1
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Fatemi E, Jung C. Pathogenicity of the root lesion nematode Pratylenchus neglectus depends on pre-culture conditions. Sci Rep 2023; 13:19642. [PMID: 37949971 PMCID: PMC10638436 DOI: 10.1038/s41598-023-46551-9] [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: 09/01/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
The ability of a plant parasitic nematode to infect and reproduce within a host plant depends on its genotype and the environmental conditions before and during infection. We studied the culturing conditions of the root lesion nematode Pratylenchus neglectus to produce inoculum for plant infection tests. Nematodes were either cultivated on carrot calli for different periods or directly isolated from the roots of the host plants. After infection of wheat and barley plants in the greenhouse, nematodes were quantified by RT-qPCR and by visual counting of the nematodes. We observed drastically reduced infection rates after long-term (> 96 weeks) cultivation on carrot callus. In contrast, fresh isolates from cereal roots displayed much higher pathogenicity. We recommend using root lesion nematodes cultivated on carrot calli no longer than 48 weeks to guarantee uniform infection rates.
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Affiliation(s)
- Ehsan Fatemi
- Plant Breeding Institute, Christian-Albrechts University, Kiel, Germany
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts University, Kiel, Germany.
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2
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Qi Y, Sun X, Peng S, Tan X, Zhou S. Effects of fertilization on soil nematode communities in an alpine meadow of Qinghai-Tibet plateau. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1122505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Nitrogen and phosphorus are important nutrient elements for plants and underground organisms. The nematode is an important part of the soil food web. Although many studies have explored the effects of fertilization on soil nematode community structure, little is known about the response mechanism of the nematode community to fertilization. In this study, we investigated the diversity and functional diversity of soil nematode communities, as well as soil physicochemical properties, root functional traits, and plant richness. We explored the response mechanism of soil nematode communities to nitrogen and phosphorus fertilizer. Nitrogen fertilizer increased the abundance and richness of bacterivorous nematodes, while phosphorus fertilizer decreased the total abundance of bacterivorous nematodes. Meanwhile, the diversity of the nematode community was significantly affected by soil physicochemical properties and plant root functional traits. Therefore, our study revealed the effects of nitrogen and phosphorus fertilizer on soil nematode community diversity and functional diversity. Exploring the response mechanism of soil nematode communities to fertilization interference provides further evidence for the role of nematodes in maintaining the function of subsurface ecosystems.
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3
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Wu S, Wen L, Dong S, Gao X, Xu Y, Li S, Dong Q, Wessell K. The Plant Interspecific Association in the Revegetated Alpine Grasslands Determines the Productivity Stability of Plant Community Across Restoration Time on Qinghai-Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2022; 13:850854. [PMID: 35386668 PMCID: PMC8978524 DOI: 10.3389/fpls.2022.850854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Grassland cultivation is the key measure for restoring "Black Beach," the extremely degraded alpine meadow in the Three River Headwater Area of the Qinghai-Tibetan Plateau. In this study, we examined the inter-specific relationship in the vegetation community of cultivated grasslands with different restoration times through the network analysis method. The results showed that with the extension of restoration time, the development of cultivated grassland would lead to increasing neutral interactions among the plant species. The proportion of species with positive and negative associations in the community decreased, while the number of species-independent pairs increased significantly. The complexity of plant interspecific association (species network density) had more influence on community stability with the extension of recovery time, which can be used to quantify the characteristics of community structure.
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Affiliation(s)
- Shengnan Wu
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Lu Wen
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Shikui Dong
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Xiaoxia Gao
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yudan Xu
- College of Grassland Science, Shanxi Agricultural University, Jinzhong, China
| | - Shuai Li
- College of Resources and Environment, Shanxi Agricultural University, Jinzhong, China
| | - Quanming Dong
- Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining, China
| | - Kelly Wessell
- Tompkins Cortland Community College, Dryden, NY, United States
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4
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Dietrich P, Cesarz S, Liu T, Roscher C, Eisenhauer N. Effects of plant species diversity on nematode community composition and diversity in a long-term biodiversity experiment. Oecologia 2021; 197:297-311. [PMID: 34091787 PMCID: PMC8505370 DOI: 10.1007/s00442-021-04956-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/26/2021] [Indexed: 11/04/2022]
Abstract
Diversity loss has been shown to change the soil community; however, little is known about long-term consequences and underlying mechanisms. Here, we investigated how nematode communities are affected by plant species richness and whether this is driven by resource quantity or quality in 15-year-old plant communities of a long-term grassland biodiversity experiment. We extracted nematodes from 93 experimental plots differing in plant species richness, and measured above- and belowground plant biomass production and soil organic carbon concentrations (Corg) as proxies for resource quantity, as well as C/Nleaf ratio and specific root length (SRL) as proxies for resource quality. We found that nematode community composition and diversity significantly differed among plant species richness levels. This was mostly due to positive plant diversity effects on the abundance and genus richness of bacterial-feeding, omnivorous, and predatory nematodes, which benefited from higher shoot mass and soil Corg in species-rich plant communities, suggesting control via resource quantity. In contrast, plant-feeding nematodes were negatively influenced by shoot mass, probably due to higher top–down control by predators, and were positively related to SRL and C/Nleaf, indicating control via resource quality. The decrease of the grazing pressure ratio (plant feeders per root mass) with plant species richness indicated a higher accumulation of plant-feeding nematodes in species-poor plant communities. Our results, therefore, support the hypothesis that soil-borne pathogens accumulate in low-diversity communities over time, while soil mutualists (bacterial-feeding, omnivorous, predatory nematodes) increase in abundance and richness in high-diversity plant communities, which may contribute to the widely-observed positive plant diversity–productivity relationship.
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Affiliation(s)
- Peter Dietrich
- Department of Physiological Diversity, UFZ, Helmholtz Centre for Environmental Research, Permoser Straße 15, 04318, Leipzig, Germany. .,German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.
| | - Simone Cesarz
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.,Department of Experimental Interaction Ecology, Institute of Biology, Leipzig University, Puschstraße 4, 04103, Leipzig, Germany
| | - Tao Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Christiane Roscher
- Department of Physiological Diversity, UFZ, Helmholtz Centre for Environmental Research, Permoser Straße 15, 04318, Leipzig, Germany.,German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
| | - Nico Eisenhauer
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.,Department of Experimental Interaction Ecology, Institute of Biology, Leipzig University, Puschstraße 4, 04103, Leipzig, Germany
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5
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Seasonal Stabilities of Soil Nematode Communities and Their Relationships with Environmental Factors in Different Temperate Forest Types on the Chinese Loess Plateau. FORESTS 2021. [DOI: 10.3390/f12020246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The bottom-up effects of vegetation have been documented to be strong drivers of the soil food web structure and functioning in temperate forests. However, how the forest type affects the stability of the soil food web is not well known. In the Ziwuling forest region of the Loess Plateau, we selected three typical forests, Pinus tabuliformis Carrière (PT), Betula platyphylla Sukaczev (BP), and Quercus liaotungensis Koidz. (QL), to investigate the soil nematode community characteristics in the dry (April) and rainy (August) season, and analyzed their relationships with the soil properties. The results showed that the characteristics of the soil nematode communities and their seasonal variations differed markedly among the forest types. Compared to P. tabuliformis (PT), the B. platyphylla (BP) and Q. liaotungensis (QL) forests had higher plant diversity and more easily decomposed litters, which were more effective for improving the soil resource availability, thus, leading to more beneficial effects on the soil nematode community. In both the dry and rainy season, the soil nematode abundance was the highest in the BP forest. The Shannon–Wiener diversity index (H’), Pielou’s evenness index (J’), and nematode channel ratio index (NCR) were higher, while the Simpson dominance index (λ) and plant parasite index (PPI) were lower, in the BP and QL forests compared with in the PT forest. From the dry to rainy season, the total nematode abundance and the abundance of fungivores, bacterivores, and omnivore-predators, significantly increased in the QL and PT forests, and the values of the Wasilewska index (WI), maturity index (MI), H’, J’, λ, and NCR showed the most significant seasonal variability in the PT forest, which were mainly driven by changes in the soil labile C and N and the moisture content between the two seasons. Generally, the seasonal stability of the soil nematode communities was the highest in the BP forest and the poorest in the PT forest, probably due to variations in the plant diversity. Our results suggest the importance of tree species and diversity as bottom-up regulating factors of the soil food web structure, function, and seasonal stability, which has important implications for sustainable forest management in the Loess Plateau and other temperate regions.
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6
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Orwin KH, Mason NWH, Aalders L, Bell NL, Schon N, Mudge PL. Relationships of plant traits and soil biota to soil functions change as nitrogen fertiliser rates increase in an intensively managed agricultural system. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.13771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Kate H. Orwin
- Manaaki Whenua – Landcare Research Lincoln New Zealand
| | | | | | | | | | - Paul L. Mudge
- Manaaki Whenua – Landcare Research Hamilton New Zealand
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7
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Yan J, Zhang Y, Crawford KM, Chen X, Yu S, Wu J. Plant genotypic diversity effects on soil nematodes vary with trophic level. THE NEW PHYTOLOGIST 2021; 229:575-584. [PMID: 32813893 DOI: 10.1111/nph.16829] [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: 12/16/2019] [Accepted: 07/15/2020] [Indexed: 06/11/2023]
Abstract
At local spatial scales, loss of genetic diversity within species can lead to species loss. Few studies, however, have examined plant genotypic diversity effects across trophic levels. We investigated genotypic diversity effects of Phragmites australis on belowground biomass and soil nematode communities. Our results revealed that belowground plant biomass and nematode abundance responses to plant genotypic diversity were uncoupled. Decreasing plant genotypic diversity decreased the abundance of lower, but not higher trophic level nematodes. Low plant genotypic diversity also decreased the structural footprint and functional indices of nematodes, indicating lowered metabolic functioning of higher trophic level nematodes and decreased soil food web stability. Our study suggests that plant genotypic diversity effects differ across trophic levels, taxonomic groups and ecosystem functions and that decreasing plant genotypic diversity could destabilise belowground food webs. This highlights the importance of conserving intraspecific plant diversity.
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Affiliation(s)
- Jun Yan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Youzheng Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Kerri M Crawford
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, 77204, USA
| | - Xiaoyong Chen
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
| | - Shuo Yu
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
- Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, 536000, China
| | - Jihua Wu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, 200433, China
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8
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Girgan C, du Preez G, Marais M, Swart A, Fourie H. Nematodes and the effect of seasonality in grassland habitats of South Africa. J Nematol 2020; 52:e2020-118. [PMID: 33829209 PMCID: PMC8015383 DOI: 10.21307/jofnem-2020-118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Indexed: 11/22/2022] Open
Abstract
Nematodes in South Africa have mainly been studied for their diversity and agricultural importance. However, the ecological status of nematodes and the effect of seasonal variation in local grasslands remain unknown. For this reason, a nematode study was conducted in the Telperion Nature Reserve and represented the first ecological study in a natural grassland area in South Africa. In total, 104 soil samples were collected during four consecutive seasons from 2015 until 2016 in three habitats, viz. (i) open grassland, (ii) shrubland with rocky outcrops, and (iii) riparian zone. From these the nematode community structure and soil ecosystem status were studied. In total, 93 genera from 50 families were recorded with herbivores and bacterivores being the most abundant trophic groups in all three habitats. Linear mixed models revealed that season had an overwhelmingly dominant impact on the condition, food web status, and functioning of the soil ecosystems with pairwise comparisons indicating that significantly higher values were recorded during winter. Interestingly, this seasonal shift can largely be attributed to fluctuations in the populations of only a few nematode groups (namely Aporcelaimellus, Dorylaimidae, Iotonchus, and Mononchus) with high colonizer-persister values. Although the reason for the higher abundance of specific nematode groups recorded during the winter is not explicitly clear, it is possibly linked to reduced competition from other soil fauna. This study clearly shows that further investigations are required to better understand the dynamics of grassland ecosystems.
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Affiliation(s)
- Chantelle Girgan
- Nematology Unit, Biosystematics, Agricultural Research Council-Plant Health and Protection (ARC-PHP), Private Bag X134, Queenswood, 0121, South Africa
| | - Gerhard du Preez
- Unit for Environmental Sciences and Management, North-West University (NWU), Private Bag X6001 Potchefstroom, 2520, South Africa.,Agricultural Research Council - Tropical and Subtropical Crops (ARC-TSC), Private Bag X11208, Nelspruit, 1200, South Africa
| | - Mariette Marais
- Nematology Unit, Biosystematics, Agricultural Research Council-Plant Health and Protection (ARC-PHP), Private Bag X134, Queenswood, 0121, South Africa
| | - Antoinette Swart
- Nematology Unit, Biosystematics, Agricultural Research Council-Plant Health and Protection (ARC-PHP), Private Bag X134, Queenswood, 0121, South Africa.,Department of Zoology, University of Johannesburg, P.O. Box 524, Auckland Park, Johannesburg, 2006, South Africa
| | - Hendrika Fourie
- Unit for Environmental Sciences and Management, North-West University (NWU), Private Bag X6001 Potchefstroom, 2520, South Africa
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9
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Steinauer K, Heinen R, Hannula SE, De Long JR, Huberty M, Jongen R, Wang M, Bezemer TM. Above‐belowground linkages of functionally dissimilar plant communities and soil properties in a grassland experiment. Ecosphere 2020. [DOI: 10.1002/ecs2.3246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Katja Steinauer
- Department of Terrestrial Ecology Netherlands Institute of Ecology Droevendaalsesteeg 10 Wageningen6700 ABThe Netherlands
| | - Robin Heinen
- Department of Terrestrial Ecology Netherlands Institute of Ecology Droevendaalsesteeg 10 Wageningen6700 ABThe Netherlands
- Institute of Biology Section Plant Ecology and Phytochemistry Leiden University P.O. Box 9505 Leiden2300 RAThe Netherlands
- Lehrstuhl für Terrestrische Ökologie Landnutzung und Umwelt Technische Universität München Wissenschaftszentrum Weihenstephan für Ernährung, Hans‐Carl‐von‐Carlowitz‐Platz 2 FreisingD‐85354Germany
| | - S. Emilia Hannula
- Department of Terrestrial Ecology Netherlands Institute of Ecology Droevendaalsesteeg 10 Wageningen6700 ABThe Netherlands
| | - Jonathan R. De Long
- Department of Terrestrial Ecology Netherlands Institute of Ecology Droevendaalsesteeg 10 Wageningen6700 ABThe Netherlands
| | - Martine Huberty
- Department of Terrestrial Ecology Netherlands Institute of Ecology Droevendaalsesteeg 10 Wageningen6700 ABThe Netherlands
- Institute of Biology Section Plant Ecology and Phytochemistry Leiden University P.O. Box 9505 Leiden2300 RAThe Netherlands
| | - Renske Jongen
- Department of Terrestrial Ecology Netherlands Institute of Ecology Droevendaalsesteeg 10 Wageningen6700 ABThe Netherlands
| | - Minggang Wang
- Department of Plant Protection Biology Swedish University of Agricultural Sciences P.O. Box 102 AlnarpSE‐23053Sweden
| | - T. Martijn Bezemer
- Department of Terrestrial Ecology Netherlands Institute of Ecology Droevendaalsesteeg 10 Wageningen6700 ABThe Netherlands
- Institute of Biology Section Plant Ecology and Phytochemistry Leiden University P.O. Box 9505 Leiden2300 RAThe Netherlands
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10
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Biodiversity increases multitrophic energy use efficiency, flow and storage in grasslands. Nat Ecol Evol 2020; 4:393-405. [PMID: 32094542 DOI: 10.1038/s41559-020-1123-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 01/15/2020] [Indexed: 11/08/2022]
Abstract
The continuing loss of global biodiversity has raised questions about the risk that species extinctions pose for the functioning of natural ecosystems and the services that they provide for human wellbeing. There is consensus that, on single trophic levels, biodiversity sustains functions; however, to understand the full range of biodiversity effects, a holistic and multitrophic perspective is needed. Here, we apply methods from ecosystem ecology that quantify the structure and dynamics of the trophic network using ecosystem energetics to data from a large grassland biodiversity experiment. We show that higher plant diversity leads to more energy stored, greater energy flow and higher community-energy-use efficiency across the entire trophic network. These effects of biodiversity on energy dynamics were not restricted to only plants but were also expressed by other trophic groups and, to a similar degree, in aboveground and belowground parts of the ecosystem, even though plants are by far the dominating group in the system. The positive effects of biodiversity on one trophic level were not counteracted by the negative effects on adjacent levels. Trophic levels jointly increased the performance of the community, indicating ecosystem-wide multitrophic complementarity, which is potentially an important prerequisite for the provisioning of ecosystem services.
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11
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Singh D, Slik JWF, Jeon YS, Tomlinson KW, Yang X, Wang J, Kerfahi D, Porazinska DL, Adams JM. Tropical forest conversion to rubber plantation affects soil micro- & mesofaunal community & diversity. Sci Rep 2019; 9:5893. [PMID: 30971738 PMCID: PMC6458137 DOI: 10.1038/s41598-019-42333-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 03/25/2019] [Indexed: 11/10/2022] Open
Abstract
Tropical rainforests play important roles in carbon sequestration and are hot spots for biodiversity. Tropical forests are being replaced by rubber (Hevea brasiliensis) plantations, causing widespread concern of a crash in biodiversity. Such changes in aboveground vegetation might have stronger impacts on belowground biodiversity. We studied tropical rainforest fragments and derived rubber plantations at a network of sites in Xishuangbanna, China, hypothesizing a major decrease in diversity with conversion to plantations. We used metabarcoding of the 18S rRNA gene and recovered 2313 OTUs, with a total of 449 OTUs shared between the two land-use types. The most abundant phyla detected were Annelida (66.4% reads) followed by arthropods (15.5% reads) and nematodes (8.9% reads). Of these, only annelids were significantly more abundant in rubber plantation. Taken together, α- and β-diversity were significantly higher in forest than rubber plantation. Soil pH and spatial distance explained a significant portion of the variability in phylogenetic community structure for both land-use types. Community assembly was primarily influenced by stochastic processes. Overall it appears that forest replacement by rubber plantation results in an overall loss and extensive replacement of soil micro- and mesofaunal biodiversity, which should be regarded as an additional aspect of the impact of forest conversion.
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Affiliation(s)
- Dharmesh Singh
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
- Environmental Biotechnology & Genomics Division, CSIR-NEERI, Nehru Marg, Nagpur, MH, 440020, India
| | - J W Ferry Slik
- Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku, BE1410, Brunei Darussalam
| | - Yoon-Seong Jeon
- ChunLab Inc., Bldg. 105-1, Suite #307, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-742, Republic of Korea
| | - Kyle W Tomlinson
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Xiaodong Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Jin Wang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Dorsaf Kerfahi
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Gwanak-Gu, Seoul, 151-742, Republic of Korea
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, IFAS, 1881 Natural Area Drive, Gainesville, 32611, Florida, USA
| | - Jonathan M Adams
- School of Geography and Ocean Sciences, Nanjing University, Nanjing, 210023, Jiangsu Province, China.
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12
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Guerrero‐Ramírez NR, Reich PB, Wagg C, Ciobanu M, Eisenhauer N. Diversity‐dependent plant–soil feedbacks underlie long‐term plant diversity effects on primary productivity. Ecosphere 2019. [DOI: 10.1002/ecs2.2704] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Nathaly R. Guerrero‐Ramírez
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Deutscher Platz 5e Leipzig 04103 Germany
- Institute of Biology Leipzig University Deutscher Platz 5e Leipzig 04103 Germany
| | - Peter B. Reich
- Department of Forest Resources University of Minnesota St. Paul Minnesota 55108 USA
- Hawkesbury Institute for the Environment Western Sydney University Richmond New South Wales 2753 Australia
| | - Cameron Wagg
- Department of Evolutionary Biology and Environmental Studies University of Zürich Winterthurerstrasse 190 Zurich CH‐8047 Switzerland
| | - Marcel Ciobanu
- Institute of Biological Research Branch of the National Institute of Research and Development for Biological Sciences Cluj‐Napoca Romania
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Deutscher Platz 5e Leipzig 04103 Germany
- Institute of Biology Leipzig University Deutscher Platz 5e Leipzig 04103 Germany
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13
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Peters K, Worrich A, Weinhold A, Alka O, Balcke G, Birkemeyer C, Bruelheide H, Calf OW, Dietz S, Dührkop K, Gaquerel E, Heinig U, Kücklich M, Macel M, Müller C, Poeschl Y, Pohnert G, Ristok C, Rodríguez VM, Ruttkies C, Schuman M, Schweiger R, Shahaf N, Steinbeck C, Tortosa M, Treutler H, Ueberschaar N, Velasco P, Weiß BM, Widdig A, Neumann S, Dam NMV. Current Challenges in Plant Eco-Metabolomics. Int J Mol Sci 2018; 19:E1385. [PMID: 29734799 PMCID: PMC5983679 DOI: 10.3390/ijms19051385] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 12/22/2022] Open
Abstract
The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms. Traditionally, research in biochemistry and ecology comes from two different directions and is performed at distinct spatiotemporal scales. Biochemical studies most often focus on intrinsic processes in individuals at physiological and cellular scales. Generally, they take a bottom-up approach scaling up cellular processes from spatiotemporally fine to coarser scales. Ecological studies usually focus on extrinsic processes acting upon organisms at population and community scales and typically study top-down and bottom-up processes in combination. Eco-Metabolomics is a transdisciplinary research discipline that links biochemistry and ecology and connects the distinct spatiotemporal scales. In this review, we focus on approaches to study chemical and biochemical interactions of plants at various ecological levels, mainly plant⁻organismal interactions, and discuss related examples from other domains. We present recent developments and highlight advancements in Eco-Metabolomics over the last decade from various angles. We further address the five key challenges: (1) complex experimental designs and large variation of metabolite profiles; (2) feature extraction; (3) metabolite identification; (4) statistical analyses; and (5) bioinformatics software tools and workflows. The presented solutions to these challenges will advance connecting the distinct spatiotemporal scales and bridging biochemistry and ecology.
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Affiliation(s)
- Kristian Peters
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Anja Worrich
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany.
- UFZ-Helmholtz-Centre for Environmental Research, Department Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany.
| | - Alexander Weinhold
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany.
| | - Oliver Alka
- Applied Bioinformatics Group, Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany.
| | - Gerd Balcke
- Leibniz Institute of Plant Biochemistry, Cell and Metabolic Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Claudia Birkemeyer
- Institute of Analytical Chemistry, University of Leipzig, Linnéstr. 3, 04103 Leipzig, Germany.
| | - Helge Bruelheide
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle (Saale), Germany.
| | - Onno W Calf
- Molecular Interaction Ecology, Institute for Water and Wetland Research (IWWR), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Sophie Dietz
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Kai Dührkop
- Department of Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany.
| | - Emmanuel Gaquerel
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany.
| | - Uwe Heinig
- Weizmann Institute of Science, Faculty of Biochemistry, Department of Plant Sciences, 234 Herzl St., P.O. Box 26, Rehovot 7610001, Israel.
| | - Marlen Kücklich
- Institute of Biology, University of Leipzig, Talstraße 33, 04109 Leipzig, Germany.
| | - Mirka Macel
- Molecular Interaction Ecology, Institute for Water and Wetland Research (IWWR), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Caroline Müller
- Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Yvonne Poeschl
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Informatics, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle (Saale), Germany.
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany.
| | - Christian Ristok
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
| | - Victor Manuel Rodríguez
- Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain.
| | - Christoph Ruttkies
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Meredith Schuman
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany.
| | - Rabea Schweiger
- Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Nir Shahaf
- Weizmann Institute of Science, Faculty of Biochemistry, Department of Plant Sciences, 234 Herzl St., P.O. Box 26, Rehovot 7610001, Israel.
| | - Christoph Steinbeck
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany.
| | - Maria Tortosa
- Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain.
| | - Hendrik Treutler
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Nico Ueberschaar
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany.
| | - Pablo Velasco
- Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain.
| | - Brigitte M Weiß
- Institute of Biology, University of Leipzig, Talstraße 33, 04109 Leipzig, Germany.
| | - Anja Widdig
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biology, University of Leipzig, Talstraße 33, 04109 Leipzig, Germany.
- Research Group of Primate Kin Selection, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
| | - Nicole M van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany.
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14
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Geisen S, Snoek LB, ten Hooven FC, Duyts H, Kostenko O, Bloem J, Martens H, Quist CW, Helder JA, der Putten WH. Integrating quantitative morphological and qualitative molecular methods to analyse soil nematode community responses to plant range expansion. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.12999] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefan Geisen
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
- Laboratory of NematologyWageningen University Wageningen The Netherlands
| | - L. Basten Snoek
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
- Laboratory of NematologyWageningen University Wageningen The Netherlands
- Theoretical Biology and BioinformaticsUtrecht University Utrecht The Netherlands
| | - Freddy C. ten Hooven
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Henk Duyts
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Olga Kostenko
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Janneke Bloem
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Henk Martens
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Casper W. Quist
- Laboratory of NematologyWageningen University Wageningen The Netherlands
| | - Johannes A. Helder
- Laboratory of NematologyWageningen University Wageningen The Netherlands
| | - Wim H. der Putten
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
- Laboratory of NematologyWageningen University Wageningen The Netherlands
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15
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Abstract
There are great concerns about the impacts of soil biodiversity loss on ecosystem functions and services such as nutrient cycling, food production, and carbon storage. A diverse community of soil organisms that together comprise a complex food web mediates such ecosystem functions and services. Recent advances have shed light on the key drivers of soil food web structure, but a conceptual integration is lacking. Here, we explore how human-induced changes in plant community composition influence soil food webs. We present a framework describing the mechanistic underpinnings of how shifts in plant litter and root traits and microclimatic variables impact on the diversity, structure, and function of the soil food web. We then illustrate our framework by discussing how shifts in plant communities resulting from land-use change, climatic change, and species invasions affect soil food web structure and functioning. We argue that unravelling the mechanistic links between plant community trait composition and soil food webs is essential to understanding the cascading effects of anthropogenic shifts in plant communities on ecosystem functions and services.
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Affiliation(s)
- Paul Kardol
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jonathan R. De Long
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
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