil OTUs was not transmitted to water. Flooding duration affected the community structure (abundance) more than composition (occurrence). Terrestrial communities responded immediately to flooding and the flooding duration influenced the community changes. Independent from flooding duration, all terrestrial communities recovered largely after flooding, indicating a remarkable resilience to the applied disturbances. Aquatic communities responded immediately to the applied inundations too. At the end of the experiment, they grouped according to the applied flooding duration and the amount of ammonium and chloride that leached from the soil. This indicates a sustained long-term response of the aquatic communities to flooding events.
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Affiliation(s)
- Oliver Röhl
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany.
| | - Nadine Graupner
- Department of Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Derek Peršoh
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Martin Kemler
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Moritz Mittelbach
- AG Ökologie der Pflanzen; Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
| | - Jens Boenigk
- Department of Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Dominik Begerow
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
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47
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Seasonal Effects on Microbial Community Structure and Nitrogen Dynamics in Temperate Forest Soil. FORESTS 2018. [DOI: 10.3390/f9030153] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
Most tropical evergreen rain forests are characterised by varying degrees of precipitation seasonality that influence plant phenology and litterfall dynamics. Soil microbes are sensitive to soil water:air ratio and to nutrient availability. We studied if within-year seasonality in precipitation and litterfall-derived nutrient input resulted in predictable seasonal variation in soil bacterial diversity/microbial functional groups in an Amazonian forest. We characterised the spatio-temporal dynamics of microbial communities from the plot to the stand scales and related them to precipitation seasonality and spatial variability in soil characteristics. Community composition and functional diversity showed high spatial heterogeneity and was related to variability in soil chemistry at the stand level. Large species turnover characterised plot level changes over time, reflecting precipitation seasonality-related changes in soil nutrient and moisture regimes. The abundance of decomposers was highest during the rainy season, characterised also by anaerobic saprophytes and N2-fixers adapted to fluctuating redox conditions. In contrast, Beijerinckiaceae, likely derived from the phyllosphere, were found at higher abundances when litter inputs and accumulation were highest. We showed that in a mildly seasonal rain forest, the composition of soil microbial communities appears to be following canopy phenology patterns and the two are interlinked and drive soil nutrient availability.
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Glassman SI, Wang IJ, Bruns TD. Environmental filtering by
pH
and soil nutrients drives community assembly in fungi at fine spatial scales. Mol Ecol 2017; 26:6960-6973. [DOI: 10.1111/mec.14414] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/17/2017] [Accepted: 10/25/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Sydney I. Glassman
- Department of Environmental Science Policy and Management University of California, Berkeley CA USA
- Department of Ecology and Evolutionary Biology University of California, Irvine CA USA
- Department of Plant & Microbial Biology University of California Berkeley CA USA
| | - Ian J. Wang
- Department of Environmental Science Policy and Management University of California, Berkeley CA USA
| | - Thomas D. Bruns
- Department of Environmental Science Policy and Management University of California, Berkeley CA USA
- Department of Plant & Microbial Biology University of California Berkeley CA USA
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Halliday FW, Umbanhowar J, Mitchell CE. Interactions among symbionts operate across scales to influence parasite epidemics. Ecol Lett 2017; 20:1285-1294. [DOI: 10.1111/ele.12825] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 07/23/2017] [Indexed: 12/31/2022]
Affiliation(s)
| | - James Umbanhowar
- Department of Biology University of North Carolina Chapel Hill NC27599 USA
- Curriculum for the Environment and Ecology University of North Carolina Chapel Hill NC27599 USA
| | - Charles E. Mitchell
- Department of Biology University of North Carolina Chapel Hill NC27599 USA
- Curriculum for the Environment and Ecology University of North Carolina Chapel Hill NC27599 USA
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