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Shamshitov A, Kadžienė G, Supronienė S. The Role of Soil Microbial Consortia in Sustainable Cereal Crop Residue Management. PLANTS (BASEL, SWITZERLAND) 2024; 13:766. [PMID: 38592825 PMCID: PMC10974107 DOI: 10.3390/plants13060766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
The global escalation in cereal production, essential to meet growing population demands, simultaneously augments the generation of cereal crop residues, estimated annually at approximately 3107 × 106 Mg/year. Among different crop residue management approaches, returning them to the soil can be essential for various ecological benefits, including nutrient recycling and soil carbon sequestration. However, the recalcitrant characteristics of cereal crop residues pose significant challenges in their management, particularly in the decomposition rate. Therefore, in this review, we aim to summarize the influence of different agricultural practices on enhancing soil microbial decomposer communities, thereby effectively managing cereal crop residues. Moreover, this manuscript provides indirect estimates of cereal crop residue production in Northern Europe and Lithuania, and highlights the diverse roles of lignocellulolytic microorganisms in the decomposition process, with a particular focus on enzymatic activities. This review bridges the knowledge gap and indicates future research directions concerning the influence of agricultural practices on cereal crop residue-associated microbial consortia.
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Affiliation(s)
- Arman Shamshitov
- Laboratory of Microbiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Instituto al. 1, Akademija, LT-58344 Kedainiai, Lithuania;
| | - Gražina Kadžienė
- Department of Soil and Crop Management, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Instituto al. 1, Akademija, LT-58344 Kedainiai, Lithuania
| | - Skaidrė Supronienė
- Laboratory of Microbiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Instituto al. 1, Akademija, LT-58344 Kedainiai, Lithuania;
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García-Serquén AL, Chumbe-Nolasco LD, Navarrete AA, Girón-Aguilar RC, Gutiérrez-Reynoso DL. Traditional potato tillage systems in the Peruvian Andes impact bacterial diversity, evenness, community composition, and functions in soil microbiomes. Sci Rep 2024; 14:3963. [PMID: 38368478 PMCID: PMC10874408 DOI: 10.1038/s41598-024-54652-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/15/2024] [Indexed: 02/19/2024] Open
Abstract
The soil microbiome, a crucial component of agricultural ecosystems, plays a pivotal role in crop production and ecosystem functioning. However, its response to traditional tillage systems in potato cultivation in the Peruvian highlands is still far from understood. Here, ecological and functional aspects of the bacterial community were analyzed based on soil samples from two traditional tillage systems: 'chiwa' (minimal tillage) and 'barbecho' (full tillage), in the Huanuco region of the Peruvian central Andes. Similar soil bacterial community composition was shown for minimal tillage system, but it was heterogeneous for full tillage system. This soil bacterial community composition under full tillage system may be attributed to stochastic, and a more dynamic environment within this tillage system. 'Chiwa' and 'barbecho' soils harbored distinct bacterial genera into their communities, indicating their potential as bioindicators of traditional tillage effects. Functional analysis revealed common metabolic pathways in both tillage systems, with differences in anaerobic pathways in 'chiwa' and more diverse pathways in 'barbecho'. These findings open the possibilities to explore microbial bioindicators for minimal and full tillage systems, which are in relationship with healthy soil, and they can be used to propose adequate tillage systems for the sowing of potatoes in Peru.
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Affiliation(s)
- Aura L García-Serquén
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, 15024, Lima, Peru.
| | - Lenin D Chumbe-Nolasco
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, 15024, Lima, Peru
| | - Acacio Aparecido Navarrete
- Graduate Program in Environmental Sciences, Brazil University (UB), Estrada Projetada F1, Fazenda Santa Rita, Fernandópolis, São Paulo, 15613-899, Brazil
| | - R Carolina Girón-Aguilar
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, 15024, Lima, Peru
| | - Dina L Gutiérrez-Reynoso
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, 15024, Lima, Peru
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3
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Singh S, Singh S, Lukas SB, Machado S, Nouri A, Calderon F, Rieke ER, Cappellazzi SB. Long-term agro-management strategies shape soil bacterial community structure in dryland wheat systems. Sci Rep 2023; 13:13929. [PMID: 37626146 PMCID: PMC10457325 DOI: 10.1038/s41598-023-41216-z] [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: 08/28/2022] [Accepted: 08/23/2023] [Indexed: 08/27/2023] Open
Abstract
Soil microbes play a crucial role in soil organic matter decomposition and nutrient cycling and are influenced by management practices. Therefore, quantifying the impacts of various agricultural management practices on soil microbiomes and their activity is crucial for making informed management decisions. This study aimed to assess the impact of various management systems on soil bacterial abundance and diversity, soil enzyme activities and carbon mineralization potential in wheat-based systems. To accomplish this, soil samples from 0 to 15 cm depth were collected from ongoing long-term field trials in eastern Oregon region under wheat (Triticum aestivum L.)-fallow (WF), WF with different tillage (WT), wheat-pea (Pisum sativum L.) (WP), WF under different crop residue management (CR) and natural undisturbed/unmanaged grassland pasture (GP). These trials consisted of an array of treatments like tillage intensities, nitrogen rates, organic amendments, and seasonal residue burning. This study was a part of the Soil Health Institute's North American Project to Evaluate Soil Health measurements (NAPESHM). Bacterial community structure was determined using amplicon sequencing of the V4 region of 16SrRNA genes and followed the protocols of the Earth Microbiome Project. In addition, extracellular enzyme activities, and carbon mineralization potential (1d-CO2) were measured. Among different trials, 1d-CO2 in WT, WP, and CR studies averaged 53%, 51% and 87% lower than GP systems, respectively. Enzyme activities were significantly greater in GP compared to the other managements and followed similar trend as respiration. We observed higher evenness in GP and higher richness in spring residue burning treatment of CR study. Our results indicated that species evenness is perhaps a better indicator of soil health in comparison to other indices in dryland wheat systems.
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Affiliation(s)
- Shikha Singh
- Hermiston Agricultural Research and Extension Center, Oregon State University, 2121 S 1St, Hermiston, OR, 97838, USA
| | - Surendra Singh
- Columbia Basin Agricultural Research Center, Oregon State University, 48037 Tubbs Ranch Rd., Adams, OR, 97810, USA
| | - Scott B Lukas
- Hermiston Agricultural Research and Extension Center, Oregon State University, 2121 S 1St, Hermiston, OR, 97838, USA.
| | - Stephen Machado
- Columbia Basin Agricultural Research Center, Oregon State University, 48037 Tubbs Ranch Rd., Adams, OR, 97810, USA
| | - Amin Nouri
- Hermiston Agricultural Research and Extension Center, Oregon State University, 2121 S 1St, Hermiston, OR, 97838, USA
| | - Francisco Calderon
- Columbia Basin Agricultural Research Center, Oregon State University, 48037 Tubbs Ranch Rd., Adams, OR, 97810, USA
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Srivastava A, Verma D. Urbanization led to the abundance of Gram-negative, chemo-organo-heterotrophs, and antibiotic resistance genes in the downstream regions of the Ganga River water of India. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27552-7. [PMID: 37217817 DOI: 10.1007/s11356-023-27552-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/07/2023] [Indexed: 05/24/2023]
Abstract
The present investigation assesses the bacterial microbiome and antibiotic resistance genes (ARGs) of the river Ganga from Uttarakhand (upstream region; US group) and Uttar Pradesh (downstream region; DS group) regions using a 16S rRNA amplicon-based metagenomic approach. Gram-negative, aerobic, and chemo-organotrophic bacteria made up the majority of the bacterial genera during the overall analysis. Physicochemical analysis revealed a higher concentration of nitrate and phosphate in the downstream sites of the Ganga River. The prevalence of Gemmatimonas, Flavobacterium, Arenimonas, and Verrucomicrobia in the water of the DS region indicates a high organic load. Pseudomonas and Flavobacterium emerged as the most prevalent genera among the 35 significantly different shared genera (p-value < 0.05) in the US and DS regions, respectively. Overall antibiotic resistance analysis of the samples showed the dominance of β-lactam resistance (33.92%) followed by CAMP (cationic antimicrobial peptide) resistance (27.75%), and multidrug resistance (19.17%), vancomycin resistance (17.84%), and tetracycline resistance (0.77%). While comparing, the DS group exhibited a higher abundance of ARGs over the US group, where the CAMP resistance and β-lactam ARGs were dominant in the respective regions. The correlation (p-value < 0.05) analysis showed that most bacteria exhibit a significant correlation with tetracycline resistance followed by the phenicol antibiotic. The present findings draw attention to the need for regulated disposal of multiform human-derived wastes into the Ganga River to reduce the irrepressible ARGs dissemination.
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Affiliation(s)
- Ankita Srivastava
- Department of Environmental Microbiology, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India
| | - Digvijay Verma
- Department of Environmental Microbiology, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India.
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Kumar M, Ansari WA, Zeyad MT, Singh A, Chakdar H, Kumar A, Farooqi MS, Sharma A, Srivastava S, Srivastava AK. Core microbiota of wheat rhizosphere under Upper Indo-Gangetic plains and their response to soil physicochemical properties. FRONTIERS IN PLANT SCIENCE 2023; 14:1186162. [PMID: 37255554 PMCID: PMC10226189 DOI: 10.3389/fpls.2023.1186162] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/21/2023] [Indexed: 06/01/2023]
Abstract
Wheat is widely cultivated in the Indo-Gangetic plains of India and forms the major staple food in the region. Understanding microbial community structure in wheat rhizosphere along the Indo-Gangetic plain and their association with soil properties can be an important base for developing strategies for microbial formulations. In the present study, an attempt was made to identify the core microbiota of wheat rhizosphere through a culture-independent approach. Rhizospheric soil samples were collected from 20 different sites along the upper Indo-Gangetic plains and their bacterial community composition was analyzed based on sequencing of the V3-V4 region of the 16S rRNA gene. Diversity analysis has shown significant variation in bacterial diversity among the sites. The taxonomic profile identified Proteobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes, Planctomycetes, Verrucomicrobia, Firmicutes, and Cyanobacteria as the most dominant phyla in the wheat rhizosphere in the region. Core microbiota analysis revealed 188 taxa as core microbiota of wheat rhizosphere with eight genera recording more than 0.5% relative abundance. The order of most abundant genera in the core microbiota is Roseiflexus> Flavobacterium> Gemmatimonas> Haliangium> Iamia> Flavisolibacter> Ohtaekwangia> Herpetosiphon. Flavobacterium, Thermomonas, Massilia, Unclassified Rhizobiaceae, and Unclassified Crenarchaeota were identified as keystone taxa of the wheat rhizosphere. Correlation studies revealed, pH, organic carbon content, and contents of available nitrogen, phosphorus, and iron as the major factors driving bacterial diversity in the wheat rhizosphere. Redundancy analysis has shown the impact of different soil properties on the relative abundance of different genera of the core microbiota. The results of the present study can be used as a prelude to be developing microbial formulations based on core microbiota.
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Affiliation(s)
- Murugan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | - Waquar Akhter Ansari
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | - Mohammad Tarique Zeyad
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | - Arjun Singh
- ICAR-Central Soil Salinity Research Institute, Regional Research Station (RRS), Lucknow, Uttar Pradesh, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | - Adarsh Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
| | | | - Anu Sharma
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sudhir Srivastava
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Alok Kumar Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India
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Rugeles-Silva PA, Londoño JA, Sánchez de Prager M, Muñoz Flórez JE, López-Álvarez D. Soil Bacterial Communities from Three Agricultural Production Systems in Rural Landscapes of Palmira, Colombia. BIOLOGY 2023; 12:biology12050701. [PMID: 37237514 DOI: 10.3390/biology12050701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023]
Abstract
Soils play important roles in the proper functioning of agroecosystems. Using molecular characterization methods such as metabarcoding, soils from eight farms (57 samples) belonging to three production system types-agroecological (two farms with twenty-two sampling points), organic (three farms with twenty-one sampling points), and conventional (three farms with fourteen sampling points)-were compared from the rural villages of El Arenillo and El Mesón in Palmira, Colombia. Amplification and sequencing of the hypervariable V4 region of the 16S rRNA gene was performed using next-generation sequencing (Illumina MiSeq) to estimate the bacterial composition and the alpha and beta diversity present. Across all soil samples, we found 2 domains (Archaea and Bacteria), 56 phylum, 190 classes, 386 orders, 632 families, and 1101 genera to be present. The most abundant phyla in the three systems were Proteobacteria, (agroecological 28%, organic 30%, and conventional 27%), Acidobacteria (agroecological 22%, organic 21%, and conventional 24%), and Verrucomicrobia (agroecological 10%, organic 6%, and conventional 13%). We found 41 nitrogen-fixing and phosphate-dissolving genera which promote growth and pathogens. Alpha and beta diversity indices were very similar across the three agricultural production systems, as reflected by shared amplicon sequence variants (ASVs) among them, likely due to the proximity of the sampling sites and recent management changes.
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Affiliation(s)
- Paula Andrea Rugeles-Silva
- Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Palmira 763533, Colombia
| | - Jairo Andrés Londoño
- Sección de Identidades Digitales, Universidad Nacional de Colombia, Palmira 763533, Colombia
| | - Marina Sánchez de Prager
- Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Palmira 763533, Colombia
| | - Jaime Eduardo Muñoz Flórez
- Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Palmira 763533, Colombia
| | - Diana López-Álvarez
- Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Palmira 763533, Colombia
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Genomic microbiome analyses of surface sand samples from the Kyzyl-Kum Desert (Uzbekistan): characterization and comparative study. Arch Microbiol 2023; 205:90. [PMID: 36780035 DOI: 10.1007/s00203-023-03432-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 02/02/2023] [Indexed: 02/14/2023]
Abstract
The Kyzyl-Kum Desert extends over an area of 300,000 Km2, in the region bordering Kazakhstan, Uzbekistan and Turkmenistan and is mainly covered by sand dunes. The Kyzyl-Kum desert is also known for its large deposits of minerals of economic interests, the exploitation of which is affecting the local ecosystem and increasing the desertification. We examined the bacterial biodiversity of surface sand samples from several sites from the Kyzyl-Kum desert using pyrosequencing of PCR amplified bacterial 16S rRNA genes from total extracted soil DNA. We also examined several physicochemical parameters of the sand samples to investigate any possible correlations between bacterial community structure and environmental drivers. The predominant bacterial phyla present in the samples were found to belong to members of the Actinobacteria, Proteobacteria and Bacteroidetes. The most abundant genera in our samples were found to belong to the Arthrobacter, Adhaeribacter and Roseomonas genera. We found that the relative abundance of members belonging to the Actinobacteria phylum, commonly found in desertic areas, increase in abundance in sites with higher content of organic matter and sulfur, whereas members of the Proteobacteria and Bacteroidetes phyla seems to diminish in abundance in coarse silt and fine-grained soils and those rich in magnesium, suggesting that those parameters might influence the bacterial community composition in this desertic area. This study is the first to provide new insights into the prokaryotic community composition from this unusual desert site.
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King WL, Richards SC, Kaminsky LM, Bradley BA, Kaye JP, Bell TH. Leveraging microbiome rediversification for the ecological rescue of soil function. ENVIRONMENTAL MICROBIOME 2023; 18:7. [PMID: 36691096 PMCID: PMC9872425 DOI: 10.1186/s40793-023-00462-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Global biodiversity losses threaten ecosystem services and can impact important functional insurance in a changing world. Microbial diversity and function can become depleted in agricultural systems and attempts to rediversify agricultural soils rely on either targeted microbial introductions or retaining natural lands as biodiversity reservoirs. As many soil functions are provided by a combination of microbial taxa, rather than outsized impacts by single taxa, such functions may benefit more from diverse microbiome additions than additions of individual commercial strains. In this study, we measured the impact of soil microbial diversity loss and rediversification (i.e. rescue) on nitrification by quantifying ammonium and nitrate pools. We manipulated microbial assemblages in two distinct soil types, an agricultural and a forest soil, with a dilution-to-extinction approach and performed a microbiome rediversification experiment by re-introducing microorganisms lost from the dilution. A microbiome water control was included to act as a reference point. We assessed disruption and potential restoration of (1) nitrification, (2) bacterial and fungal composition through 16S rRNA gene and fungal ITS amplicon sequencing and (3) functional genes through shotgun metagenomic sequencing on a subset of samples. RESULTS Disruption of nitrification corresponded with diversity loss, but nitrification was successfully rescued in the rediversification experiment when high diversity inocula were introduced. Bacterial composition clustered into groups based on high and low diversity inocula. Metagenomic data showed that genes responsible for the conversion of nitrite to nitrate and taxa associated with nitrogen metabolism were absent in the low diversity inocula microcosms but were rescued with high diversity introductions. CONCLUSIONS In contrast to some previous work, our data suggest that soil functions can be rescued by diverse microbiome additions, but that the concentration of the microbial inoculum is important. By understanding how microbial rediversification impacts soil microbiome performance, we can further our toolkit for microbial management in human-controlled systems in order to restore depleted microbial functions.
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Affiliation(s)
- William L King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, 317 Buckhout Lab, University Park, PA, 16802, USA
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Sarah C Richards
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, 317 Buckhout Lab, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Laura M Kaminsky
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, 317 Buckhout Lab, University Park, PA, 16802, USA
| | - Brosi A Bradley
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jason P Kaye
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, 317 Buckhout Lab, University Park, PA, 16802, USA.
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, PA, 16802, USA.
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Du M, Zhang J, Wang G, Liu C, Wang Z. Response of bacterial community composition and co-occurrence network to straw and straw biochar incorporation. Front Microbiol 2022; 13:999399. [PMID: 36246223 PMCID: PMC9563622 DOI: 10.3389/fmicb.2022.999399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/30/2022] [Indexed: 11/22/2022] Open
Abstract
Microbial decomposition plays a crucial role in the incorporation of straw and straw biochar (SSB) into soil. Lime concretion black soil (LCBS) is a typical low-medium crop yield soil, and it is also one of the main soil types for grain production in China. However, the link between SSB additions and soil bacterial communities in LCBS remains unclear. This study explored the effects of SSB incorporation on bacterial community composition, structure and co-occurrence network patterns at different soil depths and maize growth stages. The results showed that soil PH, soil organic matter and total nitrogen significantly affected the seasonality and stratification of the soil bacterial community. The composition and diversity of bacterial communities were significantly affected by growth period and treatment rather than soil depth. Specifically, the bacterial community diversity increased significantly with crop growth at 0–20 cm, decreased the relative abundance of Actinobacteria, and increased the relative abundance of Proteobacteria and Acidobacteria. SF (straw with fertilizer) and BF (straw biochar with fertilizer) treatments decreased bacterial community diversity. Co-occurrence networks are more complex in BF, S (straw), and SF treatments, and the number of edge network patterns is increased by 92.5, 40, and 60% at the maturity stage compared with F (fertilizer) treatment, respectively. Moreover, the positive effect of straw biochar on the bacterial network pattern increased with time, while the effect of straw weakened. Notably, we found that rare species inside keystone taxa (Gemmatimonadetes and Nitrospirae) play an indispensable role in maintaining bacterial network construction in LCBS. This study offers a comprehensive understanding of the response of soil bacterial communities to SSB addition in LCBS areas, and provides a reference for further improvement of LCBS productivity.
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Affiliation(s)
- Mingcheng Du
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, China
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing, China
- Yangtze Institute for Conservation and Development, Nanjing, China
- Research Center for Climate Change, Nanjing, China
| | - Jianyun Zhang
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, China
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing, China
- Yangtze Institute for Conservation and Development, Nanjing, China
- Research Center for Climate Change, Nanjing, China
| | - Guoqing Wang
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing, China
- Yangtze Institute for Conservation and Development, Nanjing, China
- Research Center for Climate Change, Nanjing, China
- *Correspondence: Guoqing Wang,
| | - Cuishan Liu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing, China
- Yangtze Institute for Conservation and Development, Nanjing, China
- Research Center for Climate Change, Nanjing, China
| | - Zhenlong Wang
- Wudaogou Experimental Station for Hydrology and Water Resources, Bengbu, China
- Anhui Hydraulic Research Institute, Huai River Commission, Bengbu, China
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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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Dong M, Wang B, Tian Y, Chen L, Li Y, Sun H. Diversity of fungal assemblages in rhizosphere and endosphere of blueberry (Vaccinium spp.) under field conditions revealed by culturing and culture-independent molecular methods. Can J Microbiol 2022; 68:622-632. [PMID: 35926235 DOI: 10.1139/cjm-2022-0093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mycorrhizae are important to plants in improving nutrient absorption and stress resistance. To study mycorrhizal fungal diversity in blueberry, we combined culture method and culture-independent molecular method to analyze the root endosphere and rhizosphere fungi in three different cultivars. We obtained 212 isolates with a culture method and classified them into 40 types according to their morphological characteristics. Then, we amplified the internal transcribed spacer (ITS) sequence and found rich species diversity. With high-throughput sequencing, 561 operational taxonomic units (OTUs) were annotated based on a 97% similarity level cutoff. The alpha diversity index revealed that the fungal abundance and diversity in the rhizosphere were higher than in the endosphere. The dominant phyla were Ascomycota and Basidiomycota and the dominant genus was Oidiodendron. We also constructed the plant-fungus symbiotic system by inoculating in vitro stock shoots, which lays a theoretical foundation for further research to develop and utilize the dominant mycorrhizal fungi of blueberry.
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Affiliation(s)
- Mei Dong
- Jilin Agricultural University, 85112, Changchun, Jilin, China;
| | - Bowei Wang
- Jilin Agricultural University, 85112, Changchun, Jilin, China;
| | - Youwen Tian
- Jilin Agricultural University, 85112, Changchun, Jilin, China;
| | - Li Chen
- Jilin Agricultural University, 85112, Changchun, Jilin, China;
| | - Yadong Li
- Jilin Agricultural University, 85112, Changchun, Jilin, China;
| | - Haiyue Sun
- Jilin Agricultural University, 85112, Changchun, China;
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(Meta)Genomic Analysis Reveals Diverse Energy Conservation Strategies Employed by Globally Distributed Gemmatimonadota. mSystems 2022; 7:e0022822. [PMID: 35913193 PMCID: PMC9426454 DOI: 10.1128/msystems.00228-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Gemmatimonadota is a phylum-level lineage distributed widely but rarely reported. Only six representatives of Gemmatimonadota have so far been isolated and cultured in laboratory. The physiology, ecology, and evolutionary history of this phylum remain unknown. The 16S rRNA gene survey of our salt lake and deep-sea sediments, and Earth Microbiome Project (EMP) samples, reveals that Gemmatimonadota exist in diverse environments globally. In this study, we retrieved 17 metagenome-assembled genomes (MAGs) from salt lake sediments (12 MAGs) and deep-sea sediments (5 MAGs). Analysis of these MAGs and the nonredundant MAGs or genomes from public databases reveals Gemmatimonadota can degrade various complex organic substrates, and mainly employ heterotrophic pathways (e.g., glycolysis and tricarboxylic acid [TCA] cycle) for growth via aerobic respiration. And the processes of sufficient energy being stored in glucose through gluconeogenesis, followed by the synthesis of more complex compounds, are prevalent in Gemmatimonadota. A highly expandable pangenome for Gemmatimonadota has been observed, which presumably results from their adaptation to thriving in diverse environments. The enrichment of the Na+/H+ antiporter in the SG8-23 order represents their adaptation to salty habitats. Notably, we identified a novel lineage of the SG8-23 order, which is potentially anoxygenic phototrophic. This lineage is not closely related to the phototrophs in the order of Gemmatimonadales. The two orders differ distinctly in the gene organization and phylogenetic relationship of their photosynthesis gene clusters, indicating photosystems in Gemmatimonadota have evolved in two independent routes. IMPORTANCE The phylum Gemmatimonadota is widely distributed in various environments. However, their physiology, ecology and evolutionary history remain unknown, primary due to the limited cultured isolates and available genomes. We were intrigued to find out how widespread this phylum is, and how it can thrive under diverse conditions. Our results here expand the knowledge of the genetic and metabolic diversity of Gemmatimonadota, and shed light on the diverse energy conservation strategies (i.e., oxidative phosphorylation, substrate phosphorylation, and photosynthetic phosphorylation) responsible for their global distribution. Moreover, gene organization and phylogenetic analysis of photosynthesis gene clusters in Gemmatimonadota provide a valuable insight into the evolutionary history of photosynthesis.
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Li X, Chu C, Ding S, Wei H, Wu S, Xie B. Insight into how fertilization strategies increase quality of grape (Kyoho) and shift microbial community. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:27182-27194. [PMID: 34978035 DOI: 10.1007/s11356-021-17759-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Organic and bioorganic fertilizers were increasingly used for agricultural soil. However, little is known on what kind of organic fertilizer application strategies can promote grape production well and how appropriate fertilization strategies improve soil properties and shift microbial community. This study investigated the improvement in soil physicochemical properties as well as their relations with microbial community structure and grape quality under different fertilization strategies. Our results found that (bio)organic fertilizer (CF1, CF2, and BF) especially combined application of organic and bioorganic fertilization (CBF) had smaller effects on electrical conductivity (EC) and pH, while it improved soil nutrients including N, P, K, and organic matter (OM) well, thereby promoting the grape quality comparing to the group without any fertilizer (CK) and with chemical fertilizer (NPK). Especially, the concentrations of Cr, Hg, Zn, and Cu were reduced by 13.63%, 12.50%, 12.52%, and 11.75% in CBF, respectively. Additionally, CF1, CF2, and BF, especially CBF, optimized the communities' composition and increased the abundance of some plant probiotics such as Solirubrobacter and Lysobacter. Nevertheless, excessive application of organic fertilizer derived from livestock manure could cause the accumulation of heavy metals such as Zn and Cu in soil and leaves, which could further influence the grape quality. Additionally, the structure of microbial communities was also changed possibly because some bacterial genera showed distinct adaptability to the stress of heavy metals or the utilization capacity of N, P, K, and OM. Our results demonstrated that combined application of organic and bioorganic fertilization showed a great influence on soil physicochemical properties, whose positive changes could further optimize microbial communities and facilitate the promotion of grape quality.
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Affiliation(s)
- Xunan Li
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai, 200241, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Changbin Chu
- Eco-Environmental Protection Institute of Shanghai Academy of Agricultural Science, Shanghai, 201403, China
| | - Sheng Ding
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai, 200241, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Huawei Wei
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai, 200241, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Shuhang Wu
- Eco-Environmental Protection Institute of Shanghai Academy of Agricultural Science, Shanghai, 201403, China.
| | - Bing Xie
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai, 200241, China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
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Bacterial Communities in the Rhizosphere at Different Growth Stages of Maize Cultivated in Soil Under Conventional and Conservation Agricultural Practices. Microbiol Spectr 2022; 10:e0183421. [PMID: 35254138 PMCID: PMC9049951 DOI: 10.1128/spectrum.01834-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Farmers in Mexico till soil intensively, remove crop residues for fodder and grow maize often in monoculture. Conservation agriculture (CA), including minimal tillage, crop residue retention and crop diversification, is proposed as a more sustainable alternative. In this study, we determined the effect of agricultural practices and the developing maize rhizosphere on soil bacterial communities. Bulk and maize (Zea mays L.) rhizosphere soil under conventional practices (CP) and CA were sampled during the vegetative, flowering and grain filling stage, and 16S rRNA metabarcoding was used to assess bacterial diversity and community structure. The functional diversity was inferred from the bacterial taxa using PICRUSt. Conservation agriculture positively affected taxonomic and functional diversity compared to CP. The agricultural practice was the most important factor in defining the structure of bacterial communities, even more so than rhizosphere and plant growth stage. The rhizosphere enriched fast growing copiotrophic bacteria, such as Rhizobiales, Sphingomonadales, Xanthomonadales, and Burkholderiales, while in the bulk soil of CP other copiotrophs were enriched, e.g., Halomonas and Bacillus. The bacterial community in the maize bulk soil resembled each other more than in the rhizosphere of CA and CP. The bacterial community structure, and taxonomic and functional diversity in the maize rhizosphere changed with maize development and the differences between the bulk soil and the rhizosphere were more accentuated when the plant aged. Although agricultural practices did not alter the effect of the rhizosphere on the soil bacterial communities in the flowering and grain filling stage, they did in the vegetative stage. IMPORTANCE We studied the effect of sustainable conservation agricultural practices versus intensive conventional ones on the soil microbial diversity, potential functionality, and community assembly in rhizosphere of maize cultivated in a semiarid environment. We found that conservation agriculture practices increased the diversity of soil microbial species and functions and strongly affected how they were structured compared to conventional practices. Microbes affected by the roots of maize, the rhizobiome, were different and more diverse than in the surrounding soil and their diversity increased when the plant grew. The agricultural practices affected the maize rhizobiome only in the early stages of growth, but this might have an important impact on the development of maize plant.
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Govindarajan A, Crum M, Adolacion J, Kiaghadi A, Acuña-Gonzalez E, Rifai HS, Willson RC. Sediment and their bacterial communities in an industrialized estuary after Hurricane Harvey. MARINE POLLUTION BULLETIN 2022; 175:113359. [PMID: 35124375 DOI: 10.1016/j.marpolbul.2022.113359] [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: 08/29/2021] [Revised: 12/26/2021] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Estuaries experience variable physicochemical conditions, especially after hurricanes and due to anthropogenic sources of pollution. Their microbial communities are not as well understood in terms of community structure and diversity, particularly in response to stresses from pollution and severe events. This study presents a 16S rRNA-based description of sediment microbial communities in the Houston Ship Channel-Galveston Bay estuary after Hurricane Harvey in 2017. A total of 11 sites were sampled, and microbial genomic DNA was isolated from sediment. The presence and abundance of specific bacterial and archaeal taxa in the sediment indicated pollutant inputs from identified legacy sources. The abundance of certain microbial groups was explained by the mobilization of contaminated sediment and sediment transport due to Harvey. Several microorganisms involved in the biodegradation of xenobiotics were observed. The spatial occurrence of Dehalococcoidia, a degrader of persistent polychlorinated compounds, was explained in relation to sediment properties and contaminant concentrations.
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Affiliation(s)
| | - Mary Crum
- Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Jay Adolacion
- School of Engineering and Science, Tecnológico de Monterrey, Monterrey, Mexico
| | - Amin Kiaghadi
- Civil and Environmental Engineering, University of Houston, Houston, TX, USA
| | - Edgar Acuña-Gonzalez
- School of Medicine and Health Sciences, Tecnológico de Monterrey, Monterrey, Mexico
| | - Hanadi S Rifai
- Civil and Environmental Engineering, University of Houston, Houston, TX, USA.
| | - Richard C Willson
- Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
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16
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Bonomo MG, Calabrone L, Scrano L, Bufo SA, Di Tomaso K, Buongarzone E, Salzano G. Metagenomic monitoring of soil bacterial community after the construction of a crude oil flowline. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:48. [PMID: 34978609 PMCID: PMC8724107 DOI: 10.1007/s10661-021-09637-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/20/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to assess the metagenomic changes of soil bacterial community after constructing a crude oil flowline in Basilicata region, Italy. Soils identified a total of 56 taxa at the phylum level and 485 at the family level, with a different taxa distribution, especially in samples collected on 2014. Since microbiological diversity occurred in the soils collected after 2013 (the reference year), we performed a differential abundance analysis using DESeq2 by GAIA pipeline. In the forest area, 14 phyla and 126 families were differentially abundant (- 6.06 < logFC > 7.88) in 2014 compared to 2013. Nine families were differentially abundant in 2015, with logFC between - 3.16 and 4.66, while 20 families were significantly more abundant and 16 less abundant in 2016, with logFC between - 6.48 and 6.45. In the cultivated area, 33 phyla and 260 families showed differential abundance in 2014. In the next year (2015), 14 phyla were significantly more abundant and 19 less abundant, while 29 families were substantially more abundant and 139 less abundant, with fold changes ranging between - 5.67 and 4.01. In 2016, 33 phyla showed a significantly different abundance, as 14 were more abundant and 19 decreased, and 81 families showed a significantly increased amount with logFC between - 5.31 and 5.38. These results hypothesise that the analysed site is an altered soil where the development of particular bacterial groups attends to bioremediation processes, naturally occurring to restore optimal conditions.
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Affiliation(s)
| | - Luana Calabrone
- Department of Sciences, University of Basilicata, Potenza, Italy
| | - Laura Scrano
- Department of European Cultures, University of Basilicata, Potenza, Italy
| | - Sabino Aurelio Bufo
- Department of Sciences, University of Basilicata, Potenza, Italy
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, Johannesburg, South Africa
| | - Katia Di Tomaso
- Department of Sciences, University of Basilicata, Potenza, Italy
| | | | - Giovanni Salzano
- Department of Sciences, University of Basilicata, Potenza, Italy
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17
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Gómez-Godínez LJ, Martínez-Romero E, Banuelos J, Arteaga-Garibay RI. Tools and challenges to exploit microbial communities in agriculture. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100062. [PMID: 34841352 PMCID: PMC8610360 DOI: 10.1016/j.crmicr.2021.100062] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022] Open
Abstract
Plants contain diverse microbial communities. The associated microorganisms confer advantages to the host plant, which include growth promotion, nutrient absorption, stress tolerance, and pathogen and disease resistance. In this review, we explore how agriculture is implementing the use of microbial inoculants (single species or consortia) to improve crop yields, and discuss current strategies to study plant-associated microorganisms and how their diversity varies under unconventional agriculture. It is predicted that microbial inoculation will continue to be used in agriculture.
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Affiliation(s)
- Lorena Jacqueline Gómez-Godínez
- Laboratorio de Recursos Genéticos Microbianos, Centro Nacional de Recursos Genéticos. Instituto Nacional de Investigación Forestales, Agrícolas y Pecuarios. Boulevard de la Biodiversidad 400, Rancho las Cruces, C.P. 47600. Tepatitlán de Morelos, Jalisco, México
| | - Esperanza Martínez-Romero
- Centro de Ciencias genómicas, Universidad Nacional Autónoma de México Campus Morelos, Cuernavaca, Morelos México
| | - Jacob Banuelos
- Laboratorio de Organismos Benéficos, Facultad de Ciencias Agrícolas, Universidad Veracruzana. Circuito Aguirre Beltrán SN, Col. Universitaria, CP 91000, Xalapa, Veracruz, México
| | - Ramón I. Arteaga-Garibay
- Laboratorio de Recursos Genéticos Microbianos, Centro Nacional de Recursos Genéticos. Instituto Nacional de Investigación Forestales, Agrícolas y Pecuarios. Boulevard de la Biodiversidad 400, Rancho las Cruces, C.P. 47600. Tepatitlán de Morelos, Jalisco, México
- Corresponding authors.
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18
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Li W, Jiang L, Zhang Y, Teng D, Wang H, Wang J, Lv G. Structure and driving factors of the soil microbial community associated with Alhagi sparsifolia in an arid desert. PLoS One 2021; 16:e0254065. [PMID: 34242272 PMCID: PMC8270470 DOI: 10.1371/journal.pone.0254065] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/21/2021] [Indexed: 11/19/2022] Open
Abstract
Environmental properties are important factors in structuring soil microbial communities. The primary driving factors vary in different ecosystems. In the present work, we analyzed the microbial communities of rhizosphere and bulk soils associated with the halophyte Alhagi sparsifolia across three salt/water gradients in the desert area around Ebinur Lake Basin, China, using high-throughput sequencing technology. We found that there were significant differences in soil water content (SWC), soil salinity (SAL), total nitrogen (TN), and total phosphorus (TP) contents between the three water/salt gradients. In the L (low water and salt) plot, Actinobacteria was the most abundant bacterial phylum while Ascomycota was the dominant fungal phylum. The relative abundance of Actinobacteria was negatively correlated with soil pH, soil organic carbon (SOC), TP, and available phosphorus (AP). The abundance of Bacteroidetes was significantly positively correlated with soil SOC, SWC, SAL, pH, TN, and TP (P < 0.05). The abundance of fungal phylum Chytridiomycota was significantly positively correlated with pH (P < 0.01), SWC, AP, and sulfate ion (P < 0.05). SOC and nitrate nitrogen were the main factors impacting the bacterial community, while ammonium nitrogen (NH4+) and TP were the main driving forces for the fungal community. Soil nutrients were the main contributors to the dissimilarities in the bacterial and fungal communities, explaining 48.06% and 44.45% of the variation. SWC, SAL, and pH explained only a small percentage of the microbial community dissimilarity. In conclusion, soil microbial community structure was affected by SWC, SAL, pH, and soil nutrients, with soil nutrients as the main driving factors. Nitrogen has a differential effect on the different microbial communities: bacterial communities of Alhagi sparsifolia were mainly affected by nitrate nitrogen, while fungal communities were mainly driven by ammonium nitrogen.
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Affiliation(s)
- Wenjing Li
- College of Resources and Environment Science, Xinjiang University, Urumqi, China
| | - Lamei Jiang
- College of Resources and Environment Science, Xinjiang University, Urumqi, China
| | - Yang Zhang
- College of Resources and Environment Science, Xinjiang University, Urumqi, China
| | - Dexiong Teng
- College of Resources and Environment Science, Xinjiang University, Urumqi, China
| | - Hengfang Wang
- College of Resources and Environment Science, Xinjiang University, Urumqi, China
| | - Jinlong Wang
- College of Resources and Environment Science, Xinjiang University, Urumqi, China
| | - Guanghui Lv
- College of Resources and Environment Science, Xinjiang University, Urumqi, China
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Shan J, Sanford RA, Chee-Sanford J, Ooi SK, Löffler FE, Konstantinidis KT, Yang WH. Beyond denitrification: The role of microbial diversity in controlling nitrous oxide reduction and soil nitrous oxide emissions. GLOBAL CHANGE BIOLOGY 2021; 27:2669-2683. [PMID: 33547715 DOI: 10.1111/gcb.15545] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/11/2021] [Indexed: 05/02/2023]
Abstract
Many biotic and abiotic processes contribute to nitrous oxide (N2 O) production in the biosphere, but N2 O consumption in the environment has heretofore been attributed primarily to canonical denitrifying microorganisms. The nosZ genes encoding the N2 O reductase enzyme, NosZ, responsible for N2 O reduction to dinitrogen are now known to include two distinct groups: the well-studied Clade I which denitrifiers typically possess, and the novel Clade II possessed by diverse groups of microorganisms, most of which are non-denitrifiers. Clade II N2 O reducers could play an important, previously unrecognized role in controlling N2 O emissions for several reasons, including: (1) the consumption of N2 O produced by processes other than denitrification, (2) hypothesized non-respiratory functions of NosZ as an electron sink or for N2 O detoxification, (3) possible differing enzyme kinetics of Clade II NosZ compared to Clade I NosZ, and (4) greater nosZ gene abundance for Clade II compared to Clade I in soils of many ecosystems. Despite the potential ecological significance of Clade II NosZ, a census of 800 peer-reviewed original research articles discussing nosZ and published from 2013 to 2019 showed that the percentage of articles evaluating or mentioning Clade II nosZ increased from 5% in 2013 to only 22% in 2019. The census revealed that the slowly spreading awareness of Clade II nosZ may result in part from disciplinary silos, with the percentage of nosZ articles mentioning Clade II nosZ ranging from 0% in Agriculture and Agronomy journals to 32% in Multidisciplinary Sciences journals. In addition, inconsistent nomenclature for Clade I nosZ and Clade II nosZ, with 17 different terminologies used in the literature, may have created confusion about the two distinct groups of N2 O reducers. We provide recommendations to accelerate advances in understanding the role of the diversity of N2 O reducers in regulating soil N2 O emissions.
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Affiliation(s)
- Jun Shan
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Robert A Sanford
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Joanne Chee-Sanford
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture - Agricultural Research Station,, Urbana, IL, USA
| | - Sean K Ooi
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Frank E Löffler
- Center for Environmental Biotechnology, Department of Microbiology, Department of Civil and Environmental Engineering, Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wendy H Yang
- Departments of Plant Biology and Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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20
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Gabbarini LA, Figuerola E, Frene JP, Robledo NB, Ibarbalz FM, Babin D, Smalla K, Erijman L, Wall LG. Impacts of switching tillage to no-tillage and vice versa on soil structure, enzyme activities and prokaryotic community profiles in Argentinean semi-arid soils. FEMS Microbiol Ecol 2021; 97:6133470. [PMID: 33571359 DOI: 10.1093/femsec/fiab025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 02/09/2021] [Indexed: 12/19/2022] Open
Abstract
The effects of tillage on soil structure, physiology and microbiota structure were studied in a long-term field experiment, with side-to-side plots, established to compare effects of conventional tillage (CT) vs no-till (NT) agriculture. After 27 years, part of the field under CT was switched to NT and vice versa. Soil texture, soil enzymatic profiles and the prokaryotic community structure (16S rRNA genes amplicon sequencing) were analyzed at two soil depths (0-5 and 5-10 cm) in samples taken 6, 18 and 30 months after switching tillage practices. Soil enzymatic activities were higher in NT than CT, and enzymatic profiles responded to the changes much earlier than the overall prokaryotic community structure. Beta diversity measurements of the prokaryotic community indicated that the levels of stratification observed in long-term NT soils were already recovered in the new NT soils 30 months after switching from CT to NT. Bacteria and Archaea OTUs that responded to NT were associated with coarse soil fraction, soil organic carbon and C cycle enzymes, while CT responders were related to fine soil fractions and S cycle enzymes. This study showed the potential of managing the soil prokaryotic community and soil health through changes in agricultural management practices.
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Affiliation(s)
- Luciano A Gabbarini
- Laboratorio de Bioquímica y Microbiología de Suelo, Centro de Bioquímica y Microbiología de Suelos, Universidad Nacional de Quilmes, B1876BXD Bernal, Buenos Aires, Argentina
| | - Eva Figuerola
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI, CONICET), C1428ADN Buenos Aires, Argentina.,Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - Juan P Frene
- Laboratorio de Bioquímica y Microbiología de Suelo, Centro de Bioquímica y Microbiología de Suelos, Universidad Nacional de Quilmes, B1876BXD Bernal, Buenos Aires, Argentina
| | - Natalia B Robledo
- Laboratorio de Bioquímica y Microbiología de Suelo, Centro de Bioquímica y Microbiología de Suelos, Universidad Nacional de Quilmes, B1876BXD Bernal, Buenos Aires, Argentina
| | - Federico M Ibarbalz
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI, CONICET), C1428ADN Buenos Aires, Argentina
| | - Doreen Babin
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Kornelia Smalla
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Leonardo Erijman
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI, CONICET), C1428ADN Buenos Aires, Argentina.,Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
| | - Luis G Wall
- Laboratorio de Bioquímica y Microbiología de Suelo, Centro de Bioquímica y Microbiología de Suelos, Universidad Nacional de Quilmes, B1876BXD Bernal, Buenos Aires, Argentina
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21
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Cerecetto V, Smalla K, Nesme J, Garaycochea S, Fresia P, Sørensen SJ, Babin D, Leoni C. Reduced tillage, cover crops and organic amendments affect soil microbiota and improve soil health in Uruguayan vegetable farming systems. FEMS Microbiol Ecol 2021; 97:6129805. [PMID: 33547893 DOI: 10.1093/femsec/fiab023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
Conventional tillage and mineral fertilization (CTMF) jeopardize soil health in conventional vegetable production systems. Using a field experiment established in Uruguay in 2012, we aimed to compare the soil restoration potential of organic fertilization (compost and poultry manure) combined with conventional tillage and cover crop incorporated into the soil (CTOF) or with reduced tillage and the use of cover crop as mulch (RTOF). In 2017, table beet was cultivated under CTMF, CTOF and RTOF, and yields, soil aggregate composition and nutrients, as well as soil and table beet rhizosphere microbiota (here: bacteria and archaea) were evaluated. Microbiota was studied by high-throughput sequencing of 16S rRNA gene fragments amplified from total community DNA. RTOF exhibited higher soil aggregation, soil organic C, nutrient availability and microbial alpha-diversity than CTMF, and became more similar to an adjacent natural undisturbed site. The soil microbiota was strongly shaped by the fertilization source which was conveyed to the rhizosphere and resulted in differentially abundant taxa. However, 229 amplicon sequencing variants were found to form the core table beet rhizosphere microbiota shared among managements. In conclusion, our study shows that after only 5 years of implementation, RTOF improves soil health under intensive vegetable farming systems.
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Affiliation(s)
- Victoria Cerecetto
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany.,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
| | - Kornelia Smalla
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Joseph Nesme
- University of Copenhagen, Department of Biology, Section of Microbiology, Nørregade 10, 1165 Copenhagen, Denmark
| | - Silvia Garaycochea
- 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
| | - Pablo Fresia
- Unidad Mixta Institut Pasteur de Montevideo + Instituto Nacional de Investigación Agropecuaria INIA (UMPI), Mataojo 2020, 11400 Montevideo, Uruguay
| | - Søren Johannes Sørensen
- University of Copenhagen, Department of Biology, Section of Microbiology, Nørregade 10, 1165 Copenhagen, Denmark
| | - 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
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Fernandez-Gnecco G, Smalla K, Maccario L, Sørensen SJ, Barbieri P, Consolo VF, Covacevich F, Babin D. Microbial community analysis of soils under different soybean cropping regimes in the Argentinean south-eastern Humid Pampas. FEMS Microbiol Ecol 2021; 97:fiab007. [PMID: 33444447 DOI: 10.1093/femsec/fiab007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/12/2021] [Indexed: 12/13/2022] Open
Abstract
Soil microbial communities are key players of ecosystem processes and important for crop and soil health. The Humid Pampas region in Argentina concentrates 75% of the national soybean production, which is based on intensive use of agrochemicals, monocropping and no-till. A long-term field experiment under no-till management in the southeast of the Argentinean Pampas provides a unique opportunity to compare soybean under monocropping with cultivation including alternating cover crops or in a three-phase rotation. We hypothesized that cropping regimes and season affect soil microbial community composition and diversity. Amplicon sequencing of 16S rRNA genes and internal transcribed spacer fragments showed a stronger microbial seasonal dynamic in conservation regimes compared to monocropping. In addition, several bacterial (e.g. Catenulispora, Streptomyces and Bacillus) and fungal genera (e.g. Exophiala) with cropping regime-dependent differential relative abundances were identified. Despite a temporal shift in microbial and chemical parameters, this study shows that long-term cropping regimes shaped the soil microbiota. This might have important implications for soil quality and soybean performance and should therefore be considered in the development of sustainable agricultural managements.
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Affiliation(s)
- Gabriela Fernandez-Gnecco
- Instituto de Investigaciones en Biodiversidad y Biotecnología, CONICET- Fundación para Investigaciones Biológicas Aplicadas (INBIOTEC, CONICET-FIBA), Vieytes 3103, B7602FCK Mar del Plata, Buenos Aires, Argentina
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Balcarce - CONICET (INTA, EEA Balcarce - CONICET), Ruta 226 Km 73.5, 7620 Balcarce, Buenos Aires, Argentina
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Lorrie Maccario
- Department of Biology, University of Copenhagen, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Pablo Barbieri
- National Scientific and Technical Research Council (CONICET), Argentina
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Balcarce - CONICET (INTA, EEA Balcarce - CONICET), Ruta 226 Km 73.5, 7620 Balcarce, Buenos Aires, Argentina
| | - Veronica F Consolo
- Instituto de Investigaciones en Biodiversidad y Biotecnología, CONICET- Fundación para Investigaciones Biológicas Aplicadas (INBIOTEC, CONICET-FIBA), Vieytes 3103, B7602FCK Mar del Plata, Buenos Aires, Argentina
- National Scientific and Technical Research Council (CONICET), Argentina
| | - Fernanda Covacevich
- Instituto de Investigaciones en Biodiversidad y Biotecnología, CONICET- Fundación para Investigaciones Biológicas Aplicadas (INBIOTEC, CONICET-FIBA), Vieytes 3103, B7602FCK Mar del Plata, Buenos Aires, Argentina
- National Scientific and Technical Research Council (CONICET), Argentina
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Balcarce - CONICET (INTA, EEA Balcarce - CONICET), Ruta 226 Km 73.5, 7620 Balcarce, Buenos Aires, Argentina
| | - Doreen Babin
- 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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23
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Ribeiro IDA, Volpiano CG, Vargas LK, Granada CE, Lisboa BB, Passaglia LMP. Use of Mineral Weathering Bacteria to Enhance Nutrient Availability in Crops: A Review. FRONTIERS IN PLANT SCIENCE 2020; 11:590774. [PMID: 33362817 PMCID: PMC7759553 DOI: 10.3389/fpls.2020.590774] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/26/2020] [Indexed: 05/19/2023]
Abstract
Rock powders are low-cost potential sources of most of the nutrients required by higher plants for growth and development. However, slow dissolution rates of minerals represent an obstacle to the widespread use of rock powders in agriculture. Rhizosphere processes and biological weathering may further enhance mineral dissolution since the interaction between minerals, plants, and bacteria results in the release of macro- and micronutrients into the soil solution. Plants are important agents in this process acting directly in the mineral dissolution or sustaining a wide diversity of weathering microorganisms in the root environment. Meanwhile, root microorganisms promote mineral dissolution by producing complexing ligands (siderophores and organic acids), affecting the pH (via organic or inorganic acid production), or performing redox reactions. Besides that, a wide variety of rhizosphere bacteria and fungi could also promote plant development directly, synergistically contributing to the weathering activity performed by plants. The inoculation of weathering bacteria in soil or plants, especially combined with the use of crushed rocks, can increase soil fertility and improve crop production. This approach is more sustainable than conventional fertilization practices, which may contribute to reducing climate change linked to agricultural activity. Besides, it could decrease the dependency of developing countries on imported fertilizers, thus improving local development.
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Affiliation(s)
- Igor Daniel Alves Ribeiro
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Camila Gazolla Volpiano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luciano Kayser Vargas
- Laboratório de Microbiologia Agrícola, Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual da Agricultura, Pecuária e Desenvolvimento Rural, Porto Alegre, Brazil
| | | | - Bruno Brito Lisboa
- Laboratório de Microbiologia Agrícola, Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual da Agricultura, Pecuária e Desenvolvimento Rural, Porto Alegre, Brazil
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24
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Li W, Zhang Y, Mao W, Wang C, Yin S. Functional potential differences between Firmicutes and Proteobacteria in response to manure amendment in a reclaimed soil. Can J Microbiol 2020; 66:689-697. [DOI: 10.1139/cjm-2020-0143] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Manure amendment generally bolsters soil organisms but not all bacteria equally. To understand why different taxa respond differently, we used shotgun metagenomic approaches to profile functional potentials and correlate them with taxon abundances. A soil originally unproductive was reclaimed using commercial manure and finally became productive. The abundance of Firmicutes in the soil decreased, whereas that of Bacteroidetes and Proteobacteria increased after manure addition. Thirty-nine KEGG modules were significantly different across fertilizer treatments. These modules were mainly associated with the phosphoenolpyruvate-dependent phosphotransferase system (PTS), ATP-binding cassette (ABC) transporters, and two-component signal transduction systems. The Proteobacteria and Firmicutes mainly contributed to these modules. Correlation between the abundances of phyla and orthologs showed two distinctive patterns. One linked the Firmicutes to cell wall biosynthesis, PTS, and ABC transporters, and the other linked the Betaproteobacteria, Bacteroidetes, and Verrucomicrobia to lipopolysaccharide biosynthesis, bacterial motility, and carbon metabolism. Correlation between the abundances of phyla and Carbohydrate-Active Enzyme Database families also showed two distinctive patterns, one of them linking the Betaproteobacteria, Bacteroidetes, and Verrucomicrobia to very high abundances of glycosyltransferases and glycoside hydrolases. Overall, the Proteobacteria and Firmicutes were main drivers of functional potential differences across fertilizer treatments. The Firmicutes were enriched with genes associated with cell wall biosynthesis and membrane transports, while Proteobacteria with lipopolysaccharide biosynthesis and carbohydrate metabolism, which supports our hypothesis that the Firmicutes have a lower potential for utilizing manure-derived carbohydrates, while Proteobacteria have a higher potential. This explains why the Proteobacteria and Firmicutes responded to manure differently.
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Affiliation(s)
- Wenxi Li
- Yangzhou Station of Farmland Quality Protection, Agricultural Bureau of Yangzhou City, Yangzhou 225127, P.R. China
| | - Yueping Zhang
- Yangzhou Station of Farmland Quality Protection, Agricultural Bureau of Yangzhou City, Yangzhou 225127, P.R. China
| | - Wei Mao
- Yangzhou Station of Farmland Quality Protection, Agricultural Bureau of Yangzhou City, Yangzhou 225127, P.R. China
| | - Changsong Wang
- Yizheng Management Station of Farmland Quality Protection, Agricultural Bureau of Yizheng City, Yangzhou 211400, P.R. China
| | - Shixue Yin
- College of Environmental Sciences and Engineering, Yangzhou University, Yangzhou 225127, P.R. China
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25
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Aguiar LM, Souza MDF, de Laia ML, de Oliveira Melo J, da Costa MR, Gonçalves JF, Silva DV, Dos Santos JB. Metagenomic analysis reveals mechanisms of atrazine biodegradation promoted by tree species. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 267:115636. [PMID: 33254605 DOI: 10.1016/j.envpol.2020.115636] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/18/2020] [Accepted: 09/08/2020] [Indexed: 06/12/2023]
Abstract
Metagenomics has provided the discovery of genes and metabolic pathways involved in the degradation of xenobiotics. Some microorganisms can metabolize these compounds, potentiating phytoremediation in association with plant. This study aimed to study the metagenome and the occurrence of atrazine degradation genes in rhizospheric soils of the phytoremediation species Inga striata and Caesalphinea ferrea. The genera of microorganisms predominant in the rhizospheric soils of I. striata and C. ferrea were Mycobacterium, Conexibacter, Bradyrhizobium, Solirubrobacter, Rhodoplanes, Streptomyces, Geothrix, Gaiella, Nitrospira, and Haliangium. The atzD, atzE, and atzF genes were detected in the rhizospheric soils of I. striata and atzE and atzF in the rhizospheric soils of C. ferrea. The rhizodegradation by both tree species accelerates the degradation of atrazine residues, eliminating toxic effects on plants highly sensitive to this herbicide. This is the first report for the species Agrobacterium rhizogenes and Candidatus Muproteobacteria bacterium and Micromonospora genera as atrazine degraders.
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Affiliation(s)
- Luciana Monteiro Aguiar
- Plant Production Department, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Minas Gerais, Brazil
| | - Matheus de Freitas Souza
- Department of Agricultural and Forestry Sciences, Universidade Federal Rural do Semi-Árido, Rio Grande do Norte, Brazil.
| | - Marcelo Luiz de Laia
- Department of Forest Engineering, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Minas Gerais, Brazil
| | - Janaína de Oliveira Melo
- Department of Basic Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Minas Gerais, Brazil
| | - Márcia Regina da Costa
- Plant Production Department, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Minas Gerais, Brazil
| | - Janaína Fernandes Gonçalves
- Department of Forest Engineering, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Minas Gerais, Brazil
| | - Daniel Valadão Silva
- Department of Agricultural and Forestry Sciences, Universidade Federal Rural do Semi-Árido, Rio Grande do Norte, Brazil
| | - José Barbosa Dos Santos
- Plant Production Department, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Minas Gerais, Brazil
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26
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Raiger Iustman LJ, Almasqué FJ, Vullo DL. Microbiota Diversity Change as Quality Indicator of Soils Exposed to Intensive Periurban Agriculture. Curr Microbiol 2020; 78:338-346. [PMID: 33249534 DOI: 10.1007/s00284-020-02298-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 11/13/2020] [Indexed: 11/30/2022]
Abstract
In Argentina, periurban agriculture is performed by farmers with inadequate training in the use of pesticides and chemical fertilizers, developing horticulture with serious soil deterioration. The aim of this work was to monitor bacterial diversity of a horticultural soil (S) and a reference soil (R) as quality index for the design of future restoration strategies. As crops changed together with the agrochemical applications, sample collection was before harvest for strawberries, post-harvest for red peppers, pre-harvest broccoli crop and of a resting soil in treatment with poultry litter as a fertilizing amendment. Bacterial diversity was analysed by the use of high throughput sequencing of the V1-V3 region of the 16S rRNA gene. Analysis of R soils seemed relatively constant in time, enriched in Alphaproteobacteria and Acidobacteria consistent with a reference to soil health. The effect of the intensive use of S soils was proved by differences in Chloroflexi, Bacteroidetes and Proteobacteria relative abundances. The main evidence of the alteration of S soils was the increase in Bacteroidetes and Betaproteobacteria. A weak recuperation trend of S soil microbiota was registered during a post-harvest inactive period. A strong influence of the soil use routine-consisting in high crop rotation and short time-rest cycles-on microbial community structure was verified. These results indicate the microbiota perturbation, caused by the intense use of periurban agriculture soils and will contribute for further actions to improve environment quality.
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Affiliation(s)
- Laura J Raiger Iustman
- Depto. de Química Biológica, Facultad de Ciencias Exactas y Naturales (UBA), IQUIBICEN-CONICET. Pab. II, Piso 4, Ciudad Universitaria, (1428), Buenos Aires, Argentina
| | - Facundo J Almasqué
- Depto. de Química Biológica, Facultad de Ciencias Exactas y Naturales (UBA), IQUIBICEN-CONICET. Pab. II, Piso 4, Ciudad Universitaria, (1428), Buenos Aires, Argentina
| | - Diana L Vullo
- Área Química, Instituto de Ciencias, Universidad Nacional de General Sarmiento-CONICET, J.M. Gutierrez 1150, B1613GSX, Los Polvorines, Buenos Aires, Argentina.
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27
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Effect of Organic and Conventional Systems Used to Grow Pecan Trees on Diversity of Soil Microbiota. DIVERSITY 2020. [DOI: 10.3390/d12110436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Agronomic management modifies the soil bacterial communities and may alter the carbon fractions. Here, we identify differences in several chemical and biological soil variables, as well as bacterial composition between organic (Org) and conventional (Conv) agronomic management in pecan (Carya illinoinensis) orchards located in Coahuila, Mexico. The analyzed variables were pH, N, P, K, soil organic matter, organic matter quality, soil organic carbon, C/N ratio, carbon fractions, microbial biomass carbon, easily extractable Glomalin, colony-forming units, CO2 emissions, and the enzyme activity. The DNA of soil bacteria was extracted, amplified (V3-V4 16S rRNA), and sequenced using Illumina. To compare variables between agronomic managements, t tests were used. Sequences were analyzed in QIIME (Quantitative Insights Into Microbial Ecology). A canonical correspondence analysis (CCA) was used to observe associations between the ten most abundant phyla and soil variables in both types of agronomic managements. In Org management, variables related to the capture of recalcitrant carbon compounds were significant, and there was a greater diversity of bacterial communities capable of promoting organic carbon sequestration. In Conv management, variables related to the increase in carbon mineralization, as well as the enzymatic activity related to the metabolism of labile compounds, were significant. The CCA suggested a separation between phyla associated with some variables. Agronomic management impacted soil chemical and biological parameters related to carbon dynamics, including bacterial communities associated with carbon sequestration. Further research is still necessary to understand the plasticity of some bacterial communities, as well as the soil–plant dynamics.
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28
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Zarraonaindia I, Martínez-Goñi XS, Liñero O, Muñoz-Colmenero M, Aguirre M, Abad D, Baroja-Careaga I, de Diego A, Gilbert JA, Estonba A. Response of Horticultural Soil Microbiota to Different Fertilization Practices. PLANTS 2020; 9:plants9111501. [PMID: 33171888 PMCID: PMC7694448 DOI: 10.3390/plants9111501] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 01/11/2023]
Abstract
Environmentally friendly agricultural production necessitates manipulation of microbe-plant interactions, requiring a better understanding of how farming practices influence soil microbiota. We studied the effect of conventional and organic treatment on soil bacterial richness, composition, and predicted functional potential. 16S rRNA sequencing was applied to soils from adjacent plots receiving either a synthetic or organic fertilizer, where two crops were grown within treatment, homogenizing for differences in soil properties, crop, and climate. Conventional fertilizer was associated with a decrease in soil pH, an accumulation of Ag, Mn, As, Fe, Co, Cd, and Ni; and an enrichment of ammonia oxidizers and xenobiotic compound degraders (e.g., Candidatus Nitrososphaera, Nitrospira, Bacillus, Pseudomonas). Soils receiving organic fertilization were enriched in Ti (crop biostimulant), N, and C cycling bacteria (denitrifiers, e.g., Azoarcus, Anaerolinea; methylotrophs, e.g., Methylocaldum, Methanosarcina), and disease-suppression (e.g., Myxococcales). Some predicted functions, such as glutathione metabolism, were slightly, but significantly enriched after a one-time manure application, suggesting the enhancement of sulfur regulation, nitrogen-fixing, and defense of environmental stressors. The study highlights that even a single application of organic fertilization is enough to originate a rapid shift in soil prokaryotes, responding to the differential substrate availability by promoting soil health, similar to recurrent applications.
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Affiliation(s)
- Iratxe Zarraonaindia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain; (X.S.M.-G.); (M.M.-C.); (M.A.); (D.A.); (I.B.-C.); (A.E.)
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Bizkaia, Spain
- Correspondence:
| | - Xabier Simón Martínez-Goñi
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain; (X.S.M.-G.); (M.M.-C.); (M.A.); (D.A.); (I.B.-C.); (A.E.)
| | - Olaia Liñero
- Department of Analytical Chemistry, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain; (O.L.); (A.d.D.)
| | - Marta Muñoz-Colmenero
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain; (X.S.M.-G.); (M.M.-C.); (M.A.); (D.A.); (I.B.-C.); (A.E.)
| | - Mikel Aguirre
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain; (X.S.M.-G.); (M.M.-C.); (M.A.); (D.A.); (I.B.-C.); (A.E.)
| | - David Abad
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain; (X.S.M.-G.); (M.M.-C.); (M.A.); (D.A.); (I.B.-C.); (A.E.)
| | - Igor Baroja-Careaga
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain; (X.S.M.-G.); (M.M.-C.); (M.A.); (D.A.); (I.B.-C.); (A.E.)
| | - Alberto de Diego
- Department of Analytical Chemistry, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain; (O.L.); (A.d.D.)
| | - Jack A. Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA;
| | - Andone Estonba
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain; (X.S.M.-G.); (M.M.-C.); (M.A.); (D.A.); (I.B.-C.); (A.E.)
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29
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Miao S, Zhao H, Pan S, Zhang N, Qiao Y. Elevated CO 2 weakens the shift in bacterial community structure in response to 8-year soybean straw return in the same experiment. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2020; 23:505-510. [PMID: 33016108 DOI: 10.1080/15226514.2020.1825332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A potentially important source for soil organic carbon (SOC) in the agricultural ecosystem is straw, straw return has been shown to affect soil bacterial communities. Facing global climate change, the response of bacterial communities to straw return will change at CO2 enrichment. In this study, we investigate the changes of bacterial communities in response to straw return (+straw) at elevated CO2 (eCO2, 700 ppm) in a long-term field experiment of northeast China. Soil samples were taken in the eighth year and analyzed by high throughput sequencing. Soil bacterial communities exhibited distinct clustering according to straw return and eCO2, while eCO2 shortened the distance of clustering between straw return and not. The relative abundances of 10 genera (Acidobacteria_norank, Candidatus_Solibacter, Gaiella, Nocardioides, Streptomyces, C0119_norank, Roseiflexus, Gemmatimonas, Mizugakiibacter and Rhodanobacter) were significantly affected by the interaction of straw × eCO2. In addition, straw return significantly decreased the relative abundances of Gaiellales_norank, Blastococcus, Psedarthrobacter, and Bacillus and increased that of Geminatimonadaceae_norank, Tepidisphaeraceae, Nitrosomonadaceae_norank, and SC-I-84_norank. These differential responses of genera abundances are illustrative of the susceptibility of bacterial communities and indicate their importance in evaluating the fate of exogenous C. The Clusters of Orthologous Groups (COG) analysis showed that straw return had a greater effect on the relative abundances of COG categories than eCO2. The present results point to the need to focus more strongly on the turnover and storage of straw-C during a chronic straw return in the future.
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Affiliation(s)
- Shujie Miao
- School of Applied Meteorology, Nanjing University of Information Sciences & Technology, Nanjing, China
| | - Hongfei Zhao
- School of Applied Meteorology, Nanjing University of Information Sciences & Technology, Nanjing, China
| | - Shiqiu Pan
- School of Applied Meteorology, Nanjing University of Information Sciences & Technology, Nanjing, China
| | - Nan Zhang
- School of Applied Meteorology, Nanjing University of Information Sciences & Technology, Nanjing, China
| | - Yunfa Qiao
- School of Applied Meteorology, Nanjing University of Information Sciences & Technology, Nanjing, China
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30
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Kirubakaran R, ArulJothi KN, Revathi S, Shameem N, Parray JA. Emerging priorities for microbial metagenome research. BIORESOURCE TECHNOLOGY REPORTS 2020; 11:100485. [PMID: 32835181 PMCID: PMC7319936 DOI: 10.1016/j.biteb.2020.100485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022]
Abstract
Overwhelming anthropogenic activities lead to deterioration of natural resources and the environment. The microorganisms are considered desirable, due to their suitability for easy genetic manipulation and handling. With the aid of modern biotechnological techniques, the culturable microorganisms have been widely exploited for the benefit of mankind. Metagenomics, a powerful tool to access the abundant biodiversity of the environmental samples including the unculturable microbes, to determine microbial diversity and population structure, their ecological roles and expose novel genes of interest. This review focuses on the microbial adaptations to the adverse environmental conditions, metagenomic techniques employed towards microbial biotechnology. Metagenomic approach helps to understand microbial ecology and to identify useful microbial derivatives like antibiotics, toxins, and enzymes with diverse and enhanced function. It also summarizes the application of metagenomics in clinical diagnosis, improving microbial ecology, therapeutics, xenobiotic degradation and impact on agricultural crops.
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Affiliation(s)
| | - K N ArulJothi
- Department of Genetic Engineering, SRM Institute of Science and Technology, Chennai, India
- Department of Human Biology, University of Cape Town, Cape Town, South Africa
| | | | - Nowsheen Shameem
- Department of Environmental Science, Cluster University Srinagar, J&K, India
| | - Javid A Parray
- Department of Environmental Science, Govt SAM Degree College Budgam, J&K, India
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31
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Soil bacterial communities remain altered after 30 years of agriculture abandonment in Pampa grasslands. Oecologia 2020; 193:959-968. [PMID: 32851494 DOI: 10.1007/s00442-020-04736-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 08/18/2020] [Indexed: 10/23/2022]
Abstract
Old fields are spreading in the world because of agriculture abandonment, and they show a persistence of exotic plant species with little recovery towards the original vegetation composition. Soil biota may also differ between old fields and native grasslands, but were comparatively less studied than plant communities, despite their importance in biogeochemical processes. Here we compared soil bacterial communities of exotic-dominated old fields with those of remnants of native grasslands in the Inland Pampa, Argentina, using the 16S rRNA gene amplicon sequencing approach. We also characterized plant communities, soil physico-chemical properties, and soil respiration. We expected more diverse soil bacterial communities, with higher heterogeneity, in remnant grasslands than in old fields because of a more diverse and more heterogeneous plant community. However, our results showed that soil bacterial communities had higher Shannon diversity in old fields than in remnant grasslands, but richness was not significantly different. Also we found different bacterial community compositions between grasslands even at a low taxonomic level. On the other hand, old fields harbored less heterogeneous bacterial communities than remnants, and bacteria and plant beta diversity were correlated. Despite contrasting plant and bacterial composition between old fields and remnant grasslands, soil physico-chemical properties were quite similar between grasslands. Overall, our results showed that bacterial communities in grassland soils were associated with changes in plant communities after agricultural abandonment. Plant-microbial feedbacks might regulate plant and soil bacterial community assemblage in old fields, yet further research is needed to demonstrate this potential feedback mechanism.
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32
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Hu X, Liang A, Yao Q, Liu Z, Yu Z, Wang G, Liu J. Ridge Tillage Improves Soil Properties, Sustains Diazotrophic Communities, and Enhances Extensively Cooperative Interactions Among Diazotrophs in a Clay Loam Soil. Front Microbiol 2020; 11:1333. [PMID: 32714293 PMCID: PMC7344147 DOI: 10.3389/fmicb.2020.01333] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/25/2020] [Indexed: 12/30/2022] Open
Abstract
Reduced tillage practices [such as ridge tillage (RT)] have been potential solutions to the weed pressures of long-term no tillage (NT) and the soil-intensive disturbances caused by conventional tillage [such as moldboard plow (MP) tillage]. Although soil diazotrophs are significantly important in global nitrogen (N) cycling and contribute to the pool of plant-available N in agroecosystems, little is currently known about the responses of diazotrophic communities to different long-term tillage practices. In the current study, we investigated the differences among the effects of NT, RT, and MP on soil properties, diazotrophic communities, and co-occurrence network patterns in bulk and rhizosphere soils under soybean grown in clay loam soil of Northeast China. The results showed that RT and MP led to higher contents of total C, N, and available K compared to NT in both bulk and rhizosphere soils, and RT resulted in higher soybean yield than NT and MP. Compared to NT and RT, MP decreased the relative abundances of free-living diazotrophs, while it promoted the growth of copiotrophic diazotrophs. Little differences of diazotrophic community diversity, composition, and community structure were detected between RT and NT, but MP obviously decreased diazotrophic diversity and changed the diazotrophic communities in contrast to NT and RT in bulk soils. Soil nitrogenous nutrients had negative correlations with diazotrophic diversity and significantly influenced the diazotrophic community structure. Across all diazotrophs' networks, the major diazotrophic interactions transformed into a cooperatively dominated network under RT, with more intense and efficient interactions among species than NT and MP. Overall, our study suggested that RT, with minor soil disturbances, could stabilize diazotrophic diversity and communities as NT and possessed highly positive interactions among diazotrophic species relative to NT and MP.
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Affiliation(s)
- Xiaojing Hu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Aizhen Liang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qin Yao
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhuxiu Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhenhua Yu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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Saad MM, Eida AA, Hirt H. Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3878-3901. [PMID: 32157287 PMCID: PMC7450670 DOI: 10.1093/jxb/eraa111] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/09/2020] [Indexed: 05/05/2023]
Abstract
Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment, and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim of establishing sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the application of microbial inoculants in agriculture.
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Affiliation(s)
- Maged M Saad
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdul Aziz Eida
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette Cedex, France
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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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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Wu H, Xia J, Qin X, Wu H, Zhang S, Zhao Y, Rensing C, Lin W. Underlying Mechanism of Wild Radix pseudostellariae in Tolerance to Disease Under the Natural Forest Cover. Front Microbiol 2020; 11:1142. [PMID: 32528459 PMCID: PMC7266878 DOI: 10.3389/fmicb.2020.01142] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/05/2020] [Indexed: 12/31/2022] Open
Abstract
Replanting disease caused by negative plant-soil feedback in continuous monoculture of Radix pseudostellariae is a critical factor restricting the development of this common and popular Chinese medicine, although wild R. pseudostellariae plants were shown to grow well without occurrence of disease in the same site for multiple years. Therefore, we aimed to identify the changes in microbial community composition in the rhizosphere soil of wild R. pseudostellariae thus providing a potential method for controlling soil-borne diseases. We analyzed differences in soil physicochemical properties, changes in soil microbial community structure, and root exudates of wild R. pseudostellariae under different biotopes. And then, simple sequence repeats amplification was used to isolate and collect significantly different formae speciales of Fusarium oxysporum. Finally, we analyzed the pathogenicity testing and influence of root exudates on the growth of F. oxysporum. We found that the different biotopes of R. pseudostellariae had significant effects on the soil microbial diversity. The soil fungal and bacterial abundances were significantly higher and the abundance of F. oxysporum was significantly lower under the rhizosphere environment of wild R. pseudostellariae than under consecutive monoculture. The relative abundances of most genera were Penicillium, Aspergillus, Fusarium, Nitrobacter, Nitrospira, Streptomyces, Actinoplanes, and Pseudomonas. Venn diagram and LEfSe analyses indicated numerously specific microbiome across all the samples, and the numbers of specific fungi were higher than the shared ones in the four biotopes. Eight types of phenolic acids were identified across all the rhizosphere soils. Mixed phenolic acids and most of the examined single phenolic acids had negative effects on the growth of isolated pathogenic F. oxysporum strains and promoted the growth of non-pathogenic strains. Similarly, correlation analysis suggested that most of the identified phenolic acids were positively associated with beneficial Pseudomonas, Nitrobacter, Nitrospira, Streptomyces, and Bacillus. This study suggested that wild R. pseudostellariae was able to resist or tolerate disease by increasing soil microbial diversity, and reducing the accumulation of soil-borne pathogens.
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Affiliation(s)
- Hongmiao Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinshen Xia
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xianjin Qin
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huiming Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shengkai Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
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36
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Chee-Sanford JC, Connor L, Krichels A, Yang WH, Sanford RA. Hierarchical detection of diverse Clade II (atypical) nosZ genes using new primer sets for classical- and multiplex PCR array applications. J Microbiol Methods 2020; 172:105908. [PMID: 32234512 DOI: 10.1016/j.mimet.2020.105908] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 11/27/2022]
Abstract
The reduction of nitrous oxide (N2O) to N2 represents the key terminal step in canonical denitrification. Nitrous oxide reductase (NosZ), the enzyme associated with this biological step, however, is not always affiliated with denitrifying microorganisms. Such organisms were shown recently to possess a Clade II (atypical) nosZ gene, in contrast to Clade I (typical) nosZ harbored in more commonly studied denitrifiers. Subsequent phylogenetic analyses have shown that Clade II NosZ are affiliated with a much broader diversity of microorganisms than those with Clade I NosZ, the former including both non-denitrifiers and denitrifiers. Most studies attempting to characterize the nosZ gene diversity using DNA-based PCR approaches have only focused on Clade I nosZ, despite recent metagenomic sequencing studies that have demonstrated the dominance of Clade II nosZ genes in many ecosystems, particularly soil. As a result, these studies have greatly underestimated the genetic potential for N2O reduction present in ecosystems. Because the high diversity of Clade II NosZ makes it impossible to design a universal primer set that would effectively amplify all nosZ genes in this clade, we developed a suite of primer sets to specifically target seven of ten designated subclades of Clade II nosZ genes. The new primer sets yield suitable product sizes for paired end amplicon sequencing and qPCR, demonstrated here in their use for both conventional single-reaction and multiplex array platforms. In addition, we show the utility of these primers for detecting nosZ gene transcripts from mRNA extracted from soil.
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Affiliation(s)
| | | | - Alexander Krichels
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Wendy H Yang
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Robert A Sanford
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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37
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Chee-Sanford J, Tian D, Sanford R. Consumption of N 2O and other N-cycle intermediates by Gemmatimonas aurantiaca strain T-27. MICROBIOLOGY-SGM 2020; 165:1345-1354. [PMID: 31580255 DOI: 10.1099/mic.0.000847] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bacteria affiliated with the phylum Gemmatimonadetes are found in high abundance in many terrestrial and aquatic environments, yet little is known about their metabolic capabilities. Difficulty in their cultivation has prompted interest in identifying better growth conditions for metabolic studies, especially related to their ability to reduce N2O, a potent greenhouse gas. T-27 Gemmatimonas aurantiaca is one of few cultivated strains of Gemmatimonadetes available for physiological studies. Our objective was to test this organism's ability to use nitrite, nitrate, and N2O, and mineral forms of assimilable NH4 + at concentrations not typically used in tests for compound utilization. Cultures incubated under anaerobic conditions with nitrate, nitrite or N2O failed to grow or show depletion of these substrates. Nitrate and nitrite (1 mM) were not used even when cells were grown aerobically with the O2 allowed to deplete first. N2O reduction only commenced in the presence of O2 and continued to be depleted when refed to the culture under anaerobic, microaerobic and aerobic atmospheres. Carbon mineralization was coupled to the electron-accepting processes, with higher reducing equivalents needed for N2O utilization under aerobic atmospheres. N2O was reduced to N2 in the presence of 20% O2, however the rate of this reaction is reduced in the presence of high O2 concentration. This study demonstrated that G. aurantiaca T-27 possesses unique characteristics for assimilative and dissimilative N processes with new implications for cultivation strategies to better assess the metabolic abilities of Gemmatimonadetes.
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Affiliation(s)
| | - David Tian
- Department of Molecular and Cell Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Robert Sanford
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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38
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Kraut-Cohen J, Zolti A, Shaltiel-Harpaz L, Argaman E, Rabinovich R, Green SJ, Minz D. Effects of tillage practices on soil microbiome and agricultural parameters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135791. [PMID: 31810706 DOI: 10.1016/j.scitotenv.2019.135791] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/18/2019] [Accepted: 11/25/2019] [Indexed: 06/10/2023]
Abstract
No-tillage (NT) is a common soil-conservation management practice with known agricultural advantages and drawbacks. However, its short- and long-term effects on the soil microbiome have not been well established. Here, we compared conventional (CT), minimal (MT) and NT practices in two agricultural fields in the north of Israel over a period of 3 years. Edaphic properties, plant-associated pests, weed species abundance and soil microbial community structure were assessed to examine the effects of tillage. Tillage significantly altered physical and chemical soil properties, and a significant increase in hydrolytic and redox microbial activities was observed in NT soils from both sites. Consistent with this, the microbial community structure of NT samples diverged significantly over time from those of CT samples. Repetitive tillage and even a single tillage event caused significant changes in the relative abundance of microorganisms at taxonomic levels ranging from phylum to OTU. However, no significant difference between treatments was found in microbial community alpha-diversity or crop yield. Conversely, higher levels of weed diversity and some pests number were found in NT samples. Overall, we demonstrate that tillage plays a major role in shaping microbial community structure, and in influencing additional environmental, ecological and agricultural soil parameters.
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Affiliation(s)
- Judith Kraut-Cohen
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel.
| | - Avihai Zolti
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel; Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Liora Shaltiel-Harpaz
- Migal Galilee Research Institute, P.O. Box 831, Kiryat Shmona, 11016, Israel; Department of Environmental Sciences, Tel Hai College, Upper Galilee, 12210, Israel
| | - Eli Argaman
- Soil Erosion Research Station, Soil Conservation & Drainage Division, Ministry of Agriculture & Rural Development, Israel
| | | | - Stefan J Green
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Dror Minz
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
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Obermeier MM, Gnädinger F, Durai Raj AC, Obermeier WA, Schmid CAO, Balàzs H, Schröder P. Under temperate climate, the conversion of grassland to arable land affects soil nutrient stocks and bacteria in a short term. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 703:135494. [PMID: 31761356 DOI: 10.1016/j.scitotenv.2019.135494] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
Projected population growth and climate change will make it inevitable to convert neglected and marginal land into productive arable land. We investigate the influence of agricultural management practices on nutrient stocks and soil functions during the conversion of former extensively used grassland to arable land. Effects of grassland removal, tillage, intercropping with faba bean (Vicia faba) and its later incorporation were studied with respect to soil properties and bacterial community structure. Therefore, composite samples were collected with a core sampler from the topsoil (0-20 cm) in (a) the initial grassland, (b) the transitional phase during the vegetation period of V. faba, (c) after ploughing the legume in, and (d) untreated controls. In all samples, nitrate-N, ammonium-N, dissolved organic carbon (DOC) and total nitrogen bound (TNb) were analyzed and comparisons of the bacterial community structure after 16S-amplicon sequencing were performed to assess soil functions. Mineralization after grassland conversion followed by the biological nitrogen fixation of broad beans enhanced the nitrate-N content in bulk soil from 4 to almost 50 μg N g-1dw. Bacterial community structure on phylum level in bulk soil was dominated by Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Bacteroidetes and remained almost stable. However, alpha and beta-diversity analysis revealed a change of the bacterial composition at the final state of the conversion. This change was primarily driven by increasing abundances of the genera Massilia and Lysobacter, both members of the Proteobacteria, after the decay of the leguminous plant residues. Furthermore, increasing abundances of the family Gaiellaceae and its genus Gaiella fostered this change and were related to the decreasing carbon to nitrogen ratio. In short, gentle management strategies could replace the input of mineral fertilizer with the aim to contribute to future sustainable and intensified production even on converted grassland.
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Affiliation(s)
- Michael M Obermeier
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Friederike Gnädinger
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Abilash C Durai Raj
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Wolfgang A Obermeier
- Ludwig-Maximilians-Universität München, Research and Teaching Unit for Physical Geography and Land Use Systems, Luisenstraße 37, 80333 München, Germany
| | - Christoph A O Schmid
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Helga Balàzs
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Peter Schröder
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
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Khachatryan L, de Leeuw RH, Kraakman MEM, Pappas N, Te Raa M, Mei H, de Knijff P, Laros JFJ. Taxonomic classification and abundance estimation using 16S and WGS-A comparison using controlled reference samples. Forensic Sci Int Genet 2020; 46:102257. [PMID: 32058299 DOI: 10.1016/j.fsigen.2020.102257] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 12/30/2019] [Accepted: 01/27/2020] [Indexed: 12/30/2022]
Abstract
The assessment of microbiome biodiversity is the most common application of metagenomics. While 16S sequencing remains standard procedure for taxonomic profiling of metagenomic data, a growing number of studies have clearly demonstrated biases associated with this method. By using Whole Genome Shotgun sequencing (WGS) metagenomics, most of the known restrictions associated with 16S data are alleviated. However, due to the computationally intensive data analyses and higher sequencing costs, WGS based metagenomics remains a less popular option. Selecting the experiment type that provides a comprehensive, yet manageable amount of information is a challenge encountered in many metagenomics studies. In this work, we created a series of artificial bacterial mixes, each with a different distribution of skin-associated microbial species. These mixes were used to estimate the resolution of two different metagenomic experiments - 16S and WGS - and to evaluate several different bioinformatics approaches for taxonomic read classification. In all test cases, WGS approaches provide much more accurate results, in terms of taxa prediction and abundance estimation, in comparison to those of 16S. Furthermore, we demonstrate that a 16S dataset, analysed using different state of the art techniques and reference databases, can produce widely different results. In light of the fact that most forensic metagenomic analysis are still performed using 16S data, our results are especially important.
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Affiliation(s)
- Lusine Khachatryan
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.
| | - Rick H de Leeuw
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Margriet E M Kraakman
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Nikos Pappas
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, the Netherlands
| | - Marije Te Raa
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jeroen F J Laros
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands; Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
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41
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Bacteria with Different Assemblages in the Soil Profile Drive the Diverse Nutrient Cycles in the Sugarcane Straw Retention Ecosystem. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11100194] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Straw retention, an alternative to artificial fertilization, commonly mitigates soil degradation and positively affects soil fertility. In this study, we investigated the succession of soil bacteria during two sugarcane straw retention treatments (control (CK) and sugarcane straw retention (SR)) and at four depths (0–10, 10–20, 20–30, and 30–40 cm) in fallow soil in a sugarcane cropping system. Using an Illumina MiSeq (16S rRNA) and soil enzyme activity, we explored the SR influence on soil bacterial communities and enzyme activities and its inclusive impact on soil fertility, with an emphasis on topsoil (0–10 cm) and subsoil (10–40 cm). Our results show that SR effectively improved soil fertility indicators (C, N, and P), including enzyme activities (C and N cycling), throughout the soil profile: these soil parameters greatly improved in the topsoil compared to the control. Sugarcane straw retention and soil depth (0–10 cm vs. 10–40 cm) were associated with little variation in bacterial species richness and alpha diversity throughout the soil profile. Subsoil and topsoil bacterial communities differed in composition. Compared to the CK treatment, SR enriched the topsoil with Proteobacteria, Verrucomicrobia, Actinobacteria, Chloroflexi, and Nitrospirae, while the subsoil was depleted in Nitrospirae and Acidobacteria. Similarly, SR enriched the subsoil with Proteobacteria, Verrucomicrobia, Actinobacteria, Chloroflexi, Gemmatimonadetes, and Bacteroidetes, while the topsoil was depleted in Acidobacteria, Gemmatimonadetes, and Planctomycetes compared to the CK. At the genus level, SR enriched the topsoil with Gp1, Gp2, Gp5, Gp7, Gemmatimonas, Kofleria, Sphingomonas, and Gaiella, which decompose lignocellulose and contribute to nutrient cycling. In summary, SR not only improved soil physicochemical properties and enzyme activities but also enriched bacterial taxa involved in lignocellulosic decomposition and nutrient cycling (C and N) throughout the soil profile. However, these effects were stronger in topsoil than in subsoil, suggesting that SR enhanced fertility more in topsoil than in subsoil in fallow land.
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Long-Term N Fertilization Decreased Diversity and Altered the Composition of Soil Bacterial and Archaeal Communities. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9100574] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Soil microbial communities are essential in the cycling of nutrients that affect crop production. Our goal was to characterize the microbial community structure following 34 years of nitrogen (N) fertilization treatments in continuous maize production in highly fertile soils. Using 16S rRNA gene-based analysis of the V4 region via Illumina HiSeq2500 technology with downstream bioinformatics processing and analysis with QIIME 2.0, we aimed to characterize the prokaryotic communities under three increasing N fertilization rates. Factor analyses indicated that a high N level decreased the diversity of soil bacterial and archaeal communities and altered the relative abundance (RA) of the dominant (>1% RA) and minor (<1% RA) phyla. Among the 12 major phyla, we determined increases in Gemmatimonadetes, Proteobacteria, and Euryarchaeota, accompanied by reductions in Cyanobacteria, Chloroflexi, Firmicutes, and Planctomycetes with increasing N. Within the 29 minor phyla, N fertilization led to increases in Aquificae, WPS2, Parvarchaeota, AD3, FCPU426, Armatimonadetes, TM7, Chlamydiae, and OD1, along with reductions of Nitrospirae, WS3, Tenericutes, Lentisphaerae, OP3, Synergistetes, Thermotogae, and prokaryotes that could not be reliably assigned to a phylum (classified as Other).
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Analysis of the soil microbial communities in Pinus tabulaeformis Carr. and Bupleurum chinense plantations of the Xiaolongshan Mountain region, Gansu Province, China. ECOL INFORM 2019. [DOI: 10.1016/j.ecoinf.2019.100981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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A meta-barcoding analysis of soil mycobiota of the upper Andean Colombian agro-environment. Sci Rep 2019; 9:10085. [PMID: 31300737 PMCID: PMC6625999 DOI: 10.1038/s41598-019-46485-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/17/2019] [Indexed: 11/23/2022] Open
Abstract
Colombia is a country for which one of the highest biodiversity rates is reported, and one of the first in the tropical areas where an effort was made to gather information on indigenous fungi. Nevertheless, mycological data are still scarce and discontinuous, above all on soil fungi. The present study wanted to contribute to unveil the large soil fungal biodiversity in the upper Andean Colombian agro-ecosystems. The studied area is located in the department of Boyacà, considered with a notable economical value, partly devoted to subsistence agriculture. More than 150 described species were revealed in this study, belonging to 5 phyla with Ascomycota representing the dominant taxon. Basidiomycota and Zygomycota are also well represented, dominated by species of the genus Sebacina and Mortierella respectively, mainly distributed in the semi-natural plots (woodland and grassland). Most of the species are reported as first records for Colombia. Some of them are particularly interesting for their conservation significance such as Geoglossum fallax, which is the dominant species in the unimproved grassland plot. The bootstrap-based clustering analysis showed a different distribution of the species in orchards and non-cultivated areas as a possible response of the fungal community to different use of soil in the agro-environment.
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Moreira-Grez B, Muñoz-Rojas M, Kariman K, Storer P, O’Donnell AG, Kumaresan D, Whiteley AS. Reconditioning Degraded Mine Site Soils With Exogenous Soil Microbes: Plant Fitness and Soil Microbiome Outcomes. Front Microbiol 2019; 10:1617. [PMID: 31354694 PMCID: PMC6636552 DOI: 10.3389/fmicb.2019.01617] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/28/2019] [Indexed: 02/01/2023] Open
Abstract
Mining of mineral resources substantially alters both the above and below-ground soil ecosystem, which then requires rehabilitation back to a pre-mining state. For belowground rehabilitation, recovery of the soil microbiome to a state which can support key biogeochemical cycles, and effective plant colonization is usually required. One solution proposed has been to translate microbial inocula from agricultural systems to mine rehabilitation scenarios, as a means of reconditioning the soil microbiome for planting. Here, we experimentally determine both the aboveground plant fitness outcomes and belowground soil microbiome effects of a commercially available soil microbial inocula (SMI). We analyzed treatment effects at four levels of complexity; no SMI addition control, Nitrogen addition alone, SMI addition and SMI plus Nitrogen addition over a 12-week period. Our culture independent analyses indicated that SMIs had a differential response over the 12-week incubation period, where only a small number of the consortium members persisted in the semi-arid ecosystem, and generated variable plant fitness responses, likely due to plant-microbiome physiological mismatching and low survival rates of many of the SMI constituents. We suggest that new developments in custom-made SMIs to increase rehabilitation success in mine site restoration are required, primarily based upon the need for SMIs to be ecologically adapted to both the prevailing edaphic conditions and a wide range of plant species likely to be encountered.
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Affiliation(s)
- Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Miriam Muñoz-Rojas
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
- Kings Park Science, Department of Biodiversity, Conservation and Attractions, Perth, WA, Australia
| | - Khalil Kariman
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Paul Storer
- Troforte Innovations Pty Ltd., Perth, WA, Australia
| | | | - Deepak Kumaresan
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
| | - Andrew S. Whiteley
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
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Dennert F, Imperiali N, Staub C, Schneider J, Laessle T, Zhang T, Wittwer R, van der Heijden MGA, Smits THM, Schlaeppi K, Keel C, Maurhofer M. Conservation tillage and organic farming induce minor variations in Pseudomonas abundance, their antimicrobial function and soil disease resistance. FEMS Microbiol Ecol 2019; 94:4985836. [PMID: 29701793 DOI: 10.1093/femsec/fiy075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 04/23/2018] [Indexed: 01/29/2023] Open
Abstract
Conservation tillage and organic farming are strategies used worldwide to preserve the stability and fertility of soils. While positive effects on soil structure have been extensively reported, the effects on specific root- and soil-associated microorganisms are less known. The aim of this study was to investigate how conservation tillage and organic farming influence the frequency and activity of plant-beneficial pseudomonads. Amplicon sequencing using the 16S rRNA gene revealed that Pseudomonas is among the most abundant bacterial taxa in the root microbiome of field-grown wheat, independent of agronomical practices. However, pseudomonads carrying genes required for the biosynthesis of specific antimicrobial compounds were enriched in samples from conventionally farmed plots without tillage. In contrast, disease resistance tests indicated that soil from conventional no tillage plots is less resistant to the soilborne pathogen Pythium ultimum compared to soil from organic reduced tillage plots, which exhibited the highest resistance of all compared cropping systems. Reporter strain-based gene expression assays did not reveal any differences in Pseudomonas antimicrobial gene expression between soils from different cropping systems. Our results suggest that plant-beneficial pseudomonads can be favoured by certain soil cropping systems, but soil resistance against plant diseases is likely determined by a multitude of biotic factors in addition to Pseudomonas.
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Affiliation(s)
- Francesca Dennert
- ETH Zürich, Plant Pathology, Institute of Integrative Biology, Universitätsstrasse 2, 8092 Zürich, Switzerland
| | - Nicola Imperiali
- University of Lausanne, Department of Fundamental Microbiology, Quartier UNIL-Sorge, CH-1015 Lausanne, Switzerland
| | - Cornelia Staub
- ETH Zürich, Plant Pathology, Institute of Integrative Biology, Universitätsstrasse 2, 8092 Zürich, Switzerland
| | - Jana Schneider
- ETH Zürich, Plant Pathology, Institute of Integrative Biology, Universitätsstrasse 2, 8092 Zürich, Switzerland
| | - Titouan Laessle
- University of Lausanne, Department of Fundamental Microbiology, Quartier UNIL-Sorge, CH-1015 Lausanne, Switzerland
| | - Tao Zhang
- Agroscope, Division of Agroecology and Environment, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland.,Institute of Grassland Sciences, Northeast Normal University, Key Laboratory for Vegetation Ecology, Ministry of Education, 130024 Changchun, China
| | - Raphaël Wittwer
- Agroscope, Division of Agroecology and Environment, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | | | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland
| | - Klaus Schlaeppi
- Agroscope, Division of Agroecology and Environment, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Christoph Keel
- University of Lausanne, Department of Fundamental Microbiology, Quartier UNIL-Sorge, CH-1015 Lausanne, Switzerland
| | - Monika Maurhofer
- ETH Zürich, Plant Pathology, Institute of Integrative Biology, Universitätsstrasse 2, 8092 Zürich, Switzerland
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Differences in Bacterial Diversity, Composition and Function due to Long-Term Agriculture in Soils in the Eastern Free State of South Africa. DIVERSITY 2019. [DOI: 10.3390/d11040061] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Land-use change from natural to managed agricultural ecosystems significantly impacts soil bacterial diversity and function. The Eastern Free State (EFS) is one of the most productive agricultural regions in South Africa. However, no studies aiming to understand the changes in bacterial diversity, composition and function due to land-use change in this area have been conducted. This study investigated, using high-throughput 16S rRNA gene amplicon sequencing, the effects of long-term agriculture on bacterial diversity, composition and putative function in the EFS by comparing microbiomes from lands that have been under agronomic activity for over 50 years to those from uncultivated land. Results indicate that agriculture increased bacterial diversity. Soil chemical analysis showed that land-use shifted soils from being oligotrophic to copiotrophic, which changed bacterial communities from being Actinobacteria dominated to Proteobacteria dominated. Predictive functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) suggested that agricultural soil was abundant in genes associated with plant fitness and plant growth promotion, while non-agricultural soil was abundant in genes related to organic matter degradation. Together, these results suggest that edaphic factors induced by long-term agriculture resulted in shifts in bacterial diversity and putative function in the EFS.
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Cania B, Vestergaard G, Krauss M, Fliessbach A, Schloter M, Schulz S. A long-term field experiment demonstrates the influence of tillage on the bacterial potential to produce soil structure-stabilizing agents such as exopolysaccharides and lipopolysaccharides. ENVIRONMENTAL MICROBIOME 2019; 14:1. [PMID: 33902712 PMCID: PMC7989815 DOI: 10.1186/s40793-019-0341-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 05/16/2023]
Abstract
BACKGROUND Stable soil aggregates are essential for optimal crop growth and preventing soil erosion. However, tillage is often used in agriculture to loosen the soil, which disrupts the integrity of these aggregates. Soil aggregation can be enhanced by bacteria through their ability to produce exopolysaccharides and lipopolysaccharides. These compounds stabilize soil aggregates by "gluing" soil particles together. However, it has yet to be shown how tillage influences the bacterial potential to produce aggregate-stabilizing agents. Therefore, we sampled conventional and reduced tillage treatments at 0-10 cm, 10-20 cm and 20-50 cm from a long-term field trial in Frick, Switzerland. We compared the stable aggregate fraction of the soil and the bacterial potential to produce exopolysaccharides (EPS) and lipopolysaccharides (LPS) under different tillage regimes by employing a shotgun metagenomic approach. We established a method which combines hidden Markov model searches with blasts against sequences derived from the Kyoto Encyclopedia of Genes and Genomes database to analyze genes specific for the biosynthesis of these compounds. RESULTS Our data revealed that the stable aggregate fraction as well as the bacterial potential to produce EPS and LPS were comparable under both tillage regimes. The highest potential to produce these compounds was found in the upper soil layer, which was disturbed by tillage, but had higher content of organic carbon compared to the layer below the tillage horizon. Additionally, key players of EPS and LPS production differed at different sampling depths. Some families with high potential to produce EPS and LPS, such as Chitinophagaceae and Bradyrhizobiaceae, were more abundant in the upper soil layers, while others, e.g. Nitrospiraceae and Planctomycetaceae, preferred the lowest sampled soil depth. Each family had the potential to form a limited number of different aggregate-stabilizing agents. CONCLUSIONS Our results indicate that conventional tillage and reduced tillage equally promote the bacterial potential to produce EPS and LPS in the tillage horizon. However, as major bacterial groups triggering EPS and LPS formation were not the same, it is likely that gene expression pattern differ in the different treatments due to various pathways of gene induction and transcription in different bacterial species.
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Affiliation(s)
- Barbara Cania
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Maike Krauss
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), Ackerstrasse 113, 5070 Frick, Switzerland
| | - Andreas Fliessbach
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), Ackerstrasse 113, 5070 Frick, Switzerland
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Soil Science, Technical University of Munich, Emil-Ramann-Straße 2, 85354 Freising, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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Changes of paradigms in agriculture soil microbiology and new challenges in microbial ecology. ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY 2019. [DOI: 10.1016/j.actao.2019.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Fajardo C, García-Cantalejo J, Botías P, Costa G, Nande M, Martin M. New insights into the impact of nZVI on soil microbial biodiversity and functionality. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2018; 54:157-167. [PMID: 30588856 DOI: 10.1080/10934529.2018.1535159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/05/2018] [Accepted: 10/09/2018] [Indexed: 06/09/2023]
Abstract
Nanoscale zero-valent iron (nZVI) is a strong reducing agent used for in situ remediation of soil. The impacts of nZVI (5-10% w/w) on the soil microbial biodiversity and functionality of two soils (Lufa 2.2 and 2.4) were assessed. Illumina MiSeq technology was used to evaluate the structure of soil microbiomes after 21 days of exposure. Proteobacteria, Verrucomicrobia, Firmicutes and Actinobacteria were the most abundant phyla in both soils. However, the dynamics of bacterial community composition following nZVI addition differed. nZVI exposure induced pronounced shifts in the microbial composition of soil 2.4, but not in soil 2.2; an increase in Verrucomicrobia abundance was the unique common taxonomic pattern observed in both soils. The PICRUSt approach was applied to predict the functional composition of each metagenome. Environmental information processing function (membrane transport) was decreased in both nZVI-spiked soils, although soil 2.4 samples were enriched in functions involved in cellular processes and metabolism. The effects of nZVI on autochthonous bacterial communities clearly varied with the soil type assessed; changes at the phylogenetic level appeared to be more abundant than those observed at the functional level, and thus, the overall effort of the soil ecosystem might involve the maintenance of functionality following nZVI exposure.
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Affiliation(s)
- Carmen Fajardo
- a Facultad de Farmacia , Universidad de Alcalá , Alcalá de Henares , Madrid , Spain
| | - Jesús García-Cantalejo
- b Genomics Facility , Universidad Complutense, Parque Científico (UCM-PCM) , Madrid , Spain
| | - Pedro Botías
- b Genomics Facility , Universidad Complutense, Parque Científico (UCM-PCM) , Madrid , Spain
| | - Gonzalo Costa
- c Facultad de Veterinaria , Universidad Complutense , Madrid , Spain
| | - Mar Nande
- c Facultad de Veterinaria , Universidad Complutense , Madrid , Spain
| | - Margarita Martin
- c Facultad de Veterinaria , Universidad Complutense , Madrid , Spain
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