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Yan H, Wu Y, He G, Wen S, Yang L, Ji L. Fertilization regime changes rhizosphere microbial community assembly and interaction in Phoebe bournei plantations. Appl Microbiol Biotechnol 2024; 108:417. [PMID: 38995388 PMCID: PMC11245453 DOI: 10.1007/s00253-024-13106-5] [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: 09/26/2023] [Revised: 02/28/2024] [Accepted: 03/10/2024] [Indexed: 07/13/2024]
Abstract
Fertilizer input is one of the effective forest management practices, which improves soil nutrients and microbial community compositions and promotes forest productivity. However, few studies have explored the response of rhizosphere soil microbial communities to various fertilization regimes across seasonal dynamics. Here, we collected the rhizosphere soil samples from Phoebe bournei plantations to investigate the response of community assemblages and microbial interactions of the soil microbiome to the short-term application of four typical fertilizer practices (including chemical fertilizer (CF), organic fertilizer (OF), compound microbial fertilizer (CMF), and no fertilizer control (CK)). The amendments of organic fertilizer and compound microbial fertilizer altered the composition of rhizosphere soil bacterial and fungal communities, respectively. The fertilization regime significantly affected bacterial diversity rather than fungal diversity, and rhizosphere fungi responded more sensitively than bacteria to season. Fertilization-induced fungal networks were more complex than bacterial networks. Stochastic processes governed both rhizosphere soil bacterial and fungal communities, and drift and dispersal limitation dominated soil fungal and bacterial communities, respectively. Collectively, these findings demonstrate contrasting responses to community assemblages and interactions of rhizosphere bacteria and fungi to fertilizer practices. The application of organic fertilization strengthens microbial interactions and changes the succession of key taxa in the rhizosphere habitat. KEY POINTS: • Fertilization altered the key taxa and microbial interaction • Organic fertilizer facilitated the turnover of rhizosphere microbial communities • Stochasticity governed soil fungal and bacterial community assembly.
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Affiliation(s)
- Haoyu Yan
- School of Forestry, Central South University of Forestry and Technology, 410004, Changsha, People's Republic of China
| | - Yang Wu
- School of Forestry, Central South University of Forestry and Technology, 410004, Changsha, People's Republic of China
| | - Gongxiu He
- School of Forestry, Central South University of Forestry and Technology, 410004, Changsha, People's Republic of China
| | - Shizhi Wen
- School of Forestry, Central South University of Forestry and Technology, 410004, Changsha, People's Republic of China
| | - Lili Yang
- School of Forestry, Central South University of Forestry and Technology, 410004, Changsha, People's Republic of China.
| | - Li Ji
- School of Forestry, Central South University of Forestry and Technology, 410004, Changsha, People's Republic of China.
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Cena JAD, Belmok A, Kyaw CM, Dame-Teixeira N. The Archaea domain: Exploring historical and contemporary perspectives with in silico primer coverage analysis for future research in Dentistry. Arch Oral Biol 2024; 161:105936. [PMID: 38422909 DOI: 10.1016/j.archoralbio.2024.105936] [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: 01/13/2024] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
OBJECTIVE The complete picture of how the human microbiome interacts with its host is still largely unknown, particularly concerning microorganisms beyond bacteria. Although existing in very low abundance and not directly linked to causing diseases, archaea have been detected in various sites of the human body, including the gastrointestinal tract, oral cavity, skin, eyes, respiratory and urinary systems. But what exactly are these microorganisms? In the early 1990 s, archaea were classified as a distinct domain of life, sharing a more recent common ancestor with eukaryotes than with bacteria. While archaea's presence and potential significance in Dentistry remain under-recognized, there are concerns that they may contribute to oral dysbiosis. However, detecting archaea in oral samples presents challenges, including difficulties in culturing, the selection of DNA extraction methods, primer design, bioinformatic analysis, and databases. DESIGN This is a comprehensive review on the oral archaeome, presenting an in-depth in silico analysis of various primers commonly used for detecting archaea in human body sites. RESULTS Among several primer pairs used for detecting archaea in human samples across the literature, only one specifically designed for detecting methanogenic archaea in stool samples, exhibited exceptional coverage levels for the domain and various archaea phyla. CONCLUSIONS Our in silico analysis underscores the need for designing new primers targeting not only methanogenic archaea but also nanoarchaeal and thaumarchaeota groups to gain a comprehensive understanding of the archaeal oral community. By doing so, researchers can pave the way for further advancements in the field of oral archaeome research.
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Affiliation(s)
| | - Aline Belmok
- Institute of Biology, University of Brasilia, Brazil
| | | | - Naile Dame-Teixeira
- Department of Dentistry, School of Health Sciences, University of Brasilia, Brazil; Division of Oral Biology, School of Dentistry, University of Leeds, UK.
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Zhai K, Hua Y, Liang J, Li J, Wang Z, Liu L, Gao M, Sa R, Zhao M. Soil microbial diversity under different types of interference in birch secondary forest in the Greater Khingan Mountains in China. Front Microbiol 2023; 14:1267746. [PMID: 37954244 PMCID: PMC10635414 DOI: 10.3389/fmicb.2023.1267746] [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: 08/03/2023] [Accepted: 10/05/2023] [Indexed: 11/14/2023] Open
Abstract
Introduction Soil microorganisms are an important component of soil ecosystems with an indispensable role in forest ecosystems. We analyzed the soil microbial diversity in birch secondary forest formed by natural restoration or artificial reconstruction after interference by burning, clear cutting, and gradient cutting, and the Betula platyphylla Suk undisturbed forest in the Greater Khingan Mountains in China. Methods Illumina high-throughput sequencing technology was used to analyze the characteristics of the soil microbial community during the restoration process of birch secondary forest caused by the different types of interference. The relationships between bacteria and fungi were analyzed. The gene functions of the soil bacterial community and the ecological functions of soil fungi were predicted using PICRUSt and FunGuild, respectively. Results At the phylum level, the species and quantity of bacteria were more abundant than that of fungi. At the genus level, no obvious differences in the abundance of bacteria were observed; there were obvious differences in the abundance of fungi. Among the eight sample plots, the artificial larch forest belt had the highest bacterial and fungal alpha diversity, which was slightly higher than undisturbed forest, while the other sample plots were significantly lower. Gradual cutting pure birch forest bacteria and fungi had the highest beta diversity, and artificial larch forest belt bacteria and heavy burn sample plot fungi had the lowest beta diversity. Samples from the cutting and burning sample plots were significantly different from the undisturbed forest at the phylum level of Acidobacteriae, Acidimicrobiia, Mortierellomycetes and Sordariomycetes. We found statistical differences in biomarkers between bacterial and fungal communities in undisturbed forest and artificial larch forest belt and burn sample plots. PICRUSt prediction and FunGuild prediction showed that soil bacterial and fungal communities were rich in gene and ecological functions, respectively. In the microbial network, the stability or anti-interference performance of the fungal community was higher than that of bacteria. Conclusion Our data reveal the characteristics of the soil microbial community during the restoration process of Betula platyphylla Suk secondary forest under different types of disturbance, which is of great significance for understanding the role of soil microorganisms in the forest ecological cycle.
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Affiliation(s)
- Kaitao Zhai
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Yongchun Hua
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Jingwen Liang
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Jing Li
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Zirui Wang
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Lei Liu
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Minglong Gao
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Rula Sa
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Mingmin Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
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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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Arunrat N, Sereenonchai S, Sansupa C, Kongsurakan P, Hatano R. Effect of Rice Straw and Stubble Burning on Soil Physicochemical Properties and Bacterial Communities in Central Thailand. BIOLOGY 2023; 12:biology12040501. [PMID: 37106702 PMCID: PMC10135879 DOI: 10.3390/biology12040501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
Rice straw and stubble burning is widely practiced to clear fields for new crops. However, questions remain about the effects of fire on soil bacterial communities and soil properties in paddy fields. Here, five adjacent farmed fields were investigated in central Thailand to assess changes in soil bacterial communities and soil properties after burning. Samples of soil prior to burning, immediately after burning, and 1 year after burning were obtained from depths of 0 to 5 cm. The results showed that the pH, electrical conductivity, NH4-N, total nitrogen, and soil nutrients (available P, K, Ca, and Mg) significantly increased immediately after burning due to an increased ash content in the soil, whereas NO3-N decreased significantly. However, these values returned to the initial values. Chloroflexi were the dominant bacteria, followed by Actinobacteria and Proteobacteria. At 1 year after burning, Chloroflexi abundance decreased remarkably, whereas Actinobacteria, Proteobacteria, Verrucomicrobia, and Gemmatimonadetes abundances significantly increased. Bacillus, HSB OF53-F07, Conexibacter, and Acidothermus abundances increased immediately after burning, but were lower 1 year after burning. These bacteria may be highly resistant to heat, but grow slowly. Anaeromyxobacter and Candidatus Udaeobacter dominated 1 year after burning, most likely because of their rapid growth and the fact that they occupy areas with increased soil nutrient levels after fires. Amidase, cellulase, and chitinase levels increased with increased organic matter levels, whereas β-glucosidase, chitinase, and urease levels positively correlated with the soil total nitrogen level. Although clay and soil moisture strongly correlated with the soil bacterial community’s composition, negative correlations were found for β-glucosidase, chitinase, and urease. In this study, rice straw and standing stubble were burnt under high soil moisture and within a very short time, suggesting that the fire was not severe enough to raise the soil temperature and change the soil microbial community immediately after burning. However, changes in soil properties due to ash significantly increased the diversity indices, which was noticeable 1 year after burning.
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Li X, Jin Z, Xiong L, Tong L, Zhu H, Zhang X, Qin G. Effects of Land Reclamation on Soil Bacterial Community and Potential Functions in Bauxite Mining Area. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:16921. [PMID: 36554801 PMCID: PMC9778865 DOI: 10.3390/ijerph192416921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Studying the characteristics of microorganisms in mine reclamation sites can provide a scientific reference basis for mine land reclamation. Soils in the plough layer (0-20 cm) of the bauxite mine plots in Pingguo city, Guangxi Zhuang Autonomous Region, China, with different reclamation years were used as the research objects. The community structure of soil bacteria was analyzed with high-throughput sequencing technology. The results show the following: (1) Reclamation significantly increased the contents of soil nutrients (p < 0.05). (2) The relative abundances of Proteobacteria were high (22.90~41.56%) in all plots, and reclamation significantly reduced the relative abundances of Firmicutes (3.42-10.77%) compared to that in the control plot (24.74%) (p < 0.05). The relative abundances of α-proteobacteria generally increased while the reclamation year increased. The relative abundances of α-proteobacteria and γ-proteobacteria showed significant positive correlations with soil carbon, nitrogen, and phosphorus nutrients (p < 0.01). The relative abundance of Acidobacteria Group 6 showed significant positive correlations with soil exchangeable Ca and Mg (p < 0.01). (3) Bacterial co-occurrence network showed more Copresence interactions in all plots (50.81-58.39%). The reclaimed plots had more nodes, higher modularity, and longer characteristic path length than the control plot, and the keystone taxa changed in different plots. (4) The chemoheterotrophy and aerobic chemoheterotrophy were the most abundant functional groups in all plots (35.66-48.26%), while reclamation reduced the relative abundance of fermentation groups (1.75-11.21%). The above findings indicated that reclamation improved soil nutrients, changed the bacterial community structure and potential functions, and accelerated the microbial stabilization of the reclaimed soil.
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Affiliation(s)
- Xuesong Li
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Zhenjiang Jin
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
- Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area, Guilin University of Technology, Guilin 541004, China
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541004, China
| | - Liyuan Xiong
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Lingchen Tong
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Hongying Zhu
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Xiaowen Zhang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Guangfa Qin
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
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Guo Y, Song B, Li A, Wu Q, Huang H, Li N, Yang Y, Adams JM, Yang L. Higher pH is associated with enhanced co-occurrence network complexity, stability and nutrient cycling functions in the rice rhizosphere microbiome. Environ Microbiol 2022; 24:6200-6219. [PMID: 36076153 DOI: 10.1111/1462-2920.16185] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/29/2022] [Indexed: 01/12/2023]
Abstract
The rice rhizosphere microbiota is crucial for crop yields and nutrient use efficiency. However, little is known about how co-occurrence patterns, keystone taxa and functional gene assemblages relate to soil pH in the rice rhizosphere soils. Using shotgun metagenome analysis, the rice rhizosphere microbiome was investigated across 28 rice fields in east-central China. At higher pH sites, the taxonomic co-occurrence network of rhizosphere soils was more complex and compact, as defined by higher average degree, graph density and complexity. Network stability was greatest at medium pH (6.5 < pH < 7.5), followed by high pH (7.5 < pH). Keystone taxa were more abundant at higher pH and correlated significantly with key ecosystem functions. Overall functional genes involved in C, N, P and S cycling were at a higher relative abundance in higher pH rhizosphere soils, excepting C degradation genes (e.g. key genes involved in starch, cellulose, chitin and lignin degradation). Our results suggest that the rice rhizosphere soil microbial network is more complex and stable at higher pH, possibly indicating increased efficiency of nutrient cycling. These observations may indicate routes towards more efficient soil management and understanding of the potential effects of soil acidification on the rice rhizosphere system.
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Affiliation(s)
- Yaping Guo
- School of Geography and Ocean Science, Nanjing University, Nanjing, People's Republic of China
| | - Bin Song
- School of Geography and Ocean Science, Nanjing University, Nanjing, People's Republic of China
| | - Anqi Li
- School of Geography and Ocean Science, Nanjing University, Nanjing, People's Republic of China
| | - Qi Wu
- School of Geography and Ocean Science, Nanjing University, Nanjing, People's Republic of China
| | - Haili Huang
- School of Geography and Ocean Science, Nanjing University, Nanjing, People's Republic of China
| | - Na Li
- School of Geography and Ocean Science, Nanjing University, Nanjing, People's Republic of China
| | - Ying Yang
- School of Geography and Ocean Science, Nanjing University, Nanjing, People's Republic of China
| | - Jonathan Miles Adams
- School of Geography and Ocean Science, Nanjing University, Nanjing, People's Republic of China
| | - Lin Yang
- School of Geography and Ocean Science, Nanjing University, Nanjing, People's Republic of China
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Bai Z, Zheng L, Bai Z, Jia A, Wang M. Long-term cultivation alter soil bacterial community in a forest-grassland transition zone. Front Microbiol 2022; 13:1001781. [PMID: 36246280 PMCID: PMC9557053 DOI: 10.3389/fmicb.2022.1001781] [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: 07/24/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Changes in land use types can significantly affect soil porperties and microbial community composition in many areas. However, the underlying mechanism of shift in bacterial communities link to soil properties is still unclear. In this study, Illumina high-throughput sequencing was used to analyze the changes of soil bacterial communities in different land use types in a forest-grassland transition zone, North China. There are two different land use types: grassland (G) and cultivated land (CL). Meanwhile, cultivated land includes cultivated of 10 years (CL10) or 20 years (CL20). Compared with G, CL decreased soil pH, SOC and TN, and significantly increased soil EC, P and K, and soil properties varied significantly with different cultivation years. Grassland reclamation increases the diversity of bacterial communities, the relative abundance of Proteobacteria, Gemmatimonadetes and Bacteroidetes increased, while that of Actinobacteria, Acidobacteria, Rokubacteria and Verrucomicrobia decreased. However, the relative abundance of Proteobacteria decreased and the relative abundance of Chloroflexi and Nitrospirae increased with the increase of cultivated land years. Mantel test and RDA analysis showed that TP, AP, SOC and EC were the main factors affecting the diversity of composition of bacterial communities. In conclusion, soil properties and bacterial communities were significantly altered after long-term cultivation. This study provides data support for land use and grassland ecological protection in this region.
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Shu X, He J, Zhou Z, Xia L, Hu Y, Zhang Y, Zhang Y, Luo Y, Chu H, Liu W, Yuan S, Gao X, Wang C. Organic amendments enhance soil microbial diversity, microbial functionality and crop yields: A meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154627. [PMID: 35306065 DOI: 10.1016/j.scitotenv.2022.154627] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/22/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2023]
Abstract
Fertilization plays an important role in changing soil microbial diversity, which is essential for determining crop yields. Yet, the influence of organic amendments on microbial diversity remains uncertain, and few studies have addressed the relative importance of microbial diversity versus other drivers of crop yields. Here, we synthesize 219 studies worldwide and found that organic amendments significantly increased microbial diversity components (i.e., Shannon, richness, and phylogenetic diversity) and shifted microbial community structure compared to mineral-only fertilization. The performance of microbial alpha diversity varied substantially with organic amendment types, microbial groups and changes in soil pH. Both microbial diversity and community structure exhibited significantly positive relationships with microbial functionality and crop yields. In addition, soil abiotic properties and microbial functionality had a much stronger impact on crop yields than microbial diversity and climate factors. Partial least squares path modeling showed that soil microbial diversity was an important underlying factor driving crop yields via boosting soil microbial functionality. Overall, our findings provide robust evidence for the positive diversity-functions relationships, emphasizing that substituting mineral fertilizers with organic amendments is a promising way to conserve microbial diversity and promote soil microbial functions and crop yields.
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Affiliation(s)
- Xiangyang Shu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Jia He
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhenghu Zhou
- Center for Ecological Research, Northeast Forestry University, Harbin 150040, China
| | - Longlong Xia
- Institute for Meteorology and Climate Research (IMK-IFU), Karlsruhe Institute of Technology, Garmisch-Partenkirchen 82467, Germany
| | - Yufu Hu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
| | - Yulin Zhang
- Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong 999077, China
| | - Yanyan Zhang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yiqi Luo
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 21008, China
| | - Weijia Liu
- Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China
| | - Shu Yuan
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuesong Gao
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Changquan Wang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
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Zhang N, Wu M, Che Y, Kong Y, Shu F, Wang Q, Sha W, Gong Z, Zhou J. Effects of shining pondweed (Potamogeton lucens) on bacterial communities in water and rhizosphere sediments in Nansi Lake, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:51665-51673. [PMID: 35249194 DOI: 10.1007/s11356-022-19516-0] [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: 09/17/2021] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
Submerged macrophytes and microbial communities are important parts of lake ecosystems. In this study, the bacterial community composition in rhizosphere sediments and water from areas cultivated with (PL) and without (CK) shining pondweed (Potamogeton lucens Linn.) was investigated to determine the effects of P. lucens Linn. on the structure of the bacterial communities in Nansi Lake, China. Molecular techniques, including Illumina MiSeq and qPCR targeting of the 16S rRNA gene, were used to analyze the composition and abundance of the bacterial community. We found that bacterial alpha diversity was higher in PL water than in CK water, and the opposite trend was observed in sediment. In addition, 16S rRNA gene copy number in sediment was lower in PL than in CK. We found 30 (e.g., Desulfatiglans) and 29 (e.g., Limnohabitans) significantly different genera in sediment and water, respectively. P. lucens Linn. can change chemical properties in sediment and water and thereby affect the bacterial community. At the genus level, members of bacterial community clustered according to source (water/sediment) and area (PL/CK). Our study demonstrated that submerged macrophytes can affect the bacterial community composition in both sediment and water, suggesting that submerged macrophytes affect the transportation and cycling of nutrients in lake ecosystems.
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Affiliation(s)
- Nianxin Zhang
- School of Life Sciences, Qufu Normal University, Jining, 273 165, China
| | - Mengmeng Wu
- Shandong Freshwater Fisheries Research Institute, Jinan, 250013, China
| | - Yuying Che
- School of Life Sciences, Qufu Normal University, Jining, 273 165, China
| | - Yong Kong
- School of Life Sciences, Qufu Normal University, Jining, 273 165, China
| | - Fengyue Shu
- School of Life Sciences, Qufu Normal University, Jining, 273 165, China
| | - Qingfeng Wang
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Weilai Sha
- School of Life Sciences, Qufu Normal University, Jining, 273 165, China
| | - Zhijin Gong
- School of Life Sciences, Qufu Normal University, Jining, 273 165, China
| | - Jing Zhou
- School of Life Sciences, Qufu Normal University, Jining, 273 165, China.
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Ma T, He X, Chen S, Li Y, Huang Q, Xue C, Shen Q. Long-Term Organic–Inorganic Fertilization Regimes Alter Bacterial and Fungal Communities and Rice Yields in Paddy Soil. Front Microbiol 2022; 13:890712. [PMID: 35832816 PMCID: PMC9271892 DOI: 10.3389/fmicb.2022.890712] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/10/2022] [Indexed: 01/05/2023] Open
Abstract
Microorganisms are the most abundant and diverse organisms in soils and have important effects on soil fertility. In this study, effects of the long-term fertilization treatments no fertilizer (CK), chemical fertilizer (nitrogen–phosphorus–potassium (NPK)), and organic–inorganic fertilizer (NPK and organic fertilizer (NPKM)) on rice yield and soil bacterial and fungal community diversity, structure, composition, and interaction networks were evaluated. Of the three treatments, the highest rice yield was in NPKM. Bacterial richness was significantly higher in NPKM than in NPK. Fertilization treatment significantly altered β diversity of communities, species composition of bacterial and fungal communities, and structure of soil microbial networks. The most complex bacterial and fungal interaction co-occurrence network with the highest average degree and numbers of edges and nodes was in NPKM. Relative abundance of the plant growth-promoting fungus Trichoderma increased significantly in NPKM compared with CK and NPK. The results of the study indicate that bacterial richness and microbial community member interactions (network complexity) might be suitable indicators of soil biological fertility. This research provides new insights on the effects of different fertilization regimes on responses of soil bacterial and fungal communities and their contributions to crop yield. New indicators such as bacterial richness and complexity of microbial interaction networks are also identified that can be used to evaluate soil biological fertility.
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Affiliation(s)
- Tengfei Ma
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Xiaohui He
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Shanguo Chen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yujia Li
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Qiwei Huang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Chao Xue
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Green Intelligent Fertilizer Innovation MARD, Sinong Bio-organic Fertilizer Institute, Nanjing, China
- *Correspondence: Chao Xue,
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
- Qirong Shen,
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12
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Meta-analyses on the Periodontal Archaeome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1373:69-93. [DOI: 10.1007/978-3-030-96881-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Wang JL, Liu KL, Zhao XQ, Zhang HQ, Li D, Li JJ, Shen RF. Balanced fertilization over four decades has sustained soil microbial communities and improved soil fertility and rice productivity in red paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 793:148664. [PMID: 34328991 DOI: 10.1016/j.scitotenv.2021.148664] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
The influence of long-term fertilization on soil microbial communities is critical for revealing the association between belowground microbial flora and aboveground crop productivity-a relationship of great importance to food security, environmental protection, and ecosystem functions. Here, we examined shifts in soil chemical properties, microbial communities, and the nutrient uptake and yield of rice subjected to different chemical and organic fertilization treatments over a 40-year period in red paddy soil. Ten different treatments were used: a control without fertilizer, and applications of nitrogen (N), phosphorus (P), potassium (K), NP, NK, PK, NPK, double NPK, or NPK plus manure. Compared with the effects of withholding one or two nutrients (N, P, or K), the balanced application of chemical NPK and organic fertilizers markedly improved soil nutrient status and rice yield. This improvement of soil fertility and rice yield was not associated with bacterial, archaeal, or fungal alpha diversities. The bacterial abundance and community structure and archaeal abundance effectively explained the variation in rice yield, whereas those of fungi did not. The community structure of bacteria and archaea, but not that of fungi, was correlated with soil properties. Among various soil properties, P was the key factor influencing rice yield and soil microbial communities because of the extremely low content of soil available P. Seven keystones at the operational taxonomic unit level were identified: four archaea (belonging to Thermoplasmata, Methanosaeta, Bathyarchaeia, and Nitrososphaeraceae) and three bacteria (in Desulfobacteraceae and Acidobacteriales). These keystones, which were mainly related to soil C and N transformation and pH, may work cooperatively to influence rice yield by regulating soil fertility. Our results collectively suggest that four decades of balanced fertilization has sustained the bacterial and archaeal abundances, bacterial community structure, and keystones, which potentially contribute to soil fertility and rice yield in red paddy soil.
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Affiliation(s)
- Jia Lin Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Lou Liu
- National Engineering and Technology Research Center for Red Soil Improvement, Jiangxi Institute of Red Soil, Nanchang 331717, China
| | - Xue Qiang Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Hao Qing Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jiao Jiao Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ren Fang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Zhou J, Kong Y, Zhao W, Wei G, Wang Q, Ma L, Wang T, Shu F, Sha W. Comparison of bacterial and archaeal communities in two fertilizer doses and soil compartments under continuous cultivation system of garlic. PLoS One 2021; 16:e0250571. [PMID: 33989289 PMCID: PMC8121308 DOI: 10.1371/journal.pone.0250571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 04/12/2021] [Indexed: 01/10/2023] Open
Abstract
Soil microbial communities are affected by interactions between agricultural management (e.g., fertilizer) and soil compartment, but few studies have considered combinations of these factors. We compared the microbial abundance, diversity and community structure in two fertilizer dose (high vs. low NPK) and soil compartment (rhizosphere vs. bulk soils) under 6-year fertilization regimes in a continuous garlic cropping system in China. The soil contents of NO3- and available K were significantly higher in bulk soil in the high-NPK. The 16S rRNA gene-based bacterial and archaeal abundances were positively affected by both the fertilizer dose and soil compartment, and were higher in the high-NPK fertilization and rhizosphere samples. High-NPK fertilization increased the Shannon index and decreased bacterial and archaeal richness, whereas the evenness was marginally positively affected by both the fertilizer dose and soil compartment. Soil compartment exerted a greater effect on the bacterial and archaeal community structure than did the fertilization dose, as demonstrated by both the nonmetric multidimensional scaling and redundancy analysis results. We found that rhizosphere effects significantly distinguished 12 dominant classes of bacterial and archaeal communities, whereas the fertilizer dose significantly identified four dominant classes. In particular, a Linear Effect Size analysis showed that some taxa, including Alphaproteobacteria, Rhizobiales, Xanthomonadaceae and Flavobacterium, were enriched in the garlic rhizosphere of the high-NPK fertilizer samples. Overall, the fertilizer dose interacted with soil compartment to shape the bacterial and archaeal community composition, abundance, and biodiversity in the garlic rhizosphere. These results provide an important basis for further understanding adaptive garlic-microbe feedback, reframing roots as a significant moderating influence in agricultural management and shaping the microbial community.
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Affiliation(s)
- Jing Zhou
- School of Life Sciences, Qufu Normal University, Jining, PR China
| | - Yong Kong
- School of Life Sciences, Qufu Normal University, Jining, PR China
| | - Wangfeng Zhao
- College of Biological and Environmental Engineering, Binzhou University, Binzhou, PR China
| | - Guangshan Wei
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC) / School of Marine Sciences, Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources of the PR China, Third Institute of Oceanography, Xiamen, China
| | - Qingfeng Wang
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Longchuan Ma
- Shandong Engineering and Technology Research Center for Garlic, Jining, PR China
| | - Taotao Wang
- Shandong Engineering and Technology Research Center for Garlic, Jining, PR China
| | - Fengyue Shu
- School of Life Sciences, Qufu Normal University, Jining, PR China
| | - Weilai Sha
- School of Life Sciences, Qufu Normal University, Jining, PR China
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15
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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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16
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Liu Y, Gao J, Bai Z, Wu S, Li X, Wang N, Du X, Fan H, Zhuang G, Bohu T, Zhuang X. Unraveling Mechanisms and Impact of Microbial Recruitment on Oilseed Rape ( Brassica napus L.) and the Rhizosphere Mediated by Plant Growth-Promoting Rhizobacteria. Microorganisms 2021; 9:microorganisms9010161. [PMID: 33445684 PMCID: PMC7828142 DOI: 10.3390/microorganisms9010161] [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: 12/12/2020] [Revised: 12/31/2020] [Accepted: 01/06/2021] [Indexed: 01/13/2023] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) are noticeably applied to enhance plant nutrient acquisition and improve plant growth and health. However, limited information is available on the compositional dynamics of rhizobacteria communities with PGPR inoculation. In this study, we investigated the effects of three PGPR strains, Stenotrophomonas rhizophila, Rhodobacter sphaeroides, and Bacillus amyloliquefaciens on the ecophysiological properties of Oilseed rape (Brassica napus L.), rhizosphere, and bulk soil; moreover, we assessed rhizobacterial community composition using high-throughput Illumina sequencing of 16S rRNA genes. Inoculation with S. rhizophila, R. sphaeroides, and B. amyloliquefaciens, significantly increased the plant total N (TN) (p < 0.01) content. R. sphaeroides and B. amyloliquefaciens selectively enhanced the growth of Pseudomonadacea and Flavobacteriaceae, whereas S. rhizophila could recruit diazotrophic rhizobacteria, members of Cyanobacteria and Actinobacteria, whose abundance was positively correlated with inoculation, and improved the transformation of organic nitrogen into inorganic nitrogen through the promotion of ammonification. Initial colonization by PGPR in the rhizosphere affected the rhizobacterial community composition throughout the plant life cycle. Network analysis indicated that PGPR had species-dependent effects on niche competition in the rhizosphere. These results provide a better understanding of PGPR-plant-rhizobacteria interactions, which is necessary to develop the application of PGPR.
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Affiliation(s)
- Ying Liu
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China;
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (J.G.); (Z.B.); (S.W.); (X.L.); (N.W.); (X.D.); (H.F.); (G.Z.)
| | - Jie Gao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (J.G.); (Z.B.); (S.W.); (X.L.); (N.W.); (X.D.); (H.F.); (G.Z.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihui Bai
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (J.G.); (Z.B.); (S.W.); (X.L.); (N.W.); (X.D.); (H.F.); (G.Z.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanghua Wu
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (J.G.); (Z.B.); (S.W.); (X.L.); (N.W.); (X.D.); (H.F.); (G.Z.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianglong Li
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (J.G.); (Z.B.); (S.W.); (X.L.); (N.W.); (X.D.); (H.F.); (G.Z.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (J.G.); (Z.B.); (S.W.); (X.L.); (N.W.); (X.D.); (H.F.); (G.Z.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiongfeng Du
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (J.G.); (Z.B.); (S.W.); (X.L.); (N.W.); (X.D.); (H.F.); (G.Z.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haonan Fan
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (J.G.); (Z.B.); (S.W.); (X.L.); (N.W.); (X.D.); (H.F.); (G.Z.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoqiang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (J.G.); (Z.B.); (S.W.); (X.L.); (N.W.); (X.D.); (H.F.); (G.Z.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tsing Bohu
- CSIRO Mineral Resources, Kensington, WA 6151, Australia;
| | - Xuliang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (J.G.); (Z.B.); (S.W.); (X.L.); (N.W.); (X.D.); (H.F.); (G.Z.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: ; Tel.: +86-10-6284-9193
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17
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高 宏. Research Progress on the Effects of Logging and Burning on Forest Soil Microorganisms. INTERNATIONAL JOURNAL OF ECOLOGY 2021. [DOI: 10.12677/ije.2021.104053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Ma X, Du M, Liu P, Tang Y, Li H, Yuan Q, Ruan Y, Meng L, Zhang J, Lin M, Liu Z. Alternation of soil bacterial and fungal communities by tomato-rice rotation in Hainan Island in Southeast of China. Arch Microbiol 2020; 203:913-925. [PMID: 33078269 DOI: 10.1007/s00203-020-02086-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/18/2020] [Accepted: 10/06/2020] [Indexed: 11/29/2022]
Abstract
Tomato-rice rotation is prevalent in subtropical and tropical regions in China. This practice enhances crop productivity and the disease suppression property of soils against soil-borne plant pathogens. To explore the variations and dynamics of bacterial and fungal communities, bulk soil samples were collected during two consecutive years under a rotation system between tomato and rice originated from the year of 2010 in Hainan Island, and 16S rDNA and ITS amplicons were sequenced by Illumina MiSeq. The results demonstrated that potentially beneficial bacterial phyla Acidobacteria, Chloroflexi and genus Paenibacillus, as well as the fungal genus Mortierella were significantly enriched, while the potentially pathogenic fungal genus Fusarium was significantly decreased during the crop rotation. Measurements of soil physicochemical properties indicated that the soil acidification was improved. Redundancy analysis (RDA) revealed the correlation of the microbial community with soil pH and identified soil total phosphorus (TP) level as the highest determinant factor for both bacterial and fungal communities. This work provides a preliminary description of changes of the bacterial and fungal communities related to tomato-rice rotation in China and offered experimental evidences for exploring the effects of this agricultural practice on soil ecology.
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Affiliation(s)
- Xiang Ma
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Minglun Du
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Peng Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Yanqiong Tang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Hong Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Qianhua Yuan
- School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Yunze Ruan
- School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Lei Meng
- School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Jiachao Zhang
- School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhu Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China.
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Jang SW, Yoou MH, Hong WJ, Kim YJ, Lee EJ, Jung KH. Re-Analysis of 16S Amplicon Sequencing Data Reveals Soil Microbial Population Shifts in Rice Fields under Drought Condition. RICE (NEW YORK, N.Y.) 2020; 13:44. [PMID: 32617714 PMCID: PMC7332601 DOI: 10.1186/s12284-020-00403-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
Rice (Oryza sativa. L) has been intensively studied to ensure a stable global supply of this commodity in the face of rapid global climate change. A critical factor that decreases crop yield is drought, which has been analyzed in various ways through many researches. Microbiome-based studies of rice investigate the symbiosis between rice and bacteria, which has been proposed as a way to overcome problems caused by drought. Several rice-associated metagenomic profiles obtained under drought conditions have been reported since the advent of next generation sequencing (NGS) technology. To elucidate the future diversity of plants and microorganisms and to promote sustainable agriculture, we reanalyzed 64 of the publicly available 16S amplicon sequencing data produced under drought condition. In the process of integrating data sets, however, we found an inconsistency that serves as a bottleneck for microbiome-based sustainability research. While this report provides clues about the composition of the microbiome under the drought conditions, the results are affected by differences in the location of the experiments, sampling conditions, and analysis protocols. Re-analysis of amplicon sequencing data of the soil microbiome in rice fields suggests that microbial composition shifts in response to drought condition and the presence of plants. Among the bacteria involved, the phylum Proteobacteria appears to play the most important role in the survival of rice under drought condition.
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Affiliation(s)
- Seok-Won Jang
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
- Graduate School of Biotechnology, Kyung Hee University, Yongin, 17104, South Korea
| | - Myeong-Hyun Yoou
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea
| | - Yeon-Ju Kim
- Department of Oriental Medicine Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, 17104, South Korea
| | - Eun-Jin Lee
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea.
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, South Korea.
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Jin S, Jin W, Dong C, Bai Y, Jin D, Hu Z, Huang Y. Effects of rice straw and rice straw ash on rice growth and α-diversity of bacterial community in rare-earth mining soils. Sci Rep 2020; 10:10331. [PMID: 32587300 PMCID: PMC7316728 DOI: 10.1038/s41598-020-67160-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/01/2020] [Indexed: 11/13/2022] Open
Abstract
Pot experiments were carried out to study the effects of rice straw (RS) and rice straw ash (RSA) on the growth of early rice and α-diversity of bacterial community in soils around rare earth mining areas of Xunwu and Xinfeng counties in South Jiangxi of China. The results showed that the exploitation of rare earth resources leads to soil pollution around rare earth mining areas and affects the growth of rice, and the content of rare earth elements (REEs) in rice was positively correlated with that in soils and negative correlated with dry weight of rice; The addition of RS to soils around REE mining area can inhibit growth of early rice, and the dry weight of rice grains, shoots, roots is lower when compared with the controls, while the content of REEs is higher. The α-diversity of soil bacterial decreases, which promotes the growth of Pseudorhodoferax, Phenylobacterium and other bacteria of the same kind, and inhibits the growth of beneficial bacteria. The addition of RSA to soils had no significant effect on α-diversity of soil bacterial but promoted the growth of Azospira and other beneficial bacteria, inhibited the growth of Bryobacter and other bacteria of the same kind, significantly improved the dry weight of grains, shoots and roots of early rice, and reduced the content of REEs in these parts of rice. It can be concluded that RS is unsuitable to be added to the planting soil of early rice in REE mining area, while RSA is suitable.
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Affiliation(s)
- Shulan Jin
- College of History, Geography and Tourism, Shangrao Normal University, Shangrao, 334000, China
| | - Wei Jin
- Shangrao Vocational and Technical College, Shangrao, 334109, China
| | - Chengxu Dong
- College of History, Geography and Tourism, Shangrao Normal University, Shangrao, 334000, China
| | - Yijun Bai
- College of History, Geography and Tourism, Shangrao Normal University, Shangrao, 334000, China
| | - Decai Jin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Zhongjun Hu
- College of History, Geography and Tourism, Shangrao Normal University, Shangrao, 334000, China.
| | - Yizong Huang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China.
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Srour AY, Ammar HA, Subedi A, Pimentel M, Cook RL, Bond J, Fakhoury AM. Microbial Communities Associated With Long-Term Tillage and Fertility Treatments in a Corn-Soybean Cropping System. Front Microbiol 2020; 11:1363. [PMID: 32670235 PMCID: PMC7330075 DOI: 10.3389/fmicb.2020.01363] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/27/2020] [Indexed: 11/13/2022] Open
Abstract
Tillage and fertilization are common practices used to enhance soil fertility and increase yield. Changes in soil edaphic properties associated with different tillage and fertility regimes have been widely examined, yet, the microbially mediated pathways and ecological niches involved in enhancing soil fertility are poorly understood. The effects of long-term conventional tillage and no-till in parallel with three fertility treatments (No fertilization, N-only, and NPK) on soil microbial communities were investigated in a long-term field study that was established in the 1970's. Here, we used high-throughput sequencing of bacterial, fungal and oomycetes markers, followed by community-level functional and ecological assembly to discern principles governing tillage and fertility practices' influence on associated soil microbiomes. Both tillage and fertilizer significantly altered microbial community structure, but the tillage effect was more prominent than the fertilizer effect. Tillage significantly affected bacteria, fungi, fusaria, and oomycete beta-diversity, whereas fertilizer only affected bacteria and fungi beta-diversity. In our study different tillage and fertilizer regimes favored specific networks of metabolic pathways and distinct ecological guilds. No-till selected for beneficial microbes that translocate nutrients and resources and protect the host against pathogens. Notably, ecological guilds featuring arbuscular mycorrhizae, mycoparasites, and nematophagous fungi were favored in no-till soils, while fungal saprotrophs and plant pathogens dominated in tilled soils. Conventional till and fertilizer management shifted the communities toward fast growing competitors. Copiotrophic bacteria and fusarium species were favored under conventional tillage and in the presence of fertilizers. The analysis of the metagenomes revealed a higher abundance of predicted pathways associated with energy metabolism, translation, metabolism of cofactors and vitamins, glycan biosynthesis and nucleotide metabolism in no-till. Furthermore, no specific pathways were found to be enriched under the investigated fertilization regimes. Understanding how tillage and fertilizer management shift microbial diversity, structure and ecological niches, such as presented here, can assist with designing farming systems that can maintain high crop yield, while reducing soil erosion and nutrient losses.
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Affiliation(s)
- Ali Y. Srour
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, United States
| | - Hala A. Ammar
- Department of Botany, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Arjun Subedi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, United States
| | - Mirian Pimentel
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, United States
| | - Rachel L. Cook
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Jason Bond
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, United States
| | - Ahmad M. Fakhoury
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, United States
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Gamalero E, Bona E, Novello G, Boatti L, Mignone F, Massa N, Cesaro P, Berta G, Lingua G. Discovering the bacteriome of Vitis vinifera cv. Pinot Noir in a conventionally managed vineyard. Sci Rep 2020; 10:6453. [PMID: 32296119 PMCID: PMC7160115 DOI: 10.1038/s41598-020-63154-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/16/2020] [Indexed: 01/22/2023] Open
Abstract
The structure of the bacteriome associated with grapevine roots can affect plant development, health and grape quality. We previously investigated the bacterial biodiversity of the Vitis vinifera cv. Pinot Noir rhizosphere in a vineyard subjected to integrated pest management. The aim of this work is to characterize the bacteriome of V. vinifera cv. Pinot Noir in a conventionally managed vineyard using a metabarcoding approach. Comparisons between the microbial community structure in bulk soil and rhizosphere (variable space) were performed and shifts of bacteriome according to two sampling times (variable time) were characterized. Bacterial biodiversity was higher at the second than at the first sampling and did not differ according to the variable space. Actinobacteria was the dominant class, with Gaiella as the most represented genus in all the samples. Among Proteobacteria, the most represented classes were Alpha, Beta and Gamma-Proteobacteria, with higher abundance at the second than at the first sampling time. Bradyrhizobium was the most frequent genus among Alpha-Proteobacteria, while Burkholderia was the predominant Beta-Proteobacteria. Among Firmicutes, the frequency of Staphylococcus was higher than 60% in bulk soil and rhizosphere. Finally, the sampling time can be considered as one of the drivers responsible for the bacteriome variations assessed.
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Affiliation(s)
- Elisa Gamalero
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Elisa Bona
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Piazza San Eusebio 5, 13100, Vercelli, Italy
| | - Giorgia Novello
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Lara Boatti
- SmartSeq s.r.l., spin-off of the Università del Piemonte Orientale, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Flavio Mignone
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy.,SmartSeq s.r.l., spin-off of the Università del Piemonte Orientale, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Nadia Massa
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Patrizia Cesaro
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy.
| | - Graziella Berta
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Guido Lingua
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
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23
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Long XE, Yao H. Phosphorus Input Alters the Assembly of Rice (Oryza sativa L.) Root-Associated Communities. MICROBIAL ECOLOGY 2020; 79:357-366. [PMID: 31342100 DOI: 10.1007/s00248-019-01407-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
Rice root-associated microbial community play an important role in plant nutrient acquisition, biomass production, and stress tolerance. Herein, root-associated community assembly was investigated under different phosphate input levels in phosphorus (P)-deficient paddy soil. Rice was grown in a long-term P-depleted paddy soil with 0 (P0), 50 (PL), or 200 (PH) mg P2O5 kg-1 application. DNA from root endophytes was isolated after 46 days, and PCR amplicons from archaea, bacteria, and fungi were sequenced by an Illumina Miseq PE300 platform, respectively. P application had no significant effect on rice root endophytic archaea, which were dominated by ammonia-oxidizing Candidatus Nitrososphaera. By contrast, rice root endophytic community structure of the bacteria and fungi was affected by soil P. Low P input increased endophytic bacterial diversity, whereas high P input increased rhizosphere fungi diversity. Bacillus and Pleosporales, associated with phosphate solubilization and P uptake, dominated in P0 and PH treatments, and Pseudomonas were more abundant in the PL treatment than in the P0 and PH treatments. Co-occurrence network analysis revealed a close interaction between endophytic bacteria and fungi. Soil P application affected both the rice root endosphere and soil rhizosphere microbial community and interaction between rice root endophytic bacteria, and fungi, especially species related to P cycling.
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Affiliation(s)
- Xi-En Long
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen, 361021, China
- School of Geographic Sciences, Nantong University, No. 999 Tongjing Road, Nantong, 226007, China
| | - Huaiying Yao
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen, 361021, China.
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, 206 Guanggu 1st Road, Wuhan, 430205, China.
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24
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Combined Application of Organic and Inorganic Nitrogen Fertilizers Affects Soil Prokaryotic Communities Compositions. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10010132] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
As a fundamental part of the soil ecosystem, prokaryotes are involved in the preservation of soil functions. However, little is known of how the combined application of long-term organic and inorganic nitrogen fertilizer affects the prokaryotic communities’ dynamics at a paddy field. A long-term positioning experiment initiated in 2013 with four treatments (NO: no N fertilizer, CN: 100% urea N with no organic fertilizer, PM: 80% urea N plus 20% N with pig manure, CM: 80% urea N plus 20% N with compost) were applied to detect the differential responses of soil physicochemical properties, and prokaryotic community structure and composition in different fertilization regimes. The results indicated that the long-term combined application of organic and inorganic nitrogen fertilizers altered the physicochemical properties to some extent and, simultaneously, established unique prokaryotic communities. In detail, the treatment of PM and CM significantly increased the content of soil organic carbon (SOC) and total nitrogen (TN) compared to NO. Moreover, a total of 31 indicator taxa were screened across the four treatments by LDA Effect Size (LEfSe) analysis following the principle of the greatest differences, which suggests that these indicator taxa were more sensitive to the fertilization. This research suggested that the combined application of long-term organic and inorganic nitrogen fertilizers not only contributed to the soil’s physicochemical properties but also changed the prokaryotic community composition.
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25
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Madigan AP, Egidi E, Bedon F, Franks AE, Plummer KM. Bacterial and Fungal Communities Are Differentially Modified by Melatonin in Agricultural Soils Under Abiotic Stress. Front Microbiol 2019; 10:2616. [PMID: 31849848 PMCID: PMC6901394 DOI: 10.3389/fmicb.2019.02616] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/28/2019] [Indexed: 12/29/2022] Open
Abstract
An extensive body of evidence from the last decade has indicated that melatonin enhances plant resistance to a range of biotic and abiotic stressors. This has led to an interest in the application of melatonin in agriculture to reduce negative physiological effects from environmental stresses that affect yield and crop quality. However, there are no reports regarding the effects of melatonin on soil microbial communities under abiotic stress, despite the importance of microbes for plant root health and function. Three agricultural soils associated with different land usage histories (pasture, canola or wheat) were placed under abiotic stress by cadmium (100 or 280 mg kg-1 soil) or salt (4 or 7 g kg-1 soil) and treated with melatonin (0.2 and 4 mg kg-1 soil). Automated Ribosomal Intergenic Spacer Analysis (ARISA) was used to generate Operational Taxonomic Units (OTU) for microbial community analysis in each soil. Significant differences in richness (α diversity) and community structures (β diversity) were observed between bacterial and fungal assemblages across all three soils, demonstrating the effect of melatonin on soil microbial communities under abiotic stress. The analysis also indicated that the microbial response to melatonin is governed by the type of soil and history. The effects of melatonin on soil microbes need to be regarded in potential future agricultural applications.
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Affiliation(s)
- Andrew P. Madigan
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Melbourne, VIC, Australia
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia
| | - Eleonora Egidi
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Frank Bedon
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Melbourne, VIC, Australia
| | - Ashley E. Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia
- Centre for Future Landscapes, School of Life Sciences, La Trobe University, Melbourne, VIC, Australia
| | - Kim M. Plummer
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Melbourne, VIC, Australia
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26
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Lin J, He F, Su B, Sun M, Owens G, Chen Z. The stabilizing mechanism of cadmium in contaminated soil using green synthesized iron oxide nanoparticles under long-term incubation. JOURNAL OF HAZARDOUS MATERIALS 2019; 379:120832. [PMID: 31276925 DOI: 10.1016/j.jhazmat.2019.120832] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/08/2019] [Accepted: 06/26/2019] [Indexed: 05/02/2023]
Abstract
Despite numerous studies having been conducted on the stabilization of heavy metal contaminated soil, our understanding of the mechanisms involved remains limited. Here green synthesized iron oxide nanoparticles (GION) were applied to stabilize cadmium (Cd) in a contaminated soil. GION not only stabilized soil Cd, but also improved soil properties within one year of incubation. After GION application both the exchangeable and carbonate bound Cd fractions decreased by 14.2-83.5% and 18.3-85.8% respectively, and most of the Cd was translocated to the residual Cd fraction. The application of GION also strongly altered soil bacterial communities. In GION treatments, the abundance of Gemmatimonadetes, Proteobacteria, and Saccharibacteria increased which led to a shift in the dominant bacterial genera from Bacillus to Candidatus koribacter. The variation in bacteria confirmed the restoration of the contaminated soil. The most abundant bacterial genus and species found in GION treatments were related to (i) plant derived biomass decomposition; (ii) ammoxidation and denitrification; and (iii) Fe oxidation. GION application may enhance the formation of larger soil aggregates with anaerobic centers and coprecipitation coupled Fe (II) oxidization, ammoxidation and nitrite reduction followed by Fe mineral ripening may be involved in Cd stabilization. The predominant stabilization mechanism was thus coprecipitation-ripening-stabilization.
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Affiliation(s)
- Jiajiang Lin
- Fujian Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China
| | - Fengxin He
- Fujian Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China
| | - Binglin Su
- Fujian Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China
| | - Mengqiang Sun
- Fujian Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China
| | - Gary Owens
- Environmental Contaminants Group, Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Zuliang Chen
- Fujian Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China; Environmental Contaminants Group, Future Industries Institute, University of South Australia, Mawson Lakes, SA, 5095, Australia.
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27
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Hu G, Zhang L, Yun Y, Peng Y. Taking insight into the gut microbiota of three spider species: No characteristic symbiont was found corresponding to the special feeding style of spiders. Ecol Evol 2019; 9:8146-8156. [PMID: 31380078 PMCID: PMC6662400 DOI: 10.1002/ece3.5382] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 05/22/2019] [Accepted: 05/29/2019] [Indexed: 12/19/2022] Open
Abstract
Microorganisms in insect guts have been recognized as having a great impact on their hosts' nutrition, health, and behavior. Spiders are important natural enemies of pests, and the composition of the gut microbiota of spiders remains unclear. Will the bacterial taxa in spiders be same as the bacterial taxa in insects, and what are the potential functions of the gut bacteria in spiders? To gain insight into the composition of the gut bacteria in spiders and their potential function, we collected three spider species, Pardosa laura, Pardosa astrigera, and Nurscia albofasciata, in the field, and high-throughput sequencing of the 16S rRNA V3 and V4 regions was used to investigate the diversity of gut microbiota across the three spider species. A total of 23 phyla and 150 families were identified in these three spider species. The dominant bacterial phylum across all samples was Proteobacteria. Burkholderia, Ralstonia, Ochrobactrum, Providencia, Acinetobacter, Proteus, and Rhodoplanes were the dominant genera in the guts of the three spider species. The relative abundances of Wolbachia and Rickettsiella detected in N. albofasciata were significantly higher than those in the other two spider species. The relative abundance of Thermus, Amycolatopsis, Lactococcus, Acinetobacter Microbacterium, and Koribacter detected in spider gut was different among the three spider species. Biomolecular interaction networks indicated that the microbiota in the guts had complex interactions. The results of this study also suggested that at the genus level, some of the gut bacteria taxa in the three spider species were the same as the bacteria in insect guts.
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Affiliation(s)
- Guowen Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, School of Life SciencesHubei UniversityWuhanChina
| | - Lihua Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, School of Life SciencesHubei UniversityWuhanChina
| | - Yueli Yun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, School of Life SciencesHubei UniversityWuhanChina
- Centre for Behavioral Ecology & Evolution, School of Life SciencesHubei UniversityWuhanChina
| | - Yu Peng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, School of Life SciencesHubei UniversityWuhanChina
- Centre for Behavioral Ecology & Evolution, School of Life SciencesHubei UniversityWuhanChina
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28
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Tang H, Xiao X, Xu Y, Li C, Cheng K, Pan X, Li W. Utilization of carbon sources in the rice rhizosphere and nonrhizosphere soils with different long-term fertilization management. J Basic Microbiol 2019; 59:621-631. [DOI: 10.1002/jobm.201800736] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/07/2019] [Accepted: 03/31/2019] [Indexed: 01/26/2023]
Affiliation(s)
- Haiming Tang
- Farming Ecology, Hunan Academy of Agricultural Sciences; Institute of Soil and Fertilizer; Changsha China
| | - Xiaoping Xiao
- Farming Ecology, Hunan Academy of Agricultural Sciences; Institute of Soil and Fertilizer; Changsha China
| | - Yilan Xu
- Plant Science and Technology; Hunan Biological and Electromechanical Polytechnic; Changsha China
| | - Chao Li
- Farming Ecology, Hunan Academy of Agricultural Sciences; Institute of Soil and Fertilizer; Changsha China
| | - Kaikai Cheng
- Farming Ecology, Hunan Academy of Agricultural Sciences; Institute of Soil and Fertilizer; Changsha China
| | - Xiaochen Pan
- Farming Ecology, Hunan Academy of Agricultural Sciences; Institute of Soil and Fertilizer; Changsha China
| | - Weiyan Li
- Farming Ecology, Hunan Academy of Agricultural Sciences; Institute of Soil and Fertilizer; Changsha China
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29
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Short-term response of the soil bacterial community to differing wildfire severity in Pinus tabulaeformis stands. Sci Rep 2019; 9:1148. [PMID: 30718899 PMCID: PMC6362210 DOI: 10.1038/s41598-019-38541-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 12/28/2018] [Indexed: 01/22/2023] Open
Abstract
In recent years, the investigation of fire disturbance of microbial communities has gained growing attention. However, how the bacterial community varies in response to different severities of fire at different soil depths is largely unknown. We utilized Illumina MiSeq sequencing to illustrate the changing patterns of the soil bacterial community following low-, moderate- and high-severity wildfire in the topsoil (0–10 cm) and subsoil (10–20 cm), 6 months after the fire. Acidobacteria, Proteobacteria, Actinobacteria, Verrucomicrobia and Chloroflexi were the dominant phyla among all samples. Bacterial alpha diversity (i.e. Shannon and Simpson indices) in the topsoil was significantly higher than that in the subsoil after a high-severity wildfire. Non-metric multidimensional scaling (NMDS) analysis and permutational multivariate analysis of variance (PERMANOVA) revealed significant differences in the bacterial community structure between the two soil layers. Soil pH, ammonium nitrogen (NH4+-N) and total nitrogen were the main factors in shaping the bacterial community structure, of which soil pH was the most robust in both soil layers. Our study reveals that wildfire results in short-term changes in soil bacterial community. However, a long-term monitoring of microbial variation after burning is also essential.
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30
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Maarastawi SA, Frindte K, Linnartz M, Knief C. Crop Rotation and Straw Application Impact Microbial Communities in Italian and Philippine Soils and the Rhizosphere of Zea mays. Front Microbiol 2018; 9:1295. [PMID: 29963033 PMCID: PMC6013709 DOI: 10.3389/fmicb.2018.01295] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/28/2018] [Indexed: 12/18/2022] Open
Abstract
Rice is one of the most important nourishments and its cultivation binds large agricultural areas in the world. Its cultivation leads to huge water consumption and high methane emissions. To diminish these problems, crop rotation between paddy rice and maize is introduced in Asia, but can lead to losses of carbon and water by the formation of desiccation cracks. To counteract these problems rice straw can be applied. We analyzed soil microbial responses to different crop rotation systems [rice–rice (RR), maize–maize (MM), maize–rice (MR)] and to rice straw application in the soil and rhizosphere of maize. Zea mays was grown in microcosms using soils from different field locations, each including different crop rotation regimes. The bacterial and fungal community composition was analyzed by 16S rRNA gene and ITS based amplicon sequencing in the bulk soil and rhizosphere. The microbiota was clearly different in soils from the different field locations (analysis of similarity, ANOSIM: R = 0.516 for the bacterial community; R = 0.817 for the fungal community). Within the field locations, crop rotation contributed differently to the variation in microbial community composition. Strong differences were observed in communities inhabiting soils under monosuccession (RR vs. MM) (ANOSIM: R = 0.923 for the bacterial and R = 0.714 for the fungal community), while the communities in soils undergoing MR crop rotation were more similar to those of the corresponding RR soils (ANOSIM: R = 0.111–0.175). The observed differences could be explained by altered oxygen availabilities in RR and MR soils, resulting in an enrichment of anaerobic bacteria in the soils, and the presence of the different crops, leading to the enrichment of host-plant specific microbial communities. The responses of the microbial communities to the application of rice straw in the microcosms were rather weak compared to the other factors. The taxa responding in bulk soil and rhizosphere were mostly distinct. In conclusion, this study revealed that the different agricultural management practices affect microbial community composition to different extent, not only in the bulk soil but also in the rhizosphere, and that the microbial responses in bulk soil and rhizosphere are distinct.
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Affiliation(s)
- Sarah A Maarastawi
- Institute of Crop Science and Resource Conservation (INRES), Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Katharina Frindte
- Institute of Crop Science and Resource Conservation (INRES), Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Marius Linnartz
- Institute of Crop Science and Resource Conservation (INRES), Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation (INRES), Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
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31
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Zhao Y, Feng Y, Li J, Guo Y, Chen L, Liu S. Insight into the Aggregation Capacity of Anammox Consortia during Reactor Start-Up. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:3685-3695. [PMID: 29505708 DOI: 10.1021/acs.est.7b06553] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Anammox aggregates have been extensively observed in high-efficiency nitrogen-removal reactors, yet the variation and inherent cause of its aggregation capacity related to reactor operation are still unknown. Here, we used microbial detection, metabolomics, extended Derjaguin-Landau-Verwey-Overbeek theory, and multivariate statistical analysis to address this issue. The aggregation capacity of anammox consortia varied periodically during reactor operation, which was determined by the hydrophobic force and the ratio of extracellular protein (PN) to extracellular polysaccharides (PS). Fundamentally, it related to the variation of polysaccharides degradation bacteria abundance and the discrepancy of consortia metabolism. Specifically, the distinguishable up-regulation of the amino acids Phe, Leu, Ala, Thr, Gly, Glu, and Val potentially contributed to the high biosynthesis of extracellular PN. Together with the reduced extracellular PS production that was regulated via the uridine diphosphate (UDP)- N-acetyl-d-glucosamine and UDP- N-acetyl-d-galactosamine pathways, the elevated extracellular PN-to-PS ratio resulted in the obviously increased extracellular hydrophobicity and aggregation capacity. Additionally, the overtly enriched phosphatidylethanolamine biosynthesis pathway was also vital to increasing extracellular hydrophobicity to accelerate aggregation. Understanding aggregation capacity variation is useful for advancing anammox aggregation for its application in wastewater treatment.
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Affiliation(s)
- Yunpeng Zhao
- Department of Environmental Engineering , Peking University , Beijing 100871 , China
- Key Laboratory of Water and Sediment Sciences , Ministry of Education of China , Beijing 100871 , China
| | - Ying Feng
- Department of Environmental Engineering , Peking University , Beijing 100871 , China
- Key Laboratory of Water and Sediment Sciences , Ministry of Education of China , Beijing 100871 , China
| | - Jianqi Li
- Key Laboratory of Water and Sediment Sciences , Ministry of Education of China , Beijing 100871 , China
- School of Environment and Energy , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
| | - Yongzhao Guo
- Key Laboratory of Water and Sediment Sciences , Ministry of Education of China , Beijing 100871 , China
- School of Environment and Energy , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
| | - Liming Chen
- Department of Environmental Engineering , Peking University , Beijing 100871 , China
- Key Laboratory of Water and Sediment Sciences , Ministry of Education of China , Beijing 100871 , China
| | - Sitong Liu
- Department of Environmental Engineering , Peking University , Beijing 100871 , China
- Key Laboratory of Water and Sediment Sciences , Ministry of Education of China , Beijing 100871 , China
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32
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Effect of long-term fertilization strategies on bacterial community composition in a 35-year field experiment of Chinese Mollisols. AMB Express 2018; 8:20. [PMID: 29442257 PMCID: PMC5811423 DOI: 10.1186/s13568-018-0549-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/05/2018] [Indexed: 11/10/2022] Open
Abstract
Bacteria play vital roles in soil biological fertility; however, it remains poorly understood about their response to long-term fertilization in Chinese Mollisols, especially when organic manure is substituted for inorganic nitrogen (N) fertilizer. To broaden our knowledge, high-throughput pyrosequencing and quantitative PCR were used to explore the impacts of inorganic fertilizer and manure on bacterial community composition in a 35-year field experiment of Chinese Mollisols. Soils were collected from four treatments: no fertilizer (CK), inorganic phosphorus (P) and potassium (K) fertilizer (PK), inorganic P, K, and N fertilizer (NPK), and inorganic P and K fertilizer plus manure (MPK). All fertilization differently changed soil properties. Compared with CK, the PK and NPK treatments acidified soil by significantly decreasing soil pH from 6.48 to 5.53 and 6.16, respectively, while MPK application showed no significant differences of soil pH, indicating alleviation of soil acidification. Moreover, all fertilization significantly increased soil organic matter (OM) and soybean yields, with the highest observed under MPK regime. In addition, the community composition at each taxonomic level varied considerably among the fertilization strategies. Bacterial taxa, associated with plant growth promotion, OM accumulation, disease suppression, and increased soil enzyme activity, were overrepresented in the MPK regime, while they were present at low abundant levels under NPK treatment, i.e. phyla Proteobacteria and Bacteroidetes, class Alphaproteobacteria, and genera Variovorax, Chthoniobacter, Massilia, Lysobacter, Catelliglobosispora and Steroidobacter. The application of MPK shifted soil bacterial community composition towards a better status, and such shifts were primarily derived from changes in soil pH and OM.
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Abstract
Ammonia oxidation is crucial in nitrogen removal and global nitrogen dynamics since it is the first step of the nitrification process. In this review, we focus on the distribution and community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in East Asian paddy soils with variable soil properties. The available East Asian paddy soil data shows that the ammonium concentration and pH ranges from 0.4 to 370 mg/kg and 5.1 to 8.2, respectively. Our meta-analysis suggest that AOA specific gene sequences are generally more abundant than those of AOB in both acidic and alkaline paddy soils, where Nitrosophaera and Nitrosospira amoA clusters mainly dominate the microbial community, respectively. In addition, the contribution of ammonia oxidizers to the nitrification process has been demonstrated using DNA-SIP (DNA-based stable-isotope probing); the results of these studies indicate that pH is the most important factor in niche separation of AOA and AOB under a variety of edaphic conditions. Finally, we discuss a number of other environmental variables that affect the abundance, distribution, and activity of AOA and AOB in East Asian paddy soils.
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Vaksmaa A, van Alen TA, Ettwig KF, Lupotto E, Valè G, Jetten MSM, Lüke C. Stratification of Diversity and Activity of Methanogenic and Methanotrophic Microorganisms in a Nitrogen-Fertilized Italian Paddy Soil. Front Microbiol 2017; 8:2127. [PMID: 29180985 PMCID: PMC5693880 DOI: 10.3389/fmicb.2017.02127] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/18/2017] [Indexed: 11/30/2022] Open
Abstract
Paddy fields are important ecosystems, as rice is the primary food source for about half of the world's population. Paddy fields are impacted by nitrogen fertilization and are a major anthropogenic source of methane. Microbial diversity and methane metabolism were investigated in the upper 60 cm of a paddy soil by qPCR, 16S rRNA gene amplicon sequencing and anoxic 13C-CH4 turnover with a suite of electron acceptors. The bacterial community consisted mainly of Acidobacteria, Chloroflexi, Proteobacteria, Planctomycetes, and Actinobacteria. Among archaea, Euryarchaeota and Bathyarchaeota dominated over Thaumarchaeota in the upper 30 cm of the soil. Bathyarchaeota constituted up to 45% of the total archaeal reads in the top 5 cm. In the methanogenic community, Methanosaeta were generally more abundant than the versatile Methanosarcina. The measured maximum methane production rate was 444 nmol gdwh-1, and the maximum rates of nitrate-, nitrite-, and iron-dependent anaerobic oxidation of methane (AOM) were 57 nmol, 55 nmol, and 56 nmol gdwh-1, respectively, at different depths. qPCR revealed a higher abundance of 'Candidatus Methanoperedens nitroreducens' than methanotrophic NC10 phylum bacteria at all depths, except at 60 cm. These results demonstrate that there is substantial potential for AOM in fertilized paddy fields, with 'Candidatus Methanoperedens nitroreducens' archaea as a potential important contributor.
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Affiliation(s)
- Annika Vaksmaa
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Theo A. van Alen
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Katharina F. Ettwig
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Elisabetta Lupotto
- Research Centre for Food and Nutrition, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Rome, Italy
| | - Giampiero Valè
- Research Centre for Cereal and Industrial Crops, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
| | - Mike S. M. Jetten
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Claudia Lüke
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
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Dai H, Chen Y, Yang X, Cui J, Sui P. The effect of different organic materials amendment on soil bacteria communities in barren sandy loam soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:24019-24028. [PMID: 28884297 DOI: 10.1007/s11356-017-0031-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 08/24/2017] [Indexed: 06/07/2023]
Abstract
To effectively improve soil productivity and optimize organic fertilizer management while reducing environmental pollution and resource wasting in farmland system, the present study was conducted in Wuqiao Experiment Station of China Agricultural University, Hebei Province. Taking crop straw treatment as control, four kinds of organic materials including pig manure (PM), biogas residue (BR), biochar (BC) and crop straw (ST) were applied to soil at the same nitrogen (N) level. The soil bacteria community characteristics were explored using Illumina Miseq high-throughput sequencing technologies. The results were as follows: (1) Compared with ST, PM, BR and BC had no significant effect on Chao 1 and Shannon index. The dominant bacterial groups include Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Chloroflexi in sandy loam soil after the application of different organic materials. The abundance of Proteobacteria in BC treatment was significantly lower than that of ST (control) treatment (p < 0.05). On the contrary, compared to ST, the abundances of Acidobacteria increased by 65.0, 40.7, and 58.7% in the BC, BR, and PM treatments, respectively. (2) Compared to ST, the BC treatment significantly (p < 0.05) increased in soil organic carbon (SOC) and pH in the arable layer (0-20 cm) in the farmland (p < 0.05), and significantly increased the soil pH with a value of 0.26 level (p < 0.05). (3) Pearson correlation analysis results showed that the PCoA1 scores and soil pH were closely correlated (R 2 = 0.3738, p < 0.05). In addition, pairwise regression between PCoA1 scores and SOC (R 2 = 0.5008, p < 0.05), PCoA2 scores and SOC (R 2 = 0.4053, p < 0.05) were both closely correlated. In general, our results indicated that organic materials amendment shaped the bacterial community in sandy loam soil through changing the soil pH and SOC.
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Affiliation(s)
- Hongcui Dai
- Circular Agriculture Research Center/College of Agronomy and Biotechnology, China Agricultural University, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Yuanquan Chen
- Circular Agriculture Research Center/College of Agronomy and Biotechnology, China Agricultural University, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Xiaolei Yang
- Circular Agriculture Research Center/College of Agronomy and Biotechnology, China Agricultural University, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Jixiao Cui
- Circular Agriculture Research Center/College of Agronomy and Biotechnology, China Agricultural University, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Peng Sui
- Circular Agriculture Research Center/College of Agronomy and Biotechnology, China Agricultural University, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China.
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36
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Zhou J, Jiang X, Wei D, Zhao B, Ma M, Chen S, Cao F, Shen D, Guan D, Li J. Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China. Sci Rep 2017; 7:3267. [PMID: 28607352 PMCID: PMC5468298 DOI: 10.1038/s41598-017-03539-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/01/2017] [Indexed: 01/08/2023] Open
Abstract
Long-term use of inorganic nitrogen (N) fertilization has greatly influenced the bacterial community in black soil of northeast China. It is unclear how N affects the bacterial community in two successive crop seasons in the same field for this soil type. We sampled soils from a long-term fertilizer experimental field in Harbin city with three N gradients. We applied sequencing and quantitative PCR targeting at the 16S rRNA gene to examine shifts in bacterial communities and test consistent shifts and driving-factors bacterial responses to elevated N additions. N addition decreased soil pH and bacterial 16S rDNA copy numbers, and increased soil N and crop yield. N addition consistently decreased bacterial diversity and altered bacterial community composition, by increasing the relative abundance of Proteobacteria, and decreasing that of Acidobacteria and Nitrospirae in both seasons. Consistent changes in the abundant classes and genera, and the structure of the bacterial communities across both seasons were observed. Our results suggest that increases in N inputs had consistent effects on the richness, diversity and composition of soil bacterial communities across the crop seasons in two continuous years, and the N addition and the subsequent edaphic changes were important factors in shaping bacterial community structures.
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Affiliation(s)
- Jing Zhou
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.,College of Biological Sciences, China Agricultural University, Beijing, 100094, PR China
| | - Xin Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China. .,Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, PR China.
| | - Dan Wei
- The Institute of Soil Fertility and Environmental Sources, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, PR China
| | - Baisuo Zhao
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, PR China
| | - Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, PR China
| | - Sanfeng Chen
- College of Biological Sciences, China Agricultural University, Beijing, 100094, PR China
| | - Fengming Cao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, PR China
| | - Delong Shen
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, PR China
| | - Dawei Guan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China. .,Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, PR China.
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37
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Reim A, Hernández M, Klose M, Chidthaisong A, Yuttitham M, Conrad R. Response of Methanogenic Microbial Communities to Desiccation Stress in Flooded and Rain-Fed Paddy Soil from Thailand. Front Microbiol 2017; 8:785. [PMID: 28529503 PMCID: PMC5418361 DOI: 10.3389/fmicb.2017.00785] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/18/2017] [Indexed: 11/24/2022] Open
Abstract
Rice paddies in central Thailand are flooded either by irrigation (irrigated rice) or by rain (rain-fed rice). The paddy soils and their microbial communities thus experience permanent or arbitrary submergence, respectively. Since methane production depends on anaerobic conditions, we hypothesized that structure and function of the methanogenic microbial communities are different in irrigated and rain-fed paddies and react differently upon desiccation stress. We determined rates and relative proportions of hydrogenotrophic and aceticlastic methanogenesis before and after short-term drying of soil samples from replicate fields. The methanogenic pathway was determined by analyzing concentrations and δ13C of organic carbon and of CH4 and CO2 produced in the presence and absence of methyl fluoride, an inhibitor of aceticlastic methanogenesis. We also determined the abundance (qPCR) of genes and transcripts of bacterial 16S rRNA, archaeal 16S rRNA and methanogenic mcrA (coding for a subunit of the methyl coenzyme M reductase) and the composition of these microbial communities by T-RFLP fingerprinting and/or Illumina deep sequencing. The abundances of genes and transcripts were similar in irrigated and rain-fed paddy soil. They also did not change much upon desiccation and rewetting, except the transcripts of mcrA, which increased by more than two orders of magnitude. In parallel, rates of CH4 production also increased, in rain-fed soil more than in irrigated soil. The contribution of hydrogenotrophic methanogenesis increased in rain-fed soil and became similar to that in irrigated soil. However, the relative microbial community composition on higher taxonomic levels was similar between irrigated and rain-fed soil. On the other hand, desiccation and subsequent anaerobic reincubation resulted in systematic changes in the composition of microbial communities for both Archaea and Bacteria. It is noteworthy that differences in the community composition were mostly detected on the level of operational taxonomic units (OTUs; 97% sequence similarity). The treatments resulted in change of the relative abundance of several archaeal OTUs. Some OTUs of Methanobacterium, Methanosaeta, Methanosarcina, Methanocella and Methanomassiliicoccus increased, while some of Methanolinea and Methanosaeta decreased. Bacterial OTUs within Firmicutes, Cyanobacteria, Planctomycetes and Deltaproteobacteria increased, while OTUs within other proteobacterial classes decreased.
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Affiliation(s)
- Andreas Reim
- Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
| | - Marcela Hernández
- Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany.,Centre for Biological Sciences, University of SouthamptonSouthampton, UK
| | - Melanie Klose
- Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
| | - Amnat Chidthaisong
- Joint Graduate School of Energy and Environment, King Mongkut's University of Technology ThonburiBangkok, Thailand
| | - Monthira Yuttitham
- Faculty of Environment and Resource Studies, Mahidol UniversitySalaya, Thailand
| | - Ralf Conrad
- Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
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38
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Ahn JH, Lee SA, Kim JM, Kim MS, Song J, Weon HY. Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices. J Microbiol 2016; 54:724-731. [PMID: 27796926 DOI: 10.1007/s12275-016-6463-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 11/29/2022]
Abstract
Fertilization and the response of the soil microbial community to the process significantly affect crop yield and the environment. In this study, the seasonal variation in the bacterial communities in rice field soil subjected to different fertilization treatments for more than 50 years was investigated using 16S rRNA sequencing. The simultaneous application of inorganic fertilizers and rice straw compost (CAPK) maintained the species richness of the bacterial communities at levels higher than that in the case of non-fertilization (NF) and application of inorganic fertilizers only (APK) in the initial period of rice growth. The seasonal variation in the bacterial community structure in the NF and APK plots showed cyclic behavior, suggesting that the effect of season was important; however, no such trend was observed in the CAPK plot. In the CAPK plot, the relative abundances of putative copiotrophs such as Bacteroidetes, Firmicutes, and Proteobacteria were higher and those of putative oligotrophs such as Acidobacteria and Plactomycetes were lower than those in the other plots. The relative abundances of organotrophs with respiratory metabolism, such as Actinobacteria, were lower and those of chemoautotrophs that oxidize reduced iron and sulfur compounds were higher in the CAPK plot, suggesting greater carbon storage in this plot. Increased methane emission and nitrogen deficiency, which were inferred from the higher abundances of Methylocystis and Bradyrhizobium in the CAPK plot, may be a negative effect of rice straw application; thus, a solution for these should be considered to increase the use of renewable resources in agricultural lands.
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Affiliation(s)
- Jae-Hyung Ahn
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea
| | - Shin Ae Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea
| | - Jeong Myeong Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea
| | - Myung-Sook Kim
- Soil and Ferilization Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jaekyeong Song
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea.
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39
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Vaksmaa A, Lüke C, van Alen T, Valè G, Lupotto E, Jetten MSM, Ettwig KF. Distribution and activity of the anaerobic methanotrophic community in a nitrogen-fertilized Italian paddy soil. FEMS Microbiol Ecol 2016; 92:fiw181. [PMID: 27562776 DOI: 10.1093/femsec/fiw181] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2016] [Indexed: 12/23/2022] Open
Abstract
In order to mitigate methane emissions from paddy fields, it is important to understand the sources and sinks. Most paddy fields are heavily fertilized with nitrite and nitrate, which can be used as electron acceptors by anaerobic methanotrophs. Here we show that slurry incubations of Italian paddy field soil with nitrate and 13C-labelled methane have the potential for nitrate-dependent anaerobic oxidation of methane (79.9 nmol g-1dw d-1). Community analysis based on 16S rRNA amplicon sequencing and qPCR of the water-logged soil and the rhizosphere showed that anaerobic oxidation of methane-associated archaea (AAA), including Methanoperedens nitroreducens, comprised 9% (bulk soil) and 1% (rhizosphere) of all archaeal reads. The NC10 phylum bacteria made up less than 1% of all bacterial sequences. The phylogenetic analysis was complemented by qPCR showing that AAA ranged from 0.28 × 106 to 3.9 × 106 16S rRNA gene copies g-1dw in bulk soil and 0.27 × 106 to 2.8 × 106 in the rhizosphere. The abundance of NC10 phylum bacteria was an order of magnitude lower. Revisiting published diversity studies, we found that AAA have been detected, but not linked to methane oxidation, in several paddy fields. Our data suggest an important role of AAA in methane cycling in paddy fields.
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Affiliation(s)
- A Vaksmaa
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - C Lüke
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - T van Alen
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - G Valè
- CREA - Council for Agricultural Research and Economics, Rice Research Unit, s.s.11 to Torino km 2.5, 13100 Vercelli, Italy
| | - E Lupotto
- CREA - Council for Agricultural Research and Economics, Rice Research Unit, s.s.11 to Torino km 2.5, 13100 Vercelli, Italy
| | - M S M Jetten
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - K F Ettwig
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
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40
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Wang J, Xue C, Song Y, Wang L, Huang Q, Shen Q. Wheat and Rice Growth Stages and Fertilization Regimes Alter Soil Bacterial Community Structure, But Not Diversity. Front Microbiol 2016; 7:1207. [PMID: 27536292 PMCID: PMC4971054 DOI: 10.3389/fmicb.2016.01207] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/20/2016] [Indexed: 11/13/2022] Open
Abstract
Maintaining soil fertility and the microbial communities that determine fertility is critical to sustainable agricultural strategies, and the use of different organic fertilizer (OF) regimes represents an important practice in attempts to preserve soil quality. However, little is known about the dynamic response of bacterial communities to fertilization regimes across crop growth stages. In this study, we examined microbial community structure and diversity across eight representative growth stages of wheat-rice rotation under four different fertilization treatments: no nitrogen fertilizer (NNF), chemical fertilizer (CF), organic–inorganic mixed fertilizer (OIMF), and OF. Quantitative PCR (QPCR) and high-throughput sequencing of bacterial 16S rRNA gene fragments revealed that growth stage as the best predictor of bacterial community abundance and structure. Additionally, bacterial community compositions differed between wheat and rice rotations. Relative to soils under wheat rotation, soils under rice rotation contained higher relative abundances (RA) of anaerobic and mesophilic microbes and lower RA of aerophilic microbes. With respect to fertilization regime, NNF plots had a higher abundance of nitrogen–fixing Cyanobacteria. OIMF had a lower abundance of ammonia-oxidizing Thaumarchaeota compared with CF. Application of chemical fertilizers (CF and OIMF treatments) significantly increased the abundance of some generally oligotrophic bacteria such those belonging to the Acidobacteria, while more copiotrophic of the phylum Proteobacteria increased with OF application. A high correlation coefficient was found when comparing RA of Acidobacteria based upon QPCR vs. sequence analysis, yet poor correlations were found for the α- and β- Proteobacteria, highlighting the caution required when interpreting these molecular data. In total, crop, fertilization scheme and plant developmental stage all influenced soil microbial community structure, but not total levels of alpha diversity.
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Affiliation(s)
- Jichen Wang
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural University Nanjing, China
| | - Chao Xue
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural University Nanjing, China
| | - Yang Song
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural University Nanjing, China
| | - Lei Wang
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural University Nanjing, China
| | - Qiwei Huang
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural University Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural University Nanjing, China
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Shao J, He Y, Zhang H, Chen A, Lei M, Chen J, Peng L, Gu JD. Silica fertilization and nano-MnO2 amendment on bacterial community composition in high arsenic paddy soils. Appl Microbiol Biotechnol 2015; 100:2429-37. [DOI: 10.1007/s00253-015-7131-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 10/27/2015] [Accepted: 10/29/2015] [Indexed: 12/01/2022]
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Breidenbach B, Blaser MB, Klose M, Conrad R. Crop rotation of flooded rice with upland maize impacts the resident and active methanogenic microbial community. Environ Microbiol 2015; 18:2868-85. [PMID: 26337675 DOI: 10.1111/1462-2920.13041] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/26/2015] [Accepted: 08/27/2015] [Indexed: 11/27/2022]
Abstract
Crop rotation of flooded rice with upland crops is a common management scheme allowing the reduction of water consumption along with the reduction of methane emission. The introduction of an upland crop into the paddy rice ecosystem leads to dramatic changes in field conditions (oxygen availability, redox conditions). However, the impact of this practice on the archaeal and bacterial communities has scarcely been studied. Here, we provide a comprehensive study focusing on the crop rotation between flooded rice in the wet season and upland maize (RM) in the dry season in comparison with flooded rice (RR) in both seasons. The composition of the resident and active microbial communities was assessed by 454 pyrosequencing targeting the archaeal and bacterial 16S rRNA gene and 16S rRNA. The archaeal community composition changed dramatically in the rotational fields indicated by a decrease of anaerobic methanogenic lineages and an increase of aerobic Thaumarchaeota. Members of Methanomicrobiales, Methanosarcinaceae, Methanosaetaceae and Methanocellaceae were equally suppressed in the rotational fields indicating influence on both acetoclastic and hydrogenotrophic methanogens. On the contrary, members of soil crenarchaeotic group, mainly Candidatus Nitrososphaera, were higher in the rotational fields, possibly indicating increasing importance of ammonia oxidation during drainage. In contrast, minor effects on the bacterial community were observed. Acidobacteria and Anaeromyxobacter spp. were enriched in the rotational fields, whereas members of anaerobic Chloroflexi and sulfate-reducing members of Deltaproteobacteria were found in higher abundance in the rice fields. Combining quantitative polymerase chain reaction and pyrosequencing data revealed increased ribosomal numbers per cell for methanogenic species during crop rotation. This stress response, however, did not allow the methanogenic community to recover in the rotational fields during re-flooding and rice cultivation. In summary, the analyses showed that crop rotation with upland maize led to dramatic changes in the archaeal community composition whereas the bacterial community was only little affected.
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Affiliation(s)
| | - Martin B Blaser
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Melanie Klose
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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Effect of long-term different fertilization on bacterial community structures and diversity in citrus orchard soil of volcanic ash. J Microbiol 2014; 52:995-1001. [PMID: 25467117 DOI: 10.1007/s12275-014-4129-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 09/29/2014] [Accepted: 09/29/2014] [Indexed: 10/24/2022]
Abstract
This study was conducted to assess bacterial species richness, diversity and community distribution according to different fertilization regimes for 16 years in citrus orchard soil of volcanic ash. Soil samples were collected and analyzed from Compost (cattle manure, 2,000 kg/10a), 1/2 NPK+compost (14-20-14+2,000 kg/10a), NPK+compost (28-40-28+2,000 kg/10a), NPK (28-40-28 kg/10a), 3 NPK (84-120-84 kg/10a), and Control (no fertilization) plot which have been managed in the same manners with compost and different amount of chemical fertilization. The range of pyrosequencing reads and OTUs were 4,687-7,330 and 1,790-3,695, respectively. Species richness estimates such as Ace, Chao1, and Shannon index were higher in 1/2 NPK+compost than other treatments, which were 15,202, 9,112, 7.7, respectively. Dominant bacterial groups at level of phylum were Proteobacteria, Acidobacteria, and Actinobacteria. Those were occupied at 70.9% in 1/2 NPK+compost. Dominant bacterial groups at level of genus were Pseudolabrys, Bradyrhizobium, and Acidobacteria. Those were distributed at 14.4% of a total of bacteria in Compost. Soil pH displayed significantly closely related to bacterial species richness estimates such as Ace, Chao1 (p<0.05) and Shannon index (p<0.01). However, it showed the negative correlation with exchangeable aluminum contents (p<0.05). In conclusion, diversity of bacterial community in citrus orchard soil was affected by fertilization management, soil pH changes and characteristics of volcanic ash.
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Microbial community analysis in rice paddy soils irrigated by acid mine drainage contaminated water. Appl Microbiol Biotechnol 2014; 99:2911-22. [DOI: 10.1007/s00253-014-6194-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/23/2014] [Accepted: 10/25/2014] [Indexed: 11/26/2022]
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Liu YR, Wang JJ, Zheng YM, Zhang LM, He JZ. Patterns of bacterial diversity along a long-term mercury-contaminated gradient in the paddy soils. MICROBIAL ECOLOGY 2014; 68:575-583. [PMID: 24827389 DOI: 10.1007/s00248-014-0430-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 05/01/2014] [Indexed: 06/03/2023]
Abstract
Mercury (Hg) pollution is usually regarded as an environmental stress in reducing microbial diversity and altering bacterial community structure. However, these results were based on relatively short-term studies, which might obscure the real response of microbial species to Hg contamination. Here, we analysed the bacterial abundance and community composition in paddy soils that have been potentially contaminated by Hg for more than 600 years. Expectedly, the soil Hg pollution significantly influenced the bacterial community structure. However, the bacterial abundance was significantly correlated with the soil organic matter content rather than the total Hg (THg) concentration. The bacterial alpha diversity increased at relatively low levels of THg and methylmercury (MeHg) and subsequently approached a plateau above 4.86 mg kg(-1) THg or 18.62 ng g(-1) MeHg, respectively. Contrasting with the general prediction of decreasing diversity along Hg stress, our results seem to be consistent with the intermediate disturbance hypotheses with the peak biological diversity under intermediate disturbance or stress. This result was partly supported by the inconsistent response of bacterial species to Hg stress. For instance, the relative abundance of Nitrospirae decreased, while that of Gemmatimonadetes increased significantly along the increasing soil THg and MeHg concentrations. In addition, the content of SO(4)(2-), THg, MeHg and soil depth were the four main factors influencing bacterial community structures based on the canonical correspondence analysis (CCA). Overall, our findings provide novel insight into the distribution patterns of bacterial community along the long-term Hg-contaminated gradient in paddy soils.
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Affiliation(s)
- Yu-Rong Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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46
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Lee HJ, Kim SY, Kim PJ, Madsen EL, Jeon CO. Methane emission and dynamics of methanotrophic and methanogenic communities in a flooded rice field ecosystem. FEMS Microbiol Ecol 2014; 88:195-212. [DOI: 10.1111/1574-6941.12282] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 01/03/2014] [Accepted: 01/03/2014] [Indexed: 01/19/2023] Open
Affiliation(s)
- Hyo Jung Lee
- Department of Life Science; Chung-Ang University; Seoul Korea
| | - Sang Yoon Kim
- Division of Applied Life Science; Gyeongsang National University; Jinju Korea
| | - Pil Joo Kim
- Division of Applied Life Science; Gyeongsang National University; Jinju Korea
| | | | - Che Ok Jeon
- Department of Life Science; Chung-Ang University; Seoul Korea
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Ahn JH, Choi MY, Lee HW, Kim BY, Song J, Kim MS, Weon HY. Analysis of Community Structure of Metabolically Active Bacteria in a Rice Field Subjected to Long-Term Fertilization Practices. ACTA ACUST UNITED AC 2013. [DOI: 10.7745/kjssf.2013.46.6.585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Scavino AF, Ji Y, Pump J, Klose M, Claus P, Conrad R. Structure and function of the methanogenic microbial communities in Uruguayan soils shifted between pasture and irrigated rice fields. Environ Microbiol 2013; 15:2588-602. [PMID: 23763330 DOI: 10.1111/1462-2920.12161] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/15/2013] [Indexed: 11/30/2022]
Abstract
Irrigated rice fields in Uruguay are temporarily established on soils used as cattle pastures. Typically, 4 years of cattle pasture are alternated with 2 years of irrigated rice cultivation. Thus, oxic upland conditions are rotated with seasonally anoxic wetland conditions. Only the latter conditions are suitable for the production of CH4 from anaerobic degradation of organic matter. We studied soil from a permanent pasture as well as soils from different years of the pasture-rice rotation hypothesizing that activity and structure of the bacterial and archaeal communities involved in production of CH4 change systematically with the duration of either oxic or anoxic conditions. Soil samples were taken from drained fields, air-dried and used for the experiments. Indeed, methanogenic archaeal gene copy numbers (16S rRNA, mcrA) were lower in soil from the permanent pasture than from the pasture-rice alternation fields, but within the latter, there was no significant difference. Methane production started to accumulate after 16 days and 7 days of anoxic incubation in soil from the permanent pasture and the pasture-rice alternation fields respectively. Then, CH4 production rates were slightly higher in the soils used for pasture than for rice production. Analysis of δ(13) C in CH4, CO2 and acetate in the presence and absence of methyl fluoride, an inhibitor of aceticlastic methanogenesis, indicated that CH4 was mainly (58-75%) produced from acetate, except in the permanent pasture soil (42%). Terminal restriction fragment length polymorphism (T-RFLP) of archaeal 16S rRNA genes showed no difference among the soils from the pasture-rice alternation fields with Methanocellaceae and Methanosarcinaceae as the main groups of methanogens, but in the permanent pasture soil, Methanocellaceae were relatively less abundant. T-RFLP analysis of bacterial 16S rRNA genes allowed the distinction of permanent pasture and fields from the pasture-rice rotation, but nevertheless with a high similarity. Pyrosequencing of bacterial 16S rRNA genes generally revealed Firmicutes as the dominant bacterial phylum, followed by Proteobacteria, Acidobacteria and Actinobacteria. We conclude that a stable methanogenic microbial community established once pastures have been turned into management by pasture-rice alternation despite the fact that 2 years of wetland conditions were followed by 4 years of upland conditions that were not suitable for CH4 production.
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Affiliation(s)
- Ana Fernandez Scavino
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str.10, 35043, Marburg, Germany
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