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Manfredini A, Malusà E, Pinzari F, Canfora L. Quantification of nitrogen cycle functional genes from viable archaea and bacteria in paddy soil. J Appl Microbiol 2023; 134:lxad169. [PMID: 37516446 DOI: 10.1093/jambio/lxad169] [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: 05/03/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 07/31/2023]
Abstract
AIMS One of the main challenges of culture-independent soil microbiology is distinguishing the microbial community's viable fraction from dead matter. Propidium monoazide (PMA) binds the DNA of dead cells, preventing its amplification. This dye could represent a robust means to overcome the drawbacks of other selective methods, such as ribonucleic acid-based analyses. METHODS AND RESULTS We quantified functional genes from viable archaea and bacteria in soil by combining the use of PMA and quantitative polymerase chain reaction. Four N-cycle-related functional genes (bacterial and archaeal ammonia monooxygenase, nitrate reductase, and nitrite reductase) were successfully quantified from the living fraction of bacteria and archaea of a paddy soil. The protocol was also tested with pure bacterial cultures and soils with different physical and chemical properties. CONCLUSIONS The experiment results revealed a contrasting impact of mineral and organic fertilizers on the abundance of microbial genes related to the N-cycle in paddy soil.
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Affiliation(s)
- Andrea Manfredini
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, 00184 Roma, Italy
| | - Eligio Malusà
- Council for Agricultural Research and Economics, Research Centre for Viticulture and Enology, 31015 Conegliano, Italy
- National Institute of Horticultural Research, 96-100 Skierniewice, Poland
| | - Flavia Pinzari
- Institute for Biological Systems, Council of National Research of Italy (CNR), 00010 Montelibretti, Italy
- Life Sciences Department, Natural History Museum, Cromwell Road, SW7 5BD London, UK
| | - Loredana Canfora
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, 00184 Roma, Italy
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Li M, Dai G, Mu L. Composition and diversity of soil bacterial communities under identical vegetation along an elevational gradient in Changbai Mountains, China. Front Microbiol 2022; 13:1065412. [DOI: 10.3389/fmicb.2022.1065412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 10/27/2022] [Indexed: 12/04/2022] Open
Abstract
Soil bacteria play important roles in biogeochemical cycling and biodiversity in mountain ecosystems. Past studies have investigated the bacterial community composition and diversity in elevation gradations covered by different vegetation types, but for a better assessment of elevation effects, here we studied bacterial communities in soil under identical vegetation cover. High-throughput amplicon sequencing of the V3-V4 region of bacterial 16S rDNA was used to investigate the diversity and composition bacterial communities in soil from 700 to 1,000 m above sea level collected on the north slope of Changbai Mountains, Northeast China. Obviously differences (p < 0.05) in soil physicochemical parameters (i.e., total nitrogen, nitrate and ammonium nitrogen, soil moisture content, available potassium, microbial biomass carbon and nitrogen) were observed at different elevations. Soil bacterial abundance indices (Richness, Chao1, ACE) differed significantly along the elevation gradient, whereas the Shannon index remained unchanged. Principal Coordinates Analysis indicated separated soil bacterial communities of the different elevations. The dominant phyla in all soil samples were Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Bacteroidetes, which in combination reached 80%–85%. Soil pH to some extend related to soil bacterial community along altitude gradations. The relative abundance of a multiple phyla was negatively affected by the soil nutrients, such as ammonium and nitrate nitrogen, available potassium, soil moisture content, available phosphorus, microbial biomass nitrogen and soil organic C. The strongest effects were seen for Proteobacteria. The pH either positively or negatively correlated with specific genera. The soil bacterial function differed significantly among four elevations. The chemoheterotrophy, aerobic chemoheterotrophy and nitrification were the most dominant functions of soil bacteria among four elevations. Overall, the changes in soil physicochemical properties with elevation are important in shaping the bacterial diversity, composition and function in soil with the same above-ground vegetation of Changbai Mountains.
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Sui X, Zeng X, Li M, Weng X, Frey B, Yang L, Li M. Influence of Different Vegetation Types on Soil Physicochemical Parameters and Fungal Communities. Microorganisms 2022; 10:microorganisms10040829. [PMID: 35456878 PMCID: PMC9026879 DOI: 10.3390/microorganisms10040829] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 04/05/2022] [Accepted: 04/14/2022] [Indexed: 12/18/2022] Open
Abstract
This study assessed the effects of Betula dahurica (BD), Betula platyphylla (BP), Larix gmelinii (LG), Quercus mongolica (QM), and a mixed conifer–broadleaf forest composed of LG and QM (LGQM) on the soil physicochemical parameters and community structure of fungi in the Zhongyangzhan Black-billed Capercaillie Nature Reserve. Fungal community structures were characterized via ITS rRNA sequencing. The effects of soil parameters on the community structure of soil fungi were assessed by Pearson correlation analysis and redundancy analysis (RDA). LGQM exhibited lower C/N, available nitrogen (AN), total phosphorus (TP), and available phosphorus (AP) compared with the QM broadleaf forest. The fungal Shannon and Simpson diversity indices were highest in BP, whereas LG exhibited the highest ACE index. The Basidiomycota, Ascomycota, Mortierellomycota, and Mucoromycota fungal phyla were dominant across all vegetation types. Each of the different vegetation types studied herein exhibited a unique fungal community structure. The RDA results indicated that fungal community structures were primarily shaped by the total N, available N, and available P of soil. Our findings thus indicated that forests restored with different species of trees may exhibit variations in soil quality and characteristics despite sharing the same climate. Furthermore, broadleaved and coniferous forests exhibited a unique fungal community diversity and composition.
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Affiliation(s)
- Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China; (X.S.); (X.W.)
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin 150080, China
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland;
| | - Xiannan Zeng
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin 150088, China;
| | - Mengsha Li
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China
- Correspondence: (M.L.); (L.Y.); (M.L.)
| | - Xiaohong Weng
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China; (X.S.); (X.W.)
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Beat Frey
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland;
| | - Libin Yang
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China
- Correspondence: (M.L.); (L.Y.); (M.L.)
| | - Maihe Li
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland;
- Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun 130024, China
- Erguna Forest-Steppe Ecotone Research Station, CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China
- Correspondence: (M.L.); (L.Y.); (M.L.)
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