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Ishaq SE, Ahmad T, Liang L, Xie R, Yu T, Wang Y, Wang F. Cultivation of Diverse Novel Marine Bacteria from Deep Ocean Sediment Using Spent Culture Supernatant of Ca. Bathyarchaeia Enrichment. J Microbiol 2024; 62:611-625. [PMID: 38985432 DOI: 10.1007/s12275-024-00145-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 07/11/2024]
Abstract
Most microorganisms resist pure cultivation under conventional laboratory conditions. One of the primary issues for this un-culturability is the absence of biologically produced growth-promoting factors in traditionally defined growth media. However, whether cultivating microbes by providing spent culture supernatant of pivotal microbes in the growth medium can be an effective approach to overcome this limitation is still an under-explored area of research. Here, we used the spent culture medium (SCM) method to isolate previously uncultivated marine bacteria and compared the efficiency of this method with the traditional cultivation (TC) method. In the SCM method, Ca. Bathyarchaeia-enriched supernatant (10%) was used along with recalcitrant organic substrates such as lignin, humic acid, and organic carbon mixture. Ca. Bathyarchaeia, a ubiquitous class of archaea, have the capacity to produce metabolites, making their spent culture supernatant a key source to recover new bacterial stains. Both cultivation methods resulted in the recovery of bacterial species from the phyla Pseudomonadota, Bacteroidota, Actinomycetota, and Bacillota. However, our SCM approach also led to the recovery of species from rarely cultivated groups, such as Planctomycetota, Deinococcota, and Balneolota. In terms of the isolation of new taxa, the SCM method resulted in the cultivation of 80 potential new strains, including one at the family, 16 at the genus, and 63 at the species level, with a novelty ratio of ~ 35% (80/219). In contrast, the TC method allowed the isolation of ~ 10% (19/171) novel strains at species level only. These findings suggest that the SCM approach improved the cultivation of novel and diverse bacteria.
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Affiliation(s)
- Sidra Erum Ishaq
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Tariq Ahmad
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Lewen Liang
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Ruize Xie
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Tiantian Yu
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
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Wang X, Fang J, Li L, Li X, Liu P, Song B, Adams J, Xiao Y, Fang Z. Gongronella sp. w5 hydrolyzes plant sucrose and releases fructose to recruit phosphate-solubilizing bacteria to provide plants with phosphorus. Appl Environ Microbiol 2024; 90:e0053424. [PMID: 38904410 PMCID: PMC11267922 DOI: 10.1128/aem.00534-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/22/2024] [Indexed: 06/22/2024] Open
Abstract
The mechanisms of how plant-beneficial rhizospheric fungi interact with the soil microbial community to promote plant growth by facilitating their phosphorus acquisition are poorly understood. This work supported that a Mucoromycotina fungus, Gongronella sp. w5 (w5), could promote phosphorus uptake of Medicago truncatula by increasing the available phosphorus (P) in the soil. The abundance of phosphate-solubilizing bacteria (PSB) and the activity of alkaline phosphatase (ALP) in alfalfa rhizosphere soil increased after w5 inoculation. Further analysis showed that w5 donated a portion of ALP activity and also stimulated the PSB to secrete ALP during plant-w5-PSB interaction to help release more available P in the rhizosphere of M. truncatula. Unlike most plant-beneficial rhizospheric fungi that mainly acquire hexoses from plants, w5 gained sucrose directly from the host plant and then recruited PSB to aid P acquisition by hydrolyzing sucrose and releasing mainly fructose to induce PSB to secrete ALP. IMPORTANCE This work supported that after absorbing plant sucrose, Gongronella sp. w5 mainly releases sucrose hydrolysis product fructose into the environment. Fructose was used as a carbon source and signaling molecules to induce PSB to co-produce higher alkaline phosphatase activity, releasing soil-available phosphorus and promoting M. truncatula growth. This is the first report that plant-beneficial fungi could directly metabolize sucrose from plants and then recruit PSB to aid P acquisition by providing fructose. Our findings revealed the diversity in pathways of plant-fungi-PSB interactions on soil P acquisition and deepened our understanding of the cooperation of growth-promoting microorganisms in plant rhizosphere.
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Affiliation(s)
- Xiaojie Wang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
| | - Junnan Fang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
| | - Li Li
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
| | - Xing Li
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
| | - Pu Liu
- College of Horticulture, Anhui Agricultural University, Hefei, Anhui, China
| | - Bin Song
- School of Geography and Ocean Sciences, Nanjing University, Nanjing, China
| | - Jonathan Adams
- School of Geography and Ocean Sciences, Nanjing University, Nanjing, China
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
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Yang F, Wang M, Zhao L, Fan B, Sun N, Liu J, Sun X, Dong Z. The role of cattle manure-driven polysaccharide precursors in humus formation during composting of spent mushroom substrate. Front Microbiol 2024; 15:1375808. [PMID: 39091308 PMCID: PMC11291364 DOI: 10.3389/fmicb.2024.1375808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024] Open
Abstract
The study examined the impact of adding cattle manure to the composting process of Agaricus bisporus mushroom substrate on compost humification. A control group CK comprised entirely of Agaricus bisporus mushroom substrate, while the experimental group CD (70 percent Agaricus bisporus mushroom substrate and 30 percent cattle manure) comprised the two composting treatments that were established. The study determined that the addition of cow dung has promoted the formation of humus components. Particularly, humic substance (HS-C) and humic acid (HA) increased by 41.3 and 74.7%, respectively, and the ratio of humic acid to fulvic acid (HA/FA) also increased by 2.78. It showed that the addition of cow dung accelerated the synthesis and decomposition of precursors, such as polysaccharides, polyphenols, and reducing sugars. Thereby promoting the formation of humic acid. Network analysis revealed that adding cow dung promoted microbial interactions increased the complexity and stability of the bacterial and fungal symbiotic network, enhanced cooperation and reciprocity among microbes, and assisted in transforming fulvic acid (FA) components. Structural equation modeling (SEM) is a multivariate data analysis method for analyzing complex relationships among constructs and core indicators. SEM illustrated that introducing cattle manure into the composting process resulted in alterations to the correlation between physicochemical parameters and the microbial community, in addition to humus formation. Polysaccharides are the primary precursors for polymerization to form HA, which is an essential prerequisite for the conversion of fulvic acid to humic acid. Additionally, microbes affected the formation of humus, with bacteria substantially more influential than fungi. These findings provide new ideas for regulating the degree of humification in the composting process and have important practical implications for optimizing mushroom cultivation and composting techniques today.
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Affiliation(s)
- Fengjun Yang
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, China
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Isaac A, Mohamed AR, Amin SA. Rhodobacteraceae are key players in microbiome assembly of the diatom Asterionellopsis glacialis. Appl Environ Microbiol 2024; 90:e0057024. [PMID: 38809046 PMCID: PMC11218658 DOI: 10.1128/aem.00570-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/05/2024] [Indexed: 05/30/2024] Open
Abstract
The complex interactions between bacterioplankton and phytoplankton have prompted numerous studies that investigate phytoplankton microbiomes with the aim of characterizing beneficial or opportunistic taxa and elucidating core bacterial members. Oftentimes, this knowledge is garnered through 16S rRNA gene profiling of microbiomes from phytoplankton isolated across spatial and temporal scales, yet these studies do not offer insight into microbiome assembly and structuring. In this study, we aimed to identify taxa central to structuring and establishing the microbiome of the ubiquitous diatom Asterionellopsis glacialis. We introduced a diverse environmental bacterial community to A. glacialis in nutrient-rich or nutrient-poor media in a continuous dilution culture setup and profiled the bacterial community over 7 days. 16S rRNA amplicon sequencing showed that cyanobacteria (Coleofasciculaceae) and Rhodobacteraceae dominate the microbiome early on and maintain a persistent association throughout the experiment. Differential abundance, co-abundance networks, and differential association analyses revealed that specific members of the family Rhodobacteraceae, particularly Sulfitobacter amplicon sequence variants, become integral members in microbiome assembly. In the presence of the diatom, Sulfitobacter species and other Rhodobacteraceae developed positive associations with taxa that are typically in high abundance in marine ecosystems (Pelagibacter and Synechococcus), leading to restructuring of the microbiome compared to diatom-free controls. These positive associations developed predominantly under oligotrophic conditions, highlighting the importance of investigating phytoplankton microbiomes in as close to natural conditions as possible to avoid biases that develop under routine laboratory conditions. These findings offer further insight into phytoplankton-bacteria interactions and illustrate the importance of Rhodobacteraceae, not merely as phytoplankton symbionts but as key taxa involved in microbiome assembly. IMPORTANCE Most, if not all, microeukaryotic organisms harbor an associated microbial community, termed the microbiome. The microscale interactions that occur between these partners have global-scale consequences, influencing marine primary productivity, carbon cycling, and harmful algal blooms to name but a few. Over the last decade, there has been a growing interest in the study of phytoplankton microbiomes, particularly within the context of bloom dynamics. However, long-standing questions remain regarding the process of phytoplankton microbiome assembly. The significance of our research is to tease apart the mechanism of microbiome assembly with a particular focus on identifying bacterial taxa, which may not merely be symbionts but architects of the phytoplankton microbiome. Our results strengthen the understanding of the ecological mechanisms that underpin phytoplankton-bacteria interactions in order to accurately predict marine ecosystem responses to environmental perturbations.
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Affiliation(s)
- Ashley Isaac
- Marine Microbiomics Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Amin R. Mohamed
- Marine Microbiomics Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Shady A. Amin
- Marine Microbiomics Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Mubadala ACCESS Center, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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Gong F, He C, Li X, Wang K, Li M, Zhou X, Xu M, He X. Impacts of fertilization methods on Salvia miltiorrhiza quality and characteristics of the epiphytic microbial community. FRONTIERS IN PLANT SCIENCE 2024; 15:1395628. [PMID: 38817929 PMCID: PMC11138495 DOI: 10.3389/fpls.2024.1395628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024]
Abstract
Plant epiphytic microorganisms have established a unique symbiotic relationship with plants, which has a significant impact on their growth, immune defense, and environmental adaptation. However, the impact of fertilization methods on the epiphytic microbial community and their correlation with the yield and quality of medicinal plant was still unclear. In current study, we conducted a field fertilization experiment and analyzed the composition of epiphytic bacterial and fungal communities employing high throughput sequencing data in different organs (roots, stems, and leaves) of Salvia miltiorrhiza, as well as their correlation with plant growth. The results showed that fertilization significantly affected the active ingredients and hormone content, soil physicochemical properties, and the composition of epiphytic microbial communities. After fertilization, the plant surface was enriched with a core microbial community mainly composed of bacteria from Firmicutes, Proteobacteria, and Actinobacteria, as well as fungi from Zygomycota and Ascomycota. Additionally, plant growth hormones were the principal factors leading to alterations in the epiphytic microbial community of S. miltiorrhiza. Thus, the most effective method of fertilization involved the application of base fertilizer in combination with foliar fertilizer. This study provides a new perspective for studying the correlation between microbial community function and the quality of S. miltiorrhiza, and also provides a theoretical basis for the cultivation and sustainable development of high-quality medicinal plants.
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Affiliation(s)
- Feng Gong
- College of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Chao He
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xianen Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kehan Wang
- College of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Min Li
- College of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Xiangyun Zhou
- College of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Minghui Xu
- College of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Xueli He
- College of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
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Jiang M, Dong C, Bian W, Zhang W, Wang Y. Effects of different fertilization practices on maize yield, soil nutrients, soil moisture, and water use efficiency in northern China based on a meta-analysis. Sci Rep 2024; 14:6480. [PMID: 38499586 PMCID: PMC10948899 DOI: 10.1038/s41598-024-57031-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 03/13/2024] [Indexed: 03/20/2024] Open
Abstract
The application of fertilizer to ensure the steady improvement of crop yield has become the main means of agricultural production. However, it remains to be determined whether fertilization practices with different combinations of nitrogen (N), phosphorus (P), potassium (K), and organic (O) fertilizers play a positive role in the sustainability of maize yield and the soil in which it is grown. Therefore,this meta-analysis extracted 2663 data points from 76 studies to systematically analyze and explore the effects of different fertilization measures on maize yield, soil nutrients, water content and water use efficiency (WUE) in northern China. Articles addressing this topic showed that fertilization effectively increased the soil nutrient content and maize yield. The soil organic matter (SOM) increased by 2.36 (N)-55.38% (NPO), total nitrogen content increased by 6.10 (N)-56.39% (NPO), available phosphorus content increased by 17.12 (N)-474.74% (NPO), and available potassium content changed by - 2.90 (NP)-64.40% (NPO). Soil moisture increased by 3.59% under a single organic fertilizer application and decreased by 4.27-13.40% under the other treatments. Compared with no fertilization, the yield increase of fertilized maize reached 11.65-220.42%. NP, NPK and NPKO contributed the most to increased yield in lithological, black and fluvo-aquic soils, respectively. The effects of different fertilization practices on maize yield varied in response to the same meteorological factors. The WUE increased from 9.51 to 160.72%. In conclusion, rational fertilization can improve the soil nutrient content and increase maize yield. The combined application of chemical and organic fertilizer showed the greatest increase in yield and WUE. Organic fertilizer application alone increased soil moisture. Our results provide a theoretical basis for fertilizer application and for improving the soil structure for maize cultivation in northern China.
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Affiliation(s)
- Minghao Jiang
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, 150030, China
| | - Chao Dong
- Inner Mongolia University of Technology, Hohhot, 010051, Inner Mongolia, China
| | - Wenpeng Bian
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, 150030, China
| | - Wenbei Zhang
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, 150030, China
| | - Yong Wang
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, 150030, China.
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
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Faghihinia M, Halverson LJ, Hršelová H, Bukovská P, Rozmoš M, Kotianová M, Jansa J. Nutrient-dependent cross-kingdom interactions in the hyphosphere of an arbuscular mycorrhizal fungus. Front Microbiol 2024; 14:1284648. [PMID: 38239731 PMCID: PMC10794670 DOI: 10.3389/fmicb.2023.1284648] [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: 08/28/2023] [Accepted: 11/27/2023] [Indexed: 01/22/2024] Open
Abstract
Introduction The hyphosphere of arbuscular mycorrhizal (AM) fungi is teeming with microbial life. Yet, the influence of nutrient availability or nutrient forms on the hyphosphere microbiomes is still poorly understood. Methods Here, we examined how the microbial community (prokaryotic, fungal, protistan) was affected by the presence of the AM fungus Rhizophagus irregularis in the rhizosphere and the root-free zone, and how different nitrogen (N) and phosphorus (P) supplements into the root-free compartment influenced the communities. Results The presence of AM fungus greatly affected microbial communities both in the rhizosphere and the root-free zone, with prokaryotic communities being affected the most. Protists were the only group of microbes whose richness and diversity were significantly reduced by the presence of the AM fungus. Our results showed that the type of nutrients AM fungi encounter in localized patches modulate the structure of hyphosphere microbial communities. In contrast we did not observe any effects of the AM fungus on (non-mycorrhizal) fungal community composition. Compared to the non-mycorrhizal control, the root-free zone with the AM fungus (i.e., the AM fungal hyphosphere) was enriched with Alphaproteobacteria, some micropredatory and copiotroph bacterial taxa (e.g., Xanthomonadaceae and Bacteroidota), and the poorly characterized and not yet cultured Acidobacteriota subgroup GP17, especially when phytate was added. Ammonia-oxidizing Nitrosomonas and nitrite-oxidizing Nitrospira were significantly suppressed in the presence of the AM fungus in the root-free compartment, especially upon addition of inorganic N. Co-occurrence network analyses revealed that microbial communities in the root-free compartment were complex and interconnected with more keystone species when AM fungus was present, especially when the root-free compartment was amended with phytate. Conclusion Our study showed that the form of nutrients is an important driver of prokaryotic and eukaryotic community assembly in the AM fungal hyphosphere, despite the assumed presence of a stable and specific AM fungal hyphoplane microbiome. Predictable responses of specific microbial taxa will open the possibility of using them as co-inoculants with AM fungi, e.g., to improve crop performance.
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Affiliation(s)
- Maede Faghihinia
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA, United States
| | - Larry J. Halverson
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA, United States
| | - Hana Hršelová
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Petra Bukovská
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Martin Rozmoš
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Michala Kotianová
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Jan Jansa
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
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Du C, Xu R, Zhao X, Liu Y, Zhou X, Zhang W, Zhou X, Hu N, Zhang Y, Sun Z, Wang Z. Association between host nitrogen absorption and root-associated microbial community in field-grown wheat. Appl Microbiol Biotechnol 2023; 107:7347-7364. [PMID: 37747613 DOI: 10.1007/s00253-023-12787-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/08/2023] [Accepted: 09/02/2023] [Indexed: 09/26/2023]
Abstract
Plant roots and rhizosphere soils assemble diverse microbial communities, and these root-associated microbiomes profoundly influence host development. Modern wheat has given rise to numerous cultivars for its wide range of ecological adaptations and commercial uses. Variations in nitrogen uptake by different wheat cultivars are widely observed in production practices. However, little is known about the composition and structure of the root-associated microbiota in different wheat cultivars, and it is not sure whether root-associated microbial communities are relevant in host nitrogen absorption. Therefore, there is an urgent need for systematic assessment of root-associated microbial communities and their association with host nitrogen absorption in field-grown wheat. Here, we investigated the root-associated microbial community composition, structure, and keystone taxa in wheat cultivars with different nitrogen absorption characteristics at different stages and their relationships with edaphic variables and host nitrogen uptake. Our results indicated that cultivar nitrogen absorption characteristics strongly interacted with bacterial and archaeal communities in the roots and edaphic physicochemical factors. The impact of host cultivar identity, developmental stage, and spatial niche on bacterial and archaeal community structure and network complexity increased progressively from rhizosphere soils to roots. The root microbial community had a significant direct effect on plant nitrogen absorption, while plant nitrogen absorption and soil temperature also significantly influenced root microbial community structure. The cultivar with higher nitrogen absorption at the jointing stage tended to cooperate with root microbial community to facilitate their own nitrogen absorption. Our work provides important information for further wheat microbiome manipulation to influence host nitrogen absorption. KEY POINTS: • Wheat cultivar and developmental stage affected microbiome structure and network. • The root microbial community strongly interacted with plant nitrogen absorption. • High nitrogen absorption cultivar tended to cooperate with root microbiome.
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Affiliation(s)
- Chenghang Du
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Runlai Xu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xuan Zhao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Ying Liu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiaohan Zhou
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Wanqing Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiaonan Zhou
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Naiyue Hu
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yinghua Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhencai Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Zhimin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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Chen L, Xin X, Li J, Han C, Xiong W, Luo Y, Sun R, Zhang J. Phosphorus Fertilization Boosts Mineral-Associated Soil Organic Carbon Formation Associated with Phagotrophic Protists. MICROBIAL ECOLOGY 2023; 86:2541-2551. [PMID: 37401933 DOI: 10.1007/s00248-023-02258-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 06/20/2023] [Indexed: 07/05/2023]
Abstract
Long-term fertilization affects soil organic C accumulation. A growing body of research has revealed critical roles of bacteria in soil organic C accumulation, particularly through mineral-associated organic C (MAOC) formation. Protists are essential components of soil microbiome, but the relationships between MAOC formation and protists under long-term fertilization remain unclear. Here, we used cropland soil from a long-term fertilization field trial and conducted two microcosm experiments with 13C-glucose addition to investigate the effects of N and P fertilizations on MAOC formation and the relationships with protists. The results showed that long-term fertilization (especially P fertilization) significantly (P < 0.05) increased 13C-MAOC content. Compared with P-deficient treatment, P replenishment enriched the number of protists (mainly Amoebozoa and Cercozoa) and bacteria (mainly Acidobacteriota, Bacteroidota, and Gammaproteobacteria), and significantly (P < 0.001) promoted the abundances of bacterial functional genes controlling C, N, P, and S metabolisms. The community composition of phagotrophic protists prominently (P < 0.001) correlated with the bacterial community composition, bacterial functional gene abundance, and 13C-MAOC content. Co-occurrence networks of phagotrophic protists and bacteria were more connected in soil with the N inoculum added than in soil with the NP inoculum added. P replenishment strengthened bacterial 13C assimilation (i.e., 13C-phospholipid fatty acid content), which negatively (P < 0.05) correlated with the number and relative abundance of phagotrophic Cercozoa. Together, these results suggested that P fertilization boosts MAOC formation associated with phagotrophic protists. Our study paves the way for future research to harness the potential of protists to promote belowground C accrual in agroecosystems.
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Affiliation(s)
- Lin Chen
- Fengqiu Experimental Station of National Ecosystem Research Network of China, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing, 210008, Jiangsu Province, China
| | - Xiuli Xin
- Fengqiu Experimental Station of National Ecosystem Research Network of China, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing, 210008, Jiangsu Province, China
| | - Jingwang Li
- Fengqiu Experimental Station of National Ecosystem Research Network of China, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing, 210008, Jiangsu Province, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changdong Han
- College of Land and Environment, Shenyang Agricultural University, Shenyang, 110866, China
| | - Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yu Luo
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Ruibo Sun
- Anhui Province Key Laboratory of Farmland Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Jiabao Zhang
- Fengqiu Experimental Station of National Ecosystem Research Network of China, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing, 210008, Jiangsu Province, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- College of Land and Environment, Shenyang Agricultural University, Shenyang, 110866, China.
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Li L, Meng D, Yin H, Zhang T, Liu Y. Genome-resolved metagenomics provides insights into the ecological roles of the keystone taxa in heavy-metal-contaminated soils. Front Microbiol 2023; 14:1203164. [PMID: 37547692 PMCID: PMC10402746 DOI: 10.3389/fmicb.2023.1203164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/29/2023] [Indexed: 08/08/2023] Open
Abstract
Microorganisms that exhibit resistance to environmental stressors, particularly heavy metals, have the potential to be used in bioremediation strategies. This study aimed to explore and identify microorganisms that are resistant to heavy metals in soil environments as potential candidates for bioremediation. Metagenomic analysis was conducted using microbiome metagenomes obtained from the rhizosphere of soil contaminated with heavy metals and mineral-affected soil. The analysis resulted in the recovery of a total of 175 metagenome-assembled genomes (MAGs), 73 of which were potentially representing novel taxonomic levels beyond the genus level. The constructed ecological network revealed the presence of keystone taxa, including Rhizobiaceae, Xanthobacteraceae, Burkholderiaceae, and Actinomycetia. Among the recovered MAGs, 50 were associated with these keystone taxa. Notably, these MAGs displayed an abundance of genes conferring resistance to heavy metals and other abiotic stresses, particularly those affiliated with the keystone taxa. These genes were found to combat excessive accumulation of zinc/manganese, arsenate/arsenite, chromate, nickel/cobalt, copper, and tellurite. Furthermore, the keystone taxa were found to utilize both organic and inorganic energy sources, such as sulfur, arsenic, and carbon dioxide. Additionally, these keystone taxa exhibited the ability to promote vegetation development in re-vegetated mining areas through phosphorus solubilization and metabolite secretion. In summary, our study highlights the metabolic adaptability and ecological significance of microbial keystone taxa in mineral-affected soils. The MAGs associated with keystone taxa exhibited a markedly higher number of genes related to abiotic stress resistance and plant growth promotion compared to non-keystone taxa MAGs.
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Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Teng Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
- Hunan Urban and Rural Environmental Construction Co., Ltd, Changsha, China
| | - Yongjun Liu
- Hunan Tobacco Science Institute, Changsha, China
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11
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Liu B, Dai Y, Cheng X, He X, Bei Q, Wang Y, Zhou Y, Zhu B, Zhang K, Tian X, Duan M, Xie X, Wang L. Straw mulch improves soil carbon and nitrogen cycle by mediating microbial community structure and function in the maize field. Front Microbiol 2023; 14:1217966. [PMID: 37533822 PMCID: PMC10391546 DOI: 10.3389/fmicb.2023.1217966] [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: 05/06/2023] [Accepted: 06/26/2023] [Indexed: 08/04/2023] Open
Abstract
This study was conducted to investigate the capability of the microbial community characteristics and soil variables to promote carbon and nitrogen cycles in maize fields under straw mulch. We covered the surface soil of the maize field with different amounts of wheat straw (0 kg/ha, 2,250 kg/ha, and 4,500 kg/ha) and used 16S rRNA and ITS sequencing, Biology ECO-plate, traditional enzymology, TOC analyzer, and HPLC to measure bacterial and fungal community composition and functions, characteristics of microbial carbon source metabolism, carbon and nitrogen fraction, enzyme activity, and organic acid content in the maize rhizosphere and non-rhizosphere. The results indicated that short-term straw mulch insignificantly affected the alpha diversity of bacterial and fungal communities whereas significantly influenced their beta diversity. The results of functional prediction revealed that straw mulch considerably boosted the relative abundances of bacteria belonging to chemoheterotrophy, aerobic chemoheterotrophy, ureolysis, and nitrogen fixation and inhibited fermentation and nitrate reduction in maize rhizosphere soil. These processes primarily drove the C and N cycles in soil. Straw mulch also improved fungal saprotrophs by raising the proportion of Chaetomiaceae and Chaetosphaeriaceae. The Biology ECO-plate results illustrated that straw mulch weakened the metabolism capacity of microbial labile carbon resources. As a result, the labile C and N fractions were raised under straw mulch. Our results also showed that straw mulch primarily regulated the microbial community structure in rhizosphere soil by significantly decreasing Firmicutes and Ascomycota relative abundance while increasing Basidiomycota. The fungal community structure is more than bacterial for affecting soil microbial biomass carbon, readily oxidizable organic carbon, dissolved organic carbon, available nitrogen, ammonium, and nitrate directly and indirectly through malic acid content and cellulase, protease, and amylase activity. Overall, our findings imply that straw mulch might influence the bacterial and fungal community structures, thereby boosting the production of labile C and N components and accelerating the C and N cycle in maize fields.
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Affiliation(s)
- Bangyan Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Yisha Dai
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xin Cheng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xian He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Qicheng Bei
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany
| | - Yifan Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Yuling Zhou
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Bo Zhu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Kangping Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xiaoqin Tian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Meichun Duan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xiaoyu Xie
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Longchang Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
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12
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Gomes A, Narciso R, Regalado L, Pinheiro MC, Barros F, Sario S, Santos C, Mendes RJ. Disclosing the native blueberry rhizosphere community in Portugal-an integrated metagenomic and isolation approach. PeerJ 2023; 11:e15525. [PMID: 37397024 PMCID: PMC10312161 DOI: 10.7717/peerj.15525] [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: 03/03/2023] [Accepted: 05/18/2023] [Indexed: 07/04/2023] Open
Abstract
Backgorund The production of red fruits, such as blueberry, has been threatened by several stressors from severe periods of drought, nutrient scarcity, phytopathogens, and costs with fertilization programs with adverse consequences. Thus, there is an urgent need to increase this crop's resilience whilst promoting sustainable agriculture. Plant growth-promoting microorganisms (PGPMs) constitute not only a solution to tackle water and nutrient deficits in soils, but also as a control against phytopathogens and as green compounds for agricultural practices. Methods In this study, a metagenomic approach of the local fungal and bacterial community of the rhizosphere of Vaccinium corymbosum plants was performed. At the same time, both epiphytic and endophytic microorganisms were isolated in order to disclose putative beneficial native organisms. Results Results showed a high relative abundance of Archaeorhizomyces and Serendipita genera in the ITS sequencing, and Bradyrhizobium genus in the 16S sequencing. Diversity analysis disclosed that the fungal community presented a higher inter-sample variability than the bacterial community, and beta-diversity analysis further corroborated this result. Trichoderma spp., Bacillus spp., and Mucor moelleri were isolated from the V. corymbosum plants. Discussion This work revealed a native microbial community capable of establishing mycorrhizal relationships, and with beneficial physiological traits for blueberry production. It was also possible to isolate several naturally-occurring microorganisms that are known to have plant growth-promoting activity and confer tolerance to hydric stress, a serious climate change threat. Future studies should be performed with these isolates to disclose their efficiency in conferring the needed resilience for this and several crops.
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Affiliation(s)
- Anicia Gomes
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Rodrigo Narciso
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Laura Regalado
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Margarida Cardeano Pinheiro
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Filipa Barros
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Sara Sario
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Conceição Santos
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Rafael J. Mendes
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
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13
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Kraut-Cohen J, Zolti A, Rotbart N, Bar-Tal A, Laor Y, Medina S, Shawahna R, Saadi I, Raviv M, Green SJ, Yermiyahu U, Minz D. Short- and long-term effects of continuous compost amendment on soil microbiome community. Comput Struct Biotechnol J 2023; 21:3280-3292. [PMID: 38213903 PMCID: PMC10781717 DOI: 10.1016/j.csbj.2023.05.030] [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: 02/23/2023] [Revised: 05/16/2023] [Accepted: 05/28/2023] [Indexed: 01/13/2024] Open
Abstract
Organic amendment, and especially the use of composts, is a well-accepted sustainable agricultural practice. Compost increases soil carbon and microbial biomass, changes enzymatic activity, and enriches soil carbon and nitrogen stocks. However, relatively little is known about the immediate and long-term temporal dynamics of agricultural soil microbial communities following repeated compost applications. Our study was conducted at two field sites: Newe Ya'ar (NY, Mediterranean climate) and Gilat (G, semi-arid climate), both managed organically over 4 years under either conventional fertilization (0, zero compost) or three levels of compost amendment (20, 40 and 60 m3/ha or 2, 4, 6 L/m2). Microbial community dynamics in the soils was examined by high- and low-time-resolution analyses. Annual community composition in compost-amended soils was significantly affected by compost amendment levels in G (first, second and third years) and in NY (third year). Repeated sampling at high resolution (9-10 times over 1 year) showed that at both sites, compost application initially induced a strong shift in microbial communities, lasting for up to 1 month, followed by a milder response. Compost application significantly elevated alpha diversity at both sites, but differed in the compost-dose correlation effect. We demonstrate higher abundance of taxa putatively involved in organic decomposition and characterized compost-related indicator taxa and a compost-derived core microbiome at both sites. Overall, this study describes temporal changes in the ecology of soil microbiomes in response to compost vs. conventional fertilization.
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Affiliation(s)
- Judith Kraut-Cohen
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
| | - Avihai Zolti
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Nativ Rotbart
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
- Shamir Research Institute, University of Haifa, Qatzrin, Israel
| | - Asher Bar-Tal
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
| | - Yael Laor
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization - Volcani Institute, Newe Ya’ar Research Center, Ramat Yishai 30095, Israel
| | - Shlomit Medina
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization - Volcani Institute, Newe Ya’ar Research Center, Ramat Yishai 30095, Israel
| | - Raneen Shawahna
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
| | - Ibrahim Saadi
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization - Volcani Institute, Newe Ya’ar Research Center, Ramat Yishai 30095, Israel
| | - Michael Raviv
- Institute of Plant Science, Agricultural Research Organization - Volcani Institute, Newe Ya’ar Research Center, Ramat Yishai 30095, Israel
| | - Stefan J. Green
- Genomics and Microbiome Core Facility, Rush University, Chicago, IL, USA
| | - Uri Yermiyahu
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Gilat Research Center, Israel
| | - Dror Minz
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
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14
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Dondjou DT, Diedhiou AG, Mbodj D, Mofini MT, Pignoly S, Ndiaye C, Diedhiou I, Assigbetse K, Manneh B, Laplaze L, Kane A. Rice developmental stages modulate rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization in a West African Sahelian agro-ecosystem. ENVIRONMENTAL MICROBIOME 2023; 18:42. [PMID: 37198640 PMCID: PMC10193678 DOI: 10.1186/s40793-023-00500-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/09/2023] [Indexed: 05/19/2023]
Abstract
BACKGROUND Rhizosphere microbial communities are important components of the soil-plant continuum in paddy field ecosystems. These rhizosphere communities contribute to nutrient cycling and rice productivity. The use of fertilizers is a common agricultural practice in rice paddy fields. However, the long-term impact of the fertilizers usage on the rhizosphere microbial communities at different rice developmental stages remains poorly investigated. Here, we examined the effects of long-term (27 years) N and NPK-fertilization on bacterial and archaeal community inhabiting the rice rhizosphere at three developmental stages (tillering, panicle initiation and booting) in the Senegal River Delta. RESULTS We found that the effect of long-term inorganic fertilization on rhizosphere microbial communities varied with the rice developmental stage, and between microbial communities in their response to N and NPK-fertilization. The microbial communities inhabiting the rice rhizosphere at panicle initiation appear to be more sensitive to long-term inorganic fertilization than those at tillering and booting stages. However, the effect of developmental stage on microbial sensitivity to long-term inorganic fertilization was more pronounced for bacterial than archaeal community. Furthermore, our data reveal dynamics of bacteria and archaea co-occurrence patterns in the rice rhizosphere, with differentiated bacterial and archaeal pivotal roles in the microbial inter-kingdom networks across developmental stages. CONCLUSIONS Our study brings new insights on rhizosphere bacteria and archaea co-occurrence and the long-term inorganic fertilization impact on these communities across developmental stages in field-grown rice. It would help in developing strategies for the successful manipulation of microbial communities to improve rice yields.
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Affiliation(s)
- Donald Tchouomo Dondjou
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- Centre d’Etude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, Sénégal
| | - Abdala Gamby Diedhiou
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
| | - Daouda Mbodj
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- Africa Rice Center (AfricaRice), Saint-Louis, Senegal
| | - Marie-Thérèse Mofini
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- Centre d’Etude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, Sénégal
| | - Sarah Pignoly
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Cheikh Ndiaye
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
| | - Issa Diedhiou
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
| | - Komi Assigbetse
- Laboratoire Mixte International Intensification Écologique Des Sols Cultivés en Afrique de L’Ouest (IESOL), Dakar, Sénégal
- Eco&Sols, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Baboucarr Manneh
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Africa Rice Center (AfricaRice), Saint-Louis, Senegal
| | - Laurent Laplaze
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Aboubacry Kane
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain « Environnement, Sociétés » (CEA-AGIR), UCAD, Santé, Dakar, Sénégal
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15
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Liu J, Qiu T, Peñuelas J, Sardans J, Tan W, Wei X, Cui Y, Cui Q, Wu C, Liu L, Zhou B, He H, Fang L. Crop residue return sustains global soil ecological stoichiometry balance. GLOBAL CHANGE BIOLOGY 2023; 29:2203-2226. [PMID: 36607175 DOI: 10.1111/gcb.16584] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/25/2022] [Indexed: 05/28/2023]
Abstract
Although soil ecological stoichiometry is constrained in natural ecosystems, its responses to anthropogenic perturbations are largely unknown. Inputs of inorganic fertilizer and crop residue are key cropland anthropogenic managements, with potential to alter their soil ecological stoichiometry. We conducted a global synthesis of 682 data pairs to quantify the responses of soil carbon (C), nitrogen (N), and phosphorus (P) and grain yields to combined inputs of crop residue plus inorganic fertilizer compared with only inorganic fertilizer application. Crop residue inputs enhance soil C (10.5%-12%), N (7.63%-9.2%), and P (2.62%-5.13%) contents, with an increase in C:N (2.51%-3.42%) and C:P (7.27%-8.00%) ratios, and grain yields (6.12%-8.64%), indicating that crop residue alleviated soil C limitation caused by inorganic fertilizer inputs alone and was able to sustain balanced stoichiometry. Moreover, the increase in soil C and C:N(P) ratio reached saturation in ~13-16 years after crop residue return, while grain yield increase trend discontinued. Furthermore, we identified that the increased C, N, and P contents and C:N(P) ratios were regulated by the initial pH and C content, and the increase in grain yield was not only related to soil properties, but also negatively related to the amount of inorganic N fertilizer input to a greater extent. Given that crop residual improvement varies with soil properties and N input levels, we propose a predictive model to preliminary evaluate the potential for crop residual improvement. Particularly, we suggest that part of the global budget should be used to subsidize crop residue input management strategies, achieving to a win-win situation for agricultural production, ecological protection, and climate change mitigation.
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Affiliation(s)
- Ji Liu
- Hubei Province Key Laboratory for Geographical Process Analysis and Simulation, Central China Normal University, Wuhan, China
- Department of Ecohydrology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Tianyi Qiu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Chinese Academy of Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Catalonia, Spain
- CREAF, Cerdanyola del Vallès, Catalonia, Spain
| | - Jordi Sardans
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Catalonia, Spain
- CREAF, Cerdanyola del Vallès, Catalonia, Spain
| | - Wenfeng Tan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Xiaomeng Wei
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, China
| | - Yongxing Cui
- College of Urban and Environmental Sciences, Sino-French Institute for Earth System Science, Peking University, Beijing, China
| | - Qingliang Cui
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Chinese Academy of Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Chuanfa Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Lanfa Liu
- Hubei Province Key Laboratory for Geographical Process Analysis and Simulation, Central China Normal University, Wuhan, China
| | - Baitao Zhou
- Hubei Province Key Laboratory for Geographical Process Analysis and Simulation, Central China Normal University, Wuhan, China
| | - Haoran He
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Chinese Academy of Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Linchuan Fang
- Hubei Province Key Laboratory for Geographical Process Analysis and Simulation, Central China Normal University, Wuhan, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Chinese Academy of Sciences, Northwest A&F University, Yangling, Shaanxi, China
- School of Resource and Environmental Engineering, Wuhan University of Technology, Wuhan, China
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16
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Bech PK, Zhang SD, Henriksen NNSE, Bentzon-Tilia M, Strube ML, Gram L. The potential to produce tropodithietic acid by Phaeobacter inhibens affects the assembly of microbial biofilm communities in natural seawater. NPJ Biofilms Microbiomes 2023; 9:12. [PMID: 36959215 PMCID: PMC10036634 DOI: 10.1038/s41522-023-00379-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 03/10/2023] [Indexed: 03/25/2023] Open
Abstract
Microbial secondary metabolites play important roles in biotic interactions in microbial communities and yet, we do not understand how these compounds impact the assembly and development of microbial communities. To address the implications of microbial secondary metabolite production on biotic interactions in the assembly of natural seawater microbiomes, we constructed a model system where the assembly of a natural seawater biofilm community was influenced by the addition of the marine biofilm forming Phaeobacter inhibens that can produce the antibiotic secondary metabolite tropodithietic acid (TDA), or a mutant incapable of TDA production. Because of the broad antibiotic activity of TDA, we hypothesized that the potential of P. inhibens to produce TDA would strongly affect both biofilm and planktonic community assembly patterns. We show that 1.9 % of the microbial composition variance across both environments could be attributed to the presence of WT P. inhibens, and especially genera of the Bacteriodetes were increased by the presence of the TDA producer. Moreover, network analysis with inferred putative microbial interactions revealed that P. inhibens mainly displayed strong positive associations with genera of the Flavobacteriaceae and Alteromonadaceae, and that P. inhibens acts as a keystone OTU in the biofilm exclusively due to its potential to produce TDA. Our results demonstrate the potential impact of microbial secondary metabolites on microbial interactions and assembly dynamics of complex microbial communities.
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Affiliation(s)
| | - Sheng-Da Zhang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
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17
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Jameson BD, Murdock SA, Ji Q, Stevens CJ, Grundle DS, Kim Juniper S. Network analysis of 16S rRNA sequences suggests microbial keystone taxa contribute to marine N 2O cycling. Commun Biol 2023; 6:212. [PMID: 36823449 PMCID: PMC9950131 DOI: 10.1038/s42003-023-04597-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
The mechanisms by which large-scale microbial community function emerges from complex ecological interactions between individual taxa and functional groups remain obscure. We leveraged network analyses of 16S rRNA amplicon sequences obtained over a seven-month timeseries in seasonally anoxic Saanich Inlet (Vancouver Island, Canada) to investigate relationships between microbial community structure and water column N2O cycling. Taxa separately broadly into three discrete subnetworks with contrasting environmental distributions. Oxycline subnetworks were structured around keystone aerobic heterotrophs that correlated with nitrification rates and N2O supersaturations, linking N2O production and accumulation to taxa involved in organic matter remineralization. Keystone taxa implicated in anaerobic carbon, nitrogen, and sulfur cycling in anoxic environments clustered together in a low-oxygen subnetwork that correlated positively with nitrification N2O yields and N2O production from denitrification. Close coupling between N2O producers and consumers in the anoxic basin is indicated by strong correlations between the low-oxygen subnetwork, PICRUSt2-predicted nitrous oxide reductase (nosZ) gene abundances, and N2O undersaturation. This study implicates keystone taxa affiliated with common ODZ groups as a potential control on water column N2O cycling and provides a theoretical basis for further investigations into marine microbial interaction networks.
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Affiliation(s)
- Brett D Jameson
- School of Earth & Ocean Sciences, University of Victoria, P.O. Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada.
| | - Sheryl A Murdock
- Department of Biology, University of Victoria, P.O. Box 1700 CSC, Victoria, BC, V8W 2Y2, Canada
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE01, Bermuda
| | - Qixing Ji
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE01, Bermuda
- Thrust of Earth, Ocean & Atmospheric Sciences, Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou, Guangdong, 511400, China
| | - Catherine J Stevens
- School of Earth & Ocean Sciences, University of Victoria, P.O. Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada
| | - Damian S Grundle
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE01, Bermuda
- School of Ocean Futures & School of Earth & Space Exploration, Arizona State University, Tempe, AZ, 85287-7904, USA
| | - S Kim Juniper
- School of Earth & Ocean Sciences, University of Victoria, P.O. Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada
- Department of Biology, University of Victoria, P.O. Box 1700 CSC, Victoria, BC, V8W 2Y2, Canada
- Ocean Networks Canada, 2474 Arbutus Road, Victoria, BC, V8N 1V8, Canada
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18
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Cui W, Liu Y, Li W, Pei L, Xu S, Sun Y, Liu J, Wang F. Remediation Agents Drive Bacterial Community in a Cd-Contaminated Soil. TOXICS 2023; 11:toxics11010053. [PMID: 36668779 PMCID: PMC9861843 DOI: 10.3390/toxics11010053] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 12/31/2022] [Accepted: 01/02/2023] [Indexed: 05/04/2023]
Abstract
Soil remediation agents (SRAs) such as biochar and hydroxyapatite (HAP) have shown a promising prospect in in situ soil remediation programs and safe crop production. However, the effects of SRAs on soil microbial communities still remain unclear, particularly under field conditions. Here, a field case study was conducted to compare the effects of biochar and HAP on soil bacterial communities in a slightly Cd-contaminated farmland grown with sweet sorghum of different planting densities. We found that both biochar and HAP decreased the diversity and richness of soil bacteria, but they differently altered bacterial community structure. Biochar decreased Chao1 (-7.3%), Observed_species (-8.6%), and Shannon indexes (-1.3%), and HAP caused Shannon (-2.0%) and Simpson indexes (-0.1%) to decline. The relative abundance (RA) of some specific taxa and marker species was differently changed by biochar and HAP. Overall, sweet sorghum cultivation did not significantly alter soil bacterial diversity and richness but caused changes in the RA of some taxa. Some significant correlations were observed between soil properties and bacterial abundance. In conclusion, soil remediation with biochar and HAP caused alterations in soil bacterial communities. Our findings help to understand the ecological impacts of SRAs in soil remediation programs.
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19
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Zhang S, Zhang H, Liu H, Wang H, Xiu W, Li G, Zhang G, Zhou Z, Jiang N, Zhang H, Zhao J, Yang D. Fertilization drives distinct biotic and abiotic factors in regulating functional groups of protists in a 5-year fertilization system. Front Microbiol 2022; 13:1036362. [PMID: 36545203 PMCID: PMC9760849 DOI: 10.3389/fmicb.2022.1036362] [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: 09/04/2022] [Accepted: 11/10/2022] [Indexed: 12/12/2022] Open
Abstract
Introduction Protists play an important role in nutrient cycling, microbiome stability and soil fertility maintenance. However, the driving force of protistan functional groups remains poorly understood in agricultural ecosystems. Methods We investigated the impacts of fertilization regimes on the diversity, composition and functional groups of protists and further disentangled the effects of multiple factors shaping the community composition of functional groups in a 5-year fertilization regime (CK, no fertilization; M, organic fertilization; MNPK, combined inorganic and organic fertilization; NPK, inorganic fertilization). Results Fertilization significantly changed the community composition of protists rather than diversity. The MNPK treatment significantly increased the relative abundance of phototrophs and decreased that of the parasites and consumers. Partial least squares path modeling indicated that fertilization indirectly regulated protistan consumers via changes in the P content, which affected the composition of consumers mainly by regulating fungal community composition. Soil moisture (SM) and available phosphorus (AP) were identified as the top predictors for the composition of parasites, and the composition of phototrophs was mainly affected by SM, indicating that parasites and phototrophs were more sensitive to abiotic factors in the fertilization system. Discussion Taken together, our findings highlight that fertilization significantly affects the composition of functional groups of protists and their biotic or abiotic regulatory processes, which have implications for the potential changes in their ecosystem functions for soil management systems.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Jianning Zhao
- Agro-Environmental Protection Institute, Chinese Academy of Agricultural Sciences, Tianjin, China
| | - Dianlin Yang
- Agro-Environmental Protection Institute, Chinese Academy of Agricultural Sciences, Tianjin, China
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20
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Jia H, Chu D, You X, Li Y, Huang C, Zhang J, Zeng X, Yao H, Zhou Z. Biochar improved the composting quality of seaweeds and cow manure mixture and altered the microbial community. Front Microbiol 2022; 13:1064252. [PMID: 36504785 PMCID: PMC9731296 DOI: 10.3389/fmicb.2022.1064252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 10/31/2022] [Indexed: 11/25/2022] Open
Abstract
The beneficial effects of biochar addition during composting have been proved for many feedstocks, like manures and crop straws. However, the effect of biochar on the quality of composting product with seaweed as the feedstock and the bacterial response has not been investigated. In this study, the wheat straw biochar addition on the quality of the composting product and the bacterial response was explored at the rate of 0-10%. The results showed that biochar addition at the optimal rate (5%, w/w) could increase the germination index and the ratio of the optical density of humic acid at 460 nm to that at 660 nm (E4/E6) of the composting product, which indicated the decreased biotoxicity and enhanced compost maturity. The significant increase of the nitrate nitrogen (NO3 --N) content of the composting product proved the improvement of N cycling during composting process with biochar addition. The bacterial community of composting product was shifted and the relative abundance of some beneficial taxa (e.g., Muricauda and Woeseia) was significantly increased with biochar addition. Furthermore, the relative abundance of some bacterial genes related to amino acid metabolism and carbohydrate metabolism was also increased with biochar addition. The results of our study provided the positive effect of biochar addition on the composting of seaweed and could help to produce high quality seaweed fertilizer by composting with biochar addition.
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Affiliation(s)
- Haijiang Jia
- China Tobacco Guangxi Industrial Co., Ltd., Nanning, China
| | - Depeng Chu
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Xiangwei You
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yiqiang Li
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Chongjun Huang
- China Tobacco Guangxi Industrial Co., Ltd., Nanning, China
| | - Jili Zhang
- China Tobacco Guangxi Industrial Co., Ltd., Nanning, China
| | - Xiangnan Zeng
- China Tobacco Guangxi Industrial Co., Ltd., Nanning, China
| | - Hui Yao
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China,*Correspondence: Hui Yao, ; Zhaofeng Zhou,
| | - Zhaofeng Zhou
- China Tobacco Guangxi Industrial Co., Ltd., Nanning, China,*Correspondence: Hui Yao, ; Zhaofeng Zhou,
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21
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Du P, Cao Y, Yin B, Zhou S, Li Z, Zhang X, Xu J, Liang B. Improved tolerance of apple plants to drought stress and nitrogen utilization by modulating the rhizosphere microbiome via melatonin and dopamine. Front Microbiol 2022; 13:980327. [PMID: 36439851 PMCID: PMC9687389 DOI: 10.3389/fmicb.2022.980327] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/19/2022] [Indexed: 08/29/2024] Open
Abstract
This study explored the contributions of melatonin and dopamine to the uptake and utilization of nitrogen and the formation of rhizosphere microbial communities in 'Tianhong 2'/M. hupehensis, with the goal improving plant resistance to drought stress. Drought stress was formed by artificially controlling soil moisture content. And melatonin or dopamine solutions were applied to the soil at regular intervals for experimental treatment. After 60 days of treatment, plant indices were determined and the structure of the rhizosphere microbial community was evaluated using high-throughput sequencing technology. The findings revealed two ways through which melatonin and dopamine alleviate the inhibition of growth and development caused by drought stress by promoting nitrogen uptake and utilization in plants. First, melatonin and dopamine promote the absorption and utilization of nitrogen under drought stress by directly activating nitrogen transporters and nitrogen metabolism-related enzymes in the plant. Second, they promote the absorption of nitrogen by regulating the abundances of specific microbial populations, thereby accelerating the transformation of the soil nitrogen pool to available nitrogen that can be absorbed directly by plant roots and utilized by plants. These findings provide a new framework for understanding how melatonin and dopamine regulate the uptake and utilization of nitrogen in plants and improve their ability to cope with environmental disturbances.
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Affiliation(s)
| | | | | | | | | | | | | | - Bowen Liang
- College of Horticulture, Hebei Agricultural University, Baoding, China
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22
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Gorrochategui-Ortega J, Muñoz-Colmenero M, Kovačić M, Filipi J, Puškadija Z, Kezić N, Parejo M, Büchler R, Estonba A, Zarraonaindia I. A short exposure to a semi-natural habitat alleviates the honey bee hive microbial imbalance caused by agricultural stress. Sci Rep 2022; 12:18832. [PMID: 36336704 PMCID: PMC9637708 DOI: 10.1038/s41598-022-23287-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 10/28/2022] [Indexed: 11/08/2022] Open
Abstract
Honeybee health and the species' gut microbiota are interconnected. Also noteworthy are the multiple niches present within hives, each with distinct microbiotas and all coexisting, which we termed "apibiome". External stressors (e.g. anthropization) can compromise microbial balance and bee resilience. We hypothesised that (1) the bacterial communities of hives located in areas with different degrees of anthropization differ in composition, and (2) due to interactions between the multiple microbiomes within the apibiome, changes in the community of a niche would impact the bacteria present in other hive sections. We characterised the bacterial consortia of different niches (bee gut, bee bread, hive entrance and internal hive air) of 43 hives from 3 different environments (agricultural, semi-natural and natural) through 16S rRNA amplicon sequencing. Agricultural samples presented lower community evenness, depletion of beneficial bacteria, and increased recruitment of stress related pathways (predicted via PICRUSt2). The taxonomic and functional composition of gut and hive entrance followed an environmental gradient. Arsenophonus emerged as a possible indicator of anthropization, gradually decreasing in abundance from agriculture to the natural environment in multiple niches. Importantly, after 16 days of exposure to a semi-natural landscape hives showed intermediate profiles, suggesting alleviation of microbial dysbiosis through reduction of anthropization.
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Affiliation(s)
- June Gorrochategui-Ortega
- grid.11480.3c0000000121671098Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Marta Muñoz-Colmenero
- grid.11480.3c0000000121671098Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain ,grid.419099.c0000 0001 1945 7711Instituto de Investigaciones Marinas (CSIC)/Institute of Marine Research, Eduardo Cabello 6, 36208 Vigo, Pontevedra Spain
| | - Marin Kovačić
- grid.412680.90000 0001 1015 399XFaculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, V.Preloga 1, 31000 Osijek, Croatia
| | - Janja Filipi
- grid.424739.f0000 0001 2159 1688Department of Ecology, Agronomy and Aquaculture, University of Zadar, Trg Kneza Višeslava 9, 23000 Zadar, Croatia
| | - Zlatko Puškadija
- grid.412680.90000 0001 1015 399XFaculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, V.Preloga 1, 31000 Osijek, Croatia
| | - Nikola Kezić
- grid.4808.40000 0001 0657 4636Department of Fisheries, Apiculture and Special Zoology, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000 Zagreb, Croatia
| | - Melanie Parejo
- grid.11480.3c0000000121671098Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Ralph Büchler
- grid.506460.10000 0004 4679 6788Landesbetrieb Landwirtschaft Hessen (LLH), Bieneninstitut, Erlenstraße 9, 35274 Kirchhain, Germany
| | - Andone Estonba
- grid.11480.3c0000000121671098Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Iratxe Zarraonaindia
- grid.11480.3c0000000121671098Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain ,grid.424810.b0000 0004 0467 2314IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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23
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Yang Z, Feng Y, Zhang S, Hu Y, Tang Y, Gu H, Gu Z, Xv Y, Cai Y, Zhang H. Effects of rice-prawn (Macrobrachium nipponense) co-culture on the microbial community of soil. Appl Microbiol Biotechnol 2022; 106:7361-7372. [PMID: 36195705 DOI: 10.1007/s00253-022-12164-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/30/2022]
Abstract
In the Lixiahe region of China, co-culture has been rapidly promoted in flooded paddy fields owing to its ecological and economic benefits. Rice-prawn co-culture can reduce the damage of crab and shrimp to rice growth and paddy field and substantially change the soil microbial community and soil fertility. In this study, we compared changes in the soil microbial community and soil fertility in waterlogged paddies under conventional rice culture (CR), rice-prawn (Macrobrachium nipponense) co-culture (RP), and pond culture (PC). The microbial abundance in RP was significantly higher than that in CR. RP soil microbial diversity was significantly higher than PC soil microbial diversity. The dominant bacteria in RP soil were Proteobacteria, Chloroflexi, and Bacteroidetes. Compared with those in CR, total organic matter (TOM) and total nitrogen in RP were relatively stable, available potassium and available phosphorus (AP) decreased, and other indicators increased significantly. Soil fertility significantly benefited from co-culture, with total organic carbon (TOC) increasing. Interactive relationship analysis showed that TOM, TOC, AP, and NH4+-N were the main factors affecting the microbial community. Co-occurrence network analyses showed that network modularity increased with co-culture, indicating that a unique soil microbial community formed under co-culture, improving the adaptability and tolerance to co-culture. Thus, RP is a suitable culture method for this commercially important species. The results of this study can inform the practical operation of fertilizer use and sustainable development of rice-prawn aquaculture systems. KEY POINTS: • Microbial abundance and diversity increased under rice-prawn co-culture. • Co-culture significantly improved soil fertility, with an increase in TOC. • Rice-prawn co-culture is an ecologically suitable culture method for prawns.
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Affiliation(s)
- Zhijing Yang
- Taizhou Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Taizhou, 225300, China
| | - Yaming Feng
- Taizhou Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Taizhou, 225300, China
| | - Shuanglin Zhang
- Taizhou Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Taizhou, 225300, China
| | - Yuqi Hu
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, 315211, China.,School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Yueyao Tang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, 315211, China.,School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Hailong Gu
- Taizhou Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Taizhou, 225300, China
| | - Zhengyan Gu
- Taizhou Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Taizhou, 225300, China
| | - Ye Xv
- Taizhou Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Taizhou, 225300, China
| | - Yingchun Cai
- Taizhou Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Taizhou, 225300, China
| | - Hao Zhang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, 315211, China. .,School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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24
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Du M, Zhang J, Wang G, Liu C, Wang Z. Response of bacterial community composition and co-occurrence network to straw and straw biochar incorporation. Front Microbiol 2022; 13:999399. [PMID: 36246223 PMCID: PMC9563622 DOI: 10.3389/fmicb.2022.999399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/30/2022] [Indexed: 11/22/2022] Open
Abstract
Microbial decomposition plays a crucial role in the incorporation of straw and straw biochar (SSB) into soil. Lime concretion black soil (LCBS) is a typical low-medium crop yield soil, and it is also one of the main soil types for grain production in China. However, the link between SSB additions and soil bacterial communities in LCBS remains unclear. This study explored the effects of SSB incorporation on bacterial community composition, structure and co-occurrence network patterns at different soil depths and maize growth stages. The results showed that soil PH, soil organic matter and total nitrogen significantly affected the seasonality and stratification of the soil bacterial community. The composition and diversity of bacterial communities were significantly affected by growth period and treatment rather than soil depth. Specifically, the bacterial community diversity increased significantly with crop growth at 0–20 cm, decreased the relative abundance of Actinobacteria, and increased the relative abundance of Proteobacteria and Acidobacteria. SF (straw with fertilizer) and BF (straw biochar with fertilizer) treatments decreased bacterial community diversity. Co-occurrence networks are more complex in BF, S (straw), and SF treatments, and the number of edge network patterns is increased by 92.5, 40, and 60% at the maturity stage compared with F (fertilizer) treatment, respectively. Moreover, the positive effect of straw biochar on the bacterial network pattern increased with time, while the effect of straw weakened. Notably, we found that rare species inside keystone taxa (Gemmatimonadetes and Nitrospirae) play an indispensable role in maintaining bacterial network construction in LCBS. This study offers a comprehensive understanding of the response of soil bacterial communities to SSB addition in LCBS areas, and provides a reference for further improvement of LCBS productivity.
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Affiliation(s)
- Mingcheng Du
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, China
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing, China
- Yangtze Institute for Conservation and Development, Nanjing, China
- Research Center for Climate Change, Nanjing, China
| | - Jianyun Zhang
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, China
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing, China
- Yangtze Institute for Conservation and Development, Nanjing, China
- Research Center for Climate Change, Nanjing, China
| | - Guoqing Wang
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing, China
- Yangtze Institute for Conservation and Development, Nanjing, China
- Research Center for Climate Change, Nanjing, China
- *Correspondence: Guoqing Wang,
| | - Cuishan Liu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing, China
- Yangtze Institute for Conservation and Development, Nanjing, China
- Research Center for Climate Change, Nanjing, China
| | - Zhenlong Wang
- Wudaogou Experimental Station for Hydrology and Water Resources, Bengbu, China
- Anhui Hydraulic Research Institute, Huai River Commission, Bengbu, China
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25
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Phillips KE, Akbar S, Stevens DC. Concepts and conjectures concerning predatory performance of myxobacteria. Front Microbiol 2022; 13:1031346. [PMID: 36246230 PMCID: PMC9556981 DOI: 10.3389/fmicb.2022.1031346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/14/2022] [Indexed: 01/28/2023] Open
Abstract
Myxobacteria are excellent model organisms for investigation of predator-prey interactions and predatory shaping of microbial communities. This review covers interdisciplinary topics related to myxobacterial predation and provides current concepts and challenges for determining predatory performance. Discussed topics include the role of specialized metabolites during predation, genetic determinants for predatory performance, challenges associated with methodological differences, discrepancies between sequenced and environmental myxobacteria, and factors that influence predation.
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Affiliation(s)
- Kayleigh E. Phillips
- Department of BioMolecular Sciences, The University of Mississippi, Oxford, MS, United States
| | - Shukria Akbar
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, United States,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - D. Cole Stevens
- Department of BioMolecular Sciences, The University of Mississippi, Oxford, MS, United States,*Correspondence: D. Cole Stevens,
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26
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Sadet-Bourgeteau S, Djemiel C, Chemidlin Prévost-Bouré N, Feder F. Dynamic of bacterial and archaeal diversity in a tropical soil over 6 years of repeated organic and inorganic fertilization. Front Microbiol 2022; 13:943314. [PMID: 36051761 PMCID: PMC9425033 DOI: 10.3389/fmicb.2022.943314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
The soil microbial community plays important roles in nutrient cycling, plant pathogen suppression, decomposition of residues and degradation of pollutants; as such, it is often regarded as a good indicator of soil quality. Repeated applications of mixed organic and inorganic materials in agriculture improve the soil microbial quality and in turn crop productivity. The soil microbial quality following several years of repeated fertilizer inputs has received considerable attention, but the dynamic of this community over time has never been assessed. We used high-throughput sequencing targeting 16S ribosomal RNA genes to investigate the evolution of the bacterial and archaeal community throughout 6 years of repeated organic and inorganic fertilizer applications. Soils were sampled from a field experiment in La Mare (Reunion Island, France), where different mixed organic-inorganic fertilizer inputs characterized by more or less stable organic matter were applied regularly for 6 years. Soil samples were taken each year, more than 6 months after the latest fertilizer application. The soil molecular biomass significantly increased in some organically fertilized plots (by 35–45% on average), 3–5 years after the first fertilizers application. The significant variations in soil molecular microbial biomass were explained by the fertilization practices (cumulated organic carbon inputs) and sometimes by the soil parameters (sand and soil carbon contents). The structure of the bacterial and archaeal community was more influenced by time than by the fertilization type. However, repeated fertilizer applications over time tended to modify the abundance of the bacterial phyla Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. To conclude, the present study highlights that the soil bacterial and archaeal community is lastingly modified after 6 years of repeated fertilizer inputs. These changes depend on the nature of the organic input and on the fertilization practice (frequency and applied quantity).
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Affiliation(s)
- Sophie Sadet-Bourgeteau
- Agroécologie, INRAE, Institut Agro Dijon, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
- *Correspondence: Sophie Sadet-Bourgeteau,
| | - Christophe Djemiel
- Agroécologie, INRAE, Institut Agro Dijon, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | | | - Frederic Feder
- CIRAD, UPR Recyclage et Risque, Montpellier, France
- Recyclage et risque, Univ Montpellier, CIRAD, Montpellier, France
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Song Q, Fu H, Shi Q, Shan X, Wang Z, Sun Z, Li T. Overfertilization reduces tomato yield under long-term continuous cropping system via regulation of soil microbial community composition. Front Microbiol 2022; 13:952021. [PMID: 35992643 PMCID: PMC9386239 DOI: 10.3389/fmicb.2022.952021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/11/2022] [Indexed: 12/02/2022] Open
Abstract
Long-term monoculture cropping and overfertilization degrade soil fertility, which reduces crop growth and promotes the development of soil-borne diseases. However, it remains unclear what the temporal effects of the above factors are on the tomato yield and microbial community structure. Thus, a greenhouse experiment with different amounts of fertilization [2,196 kg ha−1 (control) and 6,588 kg ha−1 (overfertilization) of inorganic fertilizers (NPK)] was carried out with the soils used previously for 1, 2, and 12 years under monoculture of tomato. A 12-year overfertilization decreased soil pH by 1.37 units. Soil electrical conductivity (EC) and concentrations of soil nutrients are enhanced with the increase in tomato cropping duration. Higher content of soil nutrients was found under overfertilization compared to the control in the 12-year soil. Overfertilization decreased the activity of β-1,4-glucosidase (BG) and oxidase compared to the control in the 12-year soil. Bacterial diversity and richness decreased by 6 and 31%, respectively, under overfertilization in 12-year soil compared to the control. The relative abundance of Gemmatimonas and Gp6 in 12-year soil under overfertilization was 17 and 78%, respectively, lower than in control soil. Soil pH and total carbon (TC) were the major factors explaining changes in microbial composition. A 38% decrease in yield was caused by overfertilization in 12-year soil compared to the control. Microbial community composition was the main factor that moderated tomato yield. In addition, fertilization rather than cropping duration had a greater impact on tomato yield. Therefore, our results suggest that long-term overfertilization influenced soil pH, soil TC, and soil microbial community composition to regulate tomato yield.
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Affiliation(s)
- Qiaobo Song
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agriculture University, Shenyang, China
| | - Hongdan Fu
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agriculture University, Shenyang, China
- *Correspondence: Hongdan Fu
| | - Qingwen Shi
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agriculture University, Shenyang, China
| | - Xuan Shan
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agriculture University, Shenyang, China
| | - Zhen Wang
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agriculture University, Shenyang, China
| | - Zhouping Sun
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agriculture University, Shenyang, China
| | - Tianlai Li
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, China
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agriculture University, Shenyang, China
- Tianlai Li
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dos Santos RM, Cueva-Yesquén LG, Garboggini FF, Desoignies N, Rigobelo EC. Inoculum Concentration and Mineral Fertilization: Effects on the Endophytic Microbiome of Soybean. Front Microbiol 2022; 13:900980. [PMID: 35875541 PMCID: PMC9301290 DOI: 10.3389/fmicb.2022.900980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/09/2022] [Indexed: 12/13/2022] Open
Abstract
Soybean crops are of great economic importance worldwide and in Brazil. This crop is a commodity that provides large amounts of financial resources to the country. Soybean productivity is influenced by several biotic and abiotic factors, and most of these factors cannot be controlled by agricultural practices. Due to the soybean cultivars used and their required yields, the soybean crop, similar to other agriculturally important crops, requires large amounts of mineral fertilizers. There are several microorganisms that colonize soybean plant roots without causing symptoms or damage. These microorganisms that colonize plant tissues are called endophytes and can often promote plant growth and development. Little is known about the factors that influence endophyticism. The aim of the present study was to evaluate whether Bacillus subtilis inoculant concentrations and levels of mineral fertilization recommended for the crop have any influence on the endophytic microbiome of soybean plant roots. The results show that B. subtilis inoculations did not affect the endophytic community of the roots; however, the evaluation of the microbial community structure according to the alpha diversity metrics observed richness, Chao1 index, Shannon index and Simpson index showed that microbial diversity of endophytes was higher at fertilization levels of 50 and 100%, with a significant difference (p < 0.05) between 0 and 50% and 0 and 100% fertilization.
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Affiliation(s)
- Roberta Mendes dos Santos
- Graduate Program in Agricultural Microbiology, Faculty of Agrarian and Veterinary Sciences, State University of Sao Paulo (UNESP), Jaboticabal, Brazil
| | - Luis Gabriel Cueva-Yesquén
- Agricultural and Livestock Microbiology Graduation Program, São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo, Brazil
| | - Fabiana Fantinatti Garboggini
- Agricultural and Livestock Microbiology Graduation Program, São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo, Brazil
| | - Nicolas Desoignies
- Phytopathology, Microbial and Molecular Farming Lab, Centre d’Etudes et de Recherche Appliquée -Haute Ecole Provinciale du Hainaut Condorcet, Ath, Belgium
| | - Everlon Cid Rigobelo
- Graduate Program in Agricultural Microbiology, Faculty of Agrarian and Veterinary Sciences, State University of Sao Paulo (UNESP), Jaboticabal, Brazil
- *Correspondence: Everlon Cid Rigobelo,
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Li W, Lei X, Zhang R, Cao Q, Yang H, Zhang N, Liu S, Wang Y. Shifts in rhizosphere microbial communities in Oplopanax elatus Nakai are related to soil chemical properties under different growth conditions. Sci Rep 2022; 12:11485. [PMID: 35798802 PMCID: PMC9262954 DOI: 10.1038/s41598-022-15340-1] [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: 02/21/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022] Open
Abstract
Plant growth environment plays an important role in shaping soil microbial communities. To understand the response of soil rhizosphere microbial communities in Oplopanax elatus Nakai plant to a changed growth conditions from natural habitation to cultivation after transplant. Here, a comparative study of soil chemical properties and microbial community using high-throughput sequencing was conducted under cultivated conditions (CT) and natural conditions (WT), in Changbai Mountain, Northeast of China. The results showed that rhizosphere soil in CT had higher pH and lower content of soil organic matter (SOM) and available nitrogen compared to WT. These changes influenced rhizosphere soil microbial communities, resulting in higher soil bacterial and fungi richness and diversity in CT soil, and increased the relative abundance of bacterial phyla Acidobacteria, Chloroflexi, Gemmatimonadetes, Firmicutes and Patescibacteria, and the fungi phyla Mortierellomycota and Zoopagomycota, while decreased bacterial phyla Actinobacteria, WPS-2, Gemmatimonadetes, and Verrucomicrobia, and the fungi phyla Ascomycota, and Basidiomycota. Redundancy analysis analysis indicated soil pH and SOM were the primarily environmental drivers in shaping the rhizosphere soil microbial community in O. elatus under varied growth conditions. Therefore, more attention on soil nutrition management especially organic fertilizer inputs should be paid in O. elatus cultivation.
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Affiliation(s)
- Wanying Li
- College of Chinese Medicinal Materials, Jilin Agriculture University, Changchun, 130118, People's Republic of China.,National and Local Joint Engineering Research Center for Ginseng Breeding and Development, Changchun, 130118, People's Republic of China
| | - Xiujuan Lei
- College of Chinese Medicinal Materials, Jilin Agriculture University, Changchun, 130118, People's Republic of China.,National and Local Joint Engineering Research Center for Ginseng Breeding and Development, Changchun, 130118, People's Republic of China
| | - Rui Zhang
- College of Chinese Medicinal Materials, Jilin Agriculture University, Changchun, 130118, People's Republic of China.,National and Local Joint Engineering Research Center for Ginseng Breeding and Development, Changchun, 130118, People's Republic of China
| | - Qingjun Cao
- Jilin Academy of Agriculture Science, Changchun, 130033, People's Republic of China.
| | - He Yang
- College of Chinese Medicinal Materials, Jilin Agriculture University, Changchun, 130118, People's Republic of China.,National and Local Joint Engineering Research Center for Ginseng Breeding and Development, Changchun, 130118, People's Republic of China
| | - Nanqi Zhang
- College of Chinese Medicinal Materials, Jilin Agriculture University, Changchun, 130118, People's Republic of China.,National and Local Joint Engineering Research Center for Ginseng Breeding and Development, Changchun, 130118, People's Republic of China
| | - Shuangli Liu
- College of Chinese Medicinal Materials, Jilin Agriculture University, Changchun, 130118, People's Republic of China.,National and Local Joint Engineering Research Center for Ginseng Breeding and Development, Changchun, 130118, People's Republic of China
| | - Yingping Wang
- College of Chinese Medicinal Materials, Jilin Agriculture University, Changchun, 130118, People's Republic of China. .,National and Local Joint Engineering Research Center for Ginseng Breeding and Development, Changchun, 130118, People's Republic of China.
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30
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Zheng C, Yang X, Liu Z, Liu K, Huang Y. Spatial distribution of soil nutrients and evaluation of cultivated land in Xuwen county. PeerJ 2022; 10:e13239. [PMID: 35791366 PMCID: PMC9250764 DOI: 10.7717/peerj.13239] [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: 11/15/2021] [Accepted: 03/18/2022] [Indexed: 01/13/2023] Open
Abstract
It is of great significance to promote the quantitative research of soil science and the implementation of precision agriculture. On this basis, taking Xuwen County as the research object, this paper comprehensively analyzed the soil characteristics of cultivated land in Xuwen County and clarify the soil nutrient content and spatial distribution characteristics of cultivated land in Xuwen County, this paper comprehensively applied the methods of geostatistics, geographic information system (GIS) and fuzzy mathematics, and referred to the cultivated land quality grade standard (GB/T 33469-2016), to analyze the soil characteristics and evaluate the soil fertility of this region. The results show that the optimal interpolation model of soil pH and available phosphorus (AP) is a Gaussian model, and the optimal interpolation model of soil organic matter (SOM), available nitrogen (AN) and available potassium (AK) is a J-Bessel model. In addition, the spatial correlation of AK is weak, whereas pH, SOM, AN and AP show moderate spatial correlation. The proportion of excellent, good, average, medium and poor comprehensive fertility index are 26.00%, 32.67%, 19.33%, 19.00% and 3.00%, respectively. The overall level of soil fertility in Xuwen County is above the average, and the fertility quality presents an obvious trend of high in the South and low in the North. Areas that above average fertility are mainly distributed in Maichen Town, Qujie Town, Nanshan Town and Chengbei Town. The results can provide theoretical basis for improving the utilization rate of chemical fertilizer, fine management of cultivated land and ecological environment in this region, which can help in decision-making of precision fertilization.
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Affiliation(s)
- Chao Zheng
- College of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, China
| | - Xiaofei Yang
- College of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, China
| | - Zhiqiang Liu
- Centre Testing International Pinbiao (Guangzhou) Co., Ltd., Guangzhou, China
| | - Kexing Liu
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Yongxiang Huang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
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31
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Yu X, Yan M, Cui Y, Liu Z, Liu H, Zhou J, Liu J, Zeng L, Chen Q, Gu Y, Zou L, Zhao K, Xiang Q, Ma M, Li S. Effects of Co-application of Cadmium-Immobilizing Bacteria and Organic Fertilizers on Houttuynia cordata and Microbial Communities in a Cadmium-Contaminated Field. Front Microbiol 2022; 12:809834. [PMID: 35601203 PMCID: PMC9122265 DOI: 10.3389/fmicb.2021.809834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/10/2021] [Indexed: 12/21/2022] Open
Abstract
Cadmium pollution is a serious threat to the soil environment. The application of bio-based fertilizers in combination with beneficial microbial agents is a sustainable approach to solving Cd pollution in farm soil. The present study investigated the effects of co-application of a Cd-immobilizing bacterial agent and two fermented organic fertilizers (fermentative edible fungi residue; fermentative cow dung) on Houttuynia cordata and its microbial communities in a Cd-polluted field. It showed that both the application of the Cd-immobilizing bacterial agent alone and the combined application of bio-based soil amendments and the bacterial agent effectively reduced >20% of the uptake of Cd by the plant. Soil nitrogen level was significantly raised after the combined fertilization. The multivariate diversity analysis and co-occurrence network algorithm showed that a significant shift of microbial communities took place, in which the microbial populations tended to be homogeneous with reduced microbial richness and increased diversity after the co-application. The treatment of fermentative cow dung with the addition of the bacterial agent showed a significant increase in the microbial community dissimilarity (R = 0.996, p = 0.001) compared to that treated with cow dung alone. The co-application of the bacterial agent with both organic fertilizers significantly increased the abundance of Actinobacteria and Bacteroidetes. The FAPROTAX soil functional analysis revealed that the introduction of the microbial agent could potentially suppress human pathogenic microorganisms in the field fertilized with edible fungi residue. It also showed that the microbial agent can reduce the nitrite oxidation function in the soil when applied alone or with the organic fertilizers. Our study thus highlights the beneficial effects of the Cd-immobilizing bacterial inoculant on H. cordata and provides a better understanding of the microbial changes induced by the combined fertilization using the microbial agent and organic soil amendments in a Cd-contaminated field.
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Affiliation(s)
- Xiumei Yu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Min Yan
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yongliang Cui
- Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, China
| | - Zhongyi Liu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Han Liu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Jie Zhou
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Jiahao Liu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Lan Zeng
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Qiang Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yunfu Gu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Ke Zhao
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Quanju Xiang
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Menggen Ma
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Shuangcheng Li
- College of Resources, Sichuan Agricultural University, Chengdu, China
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32
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Wongkiew S, Chaikaew P, Takrattanasaran N, Khamkajorn T. Evaluation of nutrient characteristics and bacterial community in agricultural soil groups for sustainable land management. Sci Rep 2022; 12:7368. [PMID: 35513414 PMCID: PMC9072534 DOI: 10.1038/s41598-022-09818-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/28/2022] [Indexed: 11/09/2022] Open
Abstract
The soil bacterial community is critical for understanding biological processes in soils and is used for agricultural soil management. The understanding of microorganisms and ecology in different soil groups classified based on soil properties (e.g., minerals, soil texture, location, nitrogen, phosphorus, organic carbon and pH, among others), is limited. To suggest soil management strategies using bacterial data, we classified soils into four groups based on physical-chemical characteristics and elucidated their relationships with soil nutrient characteristics and the bacterial community in agricultural fields in Saraburi Province, Thailand. Results show that soil groups with high bacterial diversity had positive correlations with total Kjeldahl nitrogen and available phosphorus but were negatively affected by total organic carbon and pH levels. Dominant bacterial genera included Lactobacillus, Phascolarctobacterium, Prevotella, Clostridium, Gaiellales and Blautia. Significant key biomarkers were found (p < 0.05). Nutrient-rich soil groups (high available P, acidic pH) were found with genus Agromyces, while low nutrient soil groups (low available P, basic pH) were found with Hydrogenispora, Ignavibacterium and Bauldia. Based on co-occurrence networks, organic degrading bacteria functioned with other bacteria at high degrees of interconnections, suggesting organic amendment, biostimulation and biodegradation using nutrient-rich organic substrates could be used for agricultural soil improvements.
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Affiliation(s)
- Sumeth Wongkiew
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Water Science and Technology for Sustainable Environment Research Group, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Pasicha Chaikaew
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
| | - Natta Takrattanasaran
- Land Development Department, Land Development Regional Office 1, Pathum Thani, 12110, Thailand
| | - Thanachanok Khamkajorn
- Land Development Department, Land Development Regional Office 1, Pathum Thani, 12110, Thailand
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33
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Wang R, Liu J, Jiang W, Ji P, Li Y. Metabolomics and Microbiomics Reveal Impacts of Rhizosphere Metabolites on Alfalfa Continuous Cropping. Front Microbiol 2022; 13:833968. [PMID: 35531271 PMCID: PMC9069006 DOI: 10.3389/fmicb.2022.833968] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/09/2022] [Indexed: 11/13/2022] Open
Abstract
Alfalfa long-term continuous cropping (CC) can pose a serious threat to alfalfa production. However, the mechanism of alfalfa CC obstacle is unclear as of today. Our preliminary study showed that the main factors of CC obstacle were not the lack of nutrients or water in alfalfa rhizosphere soils. Further, we evaluated physic-chemical property, microbial population structure, and metabolite differences of alfalfa rhizosphere soils with CC for 1, 7, and 14 years based on analysis of metabolomics and microbiomics. Four phenolic acid metabolites, including p-coumaric acid, ferulic acid, vanillic acid, and p-hydroxybenzoic acid, were found to have significant differences among different CC years, which may be the key factors of CC obstacle. Among them, p-coumaric acid and ferulic acid could significantly decrease the germination rate of alfalfa seeds by 21.11 and 16.67% at the concentration of 100 μg/mL and the height (root length) of alfalfa seedlings by 21% (32.9%) and 13.72% (16.45%). Moreover, these metabolites could effectively promote the growth of some pathogenic fungi, causing alfalfa root rot. Among them, p-coumaric acid obviously and significantly aggravated the occurrence of alfalfa root rot. With the increase of CC years, soil microbial community changed from fungi to bacteria; fungi decreased by 10.83%, fungi increased by 8.08%, and beneficial microorganisms decreased with the increase of CC years. Field analysis and experimental verification showed that the above results were consistent with that of CC obstacle in the field. Among the key metabolites, the autotoxicity of p-coumaric acid was the strongest. This study fully proved that the continuous accumulation of autotoxic substances in alfalfa rhizosphere was the key factor causing alfalfa CC obstacles.
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Affiliation(s)
- Ruiting Wang
- Agricultural College, Northeast Agricultural University, Harbin, China
| | - Jinxin Liu
- Agricultural College, Northeast Agricultural University, Harbin, China
| | - Wanyi Jiang
- Agricultural College, Northeast Agricultural University, Harbin, China
| | - Pingsheng Ji
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Yonggang Li
- Agricultural College, Northeast Agricultural University, Harbin, China
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34
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Lv Y, Li Y, Liu X, Xu K. A positive response of ginger root zone and rhizome development to suitable sowing depth. PROTOPLASMA 2022; 259:327-342. [PMID: 34075471 DOI: 10.1007/s00709-021-01647-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Sowing depth significantly affects ginger (Zingiber officinale Roscoe) yields, and sowing depth can affect rhizosphere community structure through root exudates. However, the relationship between the reaction process in root zone and ginger rhizome development is unclear. In this study, we investigated the rhizome and root development and rhizosphere environment at different sowing depths (2 cm (SD2), 5 cm (SD5), and 10 cm (SD10)). It was found that SD10 significantly increased ginger yield, which is related to the development of vascular bundles and the expression of aquaporin. PLS-PM analysis found that root length, root absorption capacity, and soil enzymes have the strongest correlation with yield, while root diameter is negatively correlated with yield. Under SD10, the increase of auxin and ethylene content together with the expression of ARF7, LBD16, and PIN1 promoted the development of lateral roots. In addition, SD10 increased the secretion of root organic acids, amino acids, and carbohydrates, which in turn promoted the development of rhizosphere bacteria. The promotion of SD10 on nitrogen cycle and nitrogen fixation ability in turn promoted the development of ginger.
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Affiliation(s)
- Yao Lv
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Tai'an, 271018, China
- Key Laboratory of Biology of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Tai'an, 271018, China
- State Key Laboratory of Crop Biology, Tai'an, 271018, China
| | - Yanyan Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiaohui Liu
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Kun Xu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China.
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Tai'an, 271018, China.
- Key Laboratory of Biology of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Tai'an, 271018, China.
- State Key Laboratory of Crop Biology, Tai'an, 271018, China.
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35
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The impact of different rotation regime on the soil bacterial and fungal communities in an intensively managed agricultural region. Arch Microbiol 2022; 204:142. [PMID: 35043270 DOI: 10.1007/s00203-021-02615-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022]
Abstract
The continuous wheat-maize planting has led to the increase in epidemic frequency of wheat diseases under climate change. Analyzation of the soil microbial composition in different rotation crops is essential to select alternative rotation regime. This study investigated the bacterial and fungal community abundance and composition, and potential microbe-microbe interactions in three rotations, including wheat-maize → spring maize (WMFS), wheat-soybean (WS) and continuous wheat-maize (WM) planting. The results revealed that there were 110, 156, and 195 bacterial, and 17, 8, and 15 fungal operational taxonomic units respectively enriched by WMFS, WS, and WM. WM increased the relative abundance of Actinobacteria and α-Proteobacteria in wheat, and the relative abundance and copy number of genus Fusarium in maize. WMFS and WS could decrease the abundance of Fusarium in summer-crop across the growth stages and in wheat at elongation. WS also increased the copy number of ammonia-oxidizing bacteria in wheat at flowering and harvest. Network analysis revealed that WM resulted in simple and isolated wheat network with small modules dominating and none Nitrospirae and β-Proteobacteria in the main modules. WS formed interconnected and intricate wheat network with the maximum number of large modules and module connectors. Under WS, positive correlation between antagonistic Streptomyces (Actinobacteria) and genus Fusarium was found in wheat. Soil physicochemical properties explained the majority of the variation in bacterial and fungal β-diversity in wheat (P < 0.01). Rotation regime switching from WM to WMFS and WS may effectively damp the risk of wheat disease and maintain the wheat yield in intensive cereal production.
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36
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Metagenomic outlooks of microbial dynamics influenced by organic manure in tea garden soils of North Bengal, India. Arch Microbiol 2021; 204:33. [PMID: 34923604 DOI: 10.1007/s00203-021-02635-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 10/19/2022]
Abstract
Soil microbial diversity consisted of both culturable and non-culturable microbes. The cultivated microbes can be identified by conventional microbiological processes. However, that is not possible for the non-culturable ones. In those cases, next-generation sequencing (NGS)-based metagenomics become useful. In this study, we targeted two very popular tea gardens of Darjeeling hills-Makaibari (Mak) and Castleton (Cas). The main difference between these two study areas is the type of manure they use. Mak is solely an organic tea garden using all organic manure and fertilizers whereas Cas uses inorganic pesticides and fertilizers. The main aim was to compare the effect of organic manure over chemical fertilizers on the soil microbiomes. We have performed the 16 s metagenomics analysis based on the V3-V4 region. Downstream bioinformatics analysis including reverse ecology was performed. We found that the overall microbial diversity is higher in Mak compared to Cas. Moreover, the use of organic manure has reduced the population of pathogenic bacteria in Mak soil when compared to Cas soil. From the observations made through the metagenomics analysis of Mak and Cas soil samples, we may conclude that the application of organic manure supports the population of good bacteria in the soil which may eventually impact the tea garden workers' health.
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Stavridou E, Giannakis I, Karamichali I, Kamou NN, Lagiotis G, Madesis P, Emmanouil C, Kungolos A, Nianiou-Obeidat I, Lagopodi AL. Biosolid-Amended Soil Enhances Defense Responses in Tomato Based on Metagenomic Profile and Expression of Pathogenesis-Related Genes. PLANTS (BASEL, SWITZERLAND) 2021; 10:2789. [PMID: 34961260 PMCID: PMC8709368 DOI: 10.3390/plants10122789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 05/28/2023]
Abstract
Biosolid application is an effective strategy, alternative to synthetic chemicals, for enhancing plant growth and performance and improving soil properties. In previous research, biosolid application has shown promising results with respect to tomato resistance against Fusarium oxysporum f. sp. radicis-lycopersici (Forl). Herein, we aimed at elucidating the effect of biosolid application on the plant-microbiome response mechanisms for tomato resistance against Forl at a molecular level. More specifically, plant-microbiome interactions in the presence of biosolid application and the biocontrol mechanism against Forl in tomato were investigated. We examined whether biosolids application in vitro could act as an inhibitor of growth and sporulation of Forl. The effect of biosolid application on the biocontrol of Forl was investigated based on the enhanced plant resistance, measured as expression of pathogen-response genes, and pathogen suppression in the context of soil microbiome diversity, abundance, and predicted functions. The expression of the pathogen-response genes was variably induced in tomato plants in different time points between 12 and 72 h post inoculation in the biosolid-enriched treatments, in the presence or absence of pathogens, indicating activation of defense responses in the plant. This further suggests that biosolid application resulted in a successful priming of tomato plants inducing resistance mechanisms against Forl. Our results have also demonstrated that biosolid application alters microbial diversity and the predicted soil functioning, along with the relative abundance of specific phyla and classes, as a proxy for disease suppression. Overall, the use of biosolid as a sustainable soil amendment had positive effects not only on plant health and protection, but also on growth of non-pathogenic antagonistic microorganisms against Forl in the tomato rhizosphere and thus, on plant-soil microbiome interactions, toward biocontrol of Forl.
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Affiliation(s)
- Evangelia Stavridou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, 57001 Thessaloniki, Greece; (E.S.); (I.K.); (G.L.); (P.M.)
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Ioannis Giannakis
- School of Civil Engineering, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.G.); (A.K.)
| | - Ioanna Karamichali
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, 57001 Thessaloniki, Greece; (E.S.); (I.K.); (G.L.); (P.M.)
| | - Nathalie N. Kamou
- Laboratory of Plant Pathology, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - George Lagiotis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, 57001 Thessaloniki, Greece; (E.S.); (I.K.); (G.L.); (P.M.)
| | - Panagiotis Madesis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, 57001 Thessaloniki, Greece; (E.S.); (I.K.); (G.L.); (P.M.)
- Laboratory of Molecular Biology of Plants, School of Agricultural Sciences, University of Thessaly, 38221 Volos, Greece
| | - Christina Emmanouil
- School of Spatial Planning and Development, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Athanasios Kungolos
- School of Civil Engineering, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.G.); (A.K.)
| | - Irini Nianiou-Obeidat
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Anastasia L. Lagopodi
- Laboratory of Plant Pathology, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
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Sun L, Long M, Li J, Wu R, Ma L, Tang D, Lu Y, Wang Z. Different Effects of Thermophilic Microbiological Inoculation With and Without Biochar on Physicochemical Characteristics and Bacterial Communities in Pig Manure Composting. Front Microbiol 2021; 12:746718. [PMID: 34899633 PMCID: PMC8660119 DOI: 10.3389/fmicb.2021.746718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
This study evaluated the effects of thermophilic microbiological inoculation alone (TA) and integrated with biochar (TB) on the physicochemical characteristics and bacterial communities in pig manure (PM) composting with wheat straw. Both TA and TB accelerated the rate of temperature increase during the PM composting. TA significantly reduced total nitrogen loss by 18.03% as opposed to TB which significantly accelerated total organic carbon degradation by 12.21% compared with the control. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the major phyla in composting. Variation of the relative abundance of genera depended on the composting period and treatment. The genera Lactobacillus (26.88-46.71%) and Clostridium_sensu_stricto (9.03-31.69%) occupied a superior position in the temperature rise stage, and Bacillus (30.90-36.19%) was outstanding in the cooling stage. Temperature, total nitrogen (TN), and ammonium nitrogen significantly influenced the bacterial phyla composition. TN, water content, and nitrite nitrogen were the main drivers of the bacterial community genera. Furthermore, our results demonstrated that microbiological consortia were resistant to high temperatures and could fix nitrogen for enriched Pseudomonas; however, when interacted with biochar, total organic carbon (TOC) degradation was accelerated for higher bacterial richness and diversity as well as overrepresented Corynebacterium.
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Affiliation(s)
- Likun Sun
- College of Animal Science, Gansu Agricultural University, Lanzhou, China.,Gansu Provincial Engineering Research Center for Animal Waste Utilization, Gansu Agricultural University, Lanzhou, China
| | - Min Long
- College of Animal Science, Gansu Agricultural University, Lanzhou, China.,College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Jianshu Li
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Renfei Wu
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Lin Ma
- College of Animal Science, Gansu Agricultural University, Lanzhou, China.,Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Defu Tang
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Yongli Lu
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, China
| | - Ziyu Wang
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
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Xiong Y, Yang X, Xiong Y, Xiong C, Gou W, Ma X. Insights into soil bacterial and physicochemical properties of annual ryegrass-maize rotation (ARMR) system in southern China. Sci Rep 2021; 11:20125. [PMID: 34635706 PMCID: PMC8505654 DOI: 10.1038/s41598-021-99550-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 09/27/2021] [Indexed: 02/01/2023] Open
Abstract
The popularized application of annual ryegrass-maize rotation (ARMR) in southern China has been proposed to fully utilize the farmlands and to increase forage yield and quality. Herein, one growth cycle of ARMR was conducted and soil bacteria were analyzed by 16S rRNA sequencing for control (CK), after the preceding crop (monoculture, or mixed sowing of annual ryegrass and oat) and the successive crop (maize). Our results indicated that the α-diversity of soil bacteria was changed in the ARMR system, which was related to the activity of urease and available phosphatase. The mixed sowing of annual ryegrass and oat in preceding crop could improve the yield and quality, while it was accompanied by unbalanced soil community. With the increased sowing proportion of oat to annual ryegrass, the soil pH increased while the soil available phosphatase decreased. The ARMR system was found to benefit the soil microenvironment by increasing the beneficial soil bacteria and enzyme activity or decreasing the harmful soil bacteria. Considering the soil bacteria α-diversity index and physicochemical properties comprehensively, the recommended sowing regime is the mixed sowing of M2 (22.5 kg·hm-2 annual ryegrass with 75 kg·hm-2 oat).
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Affiliation(s)
- Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaopeng Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaohui Xiong
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wenlong Gou
- Sichuan Academy of Grassland Science, Chengdu, 611731, Sichuan, China.
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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Sherpa MT, Sharma L, Bag N, Das S. Isolation, Characterization, and Evaluation of Native Rhizobacterial Consortia Developed From the Rhizosphere of Rice Grown in Organic State Sikkim, India, and Their Effect on Plant Growth. Front Microbiol 2021; 12:713660. [PMID: 34552571 PMCID: PMC8450577 DOI: 10.3389/fmicb.2021.713660] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/02/2021] [Indexed: 11/13/2022] Open
Abstract
Eight rhizospheric bacteria were isolated from the organic paddy fields of Sikkim, India, and identified as Pseudomonas kribbensis KSB, Burkholderia cenocepacia SRD, Kosakonia oryzendophytica YMA7, Pseudomonas rhodesiae SRB, Bacillus sp. ARA, Paenibacillus polymyxa COW3, Bacillus aryabhattai PSB2, and Bacillus megaterium PSB1. They showed plant growth-promoting attributes in rice and have bio-control potential against phytopathogen Colletotrichum gloeosporioides of large cardamom (Amomum subulatum). Burkholderia cenocepacia SRD showed production of indole acetic acid and ammonia and solubilization of phosphate and potassium and also possessed nitrogen fixation potential. It showed antagonistic activity against two other plant pathogens of large cardamom, viz., Curvularia eragrostidis and Pestalotiopsis sp., under in vitro conditions. The liquid bacterial consortium was prepared using the bacterial strains SRB, PSB1, and COW3 (Consortia-1); PSB2, SRD, and COW3 (Consortia-2); and COW3, KSB, and YMA7 (Consortia-3) to increase the growth and yield of rice plants under organic farming conditions. Greenhouse and field studies showed that the Consortia-3 had the highest plant growth-promoting activity. Consortia-3 demonstrated better agronomic performance in terms of root length (9.5 cm),number of leaflets per plant (5.3), grains per panicle (110.6), test grain weight (27.4 g), dry root weight per plant (0.73 g), and total dry biomass per plant (8.26 g).
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Affiliation(s)
- Mingma Thundu Sherpa
- Department of Horticulture, School of Life Sciences, Sikkim University, Gangtok, India
| | - Laxuman Sharma
- Department of Horticulture, School of Life Sciences, Sikkim University, Gangtok, India
| | - Niladri Bag
- Department of Horticulture, School of Life Sciences, Sikkim University, Gangtok, India
| | - Sayak Das
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
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Luo Y, Liu F, Ren J, Zhu J, Luo X, Xiang Y. Effects of dominant plant growth on the nutrient composition and bacterial community structure of manganese residues. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2021; 24:525-535. [PMID: 34382471 DOI: 10.1080/15226514.2021.1957769] [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] [Indexed: 06/13/2023]
Abstract
The rhizospheres of three dominant plant species (Miscanthus floridulus, Buddleja lindleyana, and Erigeron annuus) growing in manganese residue disposal sites in eastern Guizhou Province, China, were analyzed to study the effects of plant growth on the nutrient levels and bacterial community structure of two types of manganese residues. The results showed that the growth of the three species improved the nutritional composition of manganese residues; the available nitrogen (AN) contents of the manganese mine residue significantly increased by 29.56-60.78% while the available phosphorus (AP) contents of the electrolytic manganese residue significantly increased by 30.24-44.41% compared to those in unvegetated manganese residue. The diversity of the bacterial community in the manganese mine residue increased significantly due to plant growth. Proteobacteria, Acidobacteria, and Bacteroidetes were the dominant phyla in both manganese residues. Sphingomonas and GP6 were the dominant bacterial genera. The relative abundance of the Firmicutes phylum was significantly higher in the manganese mine residue than in the control and that of the Thiobacillus genus was lower, which indicated improvements in the microenvironment. Correlation analysis showed that OM and AN were the main nutrient factors affecting the bacterial community structure in the manganese mine residue.Novelty statement At present, research on the phytoremediation of manganese residue disposal sites focuses mostly on the investigation of different plant types and their heavy metal accumulation and transformation characteristics. However, comparative studies of the differences in growth matrix characteristics between plant growth areas and exposed areas are lacking. In addition, dominant plant species are regionally distributed. The previous studies were mostly concentrated in Chongqing, Guangxi, and Hunan in China. The eastern region of Guizhou Province is located in the "Manganese Triangle" area of China, where the manganese resources account for about 50% of the national total. There is no report on the phytoremediation of manganese residue disposal sites in this region. Therefore, the rhizospheres of three dominant plant species (Miscanthus floridulus, Buddleja lindleyana, and Erigeron annuus) growing in manganese residue disposal sites in eastern Guizhou Province, China, were analyzed to study the effects of plant growth on the nutrient levels and bacterial community structure of two types of manganese residues (manganese mine residue and electrolytic manganese residue). This study could provide useful theoretical information to benefit the ecological restoration of manganese residue disposal sites.
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Affiliation(s)
- Yang Luo
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, China
- School of Geography and Resources, Guizhou Education University, Guiyang, China
| | - Fang Liu
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, China
| | - Jun Ren
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, China
- School of Geography and Resources, Guizhou Education University, Guiyang, China
| | - Jian Zhu
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, China
| | - Xuqiang Luo
- School of Geography and Resources, Guizhou Education University, Guiyang, China
| | - Yangzhou Xiang
- School of Geography and Resources, Guizhou Education University, Guiyang, China
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Wang Y, Peng S, Hua Q, Qiu C, Wu P, Liu X, Lin X. The Long-Term Effects of Using Phosphate-Solubilizing Bacteria and Photosynthetic Bacteria as Biofertilizers on Peanut Yield and Soil Bacteria Community. Front Microbiol 2021; 12:693535. [PMID: 34335521 PMCID: PMC8322663 DOI: 10.3389/fmicb.2021.693535] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 06/14/2021] [Indexed: 11/30/2022] Open
Abstract
Microbial inoculation is a promising strategy to improve crop yields and reduce the use of chemical fertilizers, thereby creating environment-friendly agriculture. In this study, the long-term (5 years) effects of a phosphate-solubilizing bacterium Burkholderia cepacia ISOP5, a purple non-sulfur bacterium Rhodopseudomonas palustris ISP-1, and a mixed inoculation of these two bacteria (MB) on peanut yield, soil microbial community structure, and microbial metabolic functions were evaluated in a field experiment. After 5 years of inoculation, total peanut yield with B. cepacia ISOP5, R. palustris ISP-1, and MB treatments increased by 8.1%, 12.5%, and 19.5%, respectively. The treatments also significantly promoted the absorption of N and increased the protein content in peanut seeds. Nutrient content also increased to some extent in the bacteria-inoculum-treated soil. However, bacterial community diversity and richness were not significantly affected by bacterial inoculums, and only minor changes occurred in the bacterial community composition. Functional prediction revealed that bacterial inoculums reduced the relative abundance of those genes associated with P uptake and transport as well as increased the abundance of genes associated with inorganic P solubilization and organic P mineralization. Bacterial inoculums also increased the total relative abundance of genes associated with N metabolism. In addition to developing sustainable and eco-friendly agricultural practice, crop inoculation with B. cepacia ISOP5 and R. palustris ISP-1 would improve soil fertility, enhance microbial metabolic activity, and increase crop yield.
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Affiliation(s)
- Yiming Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, China
| | - Shuang Peng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,College of Environment and Ecology, Jiangsu Open University, Nanjing, China
| | - Qingqing Hua
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Chongwen Qiu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Pan Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xiaoli Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,National Engineering and Technology Research Center for Red Soil Improvement, Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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Yan L, Zhang W, Duan W, Zhang Y, Zheng W, Lai X. Temporal Bacterial Community Diversity in the Nicotiana tabacum Rhizosphere Over Years of Continuous Monocropping. Front Microbiol 2021; 12:641643. [PMID: 34113322 PMCID: PMC8186668 DOI: 10.3389/fmicb.2021.641643] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/28/2021] [Indexed: 01/19/2023] Open
Abstract
Long-term continuous monocropping negatively influences the physicochemical and biological characteristics of cultivated soil, especially for the economically important crop of flue-cured tobacco that is intolerant to continuous monocropping. The underlying mechanism of soil sickness under continuous monoculture and the temporal dynamic changes over the tobacco life cycle among different monoculture time spans remain poorly characterized. In this study, high-throughput sequencing targeting the 16S rRNA gene phylogenetic marker was performed on 60 soil samples of rhizosphere soil from flue−cured tobacco in the replanting, growth and harvest period across 5, 10, and 20 years of a continuous monocropping system. Bacterial community diversity decreased with the increase in duration of continuous monocropping, and the rhizosphere microbiota was highly dynamic in the harvest period. The random forests algorithm identified 17 taxa as biomarkers and a model was established to correlate root microbiota with continuous monocropping time of flue-cured tobacco. Molecular ecological network analysis elaborated the differences and interactions in bacterial co-occurrence patterns under different monocropping systems. The co-occurrence microbial network was larger in size but there were fewer interactions among microbial communities with the increase in continuous monocropping duration. These results provide insights into the changes of flue−cured tobacco root microbiome diversity in response to continuous monocropping and suggest a model for successional dynamics of the root-associated microbiota over continuous monocropping time and development stage. This study may help elucidate the theoretical basis underlying obstacles to continuous monocropping and could contribute to improving guidance for tobacco production.
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Affiliation(s)
- Lang Yan
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agriculture Science, Xichang University, Xichang, China
| | - Wenyou Zhang
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agriculture Science, Xichang University, Xichang, China
| | - Wangjun Duan
- China Tobacco Sichuan Industrial Co., Ltd., Chengdu, China
| | - Yizheng Zhang
- Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, China
| | - Wen Zheng
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agriculture Science, Xichang University, Xichang, China
| | - Xianjun Lai
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agriculture Science, Xichang University, Xichang, China
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Frühe L, Dully V, Forster D, Keeley NB, Laroche O, Pochon X, Robinson S, Wilding TA, Stoeck T. Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms. Front Microbiol 2021; 12:637811. [PMID: 33995296 PMCID: PMC8116884 DOI: 10.3389/fmicb.2021.637811] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/23/2021] [Indexed: 01/04/2023] Open
Abstract
The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3-V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.
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Affiliation(s)
- Larissa Frühe
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Verena Dully
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Dominik Forster
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Nigel B Keeley
- Biosecurity, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Research, Bergen, Norway
| | - Olivier Laroche
- Biosecurity, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Xavier Pochon
- Biosecurity, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Shawn Robinson
- St. Andrews Biological Station, Department of Fisheries and Oceans, St. Andrews, NB, Canada
| | | | - Thorsten Stoeck
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
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Succession of the Resident Soil Microbial Community in Response to Periodic Inoculations. Appl Environ Microbiol 2021; 87:AEM.00046-21. [PMID: 33637572 PMCID: PMC8091015 DOI: 10.1128/aem.00046-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/11/2021] [Indexed: 12/03/2022] Open
Abstract
Introducing beneficial microbes to the plant-soil system is an environmentally friendly approach to improve the crop yield and soil environment. Numerous studies have attempted to reveal the impacts of inoculation on the rhizosphere microbiome. To maintain the beneficial effects of microbial inoculants on plants and soil, repeated inoculation represents a promising option. Until now, the impacts of one-off inoculation on the native microbiome have been explored, but it remains unclear how long and to what extent the periodic inoculations would affect the succession of the resident microbiome in bulk soil. Here, we examined the dynamic responses of plant growth, soil functions, and the resident bacterial community in the bulk soil to periodic inoculations of phosphate-solubilizing and N2-fixing bacteria alone or in combination. Compared to single-strain inoculation, coinoculation better stimulated plant growth and soil nutrients. However, the benefits from inoculants did not increase with repeated inoculations and were not maintained after transplantation to a different site. In response to microbial inoculants, three patterns of shifts in the bacterial composition were observed: fold increase, fold decrease, and resilience. The periodic inoculations impacted the succession course of resident bacterial communities in bulk soil, mainly driven by changes in soil pH and nitrate, resulting in the development of three main cluster types throughout the investigation. The single and mixed inoculants transiently modulated the variation in the resident community in association with soil pH and the C/N ratio, but finally, the community established and showed resilience to subsequent inoculations. Consequently, the necessity of repeated inoculations should be reconsidered, and while the different microbial inoculants showed distinct impacts on resident microbiome succession, the communities ultimately exhibited resilience. IMPORTANCE Introducing beneficial microbes to the plant-soil system is an environmentally friendly approach to improve the crop yield and soil environment. Numerous studies have attempted to reveal the impacts of inoculation on the rhizosphere microbiome. However, little is known about the effectiveness of periodic inoculations on soil functioning. In addition, the long-term impact of repeated inoculations on the native community remains unclear. Here, we track the succession traits of the resident microbiome in the bulk soil across a growing season and identify the taxon clusters that respond differently to periodic inoculation. Crucially, we compare the development of the resident community composition with and without inoculation, thus providing new insight into the interactions between resident microbes and intruders. Finally, we conclude that initial inoculation plays a more important role in influencing the whole system, and the native microbial community exhibits traits of resilience, but no resistance, to the subsequent inoculations.
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Microbial Succession under Freeze-Thaw Events and Its Potential for Hydrocarbon Degradation in Nutrient-Amended Antarctic Soil. Microorganisms 2021; 9:microorganisms9030609. [PMID: 33809442 PMCID: PMC8000410 DOI: 10.3390/microorganisms9030609] [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: 02/14/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 12/24/2022] Open
Abstract
The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 °C and (ii) a freeze–thaw cycle (FTC) alternating between −20 and 4 °C. Bacterial taxa, such as Myxococcales, Chitinophagaceae, and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes.
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Cai F, Luo P, Yang J, Irfan M, Zhang S, An N, Dai J, Han X. Effect of Long-Term Fertilization on Ammonia-Oxidizing Microorganisms and Nitrification in Brown Soil of Northeast China. Front Microbiol 2021; 11:622454. [PMID: 33613469 PMCID: PMC7890093 DOI: 10.3389/fmicb.2020.622454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
The objective of this study was to find out changes in ammonia oxidation microorganisms with respect to fertilizer as investigated by real-time polymerase chain reaction and high-throughput sequencing. The treatments included control (CK); chemical fertilizer nitrogen low (N) and high (N2); nitrogen and phosphorus (NP); nitrogen phosphorus and potassium (NPK) and organic manure fertilizer (M); MN; MN2; MNPK. The results showed that long-term fertilization influenced soil fertility and affected the abundance and community of ammonia-oxidizing microorganisms by changing the physical and chemical properties of the soil. The abundance and community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) was influenced by soil organic carbon, total nitrogen, total soil phosphorus, available phosphorus, available potassium, and soil nitrate. Soil environmental factors affected the nitrification potential by affecting the structure of ammonia-oxidizing microorganisms; specific and rare AOA and AOB rather than the whole AOA or AOB community played dominant role in nitrification.
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Affiliation(s)
- Fangfang Cai
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China.,Northeast Scientific Observation Station of Corn Nutrition and Fertilization of Ministry of Agriculture, Shenyang, China
| | - Peiyu Luo
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China.,Northeast Scientific Observation Station of Corn Nutrition and Fertilization of Ministry of Agriculture, Shenyang, China
| | - Jinfeng Yang
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China.,Northeast Scientific Observation Station of Corn Nutrition and Fertilization of Ministry of Agriculture, Shenyang, China
| | - Muhammad Irfan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Shiyu Zhang
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China.,Northeast Scientific Observation Station of Corn Nutrition and Fertilization of Ministry of Agriculture, Shenyang, China
| | - Ning An
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China.,Northeast Scientific Observation Station of Corn Nutrition and Fertilization of Ministry of Agriculture, Shenyang, China
| | - Jian Dai
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China.,Northeast Scientific Observation Station of Corn Nutrition and Fertilization of Ministry of Agriculture, Shenyang, China
| | - Xiaori Han
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China.,Northeast Scientific Observation Station of Corn Nutrition and Fertilization of Ministry of Agriculture, Shenyang, China
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Tang X, Zou L, Su S, Lu Y, Zhai W, Manzoor M, Liao Y, Nie J, Shi J, Ma LQ, Xu J. Long-Term Manure Application Changes Bacterial Communities in Rice Rhizosphere and Arsenic Speciation in Rice Grains. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:1555-1565. [PMID: 33449628 DOI: 10.1021/acs.est.0c03924] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bioavailability and speciation of arsenic (As) are impacted by fertilization and bacteria in the rice rhizosphere. In this study, we investigated the effects of long-term manure application on As bioavailability, microbial community structure, and functional genes in a rice paddy field. The results showed that manure application did not affect total As in the soil but increased soluble As forms by 19%, increasing arsenite (As(III)) accumulation in rice grains and roots by 34 and 64% compared to a control. A real-time quantitative polymerase chain reaction (qPCR) and high-throughput sequencing analysis demonstrated that manure application increased the relative abundance of Rhizobium, Burkholderia, Sphingobium, and Sphingomonas containing arsenate reductase genes (arsC) in the rhizosphere soil, consistent with the 529% increase in arsC, which may have promoted arsenate (As(V)) reduction and increased As availability in pore water. In addition, manure application significantly altered the iron (Fe)-plaque microbial community structure and diversity. The microbes, particularly, Bradyrhizobium, Burkholderia, and Ralstonia, were mostly associated with As, Fe, and sulfur (S) cycles. This result was consistent with changes in the functional genes related to As, Fe, and S transformation. Although manure application promoted As(V) reduction (arsC) in Fe-plaque by 682%, it inhibited Fe and S reduction by decreasing FeIII reduction bacteria (Geobacteraceae) and the sulfate-reducing gene (dsrA) abundance. Further, manure application changed the composition of the microbial community that contained the arsC gene. In short, caution needs to be excised even in the soil with a low As concentration as manure application increased As(III) accumulation in rice grains.
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Affiliation(s)
- Xianjin Tang
- MOE Key Lab of Environmental Remediation and Ecosystem Health, and Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lina Zou
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shiming Su
- Key Laboratory of Agro-Environment, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanhong Lu
- Soil and Fertilizer Institute of Hunan Province, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Weiwei Zhai
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Maria Manzoor
- MOE Key Lab of Environmental Remediation and Ecosystem Health, and Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yulin Liao
- Soil and Fertilizer Institute of Hunan Province, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jun Nie
- Soil and Fertilizer Institute of Hunan Province, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jiyan Shi
- MOE Key Lab of Environmental Remediation and Ecosystem Health, and Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lena Q Ma
- MOE Key Lab of Environmental Remediation and Ecosystem Health, and Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianming Xu
- MOE Key Lab of Environmental Remediation and Ecosystem Health, and Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
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Sinong GF, Yasuda M, Nara Y, Lee CG, Dastogeer KMG, Tabuchi H, Nakai H, Djedidi S, Okazaki S. Distinct Root Microbial Communities in Nature Farming Rice Harbor Bacterial Strains With Plant Growth-Promoting Traits. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2020.629942] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A nature farming system is an ecological farming practice that entails cultivating crops without using chemical fertilizers and pesticides. To understand the diversity and functions of root microbiomes associated with nature farming systems, we compared the root microbial community of rice under nature farming conditions with those under conventional farming conditions. High-throughput amplicon analysis demonstrated a higher abundance and greater diversity of the root microbiome under unfertilized nature farming conditions than under conventional conditions. The application of chemical fertilizers reduced the microbial diversity and abundance of some beneficial taxa important for plant growth and health. Subsequently, we isolated and identified 46 endo- and epiphytic bacteria from rice roots grown under nature farming conditions and examined their plant growth-promoting activity. Six potential isolates were selected for plant growth assessment in insoluble P- and K-containing media. Most of the isolates promoted rice growth, and Pseudomonas koreensis AEPR1 was able to enhance rice growth significantly in both insoluble P- and K-containing media. Our data indicated that nature farming systems create a distinct root microbiome that is comparatively more diverse and supports plant growth under low-input cultivation practices than under conventional practices. The potential isolates could be exploited as sources with potential applications in sustainable agriculture.
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50
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Yu X, Yan M, Cui Y, Liu Z, Liu H, Zhou J, Liu J, Zeng L, Chen Q, Gu Y, Zou L, Zhao K, Xiang Q, Ma M, Li S. Effects of Co-application of Cadmium-Immobilizing Bacteria and Organic Fertilizers on Houttuynia cordata and Microbial Communities in a Cadmium-Contaminated Field. Front Microbiol 2021. [PMID: 35601203 DOI: 10.3389/fmicb.2021.687888/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
Cadmium pollution is a serious threat to the soil environment. The application of bio-based fertilizers in combination with beneficial microbial agents is a sustainable approach to solving Cd pollution in farm soil. The present study investigated the effects of co-application of a Cd-immobilizing bacterial agent and two fermented organic fertilizers (fermentative edible fungi residue; fermentative cow dung) on Houttuynia cordata and its microbial communities in a Cd-polluted field. It showed that both the application of the Cd-immobilizing bacterial agent alone and the combined application of bio-based soil amendments and the bacterial agent effectively reduced >20% of the uptake of Cd by the plant. Soil nitrogen level was significantly raised after the combined fertilization. The multivariate diversity analysis and co-occurrence network algorithm showed that a significant shift of microbial communities took place, in which the microbial populations tended to be homogeneous with reduced microbial richness and increased diversity after the co-application. The treatment of fermentative cow dung with the addition of the bacterial agent showed a significant increase in the microbial community dissimilarity (R = 0.996, p = 0.001) compared to that treated with cow dung alone. The co-application of the bacterial agent with both organic fertilizers significantly increased the abundance of Actinobacteria and Bacteroidetes. The FAPROTAX soil functional analysis revealed that the introduction of the microbial agent could potentially suppress human pathogenic microorganisms in the field fertilized with edible fungi residue. It also showed that the microbial agent can reduce the nitrite oxidation function in the soil when applied alone or with the organic fertilizers. Our study thus highlights the beneficial effects of the Cd-immobilizing bacterial inoculant on H. cordata and provides a better understanding of the microbial changes induced by the combined fertilization using the microbial agent and organic soil amendments in a Cd-contaminated field.
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Affiliation(s)
- Xiumei Yu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Min Yan
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yongliang Cui
- Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, China
| | - Zhongyi Liu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Han Liu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Jie Zhou
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Jiahao Liu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Lan Zeng
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Qiang Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yunfu Gu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Ke Zhao
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Quanju Xiang
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Menggen Ma
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Shuangcheng Li
- College of Resources, Sichuan Agricultural University, Chengdu, China
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