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Lin C, Li WJ, Li LJ, Neilson R, An XL, Zhu YG. Movement of protistan trophic groups in soil-plant continuums. Environ Microbiol 2023; 25:2641-2652. [PMID: 37547979 DOI: 10.1111/1462-2920.16477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
Protists, functionally divided into consumers, phototrophs, and parasites act as integral components and vital regulators of microbiomes in soil-plant continuums. However, the drivers of community structure, assembly mechanisms, co-occurrence patterns, and the associations with human pathogens and different protistan trophic groups remain unknown. Here, we characterized the phyllosphere and soil protistan communities associated with three vegetables under different fertilization treatments (none and organic fertilization) at five growth stages. In this study, consumers were the most diverse soil protist group, had the role of inter-kingdom connector, and were the primary biomarker for rhizosphere soils which were subjected to decreasing deterministic processes during plant growth. In contrast, phototrophs had the greatest niche breadth and formed soil protistan hubs, and were the primary biomarkers for both bulk soils and the phyllosphere. Parasites had minimal input to microbial co-occurrence networks. Organic fertilization increased the relative abundance (RA) of pathogenic protists and the number of pathogen-consumer connections in rhizosphere soils but decreased protistan richness and the number of internal protistan links. This study advances our understanding of the ecological roles and potential links between human pathogens and protistan trophic groups associated with soil-plant continuums, which is fundamental to the regulation of soil-plant microbiomes and maintenance of environmental and human health.
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Affiliation(s)
- Chenshuo Lin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Jing Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li-Juan Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee, Scotland, UK
| | - Xin-Li An
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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2
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Leite MFA, Liu B, Gómez Cardozo E, Silva HRE, Luz RL, Muchavisoy KHM, Moraes FHR, Rousseau GX, Kowalchuk G, Gehring C, Kuramae EE. Microbiome resilience of Amazonian forests: Agroforest divergence to bacteria and secondary forest succession convergence to fungi. GLOBAL CHANGE BIOLOGY 2023; 29:1314-1327. [PMID: 36511762 PMCID: PMC10108277 DOI: 10.1111/gcb.16556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 05/26/2023]
Abstract
An alarming and increasing deforestation rate threatens Amazon tropical ecosystems and subsequent degradation due to frequent fires. Agroforestry systems (AFS) may offer a sustainable alternative, reportedly mimicking the plant-soil interactions of the natural mature forest (MF). However, the role of microbial community in tropical AFS remains largely unknown. This knowledge is crucial for evaluating the sustainability of AFS and practices given the key role of microbes in the aboveground-belowground interactions. The current study, by comparing different AFS and successions of secondary and MFs, showed that AFS fostered distinct groups of bacterial community, diverging from the MFs, likely a result of management practices while secondary forests converged to the same soil microbiome found in the MF, by favoring the same groups of fungi. Model simulations reveal that AFS would require profound changes in aboveground biomass and in soil factors to reach the same microbiome found in MFs. In summary, AFS practices did not result in ecosystems mimicking natural forest plant-soil interactions but rather reshaped the ecosystem to a completely different relation between aboveground biomass, soil abiotic properties, and the soil microbiome.
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Affiliation(s)
- Márcio Fernandes Alves Leite
- Department of Microbial EcologyNetherlands Institute of Ecology NIOO‐KNAWWageningenThe Netherlands
- Ecology and BiodiversityInstitute of Environmental Biology, Utrecht UniversityUtrechtThe Netherlands
| | - Binbin Liu
- Center for Agricultural Resources ResearchInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesShijiazhuangChina
| | | | | | | | | | | | | | - George Kowalchuk
- Ecology and BiodiversityInstitute of Environmental Biology, Utrecht UniversityUtrechtThe Netherlands
| | - Christoph Gehring
- Agroecology Program of Maranhão State University (UEMA)São LuísBrazil
| | - Eiko Eurya Kuramae
- Department of Microbial EcologyNetherlands Institute of Ecology NIOO‐KNAWWageningenThe Netherlands
- Ecology and BiodiversityInstitute of Environmental Biology, Utrecht UniversityUtrechtThe Netherlands
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3
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Carrasco-Espinosa K, Avitia M, Barrón-Sandoval A, Abbruzzini TF, Salazar Cabrera UI, Arroyo-Lambaer D, Uscanga A, Campo J, Benítez M, Wegier A, Rosell JA, Reverchon F, Hernández G, Boege K, Escalante AE. Land-Use Change and Management Intensification Is Associated with Shifts in Composition of Soil Microbial Communities and Their Functional Diversity in Coffee Agroecosystems. Microorganisms 2022; 10:microorganisms10091763. [PMID: 36144367 PMCID: PMC9504970 DOI: 10.3390/microorganisms10091763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Despite the central role of microorganisms in soil fertility, little understanding exists regarding the impact of management practices and soil microbial diversity on soil processes. Strong correlations among soil microbial composition, management practices, and microbially mediated processes have been previously shown. However, limited integration of the different parameters has hindered our understanding of agroecosystem functioning. Multivariate analyses of these systems allow simultaneous evaluation of the parameters and can lead to hypotheses on the microbial groups involved in specific nutrient transformations. In the present study, using a multivariate approach, we investigated the effect of microbial composition (16SrDNA sequencing) and soil properties in carbon mineralization (CMIN) (BIOLOG™, Hayward, CA, USA) across different management categories on coffee agroecosystems in Mexico. Results showed that (i) changes in soil physicochemical variables were related to management, not to region, (ii) microbial composition was associated with changes in management intensity, (iii) specific bacterial groups were associated with different management categories, and (iv) there was a broader utilization range of carbon sources in non-managed plots. The identification of specific bacterial groups, management practices, and soil parameters, and their correlation with the utilization range of carbon sources, presents the possibility to experimentally test hypotheses on the interplay of all these components and further our understanding of agroecosystem functioning and sustainable management.
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Affiliation(s)
- Karen Carrasco-Espinosa
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Morena Avitia
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Alberto Barrón-Sandoval
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - Thalita F. Abbruzzini
- Laboratorio de Biogeoquímica Terrestre y Clima, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Ulises Isaac Salazar Cabrera
- Laboratorio de Biogeoquímica Terrestre y Clima, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Denise Arroyo-Lambaer
- Laboratorio de Restauración Ecológica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Adriana Uscanga
- Laboratorio de Restauración Ecológica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Julio Campo
- Laboratorio de Biogeoquímica Terrestre y Clima, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Ana Wegier
- Laboratorio de Genética de la Conservación, Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Julieta A. Rosell
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Frédérique Reverchon
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Pátzcuaro 91070, Mexico
| | - Gerardo Hernández
- Centro Agroecológico del Café A.C. Clúster Biomimic-Inecol, Xalapa Enríquez Centro, Veracruz 91000, Mexico
| | - Karina Boege
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Ana E. Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Correspondence:
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4
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Lu M, Schneider D, Daniel R. Metagenomic Screening for Lipolytic Genes Reveals an Ecology-Clustered Distribution Pattern. Front Microbiol 2022; 13:851969. [PMID: 35756004 PMCID: PMC9226776 DOI: 10.3389/fmicb.2022.851969] [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: 01/10/2022] [Accepted: 04/28/2022] [Indexed: 12/02/2022] Open
Abstract
Lipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Chloroflexi. Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integrated classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.
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Affiliation(s)
| | | | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg August University of Göttingen, Göttingen, Germany
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5
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Land use effects on tree species diversity and soil properties of the Awudua Forest, Ghana. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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6
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Xue Y, Jin T, Gao C, Li C, Zhou T, Wan D, Yang M. Effects of biodegradable film mulching on bacterial diversity in soils. Arch Microbiol 2022; 204:195. [PMID: 35217920 DOI: 10.1007/s00203-022-02799-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 11/30/2022]
Abstract
The spread of biodegradable plastic films (BDFs) not only increases grain yield but also reduces environmental pollution from plastic film to a large extent. Soil microbes are considered to be involved in biodegradation processes. However, the study of microbe diversity in soil mulched with biodegradable plastic film remains limited. Here, we compared the diversity of microbes between soils with biodegradable film and nonbiodegradable film (NBDF) mulch. The results showed that BDFs affected total C, P and NH4+-N, especially organism C content, as well as microbe species richness (ACE; Chao1) and diversity (Simpson index; Shannon index). In terms of dominant phyla and genera, BDFs and NBDF can influence the abundance of disparate species. Furthermore, BDFs could also contribute to improving the richness of the important functional bacterial groups in soil, e.g., Pedomicrobium and Comamonas, both of which are involved in the degradation of plastic residues in soil. Finally, we found that BDFs improved the transformation of nitrogen by significantly increasing the abundances of Nitrobacter and Nitrospira. Our results highlight the impact of BDF mulch on the abundance of functional bacteria in the soil.
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Affiliation(s)
- Yinghao Xue
- College of Land and Environment, Shenyang Agricultural University, Shenyang, 110866, China.,Rural Energy and Environment Agency, Ministry of Agriculture and Rural Affairs, Beijing, 100125, China
| | - Tuo Jin
- Rural Energy and Environment Agency, Ministry of Agriculture and Rural Affairs, Beijing, 100125, China
| | - Chengyu Gao
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Chongxiao Li
- Agricultural Ecology and Resource Protection Technology Extension Station of Gansu Province, Lanzhou, 730000, Gansu, People's Republic of China
| | - Tao Zhou
- Agricultural Ecology and Resource Protection Technology Extension Station of Gansu Province, Lanzhou, 730000, Gansu, People's Republic of China
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China.
| | - Mengran Yang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China.
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7
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Singh AK, Liu W, Zakari S, Wu J, Yang B, Jiang XJ, Zhu X, Zou X, Zhang W, Chen C, Singh R, Nath AJ. A global review of rubber plantations: Impacts on ecosystem functions, mitigations, future directions, and policies for sustainable cultivation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 796:148948. [PMID: 34273842 DOI: 10.1016/j.scitotenv.2021.148948] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/06/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The growing global need for latex is driving rubber plantation (RP) expansion since the last century, with >2 Mha of cultivation area being established in the last decade. Southeast Asia is the hotspot for rubber cultivation at other land-use costs. Although rubber cultivation has improved the economic status of farmers, it has altered the habitat's ecology and ecosystem functions (EF). However, studies on the impacts of RP on EF are limited, and a clear overview is not available. To bridge this gap, we conducted an inclusive review of the EF of RP, including soil carbon storage, aboveground biomass (AGB) and belowground biomass (BGB), litter production and decomposition, respiration, and biodiversity (plants, animals, soil fauna, and microbes). We compared the EF in RP (monoculture) with those in forests because the conversion of forests to RP is prevalent in the tropics and because most RP studies used forests as reference ecosystems. We found RP generally have lower EF than forests. The impacts of RP on some EF are more severe (e.g., AGB, BGB, and plant diversity), causing decreases of >55%, and the effects are consistently negative irrespective of plantation age. However, including agroforestry or polyculture, integrated pest management, cover cropping, mulching, and composting can improve the EF in RP to some extent. We highlighted research gaps, particularly substantial research gaps concerning the influence of plant diversity treatments (i.e., agroforestry) performed in RP on EF. Additionally, more empirical data on the significance of spatial and temporal levels are required, such as how the impact on EF could vary with climate and RP age, as we showed some examples where EF differs spatially and temporally. More importantly, further research on plantation management to offset EF losses is needed. Finally, we emphasized knowledge gaps and suggested future directions and policies for improving EF in RP.
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Affiliation(s)
- Ashutosh Kumar Singh
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
| | - Wenjie Liu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
| | - Sissou Zakari
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Laboratory of Hydraulics and Environmental Modeling (HydroModE-Lab), Faculté d'Agronomie, Université de Parakou, 03 BP 351 Parakou, Benin
| | - Junen Wu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Bin Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Xiao Jin Jiang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Xiai Zhu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
| | - Xin Zou
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Wanjun Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Chunfeng Chen
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Rishikesh Singh
- Integrative Ecology Laboratory (IEL), Institute of Environment & Sustainable Development (IESD), Banaras Hindu University, Varanasi 221005, India
| | - Arun Jyoti Nath
- Department of Ecology and Environmental Science, Assam University, Silchar 788011, India
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8
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Sawada K, Watanabe S, Nguyen HL, Sugihara S, Seki M, Kobayashi H, Toyota K, Funakawa S. Comparison of the Structure and Diversity of Root-Associated and Soil Microbial Communities Between Acacia Plantations and Native Tropical Mountain Forests. Front Microbiol 2021; 12:735121. [PMID: 34659163 PMCID: PMC8511777 DOI: 10.3389/fmicb.2021.735121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/18/2021] [Indexed: 12/03/2022] Open
Abstract
Deforestation of native tropical forests has occurred extensively over several decades. The plantation of fast-growing trees, such as Acacia spp., is expanding rapidly in tropical regions, which can contribute to conserve the remaining native tropical forests. To better understand belowground biogeochemical cycles and the sustainable productivity of acacia plantations, we assessed the effects of vegetation (acacia plantations vs. native forests) and soil types (Oxisols vs. Ultisols) on soil properties, including the diversity and community structures of bacteria- and fungi-colonizing surface and subsurface roots and soil in the Central Highlands of Vietnam. The results in surface soil showed that pH was significantly higher in acacia than in native for Oxisols but not for Ultisols, while exchangeable Al was significantly lower in acacia than in native for Ultisols but not for Oxisols. Bacterial alpha diversity (especially within phylum Chloroflexi) was higher in acacia than in native only for Oxisols but not for Ultisols, which was the same statistical result as soil pH but not exchangeable Al. These results suggest that soil pH, but not exchangeable Al, can be the critical factor to determine bacterial diversity. Acacia tree roots supported greater proportions of copiotrophic bacteria, which may support lower contents of soil inorganic N, compared with native tree roots for both Oxisols and Ultisols. Acacia tree roots also supported greater proportions of plant pathogenic Mycoleptodiscus sp. but appeared to reduce the abundances and diversity of beneficial ECM fungi compared with native tree roots regardless of soil types. Such changes in fungal community structures may threaten the sustainable productivity of acacia plantations in the future.
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Affiliation(s)
- Kozue Sawada
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
| | - Shinichi Watanabe
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
| | - Ho Lam Nguyen
- University of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Soh Sugihara
- Institute of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Mayuko Seki
- Institute of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Hana Kobayashi
- Institute of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Koki Toyota
- Institute of Symbiotic Science and Technology, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Shinya Funakawa
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
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9
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Eskov AK, Zverev AO, Abakumov EV. Microbiomes in Suspended Soils of Vascular Epiphytes Differ from Terrestrial Soil Microbiomes and from Each Other. Microorganisms 2021; 9:microorganisms9051033. [PMID: 34064848 PMCID: PMC8150705 DOI: 10.3390/microorganisms9051033] [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: 03/28/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 01/04/2023] Open
Abstract
Microbial biodiversity parameters for tropical rainforests remain poorly understood. Whilst the soil microbiome accounts up to 95% of the total diversity of microorganisms in terrestrial ecosystems, the microbiome of suspended soils formed by vascular epiphytes remains completely unexplored. Samples of ground and suspended soils were collected in Cat Tien National Park, southern Vietnam. DNA extraction and sequencing were performed, and libraries of 16s rDNA gene sequences were analyzed. Alpha diversity indices of the microorganisms were the highest in the forest ground soil. In general, the microbiological diversity of all the soil types was found to be similar at the phylum level. Taxonomic composition of the bacterial communities in the suspended soils of plants from the same species are not closer than the taxonomic compositions of the communities in the suspended soils of different plant species. However, the beta diversity analysis revealed significant differences in the movement of mineral elements in terrestrial versus suspended soils. Our data showed that the suspended soils associated with vascular epiphytes were a depository of unique microbiological biodiversity. A contributing factor was the presence of large amounts of organic matter in the suspended soils-deposits collected by the epiphytes-which would have been degraded by termites if it had reached the ground. Further, the nutrient content of the suspended soils was prime for soil respiration activity and taxonomic microbial community biodiversity.
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Affiliation(s)
- Alen K. Eskov
- Faculty of Biology, Lomonosov Moscow State University, 1–12 Leninskie Gory, 119991 Moscow, Russia
- Tzitzin Main Botanical Garden, Russian Academy of Sciences, 4 Botanicheskaya ul., 117628 Moscow, Russia
- Correspondence:
| | - Alexei O. Zverev
- Faculty of Biology, Saint-Petersburg State University, 7/9 Universitetskaya nab., 199034 St. Petersburg, Russia; (A.O.Z.); (E.V.A.)
- All-Russian Research Institute for Agricultural Microbiology, 3 Podbelsky chausse, 196608 St. Petersburg, Russia
| | - Evgeny V. Abakumov
- Faculty of Biology, Saint-Petersburg State University, 7/9 Universitetskaya nab., 199034 St. Petersburg, Russia; (A.O.Z.); (E.V.A.)
- All-Russian Research Institute for Agricultural Microbiology, 3 Podbelsky chausse, 196608 St. Petersburg, Russia
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10
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Berkelmann D, Schneider D, Hennings N, Meryandini A, Daniel R. Soil bacterial community structures in relation to different oil palm management practices. Sci Data 2020; 7:421. [PMID: 33257691 PMCID: PMC7705008 DOI: 10.1038/s41597-020-00752-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/29/2020] [Indexed: 11/26/2022] Open
Abstract
We provide soil bacterial 16 S rRNA gene amplicon and geochemical data derived from an oil palm plantation management experiment. The experimental design covered two different intensities of fertilizer application and weeding practices. We sampled the topsoil of 80 plots in total and extracted DNA and RNA. 16 S rRNA gene-derived and transcript-derived amplicons were generated and sequenced to analyse community composition and beta-diversity. One year after establishing the experiment, statistically significant differences of bacterial diversity or community composition between different treatments at entire (DNA-derived) and active (RNA-derived) community level were not detected. The dominant taxa belonged to Acidobacteriota and Actinobacteriota and were more abundant in the active community compared to the entire community. Similarly, the abundant genera Candidatus Solibacter and Haliangium were more abundant at active community level. Furthermore, clustering corresponding to the different sampling site locations was detected. Beta-diversity did not change among the treatments at DNA and RNA level. This dataset is of interest for related studies on the effect of altered management practices on soilborne communities.
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Affiliation(s)
- Dirk Berkelmann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Nina Hennings
- Department of Soil Science of Temperate Ecosystems, Buesgen Institute, University of Göttingen, Göttingen, Germany
| | - Anja Meryandini
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University, Bogor, Indonesia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany.
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11
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Lai D, Hedlund BP, Xie W, Liu J, Phelps TJ, Zhang C, Wang P. Impact of Terrestrial Input on Deep-Sea Benthic Archaeal Community Structure in South China Sea Sediments. Front Microbiol 2020; 11:572017. [PMID: 33224115 PMCID: PMC7674655 DOI: 10.3389/fmicb.2020.572017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022] Open
Abstract
Archaea are widespread in marine sediments and play important roles in the cycling of sedimentary organic carbon. However, factors controlling the distribution of archaea in marine sediments are not well understood. Here we investigated benthic archaeal communities over glacial-interglacial cycles in the northern South China Sea and evaluated their responses to sediment organic matter sources and inter-species interactions. Archaea in sediments deposited during the interglacial period Marine Isotope Stage (MIS) 1 (Holocene) were significantly different from those in sediments deposited in MIS 2 and MIS 3 of the Last Glacial Period when terrestrial input to the South China Sea was enhanced based on analysis of the long-chain n-alkane C31. The absolute archaeal 16S rRNA gene abundance in subsurface sediments was highest in MIS 2, coincident with high sedimentation rates and high concentrations of total organic carbon. Soil Crenarchaeotic Group (SCG; Nitrososphaerales) species, the most abundant ammonia-oxidizing archaea in soils, increased dramatically during MIS 2, likely reflecting transport of terrestrial archaea during glacial periods with high sedimentation rates. Co-occurrence network analyses indicated significant association of SCG archaea with benthic deep-sea microbes such as Bathyarchaeota and Thermoprofundales in MIS 2 and MIS 3, suggesting potential interactions among these archaeal groups. Meanwhile, Thermoprofundales abundance was positively correlated with total organic carbon (TOC), along with n-alkane C31 and sedimentation rate, indicating that Thermoprofundales may be particularly important in processing of organic carbon in deep-sea sediments. Collectively, these results demonstrate that the composition of heterotrophic benthic archaea in the South China Sea may be influenced by terrestrial organic input in tune with glacial-interglacial cycles, suggesting a plausible link between global climate change and microbial population dynamics in deep-sea marine sediments.
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Affiliation(s)
- Dengxun Lai
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China.,School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Jingjing Liu
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Tommy J Phelps
- Earth and Planetary Sciences, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Shanghai Sheshan National Geophysical Observatory, Shanghai, China
| | - Peng Wang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
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12
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Yang Z, Sun H, Zhou Q, Zhao L, Wu W. Nitrogen removal performance in pilot-scale solid-phase denitrification systems using novel biodegradable blends for treatment of waste water treatment plants effluent. BIORESOURCE TECHNOLOGY 2020; 305:122994. [PMID: 32105842 DOI: 10.1016/j.biortech.2020.122994] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/07/2020] [Accepted: 02/08/2020] [Indexed: 06/10/2023]
Abstract
In this study, three pilot-scale solid-phase denitrification (SPD) systems filled with poly-3-hydroxybutyrate-co-hyroxyvelate (PHBV), PHBV-Rice hulls (PHBV-RH) and PHBV-Sawdust (PHBV-S) were operated to treat effluent of waste water treatment pangts (WWTPs). The fast start-up and intensified nitrogen removal performance were obtained in PHBV-RH and PHBV-S systems. Besides, the optimal total nitrogen (TN) removal efficiency was obtained in PHBV-S system (91.65 ± 4.12%) with less ammonia accumulation and dissolved organic carbon (DOC) release. The significant enrichment of amx 16S rRNA and nirS genes in PHBV-RH and PHBV-S systems indicated the possible coexistence of anammox and denitrification. Miseq sequencing analysis exhibited more complex community diversity, more abundant denitrifying and fermenting bacteria in PHBV-RH and PHBV-S systems. The co-existence of denitrification and anammox might contribute to better control of nitrogen and dissolved organic carbon in PHBV-S system. The outcomes provide an economical and eco-friendly alternative to improve nitrogen removal of WWTPs effluent.
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Affiliation(s)
- Zhongchen Yang
- Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, PR China
| | - Haimeng Sun
- Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, PR China
| | - Qi Zhou
- Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, PR China
| | - Liu Zhao
- Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, PR China
| | - Weizhong Wu
- Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, PR China.
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13
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Grass I, Kubitza C, Krishna VV, Corre MD, Mußhoff O, Pütz P, Drescher J, Rembold K, Ariyanti ES, Barnes AD, Brinkmann N, Brose U, Brümmer B, Buchori D, Daniel R, Darras KFA, Faust H, Fehrmann L, Hein J, Hennings N, Hidayat P, Hölscher D, Jochum M, Knohl A, Kotowska MM, Krashevska V, Kreft H, Leuschner C, Lobite NJS, Panjaitan R, Polle A, Potapov AM, Purnama E, Qaim M, Röll A, Scheu S, Schneider D, Tjoa A, Tscharntke T, Veldkamp E, Wollni M. Trade-offs between multifunctionality and profit in tropical smallholder landscapes. Nat Commun 2020; 11:1186. [PMID: 32132531 PMCID: PMC7055322 DOI: 10.1038/s41467-020-15013-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 02/11/2020] [Indexed: 11/23/2022] Open
Abstract
Land-use transitions can enhance the livelihoods of smallholder farmers but potential economic-ecological trade-offs remain poorly understood. Here, we present an interdisciplinary study of the environmental, social and economic consequences of land-use transitions in a tropical smallholder landscape on Sumatra, Indonesia. We find widespread biodiversity-profit trade-offs resulting from land-use transitions from forest and agroforestry systems to rubber and oil palm monocultures, for 26,894 aboveground and belowground species and whole-ecosystem multidiversity. Despite variation between ecosystem functions, profit gains come at the expense of ecosystem multifunctionality, indicating far-reaching ecosystem deterioration. We identify landscape compositions that can mitigate trade-offs under optimal land-use allocation but also show that intensive monocultures always lead to higher profits. These findings suggest that, to reduce losses in biodiversity and ecosystem functioning, changes in economic incentive structures through well-designed policies are urgently needed. Identifying economic and ecological trade-offs of land-use transitions is important to ensure sustainability. Here, Grass et al. find biodiversity-profit trade-offs in tropical land-use transitions in Sumatra, and show that targeted landscape planning is needed to increase land-use efficiency while ensuring socio-ecological sustainability.
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Affiliation(s)
- Ingo Grass
- Ecology of Tropical Agricultural Systems, University of Hohenheim, Garbenstrasse 13, 70599, Stuttgart, Germany. .,Agroecology, University of Göttingen, Grisebachstrasse 6, 37077, Göttingen, Germany.
| | - Christoph Kubitza
- Department of Agricultural Economics and Rural Development, University of Göttingen, Platz der Göttinger Sieben 5, 37073, Göttingen, Germany.,German Institute of Global and Area Studies (GIGA), Neuer Jungfernstieg 21, 20354, Hamburg, Germany
| | - Vijesh V Krishna
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Mexico
| | - Marife D Corre
- Soil Science of Tropical and Subtropical Ecosystems, University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany.,Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Oliver Mußhoff
- Department of Agricultural Economics and Rural Development, University of Göttingen, Platz der Göttinger Sieben 5, 37073, Göttingen, Germany.,Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Peter Pütz
- Chair of Statistics, Faculty of Economic Sciences, University of Göttingen, Humboldtallee 3, 37073, Göttingen, Germany
| | - Jochen Drescher
- Department of Animal Ecology, J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany
| | - Katja Rembold
- Biodiversity, Macroecology & Biogeography, University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany.,Botanical Garden of the University of Bern, Altenbergrain 21, 3013, Bern, Switzerland
| | - Eka Sulpin Ariyanti
- Magister of Environmental of Science, University of Lampung, Lampung, 35145, Indonesia
| | - Andrew D Barnes
- School of Science, University of Waikato, Private Bag 3105, Hamilton, 3240, New Zealand
| | - Nicole Brinkmann
- Forest Botany and Tree Physiology, University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Ulrich Brose
- EcoNetLab, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.,EcoNetLab, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743, Jena, Germany
| | - Bernhard Brümmer
- Department of Agricultural Economics and Rural Development, University of Göttingen, Platz der Göttinger Sieben 5, 37073, Göttingen, Germany.,Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Damayanti Buchori
- Center for Transdisciplinary and Sustainability Sciences, IPB University, Bogor Agricultural University, Jalan Pajajaran, Bogor, 16128, Indonesia
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Kevin F A Darras
- Agroecology, University of Göttingen, Grisebachstrasse 6, 37077, Göttingen, Germany
| | - Heiko Faust
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany.,Human Geography, University of Göttingen, Goldschmidtstr. 5, Göttingen, Germany
| | - Lutz Fehrmann
- Forest Inventory and Remote Sensing, University of Göttingen, Büsgenweg 5, 37077, Göttingen, Germany
| | - Jonas Hein
- Institute of Geography, Kiel University, Ludewig-Meyn-Str. 14, 24118, Kiel, Germany
| | - Nina Hennings
- Soil Science of Temperate Ecosystems, University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Purnama Hidayat
- Department of Plant Protection, Faculty of Agriculture, Bogor Agriculture University, Jln. Kamper, Kampus IPB Dramaga, Bogor, 16880, Indonesia
| | - Dirk Hölscher
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany.,Tropical Silviculture and Forest Ecology, University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Malte Jochum
- Department of Animal Ecology, J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany.,Experimental Interaction Ecology, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.,Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Alexander Knohl
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany.,Bioclimatology, University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Martyna M Kotowska
- Plant Ecology and Ecosystems Research, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany
| | - Valentyna Krashevska
- Department of Animal Ecology, J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany
| | - Holger Kreft
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany.,Biodiversity, Macroecology & Biogeography, University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Christoph Leuschner
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany.,Plant Ecology and Ecosystems Research, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany
| | - Neil Jun S Lobite
- Animal Biology Division, Institute of Biological Science, University of the Philippines, Los Baños, 4031, Philippines
| | - Rawati Panjaitan
- Department of Plant Protection, Faculty of Agriculture, Bogor Agriculture University, Jln. Kamper, Kampus IPB Dramaga, Bogor, 16880, Indonesia
| | - Andrea Polle
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany.,Forest Botany and Tree Physiology, University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Anton M Potapov
- Department of Animal Ecology, J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany.,A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky Prospect 33, 119071, Moscow, Russia
| | - Edwine Purnama
- Forest Inventory and Remote Sensing, University of Göttingen, Büsgenweg 5, 37077, Göttingen, Germany
| | - Matin Qaim
- Department of Agricultural Economics and Rural Development, University of Göttingen, Platz der Göttinger Sieben 5, 37073, Göttingen, Germany.,Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Alexander Röll
- Tropical Silviculture and Forest Ecology, University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Stefan Scheu
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany.,Department of Animal Ecology, J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany
| | - Dominik Schneider
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Aiyen Tjoa
- Agriculture Faculty, Tadulako University, Jl. Soekarno Hatta km.09, Tondo, Palu, Indonesia
| | - Teja Tscharntke
- Agroecology, University of Göttingen, Grisebachstrasse 6, 37077, Göttingen, Germany.,Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Edzo Veldkamp
- Soil Science of Tropical and Subtropical Ecosystems, University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany.,Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Meike Wollni
- Department of Agricultural Economics and Rural Development, University of Göttingen, Platz der Göttinger Sieben 5, 37073, Göttingen, Germany.,Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
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14
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Edy N, Yelianti U, Irawan B, Polle A, Pena R. Differences in Root Nitrogen Uptake Between Tropical Lowland Rainforests and Oil Palm Plantations. FRONTIERS IN PLANT SCIENCE 2020; 11:92. [PMID: 32161607 PMCID: PMC7053111 DOI: 10.3389/fpls.2020.00092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 01/21/2020] [Indexed: 06/01/2023]
Abstract
Conversion of lowland tropical rainforests to intensely fertilized agricultural land-use systems such as oil palm (Elaeis guineensis) plantations leads to changes in nitrogen (N) cycling. Although soil microbial-driven N dynamics has been largely studied, the role of the plant as a major component in N uptake has rarely been considered. We address this gap by comparing the root N contents and uptake in lowland rainforests with that in oil palm plantations on Sumatra, Indonesia. To this aim, we applied 15N-labeled ammonium to intact soil, measured the 15N recovery in soil and roots, and calculated the root relative N uptake efficiency for 10 days after label application. We found that root N contents were by one third higher in the rainforest than oil palm plantations. However, 15N uptake efficiency was similar in the two systems. This finding suggests that lower N contents in oil palm roots were likely caused by plant internal utilization of the absorbed N (e.g., N export to fruit bunches) than by lower ability to take up N from the soil. 15N recovery in roots was primarily driven by the amount of root biomass, which was higher in oil palm plantation than rainforest. The oil palms unveiled a high capacity to acquire N, offering the possibility of enhancing sustainable plantation management by reducing N fertilizer application.
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Affiliation(s)
- Nur Edy
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
- Department of Agrotechnology, Tadulako University, Palu, Indonesia
| | - Upik Yelianti
- Department of Biology, University of Jambi, Jambi, Indonesia
| | - Bambang Irawan
- Department of Forestry, University of Jambi, Jambi, Indonesia
| | - Andrea Polle
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
| | - Rodica Pena
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
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15
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Potapov AM, Dupérré N, Jochum M, Dreczko K, Klarner B, Barnes AD, Krashevska V, Rembold K, Kreft H, Brose U, Widyastuti R, Harms D, Scheu S. Functional losses in ground spider communities due to habitat structure degradation under tropical land-use change. Ecology 2020; 101:e02957. [PMID: 31840252 DOI: 10.1002/ecy.2957] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 08/31/2019] [Accepted: 11/11/2019] [Indexed: 11/10/2022]
Abstract
Deforestation and land-use change in tropical regions result in habitat loss and extinction of species that are unable to adapt to the conditions in agricultural landscapes. If the associated loss of functional diversity is not compensated by species colonizing the converted habitats, extinctions might be followed by a reduction or loss of ecosystem functions including biological control. To date, little is known about how land-use change in the tropics alters the functional diversity of invertebrate predators and which key environmental factors may mitigate the decline in functional diversity and predation in litter and soil communities. We applied litter sieving and heat extraction to study ground spider communities and assessed structural characteristics of vegetation and parameters of litter in rainforest and agricultural land-use systems (jungle rubber, rubber, and oil palm monocultures) in a Southeast Asian hotspot of rainforest conversion: Sumatra, Indonesia. We found that (1) spider density, species richness, functional diversity, and community predation (energy flux to spiders) were reduced by 57-98% from rainforest to oil palm monoculture; (2) jungle rubber and rubber monoculture sustained relatively high diversity and predation in ground spiders, but small cryptic spider species strongly declined; (3) high species turnover compensated losses of some functional trait combinations, but did not compensate for the overall loss of functional diversity and predation per unit area; (4) spider diversity was related to habitat structure such as amount of litter, understory density, and understory height, while spider predation was better explained by plant diversity. Management practices that increase habitat-structural complexity and plant diversity such as mulching, reduced weeding, and intercropping monocultures with other plants may contribute to maintaining functional diversity of and predation services provided by ground invertebrate communities in plantations.
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Affiliation(s)
- Anton M Potapov
- J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany.,A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky Prospect 33, 119071, Moscow, Russia
| | - Nadine Dupérré
- Center of Natural History, Zoological Museum, Universität Hamburg, Bundesstraße 52, 20146, Hamburg, Germany
| | - Malte Jochum
- Institute of Plant Sciences, University of Bern, Hochschulstrasse 6, 3012, Bern, Switzerland.,German Centre for Integrative Biodiversity Research (iDiv), Deutscher Pl. 5E, 04103, Leipzig, Germany.,Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Kerstin Dreczko
- Center of Natural History, Zoological Museum, Universität Hamburg, Bundesstraße 52, 20146, Hamburg, Germany
| | - Bernhard Klarner
- J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany
| | - Andrew D Barnes
- German Centre for Integrative Biodiversity Research (iDiv), Deutscher Pl. 5E, 04103, Leipzig, Germany.,School of Science, the University of Waikato, Private Bag 3105, 3240, Hamilton, New Zealand
| | - Valentyna Krashevska
- J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany
| | - Katja Rembold
- Botanical Garden of the University of Bern, Altenbergrain 21, 3013, Bern, Switzerland.,Biodiversity, Macroecology & Biogeography, University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Holger Kreft
- Biodiversity, Macroecology & Biogeography, University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany.,Centre of Biodiversity and Sustainable Land Use, Von-Siebold-Strasse 8, 37075, Göttingen, Germany
| | - Ulrich Brose
- German Centre for Integrative Biodiversity Research (iDiv), Deutscher Pl. 5E, 04103, Leipzig, Germany.,Institute of Biodiversity, Friedrich Schiller University, Dornburger Strasse 159, 07743, Jena, Germany
| | - Rahayu Widyastuti
- Department of Soil Sciences and Land Resources, Institut Pertanian Bogor (IPB), Jln. Meranti Kampus IPB Darmaga, 16680, Bogor, Indonesia
| | - Danilo Harms
- Center of Natural History, Zoological Museum, Universität Hamburg, Bundesstraße 52, 20146, Hamburg, Germany
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany.,Centre of Biodiversity and Sustainable Land Use, Von-Siebold-Strasse 8, 37075, Göttingen, Germany
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16
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Berkelmann D, Schneider D, Meryandini A, Daniel R. Unravelling the effects of tropical land use conversion on the soil microbiome. ENVIRONMENTAL MICROBIOME 2020; 15:5. [PMID: 33902736 PMCID: PMC8067294 DOI: 10.1186/s40793-020-0353-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/18/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND The consequences of deforestation and agricultural treatments are complex and affect all trophic levels. Changes of microbial community structure and composition associated with rainforest conversion to managed systems such as rubber and oil palm plantations have been shown by 16S rRNA gene analysis previously, but functional profile shifts have been rarely addressed. In this study, we analysed the effects of rainforest conversion to different converted land use systems, including agroforestry ("jungle rubber") and monoculture plantations comprising rubber and oil palm, on soilborne microbial communities by metagenomic shotgun sequencing in Sumatra, Indonesia. RESULTS The diversity of bacteria and archaea decreased whereas diversity of fungi increased in the converted land use systems. The soil microbiome was dominated by bacteria followed by fungi. We detected negative effects of land use conversion on the abundance of Proteobacteria (especially on Rhizobiales and Burkholderiales) and positive effects on the abundance of Acidobacteria and Actinobacteria. These abundance changes were mainly driven by pH, C:N ratio, and Fe, C and N content. With increasing land use intensity, the functional diversity decreased for bacteria, archaea and fungi. Gene abundances of specific metabolisms such as nitrogen metabolism and carbon fixation were affected by land use management practices. The abundance of genes related to denitrification and nitrogen fixation increased in plantations while abundance of genes involved in nitrification and methane oxidation showed no significant difference. Linking taxonomic and functional assignment per read indicated that nitrogen metabolism-related genes were mostly assigned to members of the Rhizobiales and Burkholderiales. Abundances of carbon fixation genes increased also with increasing land use intensity. Motility- and interaction-related genes, especially genes involved in flagellar assembly and chemotaxis genes, decreased towards managed land use systems. This indicated a shift in mobility and interspecific interactions in bacterial communities within these soils. CONCLUSIONS Rainforest conversion to managed land use systems drastically affects structure and functional potential of soil microbial communities. The decrease in motility- and interaction-related functions from rainforest to converted land use systems indicated not only a shift in nutrient cycling but also in community dynamics. Fertilizer application and correspondingly higher availability of nutrients in intensively managed plantations lead to an environment in which interspecific interactions are not favoured compared to rainforest soils. We could directly link effects of land management, microbial community structure and functional potential for several metabolic processes. As our study is the first study of this size and detail on soil microbial communities in tropical systems, we provide a basis for further analyses.
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Affiliation(s)
- Dirk Berkelmann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Anja Meryandini
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University, Bogor, Indonesia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Grisebachstr. 8, 37077, Göttingen, Germany.
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17
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Krashevska V, Kudrin AA, Widyastuti R, Scheu S. Changes in Nematode Communities and Functional Diversity With the Conversion of Rainforest Into Rubber and Oil Palm Plantations. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00487] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Petersen IAB, Meyer KM, Bohannan BJM. Meta-Analysis Reveals Consistent Bacterial Responses to Land Use Change Across the Tropics. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00391] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Chernov TI, Zhelezova AD, Tkhakakhova AK, Bgazhba NA, Zverev AO. Microbiomes of Virgin Soils of Southern Vietnam Tropical Forests. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719040040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Susanti WI, Pollierer MM, Widyastuti R, Scheu S, Potapov A. Conversion of rainforest to oil palm and rubber plantations alters energy channels in soil food webs. Ecol Evol 2019; 9:9027-9039. [PMID: 31463001 PMCID: PMC6706186 DOI: 10.1002/ece3.5449] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 01/31/2023] Open
Abstract
In the last decades, lowland tropical rainforest has been converted in large into plantation systems. Despite the evident changes above ground, the effect of rainforest conversion on the channeling of energy in soil food webs was not studied. Here, we investigated community-level neutral lipid fatty acid profiles in dominant soil fauna to track energy channels in rainforest, rubber, and oil palm plantations in Sumatra, Indonesia. Abundant macrofauna including Araneae, Chilopoda, and Diplopoda contained high amounts of plant and fungal biomarker fatty acids (FAs). Lumbricina had the lowest amount of plant, but the highest amount of animal-synthesized C20 polyunsaturated FAs as compared to other soil taxa. Mesofauna detritivores (Collembola and Oribatida) contained high amounts of algal biomarker FAs. The differences in FA profiles between taxa were evident if data were analyzed across land-use systems, suggesting that soil fauna of different size (macro- and mesofauna) are associated with different energy channels. Despite that, rainforest conversion changed the biomarker FA composition of soil fauna at the community level. Conversion of rainforest into oil palm plantations enhanced the plant energy channel in soil food webs and reduced the bacterial energy channel; conversion into rubber plantations reduced the AMF-based energy channel. The changes in energy distribution within soil food webs may have significant implications for the functioning of tropical ecosystems and their response to environmental changes. At present, these responses are hard to predict considering the poor knowledge on structure and functioning of tropical soil food webs.
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Affiliation(s)
- Winda Ika Susanti
- J.F. Blumenbach Institute of Zoology and AnthropologyUniversity of GöttingenGoettingenGermany
- Department of Soil Sciences and Land ResourcesInstitut Pertanian Bogor (IPB)BogorIndonesia
| | - Melanie M. Pollierer
- J.F. Blumenbach Institute of Zoology and AnthropologyUniversity of GöttingenGoettingenGermany
| | - Rahayu Widyastuti
- Department of Soil Sciences and Land ResourcesInstitut Pertanian Bogor (IPB)BogorIndonesia
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and AnthropologyUniversity of GöttingenGoettingenGermany
- Centre of Biodiversity and Sustainable Land UseGöttingenGermany
| | - Anton Potapov
- J.F. Blumenbach Institute of Zoology and AnthropologyUniversity of GöttingenGoettingenGermany
- A.N. Severtsov Institute of Ecology and EvolutionRussian Academy of SciencesMoscowRussia
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Dukunde A, Schneider D, Schmidt M, Veldkamp E, Daniel R. Tree Species Shape Soil Bacterial Community Structure and Function in Temperate Deciduous Forests. Front Microbiol 2019; 10:1519. [PMID: 31338079 PMCID: PMC6629791 DOI: 10.3389/fmicb.2019.01519] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 06/18/2019] [Indexed: 01/23/2023] Open
Abstract
Amplicon-based analysis of 16S rRNA genes and transcripts was used to assess the effect of tree species composition on soil bacterial community structure and function in a temperate deciduous forest. Samples were collected from mono and mixed stands of Fagus sylvatica (beech), Carpinus betulus (hornbeam), Tilia sp. (lime), and Quercus sp. (oak) in spring, summer, and autumn. Soil bacterial community exhibited similar taxonomic composition at total (DNA-based) and potentially active community (RNA-based) level, with fewer taxa present at active community level. Members of Rhizobiales dominated at both total and active bacterial community level, followed by members of Acidobacteriales, Solibacterales, Rhodospirillales, and Xanthomonadales. Bacterial communities at total and active community level showed a significant positive correlation with tree species identity (mono stands) and to a lesser extent with tree species richness (mixed stands). Approximately 58 and 64% of indicator operational taxonomic units (OTUs) showed significant association with only one mono stand at total and active community level, respectively, indicating a strong impact of tree species on soil bacterial community composition. Soil C/N ratio, pH, and P content similarly exhibited a significant positive correlation with soil bacterial communities, which was attributed to direct and indirect effects of forest stands. Seasonality was the strongest driver of predicted metabolic functions related to C fixation and degradation, and N metabolism. Carbon and nitrogen metabolic processes were significantly abundant in spring, while C degradation gene abundances increased from summer to autumn, corresponding to increased litterfall and decomposition. The results revealed that in a spatially homogenous forest soil, tree species diversity and richness are dominant drivers of structure and composition in soil bacterial communities.
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Affiliation(s)
- Amélie Dukunde
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Marcus Schmidt
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, Büsgen Institute, Georg-August University of Göttingen, Göttingen, Germany
| | - Edzo Veldkamp
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, Büsgen Institute, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
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Shao K, Jiang X, Hu Y, Tang X, Gao G. Thaumarchaeota affiliated with Soil Crenarchaeotic Group are prevalent in the alkaline soil of an alpine grassland in northwestern China. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01492-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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23
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Potapov AM, Klarner B, Sandmann D, Widyastuti R, Scheu S. Linking size spectrum, energy flux and trophic multifunctionality in soil food webs of tropical land-use systems. J Anim Ecol 2019; 88:1845-1859. [PMID: 31111468 DOI: 10.1111/1365-2656.13027] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 04/02/2019] [Indexed: 01/13/2023]
Abstract
Many ecosystem functions depend on the structure of food webs, which heavily relies on the body size spectrum of the community. Despite that, little is known on how the size spectrum of soil animals responds to agricultural practices in tropical land-use systems and how these responses affect ecosystem functioning. We studied land-use-induced changes in below-ground communities in tropical lowland ecosystems in Sumatra (Jambi province, Indonesia), a hot spot of tropical rainforest conversion into rubber and oil palm plantations. The study included ca. 30,000 measured individuals from 33 high-order taxa of meso- and macrofauna spanning eight orders of magnitude in body mass. Using individual body masses, we calculated the metabolism of trophic guilds and used food web models to calculate energy fluxes and infer ecosystem functions, such as decomposition, herbivory, primary and intraguild predation. Land-use change was associated with reduced abundance and taxonomic diversity of soil invertebrates, but strong increase in total biomass and moderate changes in total energy flux. These changes were due to increased biomass of large-sized decomposers in soil, in particular earthworms, with their share in community metabolism increasing from 11% in rainforest to 59%-76% in jungle rubber, and rubber and oil palm plantations. Decomposition, that is the energy flux to decomposers, stayed unchanged, but herbivory, primary and intraguild predation decreased by an order of magnitude in plantation systems. Intraguild predation was very important, being responsible for 38% of the energy flux in rainforest according to our model. Conversion of rainforest into monoculture plantations is associated by an uneven loss of size classes and trophic levels of soil invertebrates resulting in sequestration of energy in large-sized primary consumers and restricted flux of energy to higher trophic levels. Pronounced differences between rainforest and jungle rubber reflect sensitivity of rainforest soil animal communities to moderate land-use changes. Soil communities in plantation systems sustained high total energy flux despite reduced biodiversity. The high energy flux into large decomposers but low energy fluxes into other trophic guilds suggests that trophic multifunctionality of below-ground communities is compromised in plantation systems.
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Affiliation(s)
- Anton M Potapov
- J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany.,A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Bernhard Klarner
- J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Dorothee Sandmann
- J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Rahayu Widyastuti
- Department of Soil Sciences and Land Resources, Institut Pertanian Bogor (IPB), Bogor, Indonesia
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany.,Centre of Biodiversity and Sustainable Land Use, Göttingen, Germany
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Brinkmann N, Schneider D, Sahner J, Ballauff J, Edy N, Barus H, Irawan B, Budi SW, Qaim M, Daniel R, Polle A. Intensive tropical land use massively shifts soil fungal communities. Sci Rep 2019; 9:3403. [PMID: 30833601 PMCID: PMC6399230 DOI: 10.1038/s41598-019-39829-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 01/30/2019] [Indexed: 12/02/2022] Open
Abstract
Soil fungi are key players in nutrient cycles as decomposers, mutualists and pathogens, but the impact of tropical rain forest transformation into rubber or oil palm plantations on fungal community structures and their ecological functions are unknown. We hypothesized that increasing land use intensity and habitat loss due to the replacement of the hyperdiverse forest flora by nonendemic cash crops drives a drastic loss of diversity of soil fungal taxa and impairs the ecological soil functions. Unexpectedly, rain forest conversion was not associated with strong diversity loss but with massive shifts in soil fungal community composition. Fungal communities clustered according to land use system and loss of plant species. Network analysis revealed characteristic fungal genera significantly associated with different land use systems. Shifts in soil fungal community structure were particularly distinct among different trophic groups, with substantial decreases in symbiotrophic fungi and increases in saprotrophic and pathotrophic fungi in oil palm and rubber plantations in comparison with rain forests. In conclusion, conversion of rain forests and current land use systems restructure soil fungal communities towards enhanced pathogen pressure and, thus, threaten ecosystem health functions.
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Affiliation(s)
- Nicole Brinkmann
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany.
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Goettingen, Göttingen, Germany
| | - Josephine Sahner
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
| | - Johannes Ballauff
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
| | - Nur Edy
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
- Department of Agrotechnology, Faculty of Agriculture, Tadulako University, Palu, Indonesia
| | - Henry Barus
- Department of Agrotechnology, Faculty of Agriculture, Tadulako University, Palu, Indonesia
| | - Bambang Irawan
- Department of Forestry, University of Jambi, Jambi, Indonesia
| | - Sri Wilarso Budi
- Department of Silviculture, Faculty of Forestry, Bogor Agriculture University, Bogor, Indonesia
| | - Matin Qaim
- Department of Agricultural Economics and Rural Development, University of Goettingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Goettingen, Göttingen, Germany
| | - Andrea Polle
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
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25
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Schulz G, Schneider D, Brinkmann N, Edy N, Daniel R, Polle A, Scheu S, Krashevska V. Changes in Trophic Groups of Protists With Conversion of Rainforest Into Rubber and Oil Palm Plantations. Front Microbiol 2019; 10:240. [PMID: 30809219 PMCID: PMC6380168 DOI: 10.3389/fmicb.2019.00240] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 01/29/2019] [Indexed: 11/13/2022] Open
Abstract
Protists, abundant but enigmatic single-celled eukaryotes, are important soil microbiota providing numerous ecosystem functions. We employed high-throughput sequencing of environmental DNA, targeting the V4 region of the 18S rRNA gene, to characterize changes in their abundance, species richness, and community structure with conversion of lowland rainforest into rubber agroforest (jungle rubber), and rubber and oil palm plantations; typical agricultural systems in Sumatra, Indonesia. We identified 5,204 operational taxonomic units (OTUs) at 97% identity threshold of protists from 32 sites. Protists species richness was similar in rainforest, jungle rubber and oil palm plantations but significantly lower in rubber plantations. After standardization, 4,219 OTUs were assigned to five trophic groups, and inspected for effects of land-use change, and potential biotic and abiotic driving factors. The most abundant trophic group was phagotrophs (52%), followed by animal parasites (29%), photoautotrophs (12%), plant parasites (1%), and symbionts (<1%). However, the relative abundance and OTU richness of phagotrophs and photoautotrophs increased significantly with increasing land-use intensity. This was similar, but less pronounced, for the relative abundance of symbionts. Animal and plant parasites decreased significantly in abundance and species richness with increasing land-use intensity. Community compositions and factors affecting the structure of individual trophic groups differed between land-use systems. Parasites were presumably mainly driven by the abundance and species richness of their hosts, while phagotrophs by changes in soil pH and increase in Gram-positive bacteria, and photoautotrophs by light availability. Overall, the results show that relative species richness, relative abundance, and community composition of individual trophic groups of protists in tropical lowland rainforest significantly differ from that in converted ecosystems. This is likely associated with changes in ecosystem functioning. The study provides novel insight into protist communities and their changes with land-use intensity in tropical lowland ecosystems. We show, that trophic groups of protists are powerful indicators reflecting changes in the functioning of ecosystems with conversion of rainforest into monoculture plantations.
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Affiliation(s)
- Garvin Schulz
- Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Göttingen, Göttingen, Germany
| | - Nicole Brinkmann
- Department of Forest Botany and Tree Physiology, University of Göttingen, Göttingen, Germany
| | - Nur Edy
- Department of Forest Botany and Tree Physiology, University of Göttingen, Göttingen, Germany
- Department of Agrotechnology, Faculty of Agriculture, Tadulako University, Palu, Indonesia
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Göttingen, Göttingen, Germany
| | - Andrea Polle
- Department of Forest Botany and Tree Physiology, University of Göttingen, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use, University of Göttingen, Göttingen, Germany
| | - Stefan Scheu
- Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, University of Göttingen, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use, University of Göttingen, Göttingen, Germany
| | - Valentyna Krashevska
- Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, University of Göttingen, Göttingen, Germany
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26
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Transition of Ethiopian highland forests to agriculture-dominated landscapes shifts the soil microbial community composition. BMC Ecol 2018; 18:58. [PMID: 30558598 PMCID: PMC6298011 DOI: 10.1186/s12898-018-0214-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 11/30/2018] [Indexed: 11/30/2022] Open
Abstract
Background Land use changes and related land management practices significantly alter soil physicochemical properties; however, their effects on the soil microbial community structure are still unclear. In this study, we used automated ribosomal intergenic spacer analysis to determine the fungal and bacterial community composition in soils from different land use areas in the Ethiopian highlands. Soil samples were collected from five areas with different land uses, natural forest, eucalyptus plantation, exclosure, grassland and cropland, which had all historically been natural forest. Results Our results showed a significant shift in the soil bacterial and fungal community composition in response to land use change. We also identified soil physicochemical factors corresponding to the changes in bacterial and fungal communities. Although most soil attributes, including soil organic carbon, total soil nitrogen, labile P, soil pH and soil aggregate stability, were related to the change in bacterial community composition, the total soil nitrogen and soil organic carbon had the strongest relationships. The change in fungal community composition was correlated with soil nutrients, organic carbon, soil nitrogen and particularly the labile P concentration. Conclusions The fungal community composition was likely affected by the alteration of vegetation cover in response to land use change, whereas the bacterial communities were mainly sensitive to changes in soil attributes. The study highlights the higher sensitivity of fungal communities than bacterial communities to land use changes. Electronic supplementary material The online version of this article (10.1186/s12898-018-0214-8) contains supplementary material, which is available to authorized users.
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Wongkiew S, Park MR, Chandran K, Khanal SK. Aquaponic Systems for Sustainable Resource Recovery: Linking Nitrogen Transformations to Microbial Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:12728-12739. [PMID: 30264997 DOI: 10.1021/acs.est.8b04177] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Aquaponics is a technology for food production (fish and vegetables/fruits) with concomitant remediation of nitrogen-rich aquaculture effluent. There is, however, a critical need to improve the nitrogen use efficiency (NUE) in aquaponics. Here, we employed quantitative polymerase chain reactions and next-generation sequencing to evaluate the bacterial communities and their links to nitrogen transformations for improving NUEs in four bench-scale plant-based floating-raft aquaponics (pak choi, lettuce, chive, and tomato) and three pH levels (7.0, 6.0, and 5.2). Low relative abundance of nitrifiers in plant roots and biofilters suggested nitrogen loss, which decreased NUE in aquaponics. Low pH level was a major factor that shifted the microbial communities and reduced the relative abundance of nitrifiers in aquaponic systems, leading to total ammonia nitrogen accumulation in recirculating water. In plant roots, the abundance of nitrite-oxidizing bacteria (e.g., Nitrospira spp.) did not decrease at low pH levels, suggesting the benefit of growing plants in aquaponics for efficient nitrification and improving NUE. These findings on microbial communities and nitrogen transformations provided complementary strategies to improve the performance of the aquaponics regarding water quality and extent of nutrient recovery from aquaculture effluent.
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Affiliation(s)
- Sumeth Wongkiew
- Department of Molecular Biosciences and Bioengineering , University of Hawai'i at Ma̅noa , 1955 East-West Road , Honolulu , Hawai'i 96822 , United States
| | - Mee-Rye Park
- Department of Earth and Environmental Engineering , Columbia University , 500 West 120th Street , New York , New York 10027 , United States
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
- Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Kartik Chandran
- Department of Earth and Environmental Engineering , Columbia University , 500 West 120th Street , New York , New York 10027 , United States
| | - Samir Kumar Khanal
- Department of Molecular Biosciences and Bioengineering , University of Hawai'i at Ma̅noa , 1955 East-West Road , Honolulu , Hawai'i 96822 , United States
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28
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Responses of Soil Organic Carbon Sequestration Potential and Bacterial Community Structure in Moso Bamboo Plantations to Different Management Strategies in Subtropical China. FORESTS 2018. [DOI: 10.3390/f9100657] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Moso bamboo is one of the fastest-growing plants in the world. The objective of this study was to investigate the impact of converting secondary broadleaf evergreen forests (CK) to Moso bamboo plantations, and the impact of different management strategies, including no disturbance (M0), extensive management (M1), and intensive management (M2), on the soil organic carbon (SOC) sequestration potential, and relevant characteristics of the soil bacterial community. Our results showed that, in comparison with CK, M0 and M1 had significantly higher SOC and recalcitrant organic materials (aliphatic and aromatic compounds), and a lower C mineralization rate, whereas M2 had the opposite effects. The conversion from CK to Moso bamboo plantation significantly decreased the relative abundance of Acidobacteria in both the topsoil and subsoil soil layers. Compared with CK, M0 led to the enrichment of bacteria such as Alphaproteobacteria, Chloroflexi, and Bacteroidetes, which are involved in the decomposition of organic matter and the formation of humus and are, therefore, potentially beneficial for increasing the SOC. Furthermore, the ratio of the microbial biomass C (MBC) to total organic C (TOC), C mineralization rate, and bacterial diversity increased from M0 to M2, i.e., with an increase in the disturbance intensity. These findings indicate that the conversion of secondary broadleaf forest to bamboo forest alter the soil bacterial community structure. Reducing disturbance in bamboo forest management strategies should be actively taken up to improve the SOC, and maintain sustainable development in the forest industry.
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Berkelmann D, Schneider D, Engelhaupt M, Heinemann M, Christel S, Wijayanti M, Meryandini A, Daniel R. How Rainforest Conversion to Agricultural Systems in Sumatra (Indonesia) Affects Active Soil Bacterial Communities. Front Microbiol 2018; 9:2381. [PMID: 30364106 PMCID: PMC6191527 DOI: 10.3389/fmicb.2018.02381] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 09/18/2018] [Indexed: 11/13/2022] Open
Abstract
Palm oil production in Indonesia increased constantly over the last decades, which led to massive deforestation, especially on Sumatra island. The ongoing conversion of rainforest to agricultural systems results in high biodiversity loss. Here, we present the first RNA-based study on the effects of rainforest transformation to rubber and oil palm plantations in Indonesia for the active soil bacterial communities. For this purpose, bacterial communities of three different converted systems (jungle rubber, rubber plantation, and oil palm plantation) were studied in two landscapes with rainforest as reference by RT-PCR amplicon-based analysis of 16S rRNA gene transcripts. Active soil bacterial communities were dominated by Frankiales (Actinobacteria), subgroup 2 of the Acidobacteria and Alphaproteobacteria (mainly Rhizobiales and Rhodospirillales). Community composition differed significantly between the converted land use systems and rainforest reference sites. Alphaproteobacteria decreased significantly in oil palm samples compared to rainforest samples. In contrast, relative abundances of taxa within the Acidobacteria increased. Most important abiotic drivers for shaping soil bacterial communities were pH, calcium concentration, base saturation and C:N ratio. Indicator species analysis showed distinct association patterns for the analyzed land use systems. Nitrogen-fixing taxa including members of Rhizobiales and Rhodospirillales were associated with rainforest soils while nitrifiers and heat-resistant taxa including members of Actinobacteria were associated with oil palm soils. Predicted metabolic profiles revealed that the relative abundances of genes associated with fixation of nitrogen significantly decreased in plantation soils. Furthermore, predicted gene abundances regarding motility, competition or gene transfer ability indicated rainforest conversion-induced changes as well.
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Affiliation(s)
- Dirk Berkelmann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Martin Engelhaupt
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Melanie Heinemann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Stephan Christel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Marini Wijayanti
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University, Bogor, Indonesia
| | - Anja Meryandini
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University, Bogor, Indonesia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
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30
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Environmental Controls on Soil Microbial Communities in a Seasonally Dry Tropical Forest. Appl Environ Microbiol 2018; 84:AEM.00342-18. [PMID: 29959251 DOI: 10.1128/aem.00342-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/23/2018] [Indexed: 12/26/2022] Open
Abstract
Several studies have shown that rainfall seasonality, soil heterogeneity, and increased nitrogen (N) deposition may have important effects on tropical forest function. However, the effects of these environmental controls on soil microbial communities in seasonally dry tropical forests are poorly understood. In a seasonally dry tropical forest in the Yucatan Peninsula (Mexico), we investigated the influence of soil heterogeneity (which results in two different soil types, black and red soils), rainfall seasonality (in two successive seasons, wet and dry), and 3 years of repeated N enrichment on soil chemical and microbiological properties, including bacterial gene content and community structure. The soil properties varied with the soil type and the sampling season but did not respond to N enrichment. Greater organic matter content in the black soils was associated with higher microbial biomass, enzyme activities, and abundances of genes related to nitrification (amoA) and denitrification (nirK and nirS) than were observed in the red soils. Rainfall seasonality was also associated with changes in soil microbial biomass and activity levels and N gene abundances. Actinobacteria, Proteobacteria, Firmicutes, and Acidobacteria were the most abundant phyla. Differences in bacterial community composition were associated with soil type and season and were primarily detected at higher taxonomic resolution, where specific taxa drive the separation of communities between soils. We observed that soil heterogeneity and rainfall seasonality were the main correlates of soil bacterial community structure and function in this tropical forest, likely acting through their effects on soil attributes, especially those related to soil organic matter and moisture content.IMPORTANCE Understanding the response of soil microbial communities to environmental factors is important for predicting the contribution of forest ecosystems to global environmental change. Seasonally dry tropical forests are characterized by receiving less than 1,800 mm of rain per year in alternating wet and dry seasons and by high heterogeneity in plant diversity and soil chemistry. For these reasons, N deposition may affect their soils differently than those in humid tropical forests. This study documents the influence of rainfall seasonality, soil heterogeneity, and N deposition on soil chemical and microbiological properties in a seasonally dry tropical forest. Our findings suggest that soil heterogeneity and rainfall seasonality are likely the main factors controlling soil bacterial community structure and function in this tropical forest. Nitrogen enrichment was likely too low to induce significant short-term effects on soil properties, because this tropical forest is not N limited.
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Micro-decomposer communities and decomposition processes in tropical lowlands as affected by land use and litter type. Oecologia 2018; 187:255-266. [PMID: 29497833 DOI: 10.1007/s00442-018-4103-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/22/2018] [Indexed: 10/17/2022]
Abstract
We investigated how the land-use change from rainforest into jungle rubber, intensive rubber and oil palm plantations affects decomposers and litter decomposition in Sumatra, Indonesia. Litterbags containing three litter types were placed into four land-use systems and harvested after 6 and 12 months. Litter mass loss and litter element concentrations were measured, and different microbial groups including bacteria, fungi and testate amoebae were studied. After 12 months 81, 65, 63 and 53% of litter exposed in rainforest, jungle rubber in oil palm and rubber plantations was decomposed. In addition to land use, litter decomposition varied strongly with litter type and short-term effects differed markedly from long-term effects. After 6 months, oil palm and rubber litter decomposed faster than rainforest litter, but after 12 months, decomposition of rainforest litter exceeded that of oil palm and rubber litter, reflecting adaptation of bacteria and fungi to decompose structural compounds in rainforest litter but not (or less) in rubber and oil palm litter. Bacterial and fungal community composition and testate amoeba species number and density varied strongly with litter type, but little with land use. However, community composition of testate amoebae was mainly affected by land use. Generally, changes in bacteria, fungi and testate amoebae were linked to changes in litter element concentrations, suggesting that element ratios of litter material as basal resource for the decomposer food web shape the structure of decomposer communities and decomposition processes via bottom-up forces. Overall, changing rainforest to monoculture plantations shifts the decomposer community structure and negatively affects litter decomposition.
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Drylands soil bacterial community is affected by land use change and different irrigation practices in the Mezquital Valley, Mexico. Sci Rep 2018; 8:1413. [PMID: 29362388 PMCID: PMC5780513 DOI: 10.1038/s41598-018-19743-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 01/03/2018] [Indexed: 11/09/2022] Open
Abstract
Dryland agriculture nourishes one third of global population, although crop irrigation is often mandatory. As freshwater sources are scarce, treated and untreated wastewater is increasingly used for irrigation. Here, we investigated how the transformation of semiarid shrubland into rainfed farming or irrigated agriculture with freshwater, dam-stored or untreated wastewater affects the total (DNA-based) and active (RNA-based) soil bacterial community composition, diversity, and functionality. To do this we collected soil samples during the dry and rainy seasons and isolated DNA and RNA. Soil moisture, sodium content and pH were the strongest drivers of the bacterial community composition. We found lineage-specific adaptations to drought and sodium content in specific land use systems. Predicted functionality profiles revealed gene abundances involved in nitrogen, carbon and phosphorous cycles differed among land use systems and season. Freshwater irrigated bacterial community is taxonomically and functionally susceptible to seasonal environmental changes, while wastewater irrigated ones are taxonomically susceptible but functionally resistant to them. Additionally, we identified potentially harmful human and phytopathogens. The analyses of 16 S rRNA genes, its transcripts and deduced functional profiles provided extensive understanding of the short-term and long-term responses of bacterial communities associated to land use, seasonality, and water quality used for irrigation in drylands.
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Liu S, Wang H, Deng Y, Tian P, Wang Q. Forest conversion induces seasonal variation in microbial β-diversity. Environ Microbiol 2018; 20:111-123. [DOI: 10.1111/1462-2920.14017] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/30/2017] [Accepted: 11/30/2017] [Indexed: 01/10/2023]
Affiliation(s)
- Shengen Liu
- CAS Key Laboratory of Forest Ecology and Management; Institute of Applied Ecology, Huitong Experimental Station of Forest Ecology; Shenyang 110164 People's Republic of China
- University of Chinese Academy of Sciences; Beijing 100049 People's Republic of China
| | - Hang Wang
- National Plateau Wetlands Research Center; Southwest Forestry University; Kunming 650224 China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Science; Chinese Academy of Sciences; Beijing 100085 China
| | - Peng Tian
- CAS Key Laboratory of Forest Ecology and Management; Institute of Applied Ecology, Huitong Experimental Station of Forest Ecology; Shenyang 110164 People's Republic of China
- University of Chinese Academy of Sciences; Beijing 100049 People's Republic of China
| | - Qingkui Wang
- CAS Key Laboratory of Forest Ecology and Management; Institute of Applied Ecology, Huitong Experimental Station of Forest Ecology; Shenyang 110164 People's Republic of China
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34
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Szoboszlay M, Dohrmann AB, Poeplau C, Don A, Tebbe CC. Impact of land-use change and soil organic carbon quality on microbial diversity in soils across Europe. FEMS Microbiol Ecol 2017; 93:4566515. [DOI: 10.1093/femsec/fix146] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/25/2017] [Indexed: 11/12/2022] Open
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Barnes AD, Allen K, Kreft H, Corre MD, Jochum M, Veldkamp E, Clough Y, Daniel R, Darras K, Denmead LH, Farikhah Haneda N, Hertel D, Knohl A, Kotowska MM, Kurniawan S, Meijide A, Rembold K, Edho Prabowo W, Schneider D, Tscharntke T, Brose U. Direct and cascading impacts of tropical land-use change on multi-trophic biodiversity. Nat Ecol Evol 2017; 1:1511-1519. [PMID: 29185508 DOI: 10.1038/s41559-017-0275-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 07/11/2017] [Indexed: 11/09/2022]
Abstract
The conversion of tropical rainforest to agricultural systems such as oil palm alters biodiversity across a large range of interacting taxa and trophic levels. Yet, it remains unclear how direct and cascading effects of land-use change simultaneously drive ecological shifts. Combining data from a multi-taxon research initiative in Sumatra, Indonesia, we show that direct and cascading land-use effects alter biomass and species richness of taxa across trophic levels ranging from microorganisms to birds. Tropical land use resulted in increases in biomass and species richness via bottom-up cascading effects, but reductions via direct effects. When considering direct and cascading effects together, land use was found to reduce biomass and species richness, with increasing magnitude at higher trophic levels. Our analyses disentangle the multifaceted effects of land-use change on tropical ecosystems, revealing that biotic interactions on broad taxonomic scales influence the ecological outcome of anthropogenic perturbations to natural ecosystems.
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Affiliation(s)
- Andrew D Barnes
- Systemic Conservation Biology, University of Goettingen, Berliner Str. 28, 37073, Goettingen, Germany. .,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany. .,Institute of Biology, Leipzig University, Johannisallee 21, 04103, Leipzig, Germany.
| | - Kara Allen
- Soil Science of Tropical and Subtropical Ecosystems, University of Goettingen, Büsgen Institute, Büsgenweg 2, 37077, Goettingen, Germany.,Department of Ecology, Evolution, and Behavior, University of Minnesota, 306 Ecology, 1987 Upper Buford Circle, St. Paul, MN, 55108, USA
| | - Holger Kreft
- Biodiversity, Macroecology & Biogeography, University of Goettingen, Büsgenweg 1, 37077, Goettingen, Germany
| | - Marife D Corre
- Soil Science of Tropical and Subtropical Ecosystems, University of Goettingen, Büsgen Institute, Büsgenweg 2, 37077, Goettingen, Germany
| | - Malte Jochum
- Systemic Conservation Biology, University of Goettingen, Berliner Str. 28, 37073, Goettingen, Germany.,Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013, Bern, Switzerland
| | - Edzo Veldkamp
- Soil Science of Tropical and Subtropical Ecosystems, University of Goettingen, Büsgen Institute, Büsgenweg 2, 37077, Goettingen, Germany
| | - Yann Clough
- Department of Crop Sciences, Agroecology, University of Goettingen, Grisebachstr. 6, 37077, Goettingen, Germany.,Centre for Environmental and Climate Research, Lund University, Sölvegatan 37, 22362, Lund, Sweden
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Goettingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Goettingen, Grisebachstr. 8, 37077, Goettingen, Germany
| | - Kevin Darras
- Department of Crop Sciences, Agroecology, University of Goettingen, Grisebachstr. 6, 37077, Goettingen, Germany
| | - Lisa H Denmead
- Department of Crop Sciences, Agroecology, University of Goettingen, Grisebachstr. 6, 37077, Goettingen, Germany.,Marine and Environmental Management, School of Applied Sciences, Toi Ohomai Institute of Technology, 70 Windermere Drive, 3112, Tauranga, New Zealand
| | - Noor Farikhah Haneda
- Department of Silviculture, Faculty of Forestry, Bogor Agricultural University, Darmaga Campus, 16680, Bogor, Indonesia
| | - Dietrich Hertel
- Department of Plant Ecology and Ecosystems Research, University of Goettingen, Untere Karspüle 2, 37073, Goettingen, Germany
| | - Alexander Knohl
- Bioclimatology, University of Goettingen, Büsgenweg 2, 37077, Goettingen, Germany
| | - Martyna M Kotowska
- Department of Plant Ecology and Ecosystems Research, University of Goettingen, Untere Karspüle 2, 37073, Goettingen, Germany
| | - Syahrul Kurniawan
- Soil Science of Tropical and Subtropical Ecosystems, University of Goettingen, Büsgen Institute, Büsgenweg 2, 37077, Goettingen, Germany.,Department of Soil Science, Faculty of Agriculture, Brawijaya University, Malang, Indonesia
| | - Ana Meijide
- Bioclimatology, University of Goettingen, Büsgenweg 2, 37077, Goettingen, Germany
| | - Katja Rembold
- Biodiversity, Macroecology & Biogeography, University of Goettingen, Büsgenweg 1, 37077, Goettingen, Germany
| | - Walesa Edho Prabowo
- Conservation Biology Division, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland
| | - Dominik Schneider
- Department of Genomic and Applied Microbiology & Goettingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Goettingen, Grisebachstr. 8, 37077, Goettingen, Germany
| | - Teja Tscharntke
- Department of Crop Sciences, Agroecology, University of Goettingen, Grisebachstr. 6, 37077, Goettingen, Germany
| | - Ulrich Brose
- Systemic Conservation Biology, University of Goettingen, Berliner Str. 28, 37073, Goettingen, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.,Institute of Ecology, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743, Jena, Germany
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Trophic niches, diversity and community composition of invertebrate top predators (Chilopoda) as affected by conversion of tropical lowland rainforest in Sumatra (Indonesia). PLoS One 2017; 12:e0180915. [PMID: 28763453 PMCID: PMC5538669 DOI: 10.1371/journal.pone.0180915] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/22/2017] [Indexed: 11/19/2022] Open
Abstract
Conversion of tropical rainforests into plantations fundamentally alters ecological niches of animal species. Generalist predators such as centipedes (Chilopoda) may be able to persist in converted ecosystems due to their ability to adapt and switch to alternative prey populations. We investigated variations in community composition and trophic niches of soil and litter living centipedes in a range of ecosystems including rainforests, jungle rubber agroforests, and rubber and oil palm monocultures in two landscapes in Sumatra, Indonesia. Including information on environmental factors in the soil and litter habitat, we explored drivers shaping ecological niches of soil living invertebrate predators in one of the world's hotspots of rainforest conversion. Conversion of rainforests into agroforests and plantations was associated with a marked change in the composition of centipede communities. However, irrespective of major differences in habitat characteristics, changes in total abundances were small and the overall diversity and biomass of centipedes was similar in each of the systems investigated, suggesting that the number of ecological niches for this group of predators remains unchanged. By using stable isotope analysis (15N and 13C), we investigated trophic niche shifts of the centipede community; lower δ13C values of centipedes in oil palm plantations as compared to other ecosystems suggests that centipedes switch from decomposer prey to other prey, presumably understory associated herbivores, due to reduced availability of litter associated prey species. The results suggest that the ability to utilize alternative prey is a key feature enabling invertebrate predators to persist in ecosystems undergoing major structural changes due to anthropogenic land use change.
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Bai R, Wang JT, Deng Y, He JZ, Feng K, Zhang LM. Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers. Front Microbiol 2017; 8:945. [PMID: 28611747 PMCID: PMC5447084 DOI: 10.3389/fmicb.2017.00945] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/11/2017] [Indexed: 11/17/2022] Open
Abstract
Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils.
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Affiliation(s)
- Ren Bai
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of SciencesBeijing, China
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of SciencesBeijing, China
| | - Ye Deng
- Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, China.,College of Resources and Environment, University of Chinese Academy of SciencesBeijing, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of SciencesBeijing, China.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, MelbourneVIC, Australia
| | - Kai Feng
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of SciencesBeijing, China.,College of Resources and Environment, University of Chinese Academy of SciencesBeijing, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of SciencesBeijing, China.,College of Resources and Environment, University of Chinese Academy of SciencesBeijing, China
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38
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de León-Lorenzana AS, Delgado-Balbuena L, Domínguez-Mendoza C, Navarro-Noya YE, Luna-Guido M, Dendooven L. Reducing Salinity by Flooding an Extremely Alkaline and Saline Soil Changes the Bacterial Community but Its Effect on the Archaeal Community Is Limited. Front Microbiol 2017; 8:466. [PMID: 28396654 PMCID: PMC5366314 DOI: 10.3389/fmicb.2017.00466] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 03/07/2017] [Indexed: 11/13/2022] Open
Abstract
Regular flooding of the soil to reduce salinity will change soil characteristics, but also the microbial community structure. Soil of the former lake Texcoco with electrolytic conductivity (EC) 157.4 dS m-1 and pH 10.3 was flooded monthly in the laboratory under controlled conditions for 10 months while soil characteristics were determined and the archaeal and bacterial community structure monitored by means of 454 pyrosequencing of the 16S rRNA gene. The EC of the soil dropped from 157.8 to 1.7 dS m-1 and the clay content decreased from 430 to 270 g kg-1 after ten floodings, but the pH (10.3) did not change significantly over time. Flooding the soil had a limited effect on the archaeal community structure and only the relative abundance of Haloferax-like 16S rRNA phylotypes changed significantly. Differences in archaeal population structure were more defined by the initial physicochemical properties of the soil sample than by a reduction in salinity. Flooding, however, had a stronger effect on bacterial community structure than on the archaeal community structure. A wide range of bacterial taxa was affected significantly by changes in the soil characteristics, i.e., four phyla, nine classes, 17 orders, and 28 families. The most marked change occurred after only one flooding characterized by a sharp decrease in the relative abundance of bacterial groups belonging to the Gammaproteobacteria, e.g., Halomonadaceae (Oceanospirillales), Pseudomonadaceae, and Xanthomonadaceae and an increase in that of the [Rhodothermales] (Bacteroidetes), Nitriliruptorales (Actinobacteria), and unassigned Bacteria. It was found that flooding the soil sharply reduced the EC, but also the soil clay content. Flooding the soil had a limited effect on the archaeal community structure, but altered the bacterial community structure significantly.
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Affiliation(s)
- Arit S de León-Lorenzana
- Soil Ecology Lab, Centro de Investigación y de Estudios Avanzados del IPN, CINVESTAV Mexico, Mexico
| | - Laura Delgado-Balbuena
- Soil Ecology Lab, Centro de Investigación y de Estudios Avanzados del IPN, CINVESTAV Mexico, Mexico
| | | | - Yendi E Navarro-Noya
- Centro Tlaxcala de Biología de la Conducta, Cátedras CONACYT, Universidad Autónoma de Tlaxcala Tlaxcala, Mexico
| | - Marco Luna-Guido
- Soil Ecology Lab, Centro de Investigación y de Estudios Avanzados del IPN, CINVESTAV Mexico, Mexico
| | - Luc Dendooven
- Soil Ecology Lab, Centro de Investigación y de Estudios Avanzados del IPN, CINVESTAV Mexico, Mexico
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39
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Monkai J, Hyde KD, Xu J, Mortimer PE. Diversity and ecology of soil fungal communities in rubber plantations. FUNGAL BIOL REV 2017. [DOI: 10.1016/j.fbr.2016.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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40
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Ambika Manirajan B, Ratering S, Rusch V, Schwiertz A, Geissler-Plaum R, Cardinale M, Schnell S. Bacterial microbiota associated with flower pollen is influenced by pollination type, and shows a high degree of diversity and species-specificity. Environ Microbiol 2016; 18:5161-5174. [DOI: 10.1111/1462-2920.13524] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/04/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Binoy Ambika Manirajan
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University; Giessen Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University; Giessen Germany
| | - Volker Rusch
- Institut für Integrative Biologie, Stiftung Old Herborn University; Herborn Germany
| | | | - Rita Geissler-Plaum
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University; Giessen Germany
| | - Massimiliano Cardinale
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University; Giessen Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University; Giessen Germany
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41
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Kerfahi D, Tripathi BM, Dong K, Go R, Adams JM. Rainforest Conversion to Rubber Plantation May Not Result in Lower Soil Diversity of Bacteria, Fungi, and Nematodes. MICROBIAL ECOLOGY 2016; 72:359-71. [PMID: 27221090 DOI: 10.1007/s00248-016-0790-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/17/2016] [Indexed: 05/27/2023]
Abstract
Large areas of rainforest in Asia have been converted to plantations, with uncertain effects on soil biodiversity. Using standard metagenetic methods, we compared the soil biota of bacteria, fungi, and nematodes at three rainforest sites in Malaysia with two rubber plantation sites with similar soils and geology. We predicted the following: (1) that the rubber sites would have a lower α- and β-diversity than the rainforest sites, due to the monospecific canopy cover and intensive management with herbicides, pesticides, and fertilizers, and (2) that due to differences in the physical and biotic environment associated with cultivation, there would be distinct communities of bacteria, fungi, and nematodes. However, regarding (1), the results showed no consistent difference in α- and β-diversity of bacteria, fungi, or nematodes between rainforest and rubber plantation sites. It appears that conversion of rainforest to rubber plantations does not necessarily result in a decrease in diversity of soil biota. It may be that heterogeneity associated with the cultivation regimen compensates for loss of biotically imposed heterogeneity of the original rainforest. Regarding (2), as predicted there were statistically significant differences in community composition between rainforest and rubber plantation for bacteria, fungi, and nematodes. These differences could be related to a range of factors including light level, litter fall composition, pH, C and N, selecting a distinct set of soil taxa, and it is possible that this in itself would affect long-term soil function.
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Affiliation(s)
- Dorsaf Kerfahi
- Department of Biological Sciences, Seoul National University, Gwanak-Gu, Seoul, 151-747, Republic of Korea
| | - Binu M Tripathi
- Arctic Research Center, Korea Polar Research Institute, Incheon, 406-840, Korea
| | - Ke Dong
- Department of Biological Sciences, Seoul National University, Gwanak-Gu, Seoul, 151-747, Republic of Korea
| | - Rusea Go
- Department of Biology, Faculty of Sciences, Universiti Putra Malaysia, Serdang, Selangor, 43400, Malaysia
| | - Jonathan M Adams
- Department of Biological Sciences, Seoul National University, Gwanak-Gu, Seoul, 151-747, Republic of Korea.
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42
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Krashevska V, Klarner B, Widyastuti R, Maraun M, Scheu S. Changes in Structure and Functioning of Protist (Testate Amoebae) Communities Due to Conversion of Lowland Rainforest into Rubber and Oil Palm Plantations. PLoS One 2016; 11:e0160179. [PMID: 27463805 PMCID: PMC4963170 DOI: 10.1371/journal.pone.0160179] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/14/2016] [Indexed: 11/22/2022] Open
Abstract
Large areas of tropical rainforest are being converted to agricultural and plantation land uses, but little is known of biodiversity and ecological functioning under these replacement land uses. We investigated the effects of conversion of rainforest into jungle rubber, intensive rubber and oil palm plantations on testate amoebae, diverse and functionally important protists in litter and soil. Living testate amoebae species richness, density and biomass were all lower in replacement land uses than in rainforest, with the impact being more pronounced in litter than in soil. Similar abundances of species of high and low trophic level in rainforest suggest that trophic interactions are more balanced, with a high number of functionally redundant species, than in rubber and oil palm. In contrast, plantations had a low density of high trophic level species indicating losses of functions. This was particularly so in oil palm plantations. In addition, the relative density of species with siliceous shells was >50% lower in the litter layer of oil palm and rubber compared to rainforest and jungle rubber. This difference suggests that rainforest conversion changes biogenic silicon pools and increases silicon losses. Overall, the lower species richness, density and biomass in plantations than in rainforest, and the changes in the functional composition of the testate amoebae community, indicate detrimental effects of rainforest conversion on the structure and functioning of microbial food webs.
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Affiliation(s)
- Valentyna Krashevska
- Georg August University Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Göttingen, Germany
| | - Bernhard Klarner
- Georg August University Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Göttingen, Germany
| | - Rahayu Widyastuti
- Institut Pertanian Bogor—IPB, Department of Soil Sciences and Land Resources, Damarga Campus, Bogor, Indonesia
| | - Mark Maraun
- Georg August University Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Göttingen, Germany
| | - Stefan Scheu
- Georg August University Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Göttingen, Germany
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