1
|
Farooqi ZUR, Qadir AA, Alserae H, Raza A, Mohy-Ud-Din W. Organic amendment-mediated reclamation and build-up of soil microbial diversity in salt-affected soils: fostering soil biota for shaping rhizosphere to enhance soil health and crop productivity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:109889-109920. [PMID: 37792186 DOI: 10.1007/s11356-023-30143-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/25/2023] [Indexed: 10/05/2023]
Abstract
Soil salinization is a serious environmental problem that affects agricultural productivity and sustainability worldwide. Organic amendments have been considered a practical approach for reclaiming salt-affected soils. In addition to improving soil physical and chemical properties, organic amendments have been found to promote the build-up of new halotolerant bacterial species and microbial diversity, which plays a critical role in maintaining soil health, carbon dynamics, crop productivity, and ecosystem functioning. Many reported studies have indicated the development of soil microbial diversity in organic amendments amended soil. But they have reported only the development of microbial diversity and their identification. This review article provides a comprehensive summary of the current knowledge on the use of different organic amendments for the reclamation of salt-affected soils, focusing on their effects on soil properties, microbial processes and species, development of soil microbial diversity, and microbial processes to tolerate salinity levels and their strategies to cope with it. It also discusses the factors affecting the microbial species developments, adaptation and survival, and carbon dynamics. This review is based on the concept of whether addition of specific organic amendment can promote specific halotolerant microbe species, and if it is, then which amendment is responsible for each microbial species' development and factors responsible for their survival in saline environments.
Collapse
Affiliation(s)
- Zia Ur Rahman Farooqi
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan.
| | - Ayesha Abdul Qadir
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Hussein Alserae
- Department of Soil Sciences and Water Resources, College of Agricultural Engineering Science, Baghdad University, Baghdad, Iraq
| | - Ali Raza
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Waqas Mohy-Ud-Din
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
- Department of Soil and Environmental Sciences, Ghazi University, Dera Ghazi Khan, 32200, Pakistan
| |
Collapse
|
2
|
Aqeel M, Ran J, Hu W, Irshad MK, Dong L, Akram MA, Eldesoky GE, Aljuwayid AM, Chuah LF, Deng J. Plant-soil-microbe interactions in maintaining ecosystem stability and coordinated turnover under changing environmental conditions. CHEMOSPHERE 2023; 318:137924. [PMID: 36682633 DOI: 10.1016/j.chemosphere.2023.137924] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/07/2023] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
Ecosystem functions directly depend upon biophysical as well as biogeochemical reactions occurring at the soil-microbe-plant interface. Environment is considered as a major driver of any ecosystem and for the distributions of living organisms. Any changes in climate may potentially alter the composition of communities i.e., plants, soil microbes and the interactions between them. Since the impacts of global climate change are not short-term, it is indispensable to appraise its effects on different life forms including soil-microbe-plant interactions. This article highlights the crucial role that microbial communities play in interacting with plants under environmental disturbances, especially thermal and water stress. We reviewed that in response to the environmental changes, actions and reactions of plants and microbes vary markedly within an ecosystem. Changes in environment and climate like warming, CO2 elevation, and moisture deficiency impact plant and microbial performance, their diversity and ultimately community structure. Plant and soil feedbacks also affect interacting species and modify community composition. The interactive relationship between plants and soil microbes is critically important for structuring terrestrial ecosystems. The anticipated climate change is aggravating the living conditions for soil microbes and plants. The environmental insecurity and complications are not short-term and limited to any particular type of organism. We have appraised effects of climate change on the soil inhabiting microbes and plants in a broader prospect. This article highlights the unique qualities of tripartite interaction between plant-soil-microbe under climate change.
Collapse
Affiliation(s)
- Muhammad Aqeel
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, PR China
| | - Jinzhi Ran
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, PR China
| | - Weigang Hu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, PR China
| | - Muhammad Kashif Irshad
- Department of Environmental Sciences, Government College University Faisalabad, (38000), Pakistan
| | - Longwei Dong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, PR China
| | - Muhammad Adnan Akram
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Department of Materials Engineering, KU Leuven, Kasteelpark Arenberg 44, Leuven 3001, Belgium
| | - Gaber E Eldesoky
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Ahmed Muteb Aljuwayid
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Lai Fatt Chuah
- Faculty of Maritime Studies, Universiti Malaysia Terengganu, Terengganu, Malaysia.
| | - Jianming Deng
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| |
Collapse
|
3
|
Marois J, Lerch TZ, Dunant U, Farnet Da Silva AM, Christen P. Chemical and Microbial Characterization of Fermented Forest Litters Used as Biofertilizers. Microorganisms 2023; 11:microorganisms11020306. [PMID: 36838270 PMCID: PMC9959058 DOI: 10.3390/microorganisms11020306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/25/2022] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
The excessive use of chemicals in intensive agriculture has had a negative impact on soil diversity and fertility. A strategy for developing sustainable agriculture could rely on the use of microbial-based fertilizers, known as biofertilizers. An alternative to marketed products could be offered to small farmers if they could produce their own biofertilizers using forest litters, which harbor one of the highest microbial diversities. The aim of this study is to characterize microbial communities of Fermented Forest Litters (FFL), assuming that the fermentation process will change both their abundance and diversity. We investigated two types of differing in the chemical composition of the initial litters used and the climatic context of the forest where they are originated from. The abundance and diversity of bacterial and fungal communities were assessed using quantitative PCR and molecular genotyping techniques. The litter chemical compositions were compared before and after fermentation using Infrared spectrometry. Results obtained showed that fermentation increased the abundance of bacteria but decreased that of fungi. Low pH and change in organic matter composition observed after fermentation also significantly reduced the α-diversity of both bacterial and fungal communities. The higher proportion of aliphatic molecules and lower C/N of the FFLs compared to initial litters indicate that FFLs should be rapidly decomposed once added into the soil. This preliminary study suggests that the agronomic interest of FFLs used as biofertilizers is probably more related to the contribution of nutrients easily assimilated by plants than to the diversity of microorganisms that compose it. Further studies must be conducted with sequencing techniques to identify precisely the microbial species likely to be beneficial to plant growth.
Collapse
Affiliation(s)
- Johann Marois
- Institute of Ecology and Environnemental Sciences of Paris, UMR 7618 (CNRS, SU, IRD, UPEC, INRAe, UPC), 94010 Créteil, France
| | - Thomas Z. Lerch
- Institute of Ecology and Environnemental Sciences of Paris, UMR 7618 (CNRS, SU, IRD, UPEC, INRAe, UPC), 94010 Créteil, France
| | - Ugo Dunant
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et Continentale, UMR 7263 (CNRS, AMU, IRD, AU), 13397 Marseille, France
| | - Anne-Marie Farnet Da Silva
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et Continentale, UMR 7263 (CNRS, AMU, IRD, AU), 13397 Marseille, France
| | - Pierre Christen
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et Continentale, UMR 7263 (CNRS, AMU, IRD, AU), 13397 Marseille, France
- Correspondence:
| |
Collapse
|
4
|
Castañeda-Gómez L, Lajtha K, Bowden R, Mohammed Jauhar FN, Jia J, Feng X, Simpson MJ. Soil organic matter molecular composition with long-term detrital alterations is controlled by site-specific forest properties. GLOBAL CHANGE BIOLOGY 2023; 29:243-259. [PMID: 36169977 DOI: 10.1111/gcb.16456] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/11/2022] [Indexed: 06/16/2023]
Abstract
Forest ecosystems are important global soil carbon (C) reservoirs, but their capacity to sequester C is susceptible to climate change factors that alter the quantity and quality of C inputs. To better understand forest soil C responses to altered C inputs, we integrated three molecular composition published data sets of soil organic matter (SOM) and soil microbial communities for mineral soils after 20 years of detrital input and removal treatments in two deciduous forests: Bousson Forest (BF), Harvard Forest (HF), and a coniferous forest: H.J. Andrews Forest (HJA). Soil C turnover times were estimated from radiocarbon measurements and compared with the molecular-level data (based on nuclear magnetic resonance and specific analysis of plant- and microbial-derived compounds) to better understand how ecosystem properties control soil C biogeochemistry and dynamics. Doubled aboveground litter additions did not increase soil C for any of the forests studied likely due to long-term soil priming. The degree of SOM decomposition was higher for bacteria-dominated sites with higher nitrogen (N) availability while lower for the N-poor coniferous forest. Litter exclusions significantly decreased soil C, increased SOM decomposition state, and led to the adaptation of the microbial communities to changes in available substrates. Finally, although aboveground litter determined soil C dynamics and its molecular composition in the coniferous forest (HJA), belowground litter appeared to be more influential in broadleaf deciduous forests (BH and HF). This synthesis demonstrates that inherent ecosystem properties regulate how soil C dynamics change with litter manipulations at the molecular-level. Across the forests studied, 20 years of litter additions did not enhance soil C content, whereas litter reductions negatively impacted soil C concentrations. These results indicate that soil C biogeochemistry at these temperate forests is highly sensitive to changes in litter deposition, which are a product of environmental change drivers.
Collapse
Affiliation(s)
- Laura Castañeda-Gómez
- Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Kate Lajtha
- Department of Crop and Soil Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Richard Bowden
- Department of Environmental Science and Sustainability, Allegheny College, Meadville, Pennsylvania, USA
| | | | - Juan Jia
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiaojuan Feng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Myrna J Simpson
- Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
5
|
Agarwal P, Saha S, Hariprasad P. Agro-industrial-residues as potting media: physicochemical and biological characters and their influence on plant growth. BIOMASS CONVERSION AND BIOREFINERY 2021; 13:1-24. [PMID: 34660165 PMCID: PMC8500816 DOI: 10.1007/s13399-021-01998-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/09/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Nursery cultivation is recognized globally as an intensive production system to support quality seedlings as well as to manage resources efficiently. Apart from other factors, potting media (PM) play a crucial role in determining the success of nursery cultivation. Worldwide, peat is the most commonly used substrate in PM because of its favorable physicochemical properties. However, due to ascending environmental and ecological concerns regarding the use of peat, a variety of new substrates have been used/tested by researchers/practitioners/growers as PM. Bark, coir pith, wood fiber, compost derived from various agro-residues, and vermicompost either alone or in combination are some of the commonly explored substrates and found to have the potential to replace peat to a greater extent. In lieu of availability, abundance, low cost, and no/low processing requirement, the use of agro-industrial residue (AIR) in the PM is the current trend. However, challenges associated with their adoption cannot be ignored. The present review is focused on providing collective information, scientific knowledge and detailed analysis of various AIR used in PM. The critical evidence-based review would help in developing a consistent approach for the identification, selection and characterization of a new renewable substrate. In addition, it would help in developing a rationale understanding of the practical and economic realities involved in the adoption of the same in PM. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13399-021-01998-6.
Collapse
Affiliation(s)
- Pratibha Agarwal
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi India
| | - Sampa Saha
- Department of Materials Science and Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi India
| | - P. Hariprasad
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi India
| |
Collapse
|
6
|
Viketoft M, Riggi LG, Bommarco R, Hallin S, Taylor AR. Type of organic fertilizer rather than organic amendment per se increases abundance of soil biota. PeerJ 2021; 9:e11204. [PMID: 34012726 PMCID: PMC8109005 DOI: 10.7717/peerj.11204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/11/2021] [Indexed: 11/30/2022] Open
Abstract
Addition of organic amendments is a commonly used practice to offset potential loss of soil organic matter from agricultural soils. The aim of the present study was to examine how long-term addition of organic matter affects the abundance of different soil biota across trophic levels and the role that the quality of the organic amendments plays. Here we used a 17-year-old fertilization experiment to investigate soil biota responses to four different organic fertilizers, compared with two mineral nitrogen fertilizers and no fertilization, where the organic fertilizers had similar carbon content but varied in their carbon to nitrogen ratios. We collected soil samples and measured a wide range of organisms belonging to different functional groups and trophic levels of the soil food web. Long-term addition of organic and mineral fertilizers had beneficial effects on the abundances of most soil organisms compared with unfertilized soil, but the responses differed between soil biota. The organic fertilizers generally enhanced bacteria and earthworms. Fungi and nematodes responded positively to certain mineral and organic fertilizers, indicating that multiple factors influenced by the fertilization may affect these heterogeneous groups. Springtails and mites were less affected by fertilization than the other groups, as they were present at relatively high abundances even in the unfertilized treatment. However, soil pH had a great influence on springtail abundance. In summary, the specific fertilizer was more important in determining the numerical and compositional responses of soil biota than whether it was mineral or organic. Overall, biennial organic amendments emerge as insufficient, by themselves, to promote soil organisms in the long run, and would need to be added annually or combined with other practices affecting soil quality, such as no or reduced tillage and other crop rotations, to have a beneficial effect.
Collapse
Affiliation(s)
- Maria Viketoft
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Laura G.A. Riggi
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Riccardo Bommarco
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Astrid R. Taylor
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| |
Collapse
|
7
|
Pozo MJ, Zabalgogeazcoa I, Vazquez de Aldana BR, Martinez-Medina A. Untapping the potential of plant mycobiomes for applications in agriculture. CURRENT OPINION IN PLANT BIOLOGY 2021; 60:102034. [PMID: 33827007 DOI: 10.1016/j.pbi.2021.102034] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/11/2021] [Accepted: 02/21/2021] [Indexed: 05/20/2023]
Abstract
Plant-fungal interactions are widespread in nature, and their multiple benefits for plant growth and health have been amply demonstrated. Endophytic and epiphytic fungi can significantly increase plant resilience, improving plant nutrition, stress tolerance and defence. Although some of these interactions have been known for decades, the relevance of the plant mycobiome within the plant microbiome has been largely underestimated. Our limited knowledge of fungal biology and their interactions with plants in the broader phytobiome context has hampered the development of optimal biotechnological applications in agrosystems and natural ecosystems. Exciting recent technical and knowledge advances in the context of molecular and systems biology open a plethora of opportunities for developing this field of research.
Collapse
Affiliation(s)
- Maria J Pozo
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Granada, Spain.
| | - Iñigo Zabalgogeazcoa
- Plant-Microbe Interactions, Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Salamanca, Spain
| | - Beatriz R Vazquez de Aldana
- Plant-Microbe Interactions, Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Salamanca, Spain
| | - Ainhoa Martinez-Medina
- Plant-Microbe Interactions, Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Salamanca, Spain
| |
Collapse
|
8
|
Zhou X, Leite MFA, Zhang Z, Tian L, Chang J, Ma L, Li X, van Veen JA, Tian C, Kuramae EE. Facilitation in the soil microbiome does not necessarily lead to niche expansion. ENVIRONMENTAL MICROBIOME 2021; 16:4. [PMID: 33902741 PMCID: PMC8067652 DOI: 10.1186/s40793-021-00373-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 01/21/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND The soil microbiome drives soil ecosystem function, and soil microbial functionality is directly linked to interactions between microbes and the soil environment. However, the context-dependent interactions in the soil microbiome remain largely unknown. RESULTS Using latent variable models (LVMs), we disentangle the biotic and abiotic interactions of soil bacteria, fungi and environmental factors using the Qinghai-Tibetan Plateau soil ecosystem as a model. Our results show that soil bacteria and fungi not only interact with each other but also shift from competition to facilitation or vice versa depending on environmental variation; that is, the nature of their interactions is context-dependent. CONCLUSIONS Overall, elevation is the environmental gradient that most promotes facilitative interactions among microbes but is not a major driver of soil microbial community composition, as evidenced by variance partitioning. The larger the tolerance of a microbe to a specific environmental gradient, the lesser likely it is to interact with other soil microbes, which suggests that facilitation does not necessarily lead to niche expansion.
Collapse
Affiliation(s)
- Xue Zhou
- College of Resources and Environment, Jilin Agricultural University, Changchun, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Márcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands
| | - Zhenqing Zhang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Jingjing Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Lina Ma
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xiujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Johannes A van Veen
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands.
- Ecology and biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.
| |
Collapse
|
9
|
Siedt M, Schäffer A, Smith KEC, Nabel M, Roß-Nickoll M, van Dongen JT. Comparing straw, compost, and biochar regarding their suitability as agricultural soil amendments to affect soil structure, nutrient leaching, microbial communities, and the fate of pesticides. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141607. [PMID: 32871314 DOI: 10.1016/j.scitotenv.2020.141607] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/06/2020] [Accepted: 08/08/2020] [Indexed: 06/11/2023]
Abstract
The emission of nutrients and pesticides from agricultural soils endangers natural habitats. Here, we review to which extent carbon-rich organic amendments help to retain nutrients and pesticides in agricultural soils and to reduce the contamination of surrounding areas and groundwater. We compare straw, compost, and biochar to see whether biochar outperforms the other two more traditional and cheaper materials. We present a list of criteria to evaluate the suitability of organic materials to be used as soil amendments and discuss differences in elemental compositions of straw, compost, and biochar to understand, how soil microorganisms utilize those materials. We review their effects on physical and chemical soil characteristics, soil microbial communities, as well as effects on the transformation and retention of nutrients and pesticides in detail. It becomes clear that for all three amendments their effects can vary greatly depending on numerous aspects, such as the type of soil, application rate, and production procedure of the organic material. Biochar is most effective in increasing the sorption capacity of soils but does not outperform straw and compost with regards to the other aspects investigated. Nevertheless, the possibility to design biochar properties makes it a very promising material. Finally, we provide critical comments about how to make studies about organic amendments more comparable (comprehensive provision of material properties), how to improve concepts of future work (meta-analysis, long-term field studies, use of deep-insight microbial DNA sequencing), and what needs to be further investigated (the link between structural and functional microbial parameters, the impact of biochar on pesticide efficiency).
Collapse
Affiliation(s)
- Martin Siedt
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
| | - Andreas Schäffer
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Kilian E C Smith
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Moritz Nabel
- Federal Agency for Nature Conservation (BfN), Konstantinstr. 110, 53179 Bonn, Germany
| | - Martina Roß-Nickoll
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Joost T van Dongen
- Molecular Ecology of the Rhizosphere, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| |
Collapse
|
10
|
Effects of Different Fertilizer Treatments on Rhizosphere Soil Microbiome Composition and Functions. LAND 2020. [DOI: 10.3390/land9090329] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fertilization influences the soil microbiome. However, little is known about the effects of long-term fertilization on soil microbial metabolic pathways. In this study, we investigated the soil microbiome composition and function and microbial participation in the N cycle according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) functional annotation of different genes in a metagenomic analysis after long-term fertilization. Fertilizer application significantly changed the soil C/N ratio. Chemical fertilizer (NPK) treatment decreased soil pH, and chemical fertilizer combined with straw (NPK+S0.5) treatment increased ammonium nitrogen (NH4+-N) but decreased nitrate nitrogen (NO3−-N). NPK, NPK+S0.5 and S0.5 applications did not change the soil microbiome composition or dominant phylum but changed the relative abundances of microbiome components. Moreover, fertilizer significantly influenced metabolic processes, cellular processes and single-organism processes. Compared with a no-fertilizer treatment (CK), the NPK treatment resulted in more differentially expressed gene (DEG) pathways than the NPK+S0.5 and S0.5 treatments, and these pathways significantly correlated with soil nitrate nitrogen (NO3−-N), available phosphorus (AP) and the moisture content of soil (MC). KEGG analysis found that fertilizer application mainly affected the ribosome, photosynthesis and oxidative phosphorylation pathways. S0.5 and NPK+S0.5 increased microbial nitrogen fixation, and NPK and NPK+S0.5 decreased amoA and amoB and accelerated denitrification. Thus, organic fertilizer increased N fixation and nitrification, and inorganic N fertilizer accelerated denitrification. We found that the function of the soil microbiome under different fertilizer applications could be important for the rational application of fertilizer and for environmental and sustainable development.
Collapse
|
11
|
Lourenço KS, Suleiman AKA, Pijl A, Cantarella H, Kuramae EE. Dynamics and resilience of soil mycobiome under multiple organic and inorganic pulse disturbances. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 733:139173. [PMID: 32454291 DOI: 10.1016/j.scitotenv.2020.139173] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
Disturbances in soil can cause short-term soil changes, consequently changes in microbial community what may result in long-lasting ecological effects. Here, we evaluate how multiple pulse disturbances effect the dynamics and resilience of fungal community, and the co-occurrence of fungal and bacterial communities in a 389 days field experiment. We used soil under sugarcane cultivation as soil ecosystem model, and organic residue (vinasse - by-product of sugarcane ethanol production) combined or not with inorganic (organic residue applied 30 days before or together with mineral N fertilizer) amendments as disturbances. Application of organic residue alone as a single disturbance or 30 days prior to a second disturbance with mineral N resulted in similar changes in the fungal community. The simultaneous application of organic and mineral N as a single pulse disturbance had the greatest impact on the fungal community. Organic amendment increased the abundance of saprotrophs, fungal species capable of denitrification, and fungi described to have copiotrophic and oligotrophic lifestyles. Furthermore, the changes in the fungal community were not correlated with the changes in the bacterial community. The fungal community was neither resistant nor resilient to organic and inorganic disturbances over the one-year sampling period. Our findings provide insights on the immediate and delayed responses of the fungal community over one year to disturbance by organic and inorganic amendments.
Collapse
Affiliation(s)
- Késia Silva Lourenço
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708, PB, Wageningen, the Netherlands; Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, 13020-902 Campinas, SP, Brazil
| | - Afnan Khalil Ahmad Suleiman
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708, PB, Wageningen, the Netherlands; KWR Watercycle Research Institute, Groningenhaven 7, 3433, PE, Nieuwegein, The Netherlands
| | - Agata Pijl
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708, PB, Wageningen, the Netherlands
| | - Heitor Cantarella
- Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, 13020-902 Campinas, SP, Brazil
| | - Eiko Eurya Kuramae
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708, PB, Wageningen, the Netherlands; Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.
| |
Collapse
|
12
|
Song H, Wang J, Zhang K, Zhang M, Hui R, Sui T, Yang L, Du W, Dong Z. A 4-year field measurement of N 2O emissions from a maize-wheat rotation system as influenced by partial organic substitution for synthetic fertilizer. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 263:110384. [PMID: 32174526 DOI: 10.1016/j.jenvman.2020.110384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/11/2020] [Accepted: 03/01/2020] [Indexed: 06/10/2023]
Abstract
Soil N2O emissions depend on the status of stoichiometric balance between organic C and inorganic N. As a beneficial management practice to sustain soil fertility and crop productivity, partial substitution of organic fertilizers (OFs) for synthetic fertilizers (SFs) can directly affect this balance status and regulate N2O emissions. However, no multi-year field studies of N2O emissions under different ratios of OFS to SFs have been performed. We conducted a 4-year experiment to measure N2O emissions in a maize-wheat rotation in central China. Six treatments were included: total SF (TS), total OF, no N fertilizer, and ratios of to SF with 1: 2 (LO), 1: 1 (MO), and 2: 1 (HO), based on N content. Two incubation experiments were performed to further interpret the field data. In the first year, cumulative N2O emissions (kg N ha-1) in LO, MO, and HO were 4.59, 4.68, and 3.59, respectively, significantly lower than in TS (6.67). However, from the second year onwards, organic substitution did not reduce N2O emissions and even significantly enhanced them in the fourth year relative to TS. Soil respiration under OF-amended soils increased over the course of the experiment. From the second year onwards, there was no marked difference in mineral N concentrations between OF- and SF-amended soils. OF caused a drop in soil pH. Cumulative N2O was negatively correlated with pH. Long-term organic substitution enhanced N2O emissions produced via denitrification rather than nitrification and resulted in higher temperature sensitivity of N2O emissions than TS. The enhanced N2O emissions from the OF-treated soils were mainly attributable to accelerated OF decomposition, increased denitrification-N2O emissions, and lessened N2O reduction due to lower pH and greater NO3-. These results indicate that OF substitution can reduce N2O emissions in the first year, but in the long-term it can increase emissions, especially as soils warm.
Collapse
Affiliation(s)
- He Song
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Jun Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Kui Zhang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Manyu Zhang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Rui Hui
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Tianyi Sui
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Lin Yang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Wenbin Du
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Zhaorong Dong
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
| |
Collapse
|
13
|
Suleiman AKA, Harkes P, van den Elsen S, Holterman M, Korthals GW, Helder J, Kuramae EE. Organic amendment strengthens interkingdom associations in the soil and rhizosphere of barley (Hordeum vulgare). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 695:133885. [PMID: 31756853 DOI: 10.1016/j.scitotenv.2019.133885] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/25/2019] [Accepted: 08/10/2019] [Indexed: 06/10/2023]
Abstract
Anthropogenic modification of soil systems has diverse impacts on food web interactions and ecosystem functioning. To understand the positive, neutral or adverse effects of agricultural practices on the associations of community members of soil microbes and microfaunal biomes, we characterized the effects of different fertilization types (organic, inorganic and a combination of organic and inorganic) on the food web active communities in the bulk soil and rhizosphere compartments in field conditions. We examined the influence of fertilization on (i) individual groups (bacteria, protozoa and fungi as microbe representatives and metazoans as microfauna representatives) and (ii) inter-kingdom interactions (focusing on the interactions between bacteria and eukaryotic groups) both neglecting and considering environmental factors in our analysis in combination with the microbial compositional data. Our results revealed different patterns of biota communities under organic versus inorganic fertilization, which shaped food web associations in both the bulk and rhizosphere compartments. Overall, organic fertilization increased the complexity of microbial-microfaunal ecological associations with inter- and intra- connections among categories of primary decomposers (bacteria and fungi) and predators (protozoa and microfauna) and differences in potential function in the soil food web in both the bulk and rhizosphere compartments. Furthermore, the inter-connections between primary decomposers and predators in bulk soil were more pronounced when environmental factors were considered. We suggest that organic fertilization selects bacterial orders with different potential ecological functions and interactions as survival, predation and cooperation due to more complex environment than those of inorganic or combined fertilization. Our findings support the importance of a comprehensive understanding of trophic food web patterns for soil management systems.
Collapse
Affiliation(s)
- Afnan K A Suleiman
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands.
| | - Paula Harkes
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Sven van den Elsen
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Martijn Holterman
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Gerard W Korthals
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands; Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Johannes Helder
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands
| | - Eiko E Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands.
| |
Collapse
|
14
|
Anastopoulos I, Omirou M, Stephanou C, Oulas A, Vasiliades MA, Efstathiou AM, Ioannides IM. Valorization of agricultural wastes could improve soil fertility and mitigate soil direct N 2O emissions. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 250:109389. [PMID: 31499464 DOI: 10.1016/j.jenvman.2019.109389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/26/2019] [Accepted: 08/10/2019] [Indexed: 06/10/2023]
Abstract
The emerging need for sustainable management of the increasing quantities of urban and industrial organic wastes creates opportunities for the development of alternative strategies for the improvement of degraded soils. The current study was performed to examine the effects of agricultural wastes application on soil bacterial community as well as CO2 and N2O direct gas emissions. Untreated soils were compared with soils, which received the same amount of N (100 μg/g soil) in the form of ammonium nitrate and organic agricultural waste. In particular, soils were incubated with three different organic agricultural wastes, orange (OP), mandarin (MP) and banana peels (BP) and ammonium nitrate (F) after adjusting soil water at 70% of its holding capacity. In the current study, soil chemical characteristics, quantitative PCR of denitrifiers (nirK, nirS, nosZI and nosZII) and16s rRNA amplicon sequencing were assessed to examine the links between the soil microbial communities and short-term soil direct N2O emissions when treated with agricultural wastes. The highest soil direct N2O emissions were recorded in soils received ammonium nitrate while soils received agricultural wastes exhibited substantially lower soil direct N2O emissions. On the contrary, agricultural wastes stimulated CO2 accumulation as well as the growth of copiotrophic bacterial groups like Proteobacteria and Firmicutes. Interestingly, direct soil N2O emissions were decoupled from the density of denitrifier community while agricultural wastes caused a substantial reduction of the relative abundance of bacterial taxa associated with N2O emissions in the soil. This study proves evidence that agricultural wastes could be integrated in a waste management strategy, which inter alia includes their direct use in agricultural ecosystems resulting in reduced N2O emissions.
Collapse
Affiliation(s)
| | - Michalis Omirou
- Agricultural Research Institute, Department of Agrobiotechnology, Cyprus.
| | - Coralea Stephanou
- Agricultural Research Institute, Department of Agrobiotechnology, Cyprus
| | - Anastasios Oulas
- Cyprus Institute of Neurology and Genetics, Bioinformatics Group, Cyprus
| | - Michalis A Vasiliades
- University of Cyprus, Department of Chemistry, Heterogeneous Catalysis Laboratory, Cyprus
| | - Angelos M Efstathiou
- University of Cyprus, Department of Chemistry, Heterogeneous Catalysis Laboratory, Cyprus
| | | |
Collapse
|
15
|
Short-Term Effects of Different Organic Amendments on Soil Fungal Composition. SUSTAINABILITY 2019. [DOI: 10.3390/su11010198] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fungi play an essential role in recovering the quality and fertility of soil. There is a limited understating of the complex response of fungal diversity to different organic materials in clay loam soil. Here, we report the response of soil fungi toward the short-term application of manure (M), sugarcane straw (S), and sugarcane straw plus manure (MS), including no organic material control (CK) at two different time points (50 and 100 days after application). Illumina sequencing was used to examine the fungal communities. Our results reveal a significant shift among the soil fungal community structure associated with each organic material application. After both time points, amendments—especially M and MS—decreased the fungal richness and stimulated the copiotrophic fungal group (Ascomycota) compared to the control soil (CK) and S-amended soil. On the contrary, as compared to the M and MS-amended soils, the CK and S-amended soils at both time points increased the fungal richness and stimulated the oligotrophic fungal groups. Organic material use, especially M and MS, showed variable results regarding pathogenic fungi enhancing the abundance of Lophodermium and Cercophora and decreasing Fusarium. Concerning the abundance of plant-beneficial fungi, Mortierella was reduced, and Podospora was increased by M and MS input. FUNGuild showed that the amendment of organic materials efficiently declined the abundance of endophytes and plant pathogens, but also enhanced the animal pathogens in terms of abundance with respect to CK at two time points. This study could be useful to provide a novel understanding of the management of soil-borne pathogens by organic amendments for the sustainable production of short-term crops.
Collapse
|
16
|
Lourenço KS, Suleiman AKA, Pijl A, van Veen JA, Cantarella H, Kuramae EE. Resilience of the resident soil microbiome to organic and inorganic amendment disturbances and to temporary bacterial invasion. MICROBIOME 2018; 6:142. [PMID: 30103819 PMCID: PMC6090642 DOI: 10.1186/s40168-018-0525-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/01/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Vinasse, a by-product of sugarcane ethanol production, is recycled by sugarcane plantations as a fertilizer due to its rich nutrient content. However, the impacts of the chemical and microbial composition of vinasse on soil microbiome dynamics are unknown. Here, we evaluate the recovery of the native soil microbiome after multiple disturbances caused by the application of organic vinasse residue, inorganic nitrogen, or a combination of both during the sugarcane crop-growing season (389 days). Additionally, we evaluated the resistance of the resident soil microbial community to the vinasse microbiome. RESULTS Vinasse applied alone or 30 days prior to N resulted in similar changes in the soil microbial community. Furthermore, the impact of the application of vinasse together with N fertilizer on the soil microbial community differed from that of N fertilizer alone. Organic vinasse is a source of microbes, nutrients, and organic matter, and the combination of these factors drove the changes in the resident soil microbial community. However, these changes were restricted to a short period of time due to the capacity of the soil community to recover. The invasive bacteria present in the vinasse microbiome were unable to survive in the soil conditions and disappeared after 31 days, with the exception of the Acetobacteraceae (native in the soil) and Lactobacillaceae families. CONCLUSION Our analysis showed that the resident soil microbial community was not resistant to vinasse and inorganic N application but was highly resilient.
Collapse
Affiliation(s)
- Késia Silva Lourenço
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, Campinas, SP, 13020-902, Brazil
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Afnan K A Suleiman
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - A Pijl
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - J A van Veen
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - H Cantarella
- Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, Campinas, SP, 13020-902, Brazil
| | - E E Kuramae
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
| |
Collapse
|
17
|
Lukiwati DR, Pujaningsih RI, Murwani R. The Effect of Organic Phosphorus and Nitrogen Enriched Manure on Nutritive Value of Sweet Corn Stover. ACTA ACUST UNITED AC 2018. [DOI: 10.1088/1755-1315/119/1/012018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
18
|
Shrestha U, Dee ME, Ownley BH, Butler DM. Anaerobic Soil Disinfestation Reduces Germination and Affects Colonization of Sclerotium rolfsii Sclerotia. PHYTOPATHOLOGY 2018; 108:342-351. [PMID: 29045190 DOI: 10.1094/phyto-04-17-0152-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Growth chamber and field studies were conducted with organic amendment mixtures of carbon (C) and nitrogen (N) at C:N ratios 10:1, 20:1, 30:1, and 40:1 and amendment rates of C at 2, 4, 6, and 8 mg/g of soil (C:N ratio 30:1) to evaluate anaerobic soil disinfestation (ASD) effects on germination and colonization of Sclerotium rolfsii. In the growth chamber, sclerotial germination was reduced in all ASD treatments regardless of C:N ratio (0.6 to 8.5% germination) or amendment rate (7.5 to 46%) as compared with nonamended controls (21 to 36% and 61 to 96%, respectively). ASD treatment increased Trichoderma spp. colonization of sclerotia, with consistently higher colonization in ASD treatments with amendment rates of C at 2 or 4 mg/g of soil (>87% colonization) compared with nonamended controls (<50% colonization). In the 2014 field study, sclerotial germination was reduced by 24 to 30% in ASD treatments when compared with the nonamended control. Sclerotial colonization by Trichoderma spp. was predominant; however, other potential mycoparasites (i.e., Aspergillus spp., Fusarium spp., zygomycetes, and other fungi) were present in the field study. Amendment C:N ratios in the range of 10:1 to 40:1 were equally effective in reducing sclerotial germination and enhancing colonization by potentially beneficial mycoparasites of sclerotia.
Collapse
Affiliation(s)
- Utsala Shrestha
- First and fourth authors: Department of Plant Sciences, and second and third authors: Department of Entomology and Plant Pathology, University of Tennessee, Knoxville
| | - Mary E Dee
- First and fourth authors: Department of Plant Sciences, and second and third authors: Department of Entomology and Plant Pathology, University of Tennessee, Knoxville
| | - Bonnie H Ownley
- First and fourth authors: Department of Plant Sciences, and second and third authors: Department of Entomology and Plant Pathology, University of Tennessee, Knoxville
| | - David M Butler
- First and fourth authors: Department of Plant Sciences, and second and third authors: Department of Entomology and Plant Pathology, University of Tennessee, Knoxville
| |
Collapse
|
19
|
Gu Y, Wang Y, Lu S, Xiang Q, Yu X, Zhao K, Zou L, Chen Q, Tu S, Zhang X. Long-term Fertilization Structures Bacterial and Archaeal Communities along Soil Depth Gradient in a Paddy Soil. Front Microbiol 2017; 8:1516. [PMID: 28861048 PMCID: PMC5559540 DOI: 10.3389/fmicb.2017.01516] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/27/2017] [Indexed: 01/23/2023] Open
Abstract
Soil microbes provide important ecosystem services. Though the effects of changes in nutrient availability due to fertilization on the soil microbial communities in the topsoil (tilled layer, 0–20 cm) have been extensively explored, the effects on communities and their associations with soil nutrients in the subsoil (below 20 cm) which is rarely impacted by tillage are still unclear. 16S rRNA gene amplicon sequencing was used to investigate bacterial and archaeal communities in a Pup-Calric-Entisol soil treated for 32 years with chemical fertilizer (CF) and CF combined with farmyard manure (CFM), and to reveal links between soil properties and specific bacterial and archaeal taxa in both the top- and subsoil. The results showed that both CF and CFM treatments increased soil organic carbon (SOC), soil moisture (MO) and total nitrogen (TN) while decreased the nitrate_N content through the profile. Fertilizer applications also increased Olsen phosphorus (OP) content in most soil layers. Microbial communities in the topsoil were significantly different from those in subsoil. Compared to the CF treatment, taxa such as Nitrososphaera, Nitrospira, and several members of Acidobacteria in topsoil and Subdivision 3 genera incertae sedis, Leptolinea, and Bellilinea in subsoil were substantially more abundant in CFM. A co-occurrence based network analysis demonstrated that SOC and OP were the most important soil parameters that positively correlated with specific bacterial and archaeal taxa in topsoil and subsoil, respectively. Hydrogenophaga was identified as the keystone genus in the topsoil, while genera Phenylobacterium and Steroidobacter were identified as the keystone taxa in subsoil. The taxa identified above are involved in the decomposition of complex organic compounds and soil carbon, nitrogen, and phosphorus transformations. This study revealed that the spatial variability of soil properties due to long-term fertilization strongly shapes the bacterial and archaeal community composition and their interactions at both high and low taxonomic levels across the whole soil profile.
Collapse
Affiliation(s)
- Yunfu Gu
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Yingyan Wang
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Sheng'e Lu
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Quanju Xiang
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Xiumei Yu
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Ke Zhao
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Likou Zou
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Qiang Chen
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Shihua Tu
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural SciencesChengdu, China
| | - Xiaoping Zhang
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| |
Collapse
|