1
|
Daraz U, Erhunmwunse AS, Dubeux JCB, Mackowiak C, Liao HL, Wang XB. Soil fungal community structure and function response to rhizoma perennial peanut cultivars. BMC PLANT BIOLOGY 2024; 24:582. [PMID: 38898415 PMCID: PMC11186081 DOI: 10.1186/s12870-024-05209-y] [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: 04/07/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Crop-associated microorganisms play a crucial role in soil nutrient cycling, and crop growth, and health. Fine-scale patterns in soil microbial community diversity and composition are commonly regulated by plant species or genotype. Despite extensive reports in different crop or its cultivar effects on the microbial community, it is uncertain how rhizoma peanut (RP, Arachis glabrata Benth.), a perennial warm-season legume forage that is well-adapted in the southern USA, affects soil microbial community across different cultivars. RESULTS This study explored the influence of seven different RP cultivars on the taxonomic composition, diversity, and functional groups of soil fungal communities through a field trial in Marianna, Florida, Southern USA, using next-generation sequencing technique. Our results showed that the taxonomic diversity and composition of the fungal community differed significantly across RP cultivars. Alpha diversity (Shannon, Simpson, and Pielou's evenness) was significantly higher in Ecoturf but lower in UF_Peace and Florigraze compared to other cultivars (p < 0.001). Phylogenetic diversity (Faith's PD) was lowest in Latitude compared to other cultivars (p < 0.0001). The dominant phyla were Ascomycota (13.34%), Mortierellomycota (3.82%), and Basidiomycota (2.99%), which were significantly greater in Florigraze, UF_Peace, and Ecoturf, respectively. The relative abundance of Neocosmospora was markedly high (21.45%) in UF_Tito and showed large variations across cultivars. The relative abundance of the dominant genera was significantly greater in Arbrook than in other cultivars. There were also significant differences in the co-occurrence network, showing different keystone taxa and more positive correlations than the negative correlations across cultivars. FUNGuild analysis showed that the relative abundance of functional guilds including pathogenic, saprotrophic, endophytic, mycorrhizal and parasitic fungi significantly differed among cultivars. Ecoturf had the greatest relative abundance of mycorrhizal fungal group (5.10 ± 0.44), whereas UF_Peace had the greatest relative abundance of endophytic (4.52 ± 0.56) and parasitic fungi (1.67 ± 0.30) compared to other cultivars. CONCLUSIONS Our findings provide evidence of crop cultivar's effect in shaping fine-scale fungal community patterns in legume-based forage systems.
Collapse
Affiliation(s)
- Umar Daraz
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral, Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China
| | | | - José C B Dubeux
- North Florida Research and Education Center, University of Florida, Marianna, FL, USA
| | - Cheryl Mackowiak
- North Florida Research and Education Center, University of Florida, Quincy, FL, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy, FL, USA
| | - Xiao-Bo Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral, Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China.
| |
Collapse
|
2
|
Xi M, Wang Y, Yang J, Bi X, Zhong S, Duan T, He Y, Tu T, Qian X. Spatial distribution and community composition of endophytic fungi within Mussaenda pubescens stems. Fungal Biol 2024; 128:1815-1826. [PMID: 38876534 DOI: 10.1016/j.funbio.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 06/16/2024]
Abstract
Endophytic fungi, pivotal in facilitating plant co-evolution, significantly enhance plant growth, stress resistance, and environmental adaptability. Despite their importance, the spatial distribution of stem endophytic fungi (SEF) within host plants remains poorly characterized. Here, we employed high-throughput sequencing to conduct a comparative analysis of SEF communities in Mussaenda pubescens on a regional scale. Our findings reveal that whole-SEF communities were overwhelmingly dominated by members of the phylum Ascomycota, accounting for 85.9 %, followed by Basidiomycota at 13.9 %, and that alpha diversity within the whole-SEF community of M. pubescens remains relatively consistent across sampling sites. However, significant variation was observed within conditionally abundant taxa (CAT), conditionally rare or abundant taxa (CRAT), and conditionally rare taxa (CRT). Climatic factors emerged as the primary influence on SEF community distribution, followed by spatial distance and stem chemical properties. Neutral community modeling results suggested that both stochastic and deterministic processes play a role in shaping whole-SEF communities, with deterministic processes having a stronger influence on CRT subcommunities. Furthermore, the CRT co-occurrence network exhibited a more complex structure, characterized by higher values of network betweenness and degree relative to CAT and CRAT subcommunities. These findings enhance our understanding of community assembly and ecological interactions between stem fungal endophytes, presenting opportunities for harnessing fungal resources for the benefit of humanity.
Collapse
Affiliation(s)
- Meijuan Xi
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yonglong Wang
- Faculty of Biological Science and Technology, Baotou Teacher's College, Baotou, China
| | - Juanjuan Yang
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaohui Bi
- Shangqiu Institute of Quality Inspection and Technical Research, Shangqiu, China
| | - Shengen Zhong
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tingting Duan
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Yimin He
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tieyao Tu
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
| | - Xin Qian
- Fujian Agriculture and Forestry University, Fuzhou, China.
| |
Collapse
|
3
|
Ma Y, Yu A, Zhang L, Zheng R. Effects of Rice-Frog Co-Cropping on the Soil Microbial Community Structure in Reclaimed Paddy Fields. BIOLOGY 2024; 13:396. [PMID: 38927276 PMCID: PMC11200385 DOI: 10.3390/biology13060396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/20/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024]
Abstract
Utilizing and improving the productivity of reclaimed land are highly significant for alleviating the problem of food production shortage in China, and the integrated rice-frog farming model can improve soil fertility. However, there are few studies on the use of integrated rice-frog farming technology to improve the fertility of reclaimed land and increase its efficiency in food production. Therefore, this study was conducted to evaluate the effects of the rice-frog co-cropping mode on the soil fertility and microbial diversity of reclaimed land. A rice monoculture group (SF), low-density rice-frog co-cropping group (SD, 5000 frogs/mu, corresponds to 8 frogs/m2), and high-density rice-frog co-cropping group (SG, 10,000 frogs/mu, corresponds to 15 frogs/m2) were established and tested. The contents of total nitrogen, soil organic matter, available potassium, and available phosphorus of the soil in the SG group were significantly higher than those in the SF group (p < 0.05) in the mature stage of rice. Compared with the SF group, the SD and SG groups improved the soil microbial diversity and changed the structure of the microbial community. This study indicates that compared with the rice monoculture mode, the rice-frog co-cropping pattern can improve the soil fertility, as well as microbial diversity, of reclaimed land.
Collapse
Affiliation(s)
- Yunshuang Ma
- Provincial Key Laboratory of Wildlife Biotechnology and Conservation and Utilization, Zhejiang Normal University, Jinhua 321004, China; (Y.M.); (A.Y.)
| | - Anran Yu
- Provincial Key Laboratory of Wildlife Biotechnology and Conservation and Utilization, Zhejiang Normal University, Jinhua 321004, China; (Y.M.); (A.Y.)
| | - Liangliang Zhang
- Xingzhi College, Zhejiang Normal University, Jinhua 321004, China;
| | - Rongquan Zheng
- Provincial Key Laboratory of Wildlife Biotechnology and Conservation and Utilization, Zhejiang Normal University, Jinhua 321004, China; (Y.M.); (A.Y.)
- Xingzhi College, Zhejiang Normal University, Jinhua 321004, China;
| |
Collapse
|
4
|
Zampolli J, De Giani A, Rossi M, Finazzi M, Di Gennaro P. Who inhabits the built environment? A microbiological point of view on the principal bacteria colonizing our urban areas. Front Microbiol 2024; 15:1380953. [PMID: 38863750 PMCID: PMC11165352 DOI: 10.3389/fmicb.2024.1380953] [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: 02/02/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024] Open
Abstract
Modern lifestyle greatly influences human well-being. Indeed, nowadays people are centered in the cities and this trend is growing with the ever-increasing population. The main habitat for modern humans is defined as the built environment (BE). The modulation of life quality in the BE is primarily mediated by a biodiversity of microbes. They derive from different sources, such as soil, water, air, pets, and humans. Humans are the main source and vector of bacterial diversity in the BE leaving a characteristic microbial fingerprint on the surfaces and spaces. This review, focusing on articles published from the early 2000s, delves into bacterial populations present in indoor and outdoor urban environments, exploring the characteristics of primary bacterial niches in the BE and their native habitats. It elucidates bacterial interconnections within this context and among themselves, shedding light on pathways for adaptation and survival across diverse environmental conditions. Given the limitations of culture-based methods, emphasis is placed on culture-independent approaches, particularly high-throughput techniques to elucidate the genetic and -omic features of BE bacteria. By elucidating these microbiota profiles, the review aims to contribute to understanding the implications for human health and the assessment of urban environmental quality in modern cities.
Collapse
Affiliation(s)
| | | | | | | | - Patrizia Di Gennaro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| |
Collapse
|
5
|
Liu S, Liu R, Zhang S, Shen Q, Chen J, Ma H, Ge C, Hao L, Zhang J, Shi S, Pang C. The Contributions of Sub-Communities to the Assembly Process and Ecological Mechanisms of Bacterial Communities along the Cotton Soil-Root Continuum Niche Gradient. Microorganisms 2024; 12:869. [PMID: 38792699 PMCID: PMC11123189 DOI: 10.3390/microorganisms12050869] [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: 03/13/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 05/26/2024] Open
Abstract
Soil microbes are crucial in shaping the root-associated microbial communities. In this study, we analyzed the effect of the soil-root niche gradient on the diversity, composition, and assembly of the bacterial community and co-occurrence network of two cotton varieties. The results revealed that the bacterial communities in cotton soil-root compartment niches exhibited a skewed species abundance distribution, dominated by abundant taxa showing a strong spatial specificity. The assembly processes of the rhizosphere bacterial communities were mainly driven by stochastic processes, dominated by the enrichment pattern and supplemented by the depletion pattern to recruit bacteria from the bulk soil, resulting in a more stable bacterial community. The assembly processes of the endosphere bacterial communities were determined by processes dominated by the depletion pattern and supplemented by the enrichment pattern to recruit species from the rhizosphere, resulting in a decrease in the stability and complexity of the community co-occurrence network. The compartment niche shaped the diversity of the bacterial communities, and the cotton variety genotype was an important source of diversity in bacterial communities within the compartment niche. We suggest that the moderate taxa contribute to significantly more changes in the diversity of the bacterial community than the rare and abundant taxa during the succession of bacterial communities in the cotton root-soil continuum.
Collapse
Affiliation(s)
- Shaodong Liu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Ruihua Liu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Siping Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Qian Shen
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Jing Chen
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Huijuan Ma
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Changwei Ge
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Lidong Hao
- Postdoctoral Mobile Station, Lanzhou University, Lanzhou 730000, China
| | - Jinshan Zhang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Shubing Shi
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Chaoyou Pang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| |
Collapse
|
6
|
Yang J, Ding D, Zhang X, Gu H. A comparative analysis of soil physicochemical properties and microbial community structure among four shelterbelt species in the northeast China plain. Microbiol Spectr 2024; 12:e0368323. [PMID: 38376351 PMCID: PMC10986494 DOI: 10.1128/spectrum.03683-23] [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: 10/18/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Conducting studies that focus on the alterations occurring in the soil microbiome within protection forests in the northeast plain is of utmost importance in evaluating the ecological rehabilitation of agricultural lands in the Mollisols region. Nevertheless, the presence of geographic factors contributes to substantial disparities in the microbiomes, and thus, addressing this aspect of influence becomes pivotal in ensuring the credibility of the collected data. Consequently, the objective is to compare the variations in soil physicochemical properties and microbial community structure within the understory of diverse shelterbelt species. In this study, we analyzed the understory soils of Juglans mandshurica (Jm), Fraxinus mandschurica (Fm), Acer mono (Am), and Betula platyphylla (Bp) from the same locality. We employed high-throughput sequencing technology and soil physicochemical data to investigate the impact of these different tree species on soil microbial communities, chemical properties, and enzyme activities in Mollisols areas. Significant variations in soil nutrients and enzyme activities were observed among tree species, with soil organic matter content ranging from 49.1 to 67.7 g/kg and cellulase content ranging from 5.3 to 524.0 μg/d/g. The impact of tree species on microbial diversities was found to be more pronounced in the bacterial community (Adnoism: R = 0.605) compared to the fungal community (Adnoism: R = 0.433). The linear discriminant analysis effect size (LEfSe) analysis revealed a total of 5 (Jm), 3 (Bp), and 6 (Am) bacterial biomarkers, as well as 2 (Jm), 6 (Fm), 4 (Bp), and 1 (Am) fungal biomarker at the genus level (LDA3). The presence of various tree species was observed to significantly alter the relative abundance of specific microbial community structures, specifically in Gammaproteobacteria, Ascomycota, and Basidiomycota. Furthermore, environmental factors, such as pH, total potassium, and available phosphorus were important factors influencing changes in bacterial communities. We propose that Fm be utilized as the primary tree species for establishing farmland protection forests in the northeastern region, owing to its superior impact on enhancing soil quality. IMPORTANCE The focal point of this study lies in the implementation of a controlled experiment conducted under field conditions. In this experiment, we deliberately selected four shelterbelts within the same field, characterized by identical planting density, and planting year. This deliberate selection effectively mitigated the potential impact of extraneous factors on the three microbiomes, thereby enhancing the reliability and validity of our findings.
Collapse
Affiliation(s)
- Jia Yang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Dang Ding
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Xiuru Zhang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Huiyan Gu
- School of Forestry, Northeast Forestry University, Harbin, China
| |
Collapse
|
7
|
Hou M, Zhu Y, Chen H, Wen Y. Chiral herbicide imazethapy influences plant-soil feedback on nitrogen metabolism by shaping rhizosphere microorganisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:18625-18635. [PMID: 38351351 DOI: 10.1007/s11356-024-32393-z] [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: 11/09/2023] [Accepted: 02/05/2024] [Indexed: 03/09/2024]
Abstract
Herbicides are known to affect the soil nitrogen cycle by shaping soil microorganisms. However, it is not clear how herbicides regulate diverse transformation processes of soil nitrogen cycling by altering rhizosphere microorganisms, subsequently influencing the feedback to plant nitrogen metabolism. Here, we investigated how imazethapyr (IM) enantiomers drive plant-soil feedback on nitrogen metabolism by altering the rhizosphere microorganisms. The results indicated that (R)- and (S)-IM significantly changed the composition and structure rhizosphere microbiome with enantioselectivity and functional changes in microbial communities were associated with soil nitrogen circulation. The determination of nitrogen-cycling functional genes further supported the above findings. The results revealed that (R)- and (S)-IM could change the abundance of nitrogen-cycling functional genes by changing specific bacteria abundances, such as Bacteroidetes, Proteobacteria, and Acidobacteria, thus resulting in diverse nitrogen transformation processes. The alternation of nitrogen transformation processes indicated (R)-IM exhibited a more notable tendency to form a nitrogen cycling pattern with lower energy cost and higher nitrogen retention than (S)-IM. Sterilization experiments demonstrated changes in soil nitrogen cycling drive plant nitrogen metabolism and rhizosphere microorganisms are responsible for the above process of plant-soil feedback for nitrogen metabolism. Under IM enantiomer treatments, rhizosphere microorganisms might stimulate glutamate synthesis by promoting NH4+ uptake and glutamine-glutamate synthesis cycling in roots, thus contributing to positive feedback, with (R)-IM treatments showing more pronounced positive feedback on nitrogen metabolism than (S)-IM treatments. Our results provide theoretical support for determining the mechanism by which IM enantiomers drive plant-soil nitrogen metabolism by changing the rhizosphere microbial communities.
Collapse
Affiliation(s)
- Mengchun Hou
- MOE Key Laboratory of Environmental Remediation & Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Youfeng Zhu
- MOE Key Laboratory of Environmental Remediation & Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hui Chen
- Ningbo Key Laboratory of Agricultural Germplasm Resources Mining and Environmental Regulation, College of Science and Technology, Ningbo University, Cixi, 315300, China
| | - Yuezhong Wen
- MOE Key Laboratory of Environmental Remediation & Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
8
|
LeBlanc NR, Harrigian FC. Green Waste Compost Impacts Microbial Functions Related to Carbohydrate Use and Active Dispersal in Plant Pathogen-Infested Soil. MICROBIAL ECOLOGY 2024; 87:44. [PMID: 38367043 PMCID: PMC10874327 DOI: 10.1007/s00248-024-02361-8] [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: 10/20/2023] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
The effects of compost on physical and chemical characteristics of soil are well-studied but impacts on soil microbiomes are poorly understood. This research tested effects of green waste compost on bacterial communities in soil infested with the plant pathogen Fusarium oxysporum. Compost was added to pathogen-infested soil and maintained in mesocosms in a greenhouse experiment and replicated growth chamber experiments. Bacteria and F. oxysporum abundance were quantified using quantitative PCR. Taxonomic and functional characteristics of bacterial communities were measured using shotgun metagenome sequencing. Compost significantly increased bacterial abundance 8 weeks after amendment in one experiment. Compost increased concentrations of chemical characteristics of soil, including phosphorus, potassium, organic matter, and pH. In all experiments, compost significantly reduced abundance of F. oxysporum and altered the taxonomic composition of soil bacterial communities. Sixteen bacterial genera were significantly increased from compost in every experiment, potentially playing a role in pathogen suppression. In all experiments, there was a consistent negative effect of compost on functions related to carbohydrate use and a positive effect on bacteria with flagella. Results from this work demonstrate that compost can reduce the abundance of soilborne plant pathogens and raise questions about the role of microbes in plant pathogen suppression.
Collapse
Affiliation(s)
- Nicholas R LeBlanc
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, 1636 E. Alisal St, Salinas, CA, 93905, USA.
| | - Fiona C Harrigian
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, 1636 E. Alisal St, Salinas, CA, 93905, USA
| |
Collapse
|
9
|
García-Serquén AL, Chumbe-Nolasco LD, Navarrete AA, Girón-Aguilar RC, Gutiérrez-Reynoso DL. Traditional potato tillage systems in the Peruvian Andes impact bacterial diversity, evenness, community composition, and functions in soil microbiomes. Sci Rep 2024; 14:3963. [PMID: 38368478 PMCID: PMC10874408 DOI: 10.1038/s41598-024-54652-2] [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: 11/09/2023] [Accepted: 02/15/2024] [Indexed: 02/19/2024] Open
Abstract
The soil microbiome, a crucial component of agricultural ecosystems, plays a pivotal role in crop production and ecosystem functioning. However, its response to traditional tillage systems in potato cultivation in the Peruvian highlands is still far from understood. Here, ecological and functional aspects of the bacterial community were analyzed based on soil samples from two traditional tillage systems: 'chiwa' (minimal tillage) and 'barbecho' (full tillage), in the Huanuco region of the Peruvian central Andes. Similar soil bacterial community composition was shown for minimal tillage system, but it was heterogeneous for full tillage system. This soil bacterial community composition under full tillage system may be attributed to stochastic, and a more dynamic environment within this tillage system. 'Chiwa' and 'barbecho' soils harbored distinct bacterial genera into their communities, indicating their potential as bioindicators of traditional tillage effects. Functional analysis revealed common metabolic pathways in both tillage systems, with differences in anaerobic pathways in 'chiwa' and more diverse pathways in 'barbecho'. These findings open the possibilities to explore microbial bioindicators for minimal and full tillage systems, which are in relationship with healthy soil, and they can be used to propose adequate tillage systems for the sowing of potatoes in Peru.
Collapse
Affiliation(s)
- Aura L García-Serquén
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, 15024, Lima, Peru.
| | - Lenin D Chumbe-Nolasco
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, 15024, Lima, Peru
| | - Acacio Aparecido Navarrete
- Graduate Program in Environmental Sciences, Brazil University (UB), Estrada Projetada F1, Fazenda Santa Rita, Fernandópolis, São Paulo, 15613-899, Brazil
| | - R Carolina Girón-Aguilar
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, 15024, Lima, Peru
| | - Dina L Gutiérrez-Reynoso
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, 15024, Lima, Peru
| |
Collapse
|
10
|
Paull GC, Lee CJ, Tyler CR. Beyond compliance: harmonising research and husbandry practices to improve experimental reproducibility using fish models. Biol Rev Camb Philos Soc 2024; 99:253-264. [PMID: 37817305 DOI: 10.1111/brv.13020] [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: 05/30/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/12/2023]
Abstract
Reproducibility in animal research is impacted by the environment, by husbandry practices in the laboratory and by the animals' provenance. These factors, however, are often not adequately considered by researchers. A disconnect between researchers and animal care staff can result in inappropriate housing and husbandry decisions for scientific studies with those animals. This is especially the case for the research in neuro-behaviour, epigenetics, and the impact of climate change, as heritable phenotypic, behavioural or physiological changes are known to result from the animals' environmental housing, husbandry, provenance and prior experience. This can lead to greater variation (even major differences) in data outcomes among studies, driving scientific uncertainties. Herein, we illustrate some of the endpoints measured in fish studies known to be intrinsically linked to the environment and husbandry conditions and assess the significance of housing and husbandry practice decisions for research adopting these endpoints for different fish species. We highlight the different priorities and challenges faced by researchers and animal care staff and how harmonising their activities and building greater understanding of how husbandry practices affect the fish will improve reproducibility in research outcomes. We furthermore illustrate how improving engagement between stakeholders, including regulatory bodies, can better underpin fish husbandry decisions and where researchers could help to drive best husbandry practices through their own research with fish models.
Collapse
Affiliation(s)
- Gregory C Paull
- Biosciences, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Carole J Lee
- Biosciences, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Charles R Tyler
- Biosciences, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| |
Collapse
|
11
|
Wang YX, Liu XY, Di HH, He XS, Sun Y, Xiang S, Huang ZB. The mechanism of microbial community succession and microbial co-occurrence network in soil with compost application. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167409. [PMID: 37769744 DOI: 10.1016/j.scitotenv.2023.167409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/17/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
The application of organic and chemical fertilizer into soil can regulate microbial communities. However, the response mechanism of microbial communities in soil to compost and chemical fertilizer application remain unclear. In this study, compost made of tobacco leaves individually and combined with chemical fertilizer was applied, respectively, to investigate their effect on soil microorganisms during the pot-culture process. High-throughput sequence, neutral community model and null model were employed to clarify how soil microbial community respond to the application of compost and chemical fertilizer. Furthermore, random forest model was applied to predict the relationships between the plant agronomical traits and the soil microorganism during the pot-culture process. The results demonstrated that the simultaneous application of compost and chemical fertilizer increased significantly the richness and diversity of the microorganisms in soil (p < 0.05), groups C and D led to a significant reduction in the number of nodes and edges in the microbial network (77.78 %-96.57 %). The dominant bacteria in the application of 50 g fertilizer accounted for the highest proportion (40 %) and organic matter was the main factors driving the change in bacterial communities. Compared to the tilled soil, the microbial communities of the soil with the simultaneous application of compost and chemical fertilizer were more susceptible to stochastic processes, and soil microorganisms had less influence on the growth of crops during pot-culture. In conclusion, the simultaneous application of compost and fertilizer altered the ecological functions of soil microbial communities, leading to an enhanced stochastic process of community formation.
Collapse
Affiliation(s)
- Yu-Xin Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xie-Yang Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China
| | - Hui-Hui Di
- Enshi Tobacco Company of Hubei Province Corporation, Enshi 445000, China
| | - Xiao-Song He
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yue Sun
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Song Xiang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Zhan-Bin Huang
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China
| |
Collapse
|
12
|
Ahsan T, Tian PC, Gao J, Wang C, Liu C, Huang YQ. Effects of microbial agent and microbial fertilizer input on soil microbial community structure and diversity in a peanut continuous cropping system. J Adv Res 2023:S2090-1232(23)00367-3. [PMID: 38030126 DOI: 10.1016/j.jare.2023.11.028] [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: 09/09/2023] [Revised: 11/11/2023] [Accepted: 11/24/2023] [Indexed: 12/01/2023] Open
Abstract
INTRODUCTION The soil harbors a diverse array of microorganisms, and these are essential components of terrestrial ecosystems. The presence of microorganisms in the soil, particularly in the rhizosphere, is closely linked to plant growth and soil fertility. OBJECTIVE The primary objective of this study is to assess the potential advantages of integrating microbial inoculants with compound fertilizer in enhancing peanut yield. METHODS We utilized Illumina MiSeq high-throughput sequencing technology to conduct our investigation. The experimental design consists of four treatment groups: compound fertilizers (CF), compound fertilizers supplemented with microbial agents (CF + MA), compound fertilizers supplemented with microbial fertilizers (CF + MF), and compound fertilizers supplemented with both microbial agents and microbial fertilizers (CF + MM). RESULTS The experimental results demonstrated a significant increase in peanut yield upon application of CF + MA, CF + MF, and CF + MM treatments. During the blossom stage and pod-setting stage, the soil's catalase, urease, and acid phosphatase activities were significantly increased in the CF + MA, and CF + MM treatments compared to the CF treatment. The application of CF + MA resulted in an increase in bacterial richness in the rhizosphere soil of peanuts, as indicated by the sequencing results. The application of CF + MA, CF + MF, and CF + MM resulted in a reduction of fungal diversity. Proteobacteria, Actinobacteria, and Acidobacteria were the dominant bacterial phyla, while Ascomycota and Basidiomycota were the dominant phyla in the fungal component of the rhizosphere soil microbiome across all experimental treatments. CONCLUSION Microbial agents and fertilizers modify the peanut rhizosphere soil's microbial community structure, as per our findings. The abundance of potentially beneficial bacteria (Bradyrhizobium, Rhizobium, and Burkholderia) and fungi (Trichoderma and Cladophialophora) could increase, while pathogenic fungi (Penicillium and Fusarium) decreased, thereby significantly promoting plant growth and yield of peanut.
Collapse
Affiliation(s)
- Taswar Ahsan
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; College of Land and Environment, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Pei-Cong Tian
- College of Land and Environment, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Jie Gao
- College of Land and Environment, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Chen Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Chuang Liu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Yu-Qian Huang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China.
| |
Collapse
|
13
|
Li T, Gao J. Attribution of dispersal limitation can better explain the assembly patterns of plant microbiota. FRONTIERS IN PLANT SCIENCE 2023; 14:1168760. [PMID: 37941678 PMCID: PMC10628812 DOI: 10.3389/fpls.2023.1168760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Disentangling community assembly processes is crucial for fully understanding the function of microbiota in agricultural ecosystems. However, numerous plant microbiome surveys have gradually revealed that stochastic processes dominate the assembly of the endophytic root microbiota in conflict with strong host filtering effects, which is an important issue. Resolving such conflicts or inconsistencies will not only help accurately predict the composition and structure of the root endophytic microbiota and its driving mechanisms, but also provide important guidance on the correlation between the relative importance of deterministic and stochastic processes in the assembly of the root endophytic microbiota, and crop productivity and nutritional quality. Here, we propose that the inappropriate division of dispersal limitation may be the main reason for such inconsistency, which can be resolved after the proportion of dispersal limitation is incorporated into the deterministic processes. The rationality of this adjustment under the framework of the formation of a holobiont between the microbiome and the plant host is herein explained, and a potential theoretical framework for dynamic assembly patterns of endophytic microbiota along the soil-plant continuum is proposed. Considering that the assembly of root endophytic microbiota is complicated, we suggest caution and level-by-level verification from deterministic processes to neutral components to stochastic processes when deciding on the attribution of dispersal limitation in the future to promote the expansion and application of microbiome engineering in sustainable agricultural development based on community assembly patterns.
Collapse
Affiliation(s)
| | - Jiangyun Gao
- Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| |
Collapse
|
14
|
Peng M, Jiang Z, Zhou F, Wang Z. From salty to thriving: plant growth promoting bacteria as nature's allies in overcoming salinity stress in plants. Front Microbiol 2023; 14:1169809. [PMID: 37426022 PMCID: PMC10327291 DOI: 10.3389/fmicb.2023.1169809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023] Open
Abstract
Soil salinity is one of the main problems that affects global crop yield. Researchers have attempted to alleviate the effects of salt stress on plant growth using a variety of approaches, including genetic modification of salt-tolerant plants, screening the higher salt-tolerant genotypes, and the inoculation of beneficial plant microbiome, such as plant growth-promoting bacteria (PGPB). PGPB mainly exists in the rhizosphere soil, plant tissues and on the surfaces of leaves or stems, and can promote plant growth and increase plant tolerance to abiotic stress. Many halophytes recruit salt-resistant microorganisms, and therefore endophytic bacteria isolated from halophytes can help enhance plant stress responses. Beneficial plant-microbe interactions are widespread in nature, and microbial communities provide an opportunity to understand these beneficial interactions. In this study, we provide a brief overview of the current state of plant microbiomes and give particular emphasis on its influence factors and discuss various mechanisms used by PGPB in alleviating salt stress for plants. Then, we also describe the relationship between bacterial Type VI secretion system and plant growth promotion.
Collapse
Affiliation(s)
- Mu Peng
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, China
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, China
| | - Zhihui Jiang
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, China
| | - Fangzhen Zhou
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, China
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, China
| | - Zhiyong Wang
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, China
| |
Collapse
|
15
|
Xia M, Ma X, Liu J, Wu M, Li Z, Liu M. Potential effect of key soil bacterial taxa on the increase of rice yield under milk vetch rotation. Front Microbiol 2023; 14:1150505. [PMID: 37283927 PMCID: PMC10241072 DOI: 10.3389/fmicb.2023.1150505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/28/2023] [Indexed: 06/08/2023] Open
Abstract
Legume crop rotation is often adopted in rice cultivation to improve soil productivity. However, little is known about the role of microbes under legume rotation in affecting soil productivity. To elucidate this, a long-term paddy cropping experiment was set up to study the relationship between crop yield, soil chemical properties, and key microbial taxa under a double-rice and milk vetch rotation. Milk vetch rotation significantly improved soil chemical properties compared to no fertilization treatment, and soil phosphorus was a major factor correlated with crop yield. Long-term legume rotation increased soil bacterial alpha diversity and changed soil bacterial community. After milk vetch rotation, the relative abundances of Bacteroidota, Desulfobacterota, Firmicutes, and Proteobacteria increased while those of Acidobacteriota, Chloroflexi, and Planctomycetota decreased. Moreover, milk vetch rotation increased the relative abundance of phosphorus-related gene K01083 (bpp), which was significantly correlated with soil phosphorus content and crop yield. Network analysis showed that taxa of Vicinamibacterales were positively correlated with total phosphorus and available phosphorus, which was a potential taxon contributing to the availability of soil phosphorus stock. Our results indicated that milk vetch rotation could enrich key taxa with latent phosphate-solubilizing ability, increase the content of soil available phosphorus, and finally enhance crop yield. This could provide scientific guidance for better crop production.
Collapse
Affiliation(s)
- Mingming Xia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinling Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jia Liu
- National Engineering and Technology Research Center for Red Soil Improvement, Soil and Fertilizer & Resources and Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Meng Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
- Ecological Experimental Station of Red Soil Academia Sinica, Nanjing, China
| |
Collapse
|
16
|
Huang Y, Huang Y, Hou J, Wu L, Christie P, Liu W. Microbial community assembly of the hyperaccumulator plant Sedum plumbizincicola in two contrasting soil types with three levels of cadmium contamination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160917. [PMID: 36529394 DOI: 10.1016/j.scitotenv.2022.160917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/24/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Microbial communities are closely related to plant performance and numerous studies have shown their involvement with the growth and development of host plants, resistance to pathogen invasion and adaptation to environmental stress. Here we described in detail the ecological process of the microbial community assembly in hyperaccumulator plant Sedum plumbizincicola. We divided the microbiota into four ecological compartments (bulk soil, rhizosphere, root endosphere and aboveground endosphere). The results showed that host selection strongly controlled the aggregation of microbial community. So that microbes occupied different niches from the bulk soil to the aboveground endosphere, and bacterial diversity and network complexity decreased gradually. Soil types were the second influencing factor, especially for the microbial community in the root endosphere. The SourceTracker analysis further confirmed the vertical migration of microbes from bulk soil to aboveground endosphere. In addition, under the condition of heavy metal pollution, the microbial community of S. plumbizincicola tended to form a microbial pool dominated by Proteobacteria and Actinobacteria. Ellin6067, Sphingomonas, Ralstonia, SC-I-84_uncultured bacterium, Burkholderiaceae_Undibacterium and Pedosphaeraceae_uncultured bacterium etc. were identified as the vital biomarker taxa. Among these genera, the relative abundance of last three was significantly positively correlated with the activation and transfer of cadmium, and they mainly enriched in paddy soil. This study provides evidence for the mechanism by which the microbial community assembly occurs and experience for regulating the microbial community and increasing the accumulation efficiency of potentially toxic metals in S. plumbizincicola.
Collapse
Affiliation(s)
- Ya Huang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongjie Huang
- School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China; Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, Anhui Normal University, Wuhu 241000, China.
| | - Jinyu Hou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Longhua Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Wuxing Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| |
Collapse
|
17
|
Li K, Chen L, Shi W, Hu C, Sha Y, Feng G, Wang E, Chen W, Sui X, Mi G. Impacts of maize hybrids with different nitrogen use efficiency on root-associated microbiota based on distinct rhizosphere soil metabolites. Environ Microbiol 2023; 25:473-492. [PMID: 36451600 DOI: 10.1111/1462-2920.16293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022]
Abstract
Plant genotypes shape root-associated microbiota that affect plant nutrient acquisition and productivity. It is unclear how maize hybrids modify root-associated microbiota and their functions and relationship with nitrogen use efficiency (NUE) by regulating rhizosphere soil metabolites. Here, two N-efficient (NE) (ZD958, DMY3) and two N-inefficient (NIE) maize hybrids (YD9953, LY99) were used to investigate this issue under low N (60 kg N ha-1 , LN) and high N (180 kg N ha-1 , HN) field conditions. NE hybrids had higher yield than NIE hybrids under LN but not HN. NE and NIE hybrids recruited only distinct root-associated bacterial microbiota in LN. The bacterial network stability was stronger in NE than NIE hybrids. Compared with NIE hybrids, NE hybrids recruited more bacterial taxa that have been described as plant growth-promoting rhizobacteria (PGPR), and less related to denitrification and N competition; this resulted in low N2 O emission and high rhizosphere NO3 - -N accumulation. NE and NIE hybrids had distinct rhizosphere soil metabolite patterns, and their specific metabolites were closely related to microbiota and specific genera under LN. Our findings reveal the relationships among plant NUE, rhizosphere soil metabolites, root-associated microbiota, and soil nutrient cycling, and this information is informative for breeding NE crops.
Collapse
Affiliation(s)
- Keke Li
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - La Chen
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wenjun Shi
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Conghui Hu
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Ye Sha
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Guozhong Feng
- College of Resources and Environmental Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, Changchun, China
| | - Entao Wang
- Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Mexico City, Mexico
| | | | - Xinhua Sui
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Guohua Mi
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| |
Collapse
|
18
|
Soil Microbial Community Responses to Different Management Strategies in Almond Crop. J Fungi (Basel) 2023; 9:jof9010095. [PMID: 36675916 PMCID: PMC9864756 DOI: 10.3390/jof9010095] [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: 12/26/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/12/2023] Open
Abstract
A comparative study of organic and conventional farming systems was conducted in almond orchards to determine the effect of management practices on their fungal and bacterial communities. Soils from two orchards under organic (OM) and conventional (CM), and nearby nonmanaged (NM) soil were analyzed and compared. Several biochemical and biological parameters were measured (soil pH, electrical conductivity, total nitrogen, organic material, total phosphorous, total DNA, and fungal and bacterial DNA copies). Massive parallel sequencing of regions from fungal ITS rRNA and bacterial 16 S genes was carried out to characterize their diversity in the soil. We report a larger abundance of bacteria and fungi in soils under OM, with a more balanced fungi:bacteria ratio, compared to bacteria-skewed proportions under CM and NM. The fungal phylum Ascomycota corresponded to around the 75% relative abundance in the soil, whereas for bacteria, the phyla Proteobacteria, Acidobacteriota and Bacteroidota integrated around 50% of their diversity. Alpha diversity was similar across practices, but beta diversity was highly clustered by soil management. Linear discriminant analysis effect size (LEfSE) identified bacterial and fungal taxa associated with each type of soil management. Analyses of fungal functional guilds revealed 3-4 times larger abundance of pathogenic fungi under CM compared to OM and NM treatments. Among them, the genus Cylindrocarpon was more abundant under CM, and Fusarium under OM.
Collapse
|
19
|
Cui Z, Li R, Li F, Jin L, Wu H, Cheng C, Ma Y, Wang Z, Wang Y. Structural characteristics and diversity of the rhizosphere bacterial communities of wild Fritillaria przewalskii Maxim. in the northeastern Tibetan Plateau. Front Microbiol 2023; 14:1070815. [PMID: 36876117 PMCID: PMC9981654 DOI: 10.3389/fmicb.2023.1070815] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/01/2023] [Indexed: 02/19/2023] Open
Abstract
Introduction Fritillaria przewalskii Maxim. is a Chinese endemic species with high medicinal value distributed in the northeastern part of the Tibetan Plateau. F. przewalskii root-associated rhizosphere bacterial communities shaped by soil properties may maintain the stability of soil structure and regulate F. przewalskii growth, but the rhizosphere bacterial community structure of wild F. przewalskii from natural populations is not clear. Methods In the current study, soil samples from 12 sites within the natural range of wild F. przewalskii were collected to investigate the compositions of bacterial communities via high-throughput sequencing of 16S rRNA genes and multivariate statistical analysis combined with soil properties and plant phenotypic characteristics. Results Bacterial communities varied between rhizosphere and bulk soil, and also between sites. Co-occurrence networks were more complex in rhizosphere soil (1,169 edges) than in bulk soil (676 edges). There were differences in bacterial communities between regions, including diversity and composition. Proteobacteria (26.47-37.61%), Bacteroidetes (10.53-25.22%), and Acidobacteria (10.45-23.54%) were the dominant bacteria, and all are associated with nutrient cycling. In multivariate statistical analysis, both soil properties and plant phenotypic characteristics were significantly associated with the bacterial community (p < 0.05). Soil physicochemical properties accounted for most community differences, and pH was a key factor (p < 0.01). Interestingly, when the rhizosphere soil environment remained alkaline, the C and N contents were lowest, as was the biomass of the medicinal part bulb. This might relate to the specific distribution of genera, such as Pseudonocardia, Ohtaekwangia, Flavobacterium (relative abundance >0.01), which all have significantly correlated with the biomass of F. przewalskii (p < 0.05). Discussion F. przewalskii is evidently averse to alkaline soil with high potassium contents, but this requires future verification. The results of the present study may provide theoretical guidance and new insights for the cultivation and domestication of F. przewalskii.
Collapse
Affiliation(s)
- Zhijia Cui
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu, China.,Northwest Collaborative Innovation Center for Traditional Chinese Medicine Co-Constructed by Gansu Province & MOE of PRC, Lanzhou, Gansu, China
| | - Ran Li
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
| | - Fan Li
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
| | - Ling Jin
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu, China.,Northwest Collaborative Innovation Center for Traditional Chinese Medicine Co-Constructed by Gansu Province & MOE of PRC, Lanzhou, Gansu, China
| | - Haixu Wu
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
| | - Chunya Cheng
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
| | - Yi Ma
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu, China.,Northwest Collaborative Innovation Center for Traditional Chinese Medicine Co-Constructed by Gansu Province & MOE of PRC, Lanzhou, Gansu, China
| | - Zhenheng Wang
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu, China.,Northwest Collaborative Innovation Center for Traditional Chinese Medicine Co-Constructed by Gansu Province & MOE of PRC, Lanzhou, Gansu, China
| | - Yuanyuan Wang
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
| |
Collapse
|
20
|
Sun P, Chen Y, Liu J, Xu Y, Zhou L, Wu Y. Periphytic biofilms function as a double-edged sword influencing nitrogen cycling in paddy fields. Environ Microbiol 2022; 24:6279-6289. [PMID: 36335557 DOI: 10.1111/1462-2920.16277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/01/2022] [Indexed: 11/07/2022]
Abstract
It remains unclear whether periphytic biofilms are beneficial to N cycling in paddy fields. Here, based on a national-scale field investigation covering 220 rice fields in China, the N accumulation potential of periphytic biofilms was found to decrease from 8.8 ± 2.4 to 4.5 ± 0.7 g/kg and 3.1 ± 0.6 g/kg with increasing habitat latitude and longitude, respectively. The difference in abundant and rare subcommunities likely accounts for their geo-difference in N accumulation potential. The N cycling pathways involved in periphytic biofilms inferred that soil N and N2 were two potential sources for N accumulation in periphytic biofilms. Meanwhile, some of the accumulated N may be lost via N2 , N2 O, NO, or NH3 outputs. Superficially, periphytic biofilms are double-edged swords to N cycling by increasing soil N through biological N fixation but accelerating greenhouse gas emissions. Essentially, augmented periphytic biofilms increased change of TN (ΔTN) content in paddy soil from -231.9 to 31.9 mg/kg, indicating that periphytic biofilms overall benefit N content enhancement in paddy fields. This study highlights the contribution of periphytic biofilms to N cycling in rice fields, thus, drawing attention to their effect on rice production and environmental security.
Collapse
Affiliation(s)
- Pengfei Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resource of the Peoples' Republic of China, Shuitianba, Zigui, Yichang, China
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Junzhuo Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resource of the Peoples' Republic of China, Shuitianba, Zigui, Yichang, China
| | - Ying Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resource of the Peoples' Republic of China, Shuitianba, Zigui, Yichang, China
| | - Lei Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resource of the Peoples' Republic of China, Shuitianba, Zigui, Yichang, China
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resource of the Peoples' Republic of China, Shuitianba, Zigui, Yichang, China
| |
Collapse
|