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Jibola-Shittu MY, Heng Z, Keyhani NO, Dang Y, Chen R, Liu S, Lin Y, Lai P, Chen J, Yang C, Zhang W, Lv H, Wu Z, Huang S, Cao P, Tian L, Qiu Z, Zhang X, Guan X, Qiu J. Understanding and exploring the diversity of soil microorganisms in tea ( Camellia sinensis) gardens: toward sustainable tea production. Front Microbiol 2024; 15:1379879. [PMID: 38680916 PMCID: PMC11046421 DOI: 10.3389/fmicb.2024.1379879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/03/2024] [Indexed: 05/01/2024] Open
Abstract
Leaves of Camellia sinensis plants are used to produce tea, one of the most consumed beverages worldwide, containing a wide variety of bioactive compounds that help to promote human health. Tea cultivation is economically important, and its sustainable production can have significant consequences in providing agricultural opportunities and lowering extreme poverty. Soil parameters are well known to affect the quality of the resultant leaves and consequently, the understanding of the diversity and functions of soil microorganisms in tea gardens will provide insight to harnessing soil microbial communities to improve tea yield and quality. Current analyses indicate that tea garden soils possess a rich composition of diverse microorganisms (bacteria and fungi) of which the bacterial Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Chloroflexi and fungal Ascomycota, Basidiomycota, Glomeromycota are the prominent groups. When optimized, these microbes' function in keeping garden soil ecosystems balanced by acting on nutrient cycling processes, biofertilizers, biocontrol of pests and pathogens, and bioremediation of persistent organic chemicals. Here, we summarize research on the activities of (tea garden) soil microorganisms as biofertilizers, biological control agents and as bioremediators to improve soil health and consequently, tea yield and quality, focusing mainly on bacterial and fungal members. Recent advances in molecular techniques that characterize the diverse microorganisms in tea gardens are examined. In terms of viruses there is a paucity of information regarding any beneficial functions of soil viruses in tea gardens, although in some instances insect pathogenic viruses have been used to control tea pests. The potential of soil microorganisms is reported here, as well as recent techniques used to study microbial diversity and their genetic manipulation, aimed at improving the yield and quality of tea plants for sustainable production.
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Affiliation(s)
- Motunrayo Y. Jibola-Shittu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiang Heng
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Nemat O. Keyhani
- Department of Biological Sciences, University of Illinois, Chicago, IL, United States
| | - Yuxiao Dang
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ruiya Chen
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sen Liu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongsheng Lin
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Pengyu Lai
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinhui Chen
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chenjie Yang
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weibin Zhang
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huajun Lv
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ziyi Wu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuaishuai Huang
- School of Ecology and Environment, Tibet University, Lhasa, China
| | - Pengxi Cao
- School of Ecology and Environment, Tibet University, Lhasa, China
| | - Lin Tian
- Tibet Plateau Institute of Biology, Lhasa, China
| | - Zhenxing Qiu
- Fuzhou Technology and Business University, Fuzhou, Fujian, China
| | - Xiaoyan Zhang
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiayu Guan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Junzhi Qiu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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Leifheit EF, Camenzind T, Lehmann A, Andrade-Linares DR, Fussan M, Westhusen S, Wineberger TM, Rillig MC. Fungal traits help to understand the decomposition of simple and complex plant litter. FEMS Microbiol Ecol 2024; 100:fiae033. [PMID: 38486354 PMCID: PMC11022653 DOI: 10.1093/femsec/fiae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/21/2024] [Accepted: 03/13/2024] [Indexed: 04/18/2024] Open
Abstract
Litter decomposition is a key ecosystem process, relevant for the release and storage of nutrients and carbon in soil. Soil fungi are one of the dominant drivers of organic matter decomposition, but fungal taxa differ substantially in their functional ability to decompose plant litter. Knowledge is mostly based on observational data and subsequent molecular analyses and in vitro studies have been limited to forest ecosystems. In order to better understand functional traits of saprotrophic soil fungi in grassland ecosystems, we isolated 31 fungi from a natural grassland and performed several in vitro studies testing for i) leaf and wood litter decomposition, ii) the ability to use carbon sources of differing complexity, iii) the enzyme repertoire. Decomposition strongly varied among phyla and isolates, with Ascomycota decomposing the most and Mucoromycota decomposing the least. The phylogeny of the fungi and their ability to use complex carbon were the most important predictors for decomposition. Our findings show that it is crucial to understand the role of individual members and functional groups within the microbial community. This is an important way forward to understand the role of microbial community composition for the prediction of litter decomposition and subsequent potential carbon storage in grassland soils.
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Affiliation(s)
- Eva F Leifheit
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
| | - Tessa Camenzind
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
| | - Anika Lehmann
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
| | - Diana R Andrade-Linares
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Research Unit for Comparative Microbiome Analyses – COMI, 85764 Neuherberg, Germany
| | - Max Fussan
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
| | - Sophia Westhusen
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
| | - Till M Wineberger
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
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3
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Terol H, Thiour-Mauprivez C, Devers M, Martin-Laurent F, Suzuki M, Calvayrac C, Barthelmebs L. "Structural responses of non-targeted bacterial and hppd communities to the herbicide tembotrione in soil". THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168198. [PMID: 37914111 DOI: 10.1016/j.scitotenv.2023.168198] [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: 08/28/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023]
Abstract
Tembotrione (TBT) is a β-triketone herbicide targeting the 4-Hydroxyphenylpyruvate dioxygenase enzyme (4-HPPD) of weeds. This molecule can also affect soil microorganisms, either through both direct and indirect toxic effects for microorganisms expressing 4-HPPD, or by promoting tolerant and/or degrading microbial populations. Our study aimed to characterize the impacts of TBT on the diversity of total- and hppd (coding for 4-HPPD) -soil bacterial communities. Soil microcosms were treated with the active ingredient TBT at the recommended field dose (100 g a.i/ha; D1) or the tenfold dose (D10). Soil samples were collected from 0 to 55 days post-treatment to study: (i) total- and hppd-bacterial diversities using 16SrRNA and hppd amplicons sequencing, respectively; (ii) TBT dissipation in soil. Both total- and hppd-bacterial community composition was not affected by TBT treatments (D1 and D10). However, D10 treatment slightly increased richness and phylogenetic diversity of the total bacterial community while decreasing hppd richness. Overall, the highest dose of TBT seemed to promote TBT-tolerant or TBT-degrading bacterial populations and to deplete TBT-sensitive ones. These effects were transient as TBT was rapidly dissipated with a DT50 of 7 days and 15 days for D1 and D10, respectively. Differential abundance analysis with a Generalized Linear Model allowed the identification of Sphingomonas, Steroidobacter and Lysobacter as genus that were influenced by TBT, and which could be used as a new class of exposure biomarkers.
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Affiliation(s)
- Hugo Terol
- Université de Perpignan Via Domitia, Biocapteurs-Analyse-Environnement, 66860 Perpignan, France; Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, F-66650 Banyuls-sur-Mer, France
| | - Clémence Thiour-Mauprivez
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Marion Devers
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Fabrice Martin-Laurent
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Marcelino Suzuki
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, F-66650 Banyuls-sur-Mer, France
| | - Christophe Calvayrac
- Université de Perpignan Via Domitia, Biocapteurs-Analyse-Environnement, 66860 Perpignan, France; Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, F-66650 Banyuls-sur-Mer, France
| | - Lise Barthelmebs
- Université de Perpignan Via Domitia, Biocapteurs-Analyse-Environnement, 66860 Perpignan, France; Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, F-66650 Banyuls-sur-Mer, France.
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Lí JT, Hicks LC, Brangarí AC, Tájmel D, Cruz-Paredes C, Rousk J. Subarctic winter warming promotes soil microbial resilience to freeze-thaw cycles and enhances the microbial carbon use efficiency. GLOBAL CHANGE BIOLOGY 2024; 30:e17040. [PMID: 38273522 DOI: 10.1111/gcb.17040] [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: 09/01/2023] [Revised: 11/01/2023] [Accepted: 11/01/2023] [Indexed: 01/27/2024]
Abstract
Climate change is predicted to cause milder winters and thus exacerbate soil freeze-thaw perturbations in the subarctic, recasting the environmental challenges that soil microorganisms need to endure. Historical exposure to environmental stressors can facilitate the microbial resilience to new cycles of that same stress. However, whether and how such microbial memory or stress legacy can modulate microbial responses to cycles of frost remains untested. Here, we conducted an in situ field experiment in a subarctic birch forest, where winter warming resulted in a substantial increase in the number and intensity of freeze-thaw events. After one season of winter warming, which raised mean surface and soil (-8 cm) temperatures by 2.9 and 1.4°C, respectively, we investigated whether the in situ warming-induced increase in frost cycles improved soil microbial resilience to an experimental freeze-thaw perturbation. We found that the resilience of microbial growth was enhanced in the winter warmed soil, which was associated with community differences across treatments. We also found that winter warming enhanced the resilience of bacteria more than fungi. In contrast, the respiration response to freeze-thaw was not affected by a legacy of winter warming. This translated into an enhanced microbial carbon-use efficiency in the winter warming treatments, which could promote the stabilization of soil carbon during such perturbations. Together, these findings highlight the importance of climate history in shaping current and future dynamics of soil microbial functioning to perturbations associated with climate change, with important implications for understanding the potential consequences on microbial-mediated biogeochemical cycles.
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Affiliation(s)
- Jin-Tao Lí
- Department of Biology, Microbial Biogeochemistry in Lund (MBLU), Lund University, Lund, Sweden
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
- Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Lettice C Hicks
- Department of Biology, Microbial Biogeochemistry in Lund (MBLU), Lund University, Lund, Sweden
- Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Albert C Brangarí
- Department of Biology, Microbial Biogeochemistry in Lund (MBLU), Lund University, Lund, Sweden
- Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Dániel Tájmel
- Department of Biology, Microbial Biogeochemistry in Lund (MBLU), Lund University, Lund, Sweden
- Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Carla Cruz-Paredes
- Department of Biology, Microbial Biogeochemistry in Lund (MBLU), Lund University, Lund, Sweden
- Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Johannes Rousk
- Department of Biology, Microbial Biogeochemistry in Lund (MBLU), Lund University, Lund, Sweden
- Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
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5
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Zhou SYD, Huang FY, Su W, Lie Z, Liu Y, Lin C, Yang K, Meng Z, Liu Z, Neilson R, Su JQ, Liu J. Distinct patterns of the soil and phyllosphere antibiotic resistome in natural forest ecosystems under an altitudinal gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165346. [PMID: 37419346 DOI: 10.1016/j.scitotenv.2023.165346] [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: 05/04/2023] [Revised: 06/25/2023] [Accepted: 07/04/2023] [Indexed: 07/09/2023]
Abstract
Warming affects microbial functioning of soil and the phyllosphere across global ecosystems. However, little is known about the impact of increasing temperature on antibiotic resistome profiles in natural forests. To address this issue, we investigated antibiotic resistance genes (ARGs) in both soil and the plant phyllosphere using an experimental platform established in a forest ecosystem that delivers a temperature difference of 2.1 °C along an altitudinal gradient. Principal Coordinate Analysis (PCoA) showed that there were significant differences in the composition of soil and plant phyllosphere ARGs at different altitudes (P = 0.001). The relative abundance of phyllosphere ARGs and mobile genetic elements (MGEs) and soil MGEs increased with temperature. More resistance gene classes increased in abundance in the phyllosphere (10 classes) than soil (2 classes), and a Random Forest model analysis suggested that phyllosphere ARGs were more sensitive to temperature change than soil. Increasing temperature as a direct consequence of an altitudinal gradient, and the relative abundance of MGEs were the main drivers that shaped the profiles of ARGs in the phyllosphere and soil. Biotic and abiotic factors affected phyllosphere ARGs indirectly via MGEs. This study enhances our understanding of the influence of altitude gradients on resistance genes in natural environments.
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Affiliation(s)
- Shu-Yi-Dan Zhou
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Fu-Yi Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Wei Su
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Zhongkai University of Agriculture and Engineering, 24 Dongsha Street, Haizhu District, Guangzhou 510225, China
| | - Zhiyang Lie
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Yue Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Chenshuo Lin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Kai Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Ze Meng
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Zhanfeng Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, Scotland, UK
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Juxiu Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China.
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Wang S, Zhou T, Zhao H, Zhang K, Cui J. Temporal and spatial changes in rhizosphere bacterial diversity of mountain Rhododendron mucronulatum. Front Microbiol 2023; 14:1201274. [PMID: 37415822 PMCID: PMC10321304 DOI: 10.3389/fmicb.2023.1201274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/05/2023] [Indexed: 07/08/2023] Open
Abstract
To better conserve the ecology of the wild Rhododendron mucronulatum range, we studied the rhizosphere microenvironment of R. mucronulatum in Beijing's Yunmeng Mountain National Forest Park. R. mucronulatum rhizosphere soil physicochemical properties and enzyme activities changed significantly with temporal and elevational gradients. The correlations between soil water content (SWC), electrical conductivity (EC), organic matter content (OM), total nitrogen content (TN), catalase activity (CAT), sucrose-converting enzyme activity (INV), and urease activity (URE) were significant and positive in the flowering and deciduous periods. The alpha diversity of the rhizosphere bacterial community was significantly higher in the flowering period than in the deciduous period, and the effect of elevation was insignificant. The diversity of the R. mucronulatum rhizosphere bacterial community changed significantly with the change in the growing period. A network analysis of the correlations revealed stronger linkages between the rhizosphere bacterial communities in the deciduous period than in the flowering period. Rhizomicrobium was the dominant genus in both periods, but its relative abundance decreased in the deciduous period. Changes in the relative abundance of Rhizomicrobium may be the main factor influencing the changes in the R. mucronulatum rhizosphere bacterial community. Moreover, the R. mucronulatum rhizosphere bacterial community and soil characteristics were significantly correlated. Additionally, the influence of soil physicochemical properties on the rhizosphere bacterial community was larger than that of enzyme activity on the bacterial community. We mainly analyzed the change patterns in the rhizosphere soil properties and rhizosphere bacterial diversity of R. mucronulatum during temporal and spatial variation, laying the foundation for further understanding of the ecology of wild R. mucronulatum.
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Affiliation(s)
- Sirui Wang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Tiantian Zhou
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Hewen Zhao
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Kezhong Zhang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Jinteng Cui
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
- Ancient Tree Health and Culture Engineering Technology Research Center, Beijing University of Agriculture, Beijing, China
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7
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Dlamini P, Sekhohola-Dlamini LM, Cowan AK. Editorial: Soil-microbial interactions. Front Microbiol 2023; 14:1213834. [PMID: 37260691 PMCID: PMC10228142 DOI: 10.3389/fmicb.2023.1213834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 06/02/2023] Open
Affiliation(s)
- Phesheya Dlamini
- Department of Plant Production, Soil Science and Agricultural Engineering, University of Limpopo, Sovenga, South Africa
| | | | - A. Keith Cowan
- Institute for Environmental Biotechnology, Rhodes University, Makhanda, South Africa
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Cruz-Paredes C, Tájmel D, Rousk J. Variation in Temperature Dependences across Europe Reveals the Climate Sensitivity of Soil Microbial Decomposers. Appl Environ Microbiol 2023; 89:e0209022. [PMID: 37162342 DOI: 10.1128/aem.02090-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Temperature is a major determinant of biological process rates, and microorganisms are key regulators of ecosystem carbon (C) dynamics. Temperature controls microbial rates of decomposition, and thus warming can stimulate C loss, creating positive feedback to climate change. If trait distributions that define temperature relationships of microbial communities can adapt to altered temperatures, they could modulate the strength of this feedback, but if this occurs remains unclear. In this study, we sampled soils from a latitudinal climate gradient across Europe. We established the temperature relationships of microbial growth and respiration rates and used these to investigate if and with what strength the community trait distributions for temperature were adapted to their local environment. Additionally, we sequenced bacterial and fungal amplicons to link the variance in community composition to changes in temperature traits. We found that microbial temperature trait distributions varied systematically with climate, suggesting that an increase in mean annual temperature (MAT) of 1°C will result in warm-shifted microbial temperature trait distributions equivalent to an increase in temperature minimum (Tmin) of 0.20°C for bacterial growth, 0.07°C for fungal growth, and 0.10°C for respiration. The temperature traits for bacterial growth were thus more responsive to warming than those for respiration and fungal growth. The microbial community composition also varied with temperature, enabling the interlinkage of taxonomic information with microbial temperature traits. Our work shows that the adaptation of microbial temperature trait distributions to a warming climate will affect the C-climate feedback, emphasizing the need to represent this to capture the microbial feedback to climate change. IMPORTANCE One of the largest uncertainties of global warming is if the microbial decomposer feedback will strengthen or weaken soil C-climate feedback. Despite decades of research effort, the strength of this feedback to warming remains unknown. We here present evidence that microbial temperature relationships vary systematically with environmental temperatures along a climate gradient and use this information to forecast how microbial temperature traits will create feedback between the soil C cycle and climate warming. We show that the current use of a universal temperature sensitivity is insufficient to represent the microbial feedback to climate change and provide new estimates to replace this flawed assumption in Earth system models. We also demonstrate that temperature relationships for rates of microbial growth and respiration are differentially affected by warming, with stronger responses to warming for microbial growth (soil C formation) than for respiration (C loss from soil to atmosphere), which will affect the atmosphere-land C balance.
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Affiliation(s)
| | - Dániel Tájmel
- Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Johannes Rousk
- Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
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Wang B, Xiao L, Xu A, Mao W, Wu Z, Hicks LC, Jiang Y, Xu J. Silicon fertilization enhances the resistance of tobacco plants to combined Cd and Pb contamination: Physiological and microbial mechanisms. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 255:114816. [PMID: 36963187 DOI: 10.1016/j.ecoenv.2023.114816] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 06/18/2023]
Abstract
Remediation of soil contaminated with cadmium (Cd) and lead (Pb) is critical for tobacco production. Silicon (Si) fertilizer can relieve heavy metal stress and promote plant growth, however, it remains unknown whether fertilization with Si can mitigate the effects of Cd and Pb on tobacco growth and alter microbial community composition in polluted soils. Here we assessed the effect of two organic (OSiFA, OSiFB) and one mineral Si fertilizer (MSiF) on Cd and Pb accumulation in tobacco plants, together with responses in plant biomass, physiological parameters and soil bacterial communities in pot experiments. Results showed that Si fertilizer relieved Cd and Pb stress on tobacco, thereby promoting plant growth: Si fertilizer reduced available Cd and Pb in the soil by 37.3 % and 28.6 %, respectively, and decreased Cd and Pb contents in the plant tissue by 42.0-55.5 % and 17.2-25.6 %, resulting in increased plant biomass by 13.0-30.5 %. Fertilization with Si alleviated oxidative damage by decreasing malondialdehyde content and increasing peroxidase and ascorbate peroxidase content. In addition, Si fertilization increased photosynthesis, chlorophyll and carotenoid content. Microbial community structure was also affected by Si fertilization. Proteobacteria and Actinobacteria were the dominant phylum in the Cd and Pb contaminated soils, but Si fertilization reduced the abundance of Actinobacteria. Si fertilization also altered microbial metabolic pathways associated with heavy metal resistance. Together, our results suggest that both organic and mineral Si fertilizers can promote tobacco growth by relieving plant physiological stress and favoring a heavy metal tolerant soil microbial community.
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Affiliation(s)
- Bin Wang
- College of Tobacco Science, Yunnan Agricultural University, Kunming, China
| | - Liang Xiao
- School of Geographic Information and Tourism, Chuzhou University, Chuzhou 239000, China
| | - Anchuan Xu
- Technical Center of China Tobacco Yunnan Industrial Co., Ltd., Kunming 650031, China
| | - Wanchong Mao
- Sichuan Management & Monitoring Center Station of Radioactive Environment, Chengdu 611139, China
| | - Zhen Wu
- School of Geographic Information and Tourism, Chuzhou University, Chuzhou 239000, China
| | - Lettice C Hicks
- Section of Microbial Ecology, Department of Biology, Lund University, Ecology Building, Lund 223 62, Sweden
| | - Yonglei Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China.
| | - Junju Xu
- College of Tobacco Science, Yunnan Agricultural University, Kunming, China.
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10
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Zhou H, Xu B, Xu S, Jiang S, Mu D, Wu X, Li X. Bacterial Communities Found in Pit-Wall Mud and Factors Driving Their Evolution. Foods 2023; 12:foods12071419. [PMID: 37048240 PMCID: PMC10093803 DOI: 10.3390/foods12071419] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Pit-wall mud (PWM) fosters bacterial communities involved in Baijiu production. PWM varies depending on pit age and height. In this study, we explored the bacterial communities in PWM and factors driving their evolution. The abundance and diversity of bacterial communities were low in new PWM (NPWM). In old PWM (OPWM), similar but diverse bacterial communities were observed at different heights. Lactobacillus was the predominant genus in NPWM, and Caproiciproducens, Aminobacterium, Hydrogenispora, Lactobacillus, Petrimonas, Syntrophomonas, and Sedimentibacter were the dominant genera in OPWM. A decrease was noted in the abundance of Lactobacillus, which indicated evolution. Among all the physicochemical properties, pH had the highest degree of interpretation with an R2 value of 0.965. pH also exerted the strongest effect on bacterial communities. The path coefficients of pH on bacterial community diversity and abundance were 0.886 and 0.810, respectively. Caproiciproducens and Clostridium sensu stricto 12 metabolized lactic acid, inhibiting the growth of Lactobacillus at a suitable pH, which led to the maturation of PWM. Our findings enrich the literature on the evolution of bacterial communities in PM and the maturation of PM.
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11
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Xin Y, Shi Y, He WM. A shift from inorganic to organic nitrogen-dominance shapes soil microbiome composition and co-occurrence networks. Front Microbiol 2022; 13:1074064. [PMID: 36601395 PMCID: PMC9807163 DOI: 10.3389/fmicb.2022.1074064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/21/2022] [Indexed: 12/23/2022] Open
Abstract
Soil microbiomes are characterized by their composition and networks, which are linked to soil nitrogen (N) availability. In nature, inorganic N dominates at one end and organic N dominates at the other end along soil N gradients; however, little is known about how this shift influences soil microbiome composition and co-occurrence networks, as well as their controls. To this end, we conducted an experiment with the host plant Solidago canadensis, which was subject to three N regimes: inorganic N-dominated, co-dominated by inorganic and organic N (CIO), and organic N-dominated. Organic N dominance exhibited stronger effects on the composition and co-occurrence networks of soil microbiomes than inorganic N dominance. The predominant control was plant traits for bacterial and fungal richness, and soil pH for keystone species. Relative to the CIO regime, inorganic N dominance did not affect fungal richness and increased keystone species; organic N dominance decreased fungal richness and keystone species. Pathogenic fungi and arbuscular mycorrhizal fungi were suppressed by organic N dominance but not by inorganic N dominance. These findings suggest that the shift from soil inorganic N-dominance to soil organic N-dominance could strongly shape soil microbiome composition and co-occurrence networks by altering species diversity and topological properties.
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Affiliation(s)
- Yue Xin
- College of Forestry, Hebei Agricultural University, Baoding, China
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Wei-Ming He
- College of Forestry, Hebei Agricultural University, Baoding, China,*Correspondence: Wei-Ming He,
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12
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Rijkers R, Rousk J, Aerts R, Sigurdsson BD, Weedon JT. Optimal growth temperature of Arctic soil bacterial communities increases under experimental warming. GLOBAL CHANGE BIOLOGY 2022; 28:6050-6064. [PMID: 35838347 PMCID: PMC9546092 DOI: 10.1111/gcb.16342] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Future climate warming in the Arctic will likely increase the vulnerability of soil carbon stocks to microbial decomposition. However, it remains uncertain to what extent decomposition rates will change in a warmer Arctic, because extended soil warming could induce temperature adaptation of bacterial communities. Here we show that experimental warming induces shifts in the temperature-growth relationships of bacterial communities, which is driven by community turnover and is common across a diverse set of 8 (sub) Arctic soils. The optimal growth temperature (Topt ) of the soil bacterial communities increased 0.27 ± 0.039 (SE) and 0.07 ± 0.028°C per °C of warming over a 0-30°C gradient, depending on the sampling moment. We identify a potential role for substrate depletion and time-lag effects as drivers of temperature adaption in soil bacterial communities, which possibly explain discrepancies between earlier incubation and field studies. The changes in Topt were accompanied by species-level shifts in bacterial community composition, which were mostly soil specific. Despite the clear physiological responses to warming, there was no evidence for a common set of temperature-responsive bacterial amplicon sequence variants. This implies that community composition data without accompanying physiological measurements may have limited utility for the identification of (potential) temperature adaption of soil bacterial communities in the Arctic. Since bacterial communities in Arctic soils are likely to adapt to increasing soil temperature under future climate change, this adaptation to higher temperature should be implemented in soil organic carbon modeling for accurate predictions of the dynamics of Arctic soil carbon stocks.
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Affiliation(s)
- Ruud Rijkers
- Amsterdam Institute for Life and Environment, Section of Systems EcologyVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Johannes Rousk
- Microbial Ecology, Department of BiologyLund UniversityLundSweden
| | - Rien Aerts
- Amsterdam Institute for Life and Environment, Section of Systems EcologyVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Bjarni D. Sigurdsson
- Faculty of Environmental and Forest SciencesAgricultural University of IcelandBorgarnesIceland
| | - James T. Weedon
- Amsterdam Institute for Life and Environment, Section of Systems EcologyVrije Universiteit AmsterdamAmsterdamThe Netherlands
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