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Naumova N, Barsukov P, Baturina O, Rusalimova O, Kabilov M. West-Siberian Chernozem: How Vegetation and Tillage Shape Its Bacteriobiome. Microorganisms 2023; 11:2431. [PMID: 37894089 PMCID: PMC10609427 DOI: 10.3390/microorganisms11102431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/15/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
Managing soil biodiversity using reduced tillage is a popular approach, yet soil bacteriobiomes in the agroecosystems of Siberia has been scarcely studied, especially as they are related to tillage. We studied bacteriobiomes in Chernozem under natural steppe vegetation and cropped for wheat using conventional or no tillage in a long-term field trial in the Novosibirsk region, Russia, by using the sequence diversity of the V3/V4 region of 16S rRNA genes. Actinobacteria, Acidobacteria, and Proteobacteria summarily accounted for 80% of the total number of sequences, with Actinobacteria alone averaging 51%. The vegetation (natural vs. crop) and tillage (ploughed vs. no-till) affected the bacterial relative abundance at all taxonomic levels and many taxa, e.g., hundreds of OTUs. However, such changes did not translate into α-biodiversity changes, i.e., observed and potential OTUs' richness, Shannon, and Simpson, excepting the slightly higher evenness and equitability in the top 0-5 cm of the undisturbed soil. As for the β-biodiversity, substituting conventional ploughing with no tillage and maintaining the latter for 12 years notably shifted the soil bacteriobiome closer to the one in the undisturbed soil. This study, presenting the first inventory of soil bacteriobiomes under different tillage in the south of West Siberia, underscores the need to investigate the seasonality and longevity aspects of tillage, especially as they are related to crop production.
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Affiliation(s)
- Natalia Naumova
- Institute of Soil Science and Agrochemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (P.B.); (O.R.)
| | - Pavel Barsukov
- Institute of Soil Science and Agrochemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (P.B.); (O.R.)
| | - Olga Baturina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.B.); (M.K.)
| | - Olga Rusalimova
- Institute of Soil Science and Agrochemistry, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (P.B.); (O.R.)
| | - Marsel Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.B.); (M.K.)
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Liu WS, Wei YX, Deng PP, Oladele OP, N'Dri Bohoussou Y, Dang YP, Zhao X, Zhang HL. Conservation tillage increases surface soil organic carbon stock by altering fungal communities and enzyme activity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:80901-80915. [PMID: 37311861 DOI: 10.1007/s11356-023-28062-2] [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: 02/23/2023] [Accepted: 05/30/2023] [Indexed: 06/15/2023]
Abstract
Fungal communities play a key role in the decomposition of crop residues and affect soil organic carbon (SOC) dynamics. Conservation tillage enhances SOC sequestration and mitigate global climate change. However, the impact of long-term tillage practices on fungal community diversity and its relation to SOC stock remains unclear. The objectives of this study were to evaluate the relationship between extracellular enzyme activities and fungal community diversity and SOC stock under different tillage practices. A field experiment was conducted with four tillage practices: (i) no-tillage with straw removal (NT0), (ii) no-tillage with straw retention (NTSR, conservation tillage), (iii) plough tillage with straw retention (PTSR), and (iv) rotary tillage with straw retention (RTSR). The results showed that the SOC stock in NTSR was higher than other treatments in the 0-10 cm soil layer. Compared to NT0, NTSR significantly increased soil β-glucosidase, xylosidase, cellobiohydrolase, and chitinase activities at 0-10 cm soil depth (P < 0.05). However, different tillage methods with straw returning had no significant effects on enzyme activity at 0-10 cm soil depth. The observed species and Chao1 index of the fungal communities under NTSR were 22.8% and 32.1% lower than under RTSR in the 0-10 cm soil layer, respectively. The composition, structure, and co-occurrence network of fungal communities differed across tillage practices. A partial least squares path model (PLS-PM) analysis indicated that C-related enzymes were the most influential factors associated with SOC stock. Soil physicochemical properties and fungal communities affected extracellular enzyme activities. Overall, conservation tillage can promote surface SOC stock, which was associated with increased enzyme activity.
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Affiliation(s)
- Wen-Sheng Liu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, People's Republic of China
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs of China, Beijing, 100193, People's Republic of China
| | - Yu-Xin Wei
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, People's Republic of China
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs of China, Beijing, 100193, People's Republic of China
| | - Ping-Ping Deng
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, People's Republic of China
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs of China, Beijing, 100193, People's Republic of China
| | - Olatunde Pelumi Oladele
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, People's Republic of China
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs of China, Beijing, 100193, People's Republic of China
| | - Yves N'Dri Bohoussou
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, People's Republic of China
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs of China, Beijing, 100193, People's Republic of China
| | - Yash Pal Dang
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, 4072, Australia
| | - Xin Zhao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, People's Republic of China
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs of China, Beijing, 100193, People's Republic of China
| | - Hai-Lin Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, People's Republic of China.
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs of China, Beijing, 100193, People's Republic of China.
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Ritzinger MG, Smith KP, Case AJ, Wodarek JR, Dill-Macky R, Curland RD, Steffenson BJ. Sources of Bacterial Leaf Streak Resistance Identified in a Diverse Collection of Barley Germplasm. PLANT DISEASE 2023; 107:802-808. [PMID: 35973078 DOI: 10.1094/pdis-04-22-0751-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacterial leaf streak (BLS) is a sporadic yet damaging disease of cereals that is growing in importance across the Upper Midwest production region. In barley (Hordeum vulgare ssp. vulgare), this disease is caused primarily by the bacterium Xanthomonas translucens pv. translucens. Accessions resistant to BLS have been reported in past studies, but few have been rigorously validated in the field. To identify accessions carrying diverse resistance alleles to BLS, a largescale germplasm screening study was undertaken against strain CIX95 of X. translucens pv. translucens in St. Paul and Crookston, Minnesota, in 2020 and 2021. The germplasm screened was diverse and included adapted breeding lines from two improvement programs, two landrace panels (one global and one from Ethiopia/Eritrea), introgression lines from wild barley (H. vulgare ssp. spontaneum) in the genetic background of barley cultivar 'Rasmusson', and an assemblage of accessions previously reported to carry BLS resistance. Of the 2,094 accessions evaluated in this study, 32 (1.5%) exhibited a consistently high level of resistance across locations and years and had heading dates similar to standard cultivars grown in the region. Accessions resistant to BLS were identified from all germplasm panels tested, providing genetically diverse sources for barley improvement programs focused on breeding for resistance to this important bacterial disease.
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Affiliation(s)
| | - Kevin P Smith
- Department of Agronomy, University of Minnesota, St. Paul, MN 55108
| | | | - Joseph R Wodarek
- Northwest Research and Outreach Center, University of Minnesota, Crookston, MN 56716
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
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Soil Mycobiome Diversity under Different Tillage Practices in the South of West Siberia. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081169. [PMID: 36013348 PMCID: PMC9409700 DOI: 10.3390/life12081169] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022]
Abstract
Managing soil biodiversity by reduced or no tillage is an increasingly popular approach. Soil mycobiome in Siberian agroecosystems has been scarcely studied; little is known about its changes due to tillage. We studied mycobiome in Chernozem under natural steppe vegetation and cropped for wheat by conventional or no tillage in a long-term field trial in West Siberia, Russia, by using ITS2 rDNA gene marker (Illumina MiSeq sequencing). Half of the identified OTUs were Ascomycota with 82% of the total number of sequence reads and showing, like other phyla (Basidiomycota, Zygomycota, Mortierellomycota, Chytridiomycota, Glomeromycota), field-related differential abundance. Several dominant genera (Mortierella, Chaetomium, Clonostachys, Gibberella, Fusarium, and Hypocrea) had increased abundance in both cropped soils as compared with the undisturbed one and therefore can be safely assumed to be associated with wheat residues. Fungal OTUs' richness in cropped soils was less than in the undisturbed one; however, no tillage shifted soil mycobiome composition closer to the latter, albeit, it was still similar to the ploughed soil, despite different organic matter and wheat residue content. The study provided the first inventory of soil mycobiome under different tillage treatments in the south of West Siberia, where wheat production is an important section of the regional economy.
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El Mujtar VA, Chirdo F, Lagares A, Wall L, Tittonell P. Soil bacterial biodiversity characterization by flow cytometry: The bottleneck of cell extraction from soil. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Verónica A. El Mujtar
- Agroecology, Environment and Systems Group, Instituto de Investigaciones Forestales y Agropecuarias de Bariloche (IFAB) INTA‐CONICET, San Carlos de Bariloche Río Negro Argentina
| | - Fernando Chirdo
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP)(UNLP‐CONICET), Facultad de Ciencias Exactas Universidad Nacional de La Plata La Plata Argentina
| | - Antonio Lagares
- IBBM—Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas Universidad Nacional de La Plata, CCT‐La Plata CONICET La Plata Argentina
| | - Luis Wall
- Laboratorio de Bioquímica y Microbiología de Suelo, Centro de Bioquímica y Microbiología de Suelos Universidad Nacional de Quilmes Bernal Argentina
| | - Pablo Tittonell
- Agroecology, Environment and Systems Group, Instituto de Investigaciones Forestales y Agropecuarias de Bariloche (IFAB) INTA‐CONICET, San Carlos de Bariloche Río Negro Argentina
- Groningen Institute of Evolutionary Life Sciences Groningen University Groningen The Netherlands
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Rivas GA, Guillade AC, Semorile LC, Delfederico L. Influence of Climate on Soil and Wine Bacterial Diversity on a Vineyard in a Non-traditional Wine Region in Argentina. Front Microbiol 2021; 12:726384. [PMID: 34475867 PMCID: PMC8406854 DOI: 10.3389/fmicb.2021.726384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 07/23/2021] [Indexed: 01/04/2023] Open
Abstract
Argentina is the fifth world-wide wine producer, with an area of emerging importance in the Southwest of Buenos Aires Province, where climatic conditions are rather challenging. We studied the variations in soil and wine bacterial diversity through three consecutive vintages, and how climatic conditions affected said diversity. During the years of our study there were two harsh climatic events, a prolonged drought that extended over two vegetative periods, and an unseasonable spring frost in 2017. We found that the bacterial diversity reacted to these climatic events, given that there was a shift in the taxa exclusive to soil and wine, and shared by both, through time. Our results show a core of microorganisms in soil as well as in wine, belonging to different phyla that are conserved across the vintage years. A trend to an enrichment in Actinobacteria was detected in soil samples, whereas a high relative abundance of the Acetobacteraceae family and a scarcity of Lactic Acid Bacteria (LAB) were detected in the wine samples. We believe our results contribute to a better understanding of the impact of climatic conditions on the soil and wine microbiota, and can provide vintners with valuable knowledge for improving their wine production.
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Affiliation(s)
- Gabriel A Rivas
- Laboratorio de Microbiología Molecular, Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes (UNQ), Bernal, Argentina.,National Scientific and Technical Research Council Argentina (CONICET), Bernal, Argentina
| | - Andrea C Guillade
- Laboratorio de Microbiología Molecular, Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes (UNQ), Bernal, Argentina
| | - Liliana C Semorile
- Laboratorio de Microbiología Molecular, Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes (UNQ), Bernal, Argentina
| | - Lucrecia Delfederico
- Laboratorio de Microbiología Molecular, Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes (UNQ), Bernal, Argentina
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Babin D, Leoni C, Neal AL, Sessitsch A, Smalla K. Editorial to the Thematic Topic "Towards a more sustainable agriculture through managing soil microbiomes". FEMS Microbiol Ecol 2021; 97:6321563. [PMID: 34263312 DOI: 10.1093/femsec/fiab094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 06/22/2021] [Indexed: 11/15/2022] Open
Affiliation(s)
- Doreen Babin
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Carolina Leoni
- Instituto Nacional de Investigación Agropecuaria (INIA), Programa de Producción y Sustentabilidad Ambiental, Estación Experimental INIA Las Brujas, Ruta 48 Km 10, 90200 Rincón del Colorado, Canelones, Uruguay
| | - Andrew L Neal
- Department of Sustainable Agriculture Sciences, Rothamsted Research, North Wyke, Devon EX20 2SB, United Kingdom
| | - Angela Sessitsch
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Bioresources Unit, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
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