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Cornell CR, Zhang Y, Ning D, Xiao N, Wagle P, Xiao X, Zhou J. Land use conversion increases network complexity and stability of soil microbial communities in a temperate grassland. THE ISME JOURNAL 2023; 17:2210-2220. [PMID: 37833523 PMCID: PMC10689820 DOI: 10.1038/s41396-023-01521-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/29/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023]
Abstract
Soils harbor highly diverse microbial communities that are critical to soil health, but agriculture has caused extensive land use conversion resulting in negative effects on critical ecosystem processes. However, the responses and adaptations of microbial communities to land use conversion have not yet been understood. Here, we examined the effects of land conversion for long-term crop use on the network complexity and stability of soil microbial communities over 19 months. Despite reduced microbial biodiversity in comparison with native tallgrass prairie, conventionally tilled (CT) cropland significantly increased network complexity such as connectivity, connectance, average clustering coefficient, relative modularity, and the number of species acting at network hubs and connectors as well as resulted in greater temporal variation of complexity indices. Molecular ecological networks under CT cropland became significantly more robust and less vulnerable, overall increasing network stability. The relationship between network complexity and stability was also substantially strengthened due to land use conversion. Lastly, CT cropland decreased the number of relationships between network structure and environmental properties instead being strongly correlated to management disturbances. These results indicate that agricultural disturbance generally increases the complexity and stability of species "interactions", possibly as a trade-off for biodiversity loss to support ecosystem function when faced with frequent agricultural disturbance.
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Affiliation(s)
- Carolyn R Cornell
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, USA
| | - Ya Zhang
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Daliang Ning
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Naijia Xiao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Pradeep Wagle
- USDA, Agricultural Research Service, Oklahoma and Central Plains Agricultural Research Center, El Reno, OK, USA
| | - Xiangming Xiao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Ok, USA.
- School of Computer Science, University of Oklahoma, Norman, OK, USA.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Varela C, Alperstein L, Sundstrom J, Solomon M, Brady M, Borneman A, Jiranek V. A special drop: Characterising yeast isolates associated with fermented beverages produced by Australia's indigenous peoples. Food Microbiol 2023; 112:104216. [PMID: 36906316 DOI: 10.1016/j.fm.2023.104216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/11/2023]
Abstract
Way-a-linah, an alcoholic beverage produced from the fermented sap of Eucalyptus gunnii, and tuba, a fermented drink made from the syrup of Cocos nucifera fructifying bud, are two of several fermented beverages produced by Australian Aboriginal and Torres Strait people. Here we describe the characterisation of yeast isolates from samples associated with the fermentation of way-a-linah and tuba. Microbial isolates were obtained from two different geographical locations in Australia - the Central Plateau in Tasmania, and Erub Island in the Torres Strait. While Hanseniaspora species and Lachancea cidri were the most abundant species in Tasmania, Candida species were the most abundant in Erub Island. Isolates were screened for tolerance to stress conditions found during the production of fermented beverages and for enzyme activities relevant to the appearance, aroma and flavour of these beverages. Based on screening results, eight isolates were evaluated for their volatile profile during the fermentation of wort, apple juice and grape juice. Diverse volatile profiles were observed for beers, ciders and wines fermented with different isolates. These findings reveal the potential of these isolates to produce fermented beverages with unique aroma and flavour profiles and highlight the vast microbial diversity associated with fermented beverages produced by Australia's Indigenous peoples.
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Affiliation(s)
- Cristian Varela
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA 5064, Australia; Department of Wine Science, The University of Adelaide, Glen Osmond, SA 5064, Australia.
| | - Lucien Alperstein
- Department of Wine Science, The University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Joanna Sundstrom
- Department of Wine Science, The University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Mark Solomon
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA 5064, Australia
| | - Maggie Brady
- Centre for Aboriginal Economic Policy Research, College of Arts and Social Sciences, The Australian National University, Acton, ACT 2601, Australia
| | - Anthony Borneman
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA 5064, Australia; Department of Wine Science, The University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Vladimir Jiranek
- Department of Wine Science, The University of Adelaide, Glen Osmond, SA 5064, Australia
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Gui H, Fan L, Wang D, Yan P, Li X, Pang Y, Zhang L, Zamanian K, Shi L, Xu J, Han W. Variations in Soil Nutrient Dynamics and Bacterial Communities After the Conversion of Forests to Long-Term Tea Monoculture Systems. Front Microbiol 2022; 13:896530. [PMID: 35814650 PMCID: PMC9263701 DOI: 10.3389/fmicb.2022.896530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/08/2022] [Indexed: 01/04/2023] Open
Abstract
The soil microbial community is a key indicator to evaluate the soil health and productivities in agricultural ecosystems. Monoculture and conversions of forests to tea plantations have been widely applied in tea plantation globally, but long-term monoculture of tea plantation could lead to soil degradation and yield decline. Understanding how long-term monoculture systems influence the soil health and ecosystem functions in tea plantation is of great importance for soil environment management. In this study, through the comparison of three independent tea plantations across eastern China composed of varying stand ages (from 3 to 90 years after conversion from forest), we found that long-term tea monoculture led to significant increases in soil total organic carbon (TOC) and microbial nitrogen (MBN). Additionally, the structure, function, and co-occurrence network of soil bacterial communities were investigated by pyrosequencing 16S rRNA genes. The pyrosequencing analysis revealed that the structures and functions of soil bacterial communities were significantly affected by different stand ages, but sampling sites and land-use conversion (from forest to tea plantation) had stronger effects than stand age on the diversity and structure of soil bacterial communities. Soil bacterial diversity can be improved with increasing stand ages in tea plantation. Further RDA analysis revealed that the C and N availability improvement in tea plantation soils led to the variation of structure and function in soil bacterial communities. Moreover, co-occurrence network analysis of soil bacterial communities also demonstrated that interactions among soil bacteria taxa were strengthened with increasing stand age. Our findings suggest that long-term monoculture with proper managements could be beneficial to soil ecosystems by increasing the C and N content and strengthening bacterial associations in tea plantations. Overall, this study provides a comprehensive understanding of the impact of land-use change and long-term monoculture stand age on soil environments in tea plantation.
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Affiliation(s)
- Heng Gui
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Lichao Fan
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen, Germany
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- *Correspondence: Lichao Fan,
| | - Donghui Wang
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Peng Yan
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Xin Li
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Yinghua Pang
- Bureau of Agriculture and Rural Affairs of the Yuhang District, Hangzhou, China
| | - Liping Zhang
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Kazem Zamanian
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen, Germany
- School of Geographical Sciences, Nanjing University of Information Science and Technology, Nanjing, China
| | - Lingling Shi
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jianchu Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Wenyan Han
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Wenyan Han,
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Temporal Dynamics of Bacterial Communities along a Gradient of Disturbance in a U.S. Southern Plains Agroecosystem. mBio 2022; 13:e0382921. [PMID: 35420482 PMCID: PMC9239210 DOI: 10.1128/mbio.03829-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Land conversion for intensive agriculture produces unfavorable changes to soil ecosystems, causing global concern. Soil bacterial communities mediate essential terrestrial ecosystem processes, making it imperative to understand their responses to agricultural perturbations. Here, we used high-throughput sequencing coupled with a functional gene array to study temporal dynamics of soil bacterial communities over 1 year under different disturbance intensities across a U.S. Southern Plains agroecosystem, including tallgrass prairie, Old World bluestem pasture, no-tillage (NT) canola, and conventional tillage (CT) wheat. Land use had the greatest impact on bacterial taxonomic diversity, whereas sampling time and its interaction with land use were central to functional diversity differences. The main drivers of taxonomic diversity were tillage > sampling time > temperature, while all measured factors explained similar amounts of variations in functional diversity. Temporal differences had the strongest correlation with total nitrogen > rainfall > nitrate. Within land uses, community variations for CT wheat were attributed to nitrogen levels, whereas soil organic matter and soil water content explained community variations for NT canola. In comparison, all measured factors contributed almost equally to variations in grassland bacterial communities. Finally, functional diversity had a stronger relationship with taxonomic diversity for CT wheat compared to phylogenetic diversity in the prairie. These findings reinforce that tillage management has the greatest impact on bacterial community diversity, with sampling time also critical. Hence, our study highlights the importance of the interaction between temporal dynamics and land use in influencing soil microbiomes, providing support for reducing agricultural disturbance to conserve soil biodiversity.
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Metagenomic insights into the microbial community structure and resistomes of a tropical agricultural soil persistently inundated with pesticide and animal manure use. Folia Microbiol (Praha) 2022; 67:707-719. [PMID: 35415828 DOI: 10.1007/s12223-022-00970-9] [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: 12/31/2021] [Accepted: 04/05/2022] [Indexed: 11/04/2022]
Abstract
Persistent use of pesticides and animal manure in agricultural soils inadvertently introduced heavy metals and antibiotic/antibiotic resistance genes (ARGs) into the soil with deleterious consequences. The microbiome and heavy metal and antibiotic resistome of a pesticide and animal manure inundated agricultural soil (SL6) obtained from a vegetable farm at Otte, Eiyenkorin, Kwara State, Nigeria, was deciphered via shotgun metagenomics and functional annotation of putative ORFs (open reading frames). Structural metagenomics of SL6 microbiome revealed 29 phyla, 49 classes, 94 orders, 183 families, 366 genera, 424 species, and 260 strains with the preponderance of the phyla Proteobacteria (40%) and Actinobacteria (36%), classes Actinobacteria (36%), Alphaproteobacteria (18%), and Gammaproteobacteria (17%), and genera Kocuria (16%), Sphingobacterium (11%), and Brevundimonas (10%), respectively. Heavy metal resistance genes annotation conducted using Biocide and Metal Resistance Gene Database (BacMet) revealed the detection of genes responsible for the uptake, transport, detoxification, efflux, and regulation of copper, cadmium, zinc, nickel, chromium, cobalt, selenium, tungsten, mercury, and several others. ARG annotation using the Antibiotic Resistance Gene-annotation (ARG-ANNOT) revealed ARGs for 11 antibiotic classes with the preponderance of β-lactamases, mobilized colistin resistance determinant (mcr-1), macrolide-lincosamide-streptogramin (MLS), glycopeptide, and aminoglycoside resistance genes, among others. The persistent use of pesticide and animal manure is strongly believed to play a major role in the proliferation of heavy metal and antibiotic resistance genes in the soil. This study revealed that agricultural soils inundated with pesticide and animal manure use are potential hotspots for ARG spread and may accentuate the spread of multidrug resistant clinical pathogens.
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6
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Singh U, Choudhary AK, Sharma S. A 3-year field study reveals that agri-management practices drive the dynamics of dominant bacterial taxa in the rhizosphere of Cajanus cajan. Symbiosis 2022. [DOI: 10.1007/s13199-022-00834-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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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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Osman JR, Wang Y, Jaubert C, Nguyen TN, Fernandes GR, DuBow MS. The bacterial communities of surface soils from desert sites in the eastern Utah (USA) portion of the Colorado Plateau. Microbiol Res 2020; 244:126664. [PMID: 33359841 DOI: 10.1016/j.micres.2020.126664] [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: 05/24/2020] [Revised: 09/11/2020] [Accepted: 11/27/2020] [Indexed: 01/05/2023]
Abstract
Desert-like areas located in the eastern portion of the state of Utah (USA) have geographic features that can resemble the surface of the planet Mars, characterized by red-colored hills, soils and sandstones. We examined the bacterial biodiversity of surface soil samples from several sites from the Colorado Plateau Desert in eastern Utah using pyrosequencing of PCR amplified bacterial 16S rRNA genes from total extracted soil DNA. The sample sites cover the Great Basin, Goblin Valley State Park and nearby regions on the Colorado Plateau. We also examined several physicochemical parameters of the soil 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 Proteobacteria, Actinobacteria, Bacteroidetes, and Gemmatimonadetes. The most abundant genera in our samples were found to belong to the Cesiribacter, Lysobacter, Adhaeribacter, Microvirga and Pontibacter genera. We found that the relative abundance of Proteobacteria and Gemmatimonadetes were significantly correlated with soil pH and a low concentration of organic matter, suggesting that, in these relatively high-altitude desert soils, these two parameters may be of primary importance to influence bacterial community composition.
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Affiliation(s)
- Jorge R Osman
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France
| | - Yang Wang
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France
| | - Chloé Jaubert
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France
| | - Tuyet-Nga Nguyen
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France
| | - Gustavo R Fernandes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France
| | - Michael S DuBow
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France.
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Discovering the indigenous microbial communities associated with the natural fermentation of sap from the cider gum Eucalyptus gunnii. Sci Rep 2020; 10:14716. [PMID: 32895409 PMCID: PMC7477236 DOI: 10.1038/s41598-020-71663-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 08/19/2020] [Indexed: 12/13/2022] Open
Abstract
Over the course of human history and in most societies, fermented beverages have had a unique economic and cultural importance. Before the arrival of the first Europeans in Australia, Aboriginal people reportedly produced several fermented drinks including mangaitch from flowering cones of Banksia and way-a-linah from Eucalyptus tree sap. In the case of more familiar fermented beverages, numerous microorganisms, including fungi, yeast and bacteria, present on the surface of fruits and grains are responsible for the conversion of the sugars in these materials into ethanol. Here we describe native microbial communities associated with the spontaneous fermentation of sap from the cider gum Eucalyptus gunnii, a Eucalyptus tree native to the remote Central Plateau of Tasmania. Amplicon-based phylotyping showed numerous microbial species in cider gum samples, with fungal species differing greatly to those associated with winemaking. Phylotyping also revealed several fungal sequences which do not match known fungal genomes suggesting novel yeast species. These findings highlight the vast microbial diversity associated with the Australian Eucalyptus gunnii and the native alcoholic beverage way-a-linah.
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Seasonal and Agricultural Response of Acidobacteria Present in Two Fynbos Rhizosphere Soils. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12070277] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Acidobacteria is one of the most abundant phyla in most soil types. Fynbos plants are endemic to South Africa, and these soils provide the ideal habitat for Acidobacteria, because of its low pH and oligotrophic properties. However, little is known about their distribution in the fynbos biome and the impact of cultivation of plants on Acidobacterial diversity. Therefore, the aim of this study was to determine the effect of seasonal changes and cultivation on the relative abundance and diversity of Acidobacteria associated with Aspalathus linearis (rooibos) and Cyclopia spp. (honeybush). This study was based on rhizosphere soil. A total of 32 and 31 operational taxonomic units (OTUs) were identified for honeybush and rooibos, respectively. The majority of these were classified as representatives of subdivisions 1, 2, 3, and 10. Significant differences in community compositions were observed between seasons for both honeybush and rooibos, as well as between the cultivated and uncultivated honeybush. Acidobacteria had a significantly positive correlation with pH, C, Ca2+, and P. In this study, we have shown the effect of seasonal changes, in summer and winter, and cultivation farming on the relative abundance and diversity of Acidobacteria present in the soil of rooibos and honeybush.
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Effects of cadmium perturbation on the microbial community structure and heavy metal resistome of a tropical agricultural soil. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00314-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractThe effects of cadmium (Cd) contamination on the microbial community structure, soil physicochemistry and heavy metal resistome of a tropical agricultural soil were evaluated in field-moist soil microcosms. A Cd-contaminated agricultural soil (SL5) and an untreated control (SL4) were compared over a period of 5 weeks. Analysis of the physicochemical properties and heavy metals content of the two microcosms revealed a statistically significant decrease in value of the soil physicochemical parameters (P < 0.05) and concentration of heavy metals (Cd, Pb, Cr, Zn, Fe, Cu, Se) content of the agricultural soil in SL5 microcosm. Illumina shotgun sequencing of the DNA extracted from the two microcosms showed the predominance of the phyla, classes, genera and species of Proteobacteria (37.38%), Actinobacteria (35.02%), Prevotella (6.93%), and Conexibacter woesei (8.93%) in SL4, and Proteobacteria (50.50%), Alphaproteobacteria (22.28%), Methylobacterium (9.14%), and Methylobacterium radiotolerans (12,80%) in SL5, respectively. Statistically significant (P < 0.05) difference between the metagenomes was observed at genus and species delineations. Functional annotation of the two metagenomes revealed diverse heavy metal resistome for the uptake, transport, efflux and detoxification of various heavy metals. It also revealed the exclusive detection in SL5 metagenome of members of RND (resistance nodulation division) protein czcCBA efflux system (czcA, czrA, czrB), CDF (cation diffusion facilitator) transporters (czcD), and genes for enzymes that protect the microbial cells against cadmium stress (sodA, sodB, ahpC). The results obtained in this study showed that Cd contamination significantly affects the soil microbial community structure and function, modifies the heavy metal resistome, alters the soil physicochemistry and results in massive loss of some autochthonous members of the community not adapted to the Cd stress.
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Sun Y, Luo C, Jiang L, Song M, Zhang D, Li J, Li Y, Ostle NJ, Zhang G. Land-use changes alter soil bacterial composition and diversity in tropical forest soil in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 712:136526. [PMID: 31945538 DOI: 10.1016/j.scitotenv.2020.136526] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 01/02/2020] [Accepted: 01/03/2020] [Indexed: 06/10/2023]
Abstract
Tropical forests, under pressure from human activities, are important reservoirs of biodiversity and regulators of global biogeochemical cycles. Land-use and management are influential drivers of environmental change and ecosystem sustainability. However, only limited studies have analysed the impacts of planting age and vegetation type under land-use change on soil microbial community in tropical forests simultaneously. Here, we assessed soil bacterial community composition and diversity under different land-use in Hainan Province, China, using high-throughput sequencing combined with PICRUSt analysis. Land-use included natural forest, 5-year-old cropland, young (5-year-old) rubber tree plantation, and old (30-year-old) rubber tree plantation. Land-use changes altered the soil bacterial community composition but had a non-significant influence on alpha diversity (P > .05). We found that bacterial beta-diversity significantly decreased in young rubber tree plantation soils and cropland soils compared to natural forest as a control. In contrast, soil bacterial beta-diversity increased in old rubber tree plantation soils, indicating the effects of time since planting. There was no difference in microbial beta-diversity between soils from cropland and young rubber tree plantation. Soil bulk density and moisture, not pH, were the main environmental factors explaining the variability in microbial diversity. PICRUSt analysis of soil bacterial predicted gene abundances within metabolic pathways and indicated that land-use change altered soil functional traits, e.g., amino acid-related enzymes, ribosomes, DNA repair/recombination proteins and oxidative phosphorylation. Also, vegetation type, not planting age, had significant impacts on soil functional traits. Overall, planting age had the greatest influence on soil bacterial beta-diversity, while vegetation type was more crucial for soil functional traits (P < .05).
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Affiliation(s)
- Yingtao Sun
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
| | - Longfei Jiang
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Mengke Song
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Jun Li
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yongtao Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Nicholas J Ostle
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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13
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Yanez-Montalvo A, Gómez-Acata S, Águila B, Hernández-Arana H, Falcón LI. The microbiome of modern microbialites in Bacalar Lagoon, Mexico. PLoS One 2020; 15:e0230071. [PMID: 32210450 PMCID: PMC7094828 DOI: 10.1371/journal.pone.0230071] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 02/20/2020] [Indexed: 11/18/2022] Open
Abstract
Microbialites are highly diverse microbial communities that represent modern examples of the oldest life forms, stromatolites (dated >3.7 Ga). Bacalar Lagoon, in Mexico, harbors the largest freshwater microbialite occurrences of the world; yet diverse anthropogenic activities are changing the oligotrophic conditions of the lagoon. The objective of this work was to perform a spatial exploration of the microbialites of Bacalar Lagoon, analyze their prokaryote diversity, following a high throughput sequencing approach of the V4 region of the 16S rDNA, and correlate to the environmental parameters that influence the structure of these communities. The results indicate the presence of microbialites throughout the periphery of the lagoon. The microbiome of the microbialites is composed primarily of Proteobacteria (40-80%), Cyanobacteria (1-11%), Bacteroidetes (7-8%), Chloroflexi (8-14%), Firmicutes (1-23%), Planctomycetes (1-8%), and Verrucomicrobia (1-4%). Phylogenetic distance analyses suggests two distinct groups of microbialites associated with regions in the lagoon that have differences in their environmental parameters, including soluble reactive silicate (in the north), bicarbonates and available forms of nitrogen (ammonium, nitrates and nitrites) (in the south). These microbialite groups had differences in their microbiome composition associated to strong anthropogenic pressure on water quality (agriculture, landfill leachate, lack of water treatment infrastructure and intensive tourism), which were related to a loss of microbial diversity.
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Affiliation(s)
- Alfredo Yanez-Montalvo
- UNAM, Instituto de Ecología, Parque Científico y Tecnológico de Yucatán, Sierra Papacal, Yucatán, México
- El Colegio de la Frontera Sur Unidad Chetumal, Chetumal, Quintana Roo, Mexico
| | - Selene Gómez-Acata
- UNAM, Instituto de Ecología, Parque Científico y Tecnológico de Yucatán, Sierra Papacal, Yucatán, México
| | - Bernardo Águila
- UNAM, Instituto de Ecología, Parque Científico y Tecnológico de Yucatán, Sierra Papacal, Yucatán, México
| | | | - Luisa I. Falcón
- UNAM, Instituto de Ecología, Parque Científico y Tecnológico de Yucatán, Sierra Papacal, Yucatán, México
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14
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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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15
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Qi X, Liu B, Wu H, Song Q, Jiang J, Bu Y, Rui J, Zou B, Zhou G. Bacterial communities under long-term conventional and transgenic cotton farming systems using V3-V5 and V5-V9 of 16s rDNA. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 164:618-628. [PMID: 30165339 DOI: 10.1016/j.ecoenv.2018.08.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/20/2018] [Accepted: 08/10/2018] [Indexed: 06/08/2023]
Abstract
Understanding the community structure of soil microbes is required to evaluate the potential effects of genetically modified (GM) plants on ecological environments. Bacterial communities in soil planted with conventional cotton (CC) and transgenic cultivar (TC) in a natural ecosystem for three years were characterized by 454 pyrosequencing of the V3-V5 and V5-V9 regions of 16S rDNA from June to September 2013. V3-V5 and V5-V9 regions yielded a total of 12,848 and 10,541 OTUs, respectively. The V5-V9 amplicon was additionally used to detect phyla that were poorly sequenced by V3-V5 (such as Chlamydiae, Crenarchaeota and Archaea). Among the species detected by each primer pair, 46% of the species identified from V3-V5 and 60% of those identified from V5-V9 were detected by both primer pairs. Although distinct bacterial compositions existed between the two amplified regions, statistical analysis revealed no significant difference in the diversity indexes or phylogenetic patterns in TC versus compared to those in the CC control. Further, clustering analysis in both regions indicated that there was no unambiguous aggregation in TC compared to that in CC control. Of all 26 phyla detected by both regions, each region detected 2 distinct phyla exhibiting significant variations in abundance. The species unique to each treatment field accounted for less than 27% of all species and were rare taxa (abundance < 0.15%). However, a small fraction of diagnostic taxa with specific ecological functions differed significantly between TC and CC. These differences were not driven by any obvious environmental factors. The results established a comprehensive inventory of the bacterial communities associated with GM plants and indicated that transgenic cotton may not significantly affect soil microorganisms compared with conventional cotton over a three-year period. Furthermore, diagnostic taxa were provided for monitoring the perturbation in soil, but further verification in future studies is required.
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Affiliation(s)
- Xiemin Qi
- Department of Pharmacology, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, School of Medicine, Nanjing University, Nanjing 210002, China
| | - Biao Liu
- Key Laboratory of Biosafety, Ministry of Environmental Protection of China, Nanjing Institute of Environmental Sciences, Nanjing 210042, China
| | - Haiping Wu
- Huadong Research Institute for Medicine and Biotechnics, Nanjing 210002, China
| | - Qinxin Song
- Department of Pharmacology, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, School of Medicine, Nanjing University, Nanjing 210002, China; Department of Pharmaceutical Analysis, Jiangsu key lab of drug screening, China Pharmaceutical University, Nanjing 210009, China
| | - Jingwei Jiang
- Department of Pharmaceutical Analysis, Jiangsu key lab of drug screening, China Pharmaceutical University, Nanjing 210009, China
| | - Ying Bu
- Huadong Research Institute for Medicine and Biotechnics, Nanjing 210002, China
| | - Jianzhong Rui
- Department of Pharmacology, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, School of Medicine, Nanjing University, Nanjing 210002, China
| | - Bingjie Zou
- Department of Pharmacology, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, School of Medicine, Nanjing University, Nanjing 210002, China.
| | - Guohua Zhou
- Department of Pharmacology, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, School of Medicine, Nanjing University, Nanjing 210002, China.
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16
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Lin YT, Whitman WB, Coleman DC, Chiu CY. Effects of Reforestation on the Structure and Diversity of Bacterial Communities in Subtropical Low Mountain Forest Soils. Front Microbiol 2018; 9:1968. [PMID: 30186273 PMCID: PMC6110939 DOI: 10.3389/fmicb.2018.01968] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 08/02/2018] [Indexed: 11/15/2022] Open
Abstract
Reforestation with different tree species could alter soil properties and in turn affect the bacterial community. However, the effects of long-term reforestation on bacterial community structure and diversity of subtropical forest soils are poorly understood. In the current study, we applied error-corrected barcoded pyrosequencing to characterize the differences in the soil bacterial community in a low mountain, subtropical forest subjected to reforestation. The communities were sampled in the summer and winter from a native broadleaved forest (BROAD-Nat) and two adjacent coniferous plantations, a Calocedrus formosana forest of 80 years (CONIF-80) and a Cunninghamia konishii forest of 40 years (CONIF-40). The soil bacterial communities among three forest types were dominated by Acidobacteria and Alphaproteobacteria. The distribution of abundant genera among communities was different. Based on the Shannon diversity index, the bacterial alpha diversity of CONIF-40 community was significantly higher than that in the CONIF-80 and BROAD-Nat soils. In both of the coniferous plantations, the soil bacterial diversity in summer was also higher than that in winter. Distribution of some abundant phylogenetic groups, K-shuff and redundancy analysis of beta diversity among communities showed that the bacterial structure of three soil communities differed between two seasons. These results suggest that seasonal differences influence the diversity and structure of bacterial soil communities and that the communities remain different even after a long period of reforestation.
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Affiliation(s)
- Yu-Te Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - David C Coleman
- Odum School of Ecology, University of Georgia, Athens, GA, United States
| | - Chih-Yu Chiu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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17
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Tian T, Chen Z, Tian Y, Gao L. Microbial diversity in solar greenhouse soils in Round-Bohai Bay-Region, China: The influence of cultivation year and environmental condition. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:23236-23249. [PMID: 28831706 DOI: 10.1007/s11356-017-9837-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 07/26/2017] [Indexed: 06/07/2023]
Abstract
Round-Bohai Bay (RBB)-Region is an important crop production area in China, where vegetables are mainly produced in solar greenhouses. However, excessive fertilization and monoculture have caused serious deterioration of soil quality in this region. Soil microbial communities play pivotal roles in many ecosystem processes and are recognized as integrative components of soil quality. Therefore, in this study, we investigated bacterial and fungal diversity in solar greenhouse soils covering a wide range of cultivation year (CY) and sampling site (SS), by using pyrosequencing technology. Surprisingly, CY and SS had little influence on bacterial and fungal relative abundance and diversity. However, environmental factors (EF) and soil available potassium (K) in particular made a significant contribution to the variation of soil bacterial and fungal communities. Specifically, K showed significant (P < 0.05) correlations with dominant bacterial phyla Bacteroidetes, Acidobacteria, Chloroflexi, and Planctomycetes and fungal phyla Ascomycota and Basidiomycota. These results suggested that soil EF appeared more important than CY and SS in shaping the compositions of bacterial and fungal communities. In addition, since fertilizer K has been in the long-term abused in RBB-Region, future vegetable production should pay more attention to K input to reduce the negative effect on soil microbial communities.
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Affiliation(s)
- Tian Tian
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, 2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Zhiqun Chen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, 2 Yuanmingyuan Xilu, Beijing, 100193, China
- College of Life Science, Linyi University, Shuangling Road, Linyi, 276005, China
| | - Yongqiang Tian
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, 2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Lihong Gao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, 2 Yuanmingyuan Xilu, Beijing, 100193, China.
- Round-Bohai Bay-Region Collaborative Innovation Center for Protected Vegetables, Shenyang Agricultural University, Dongling Road 120, Liaoning, 110866, China.
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18
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Rathore R, Dowling DN, Forristal PD, Spink J, Cotter PD, Bulgarelli D, Germaine KJ. Crop Establishment Practices Are a Driver of the Plant Microbiota in Winter Oilseed Rape ( Brassica napus). Front Microbiol 2017; 8:1489. [PMID: 28848510 PMCID: PMC5553296 DOI: 10.3389/fmicb.2017.01489] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/24/2017] [Indexed: 02/01/2023] Open
Abstract
Gaining a greater understanding of the plant microbiota and its interactions with its host plant heralds a new era of scientific discovery in agriculture. Different agricultural management practices influence soil microbial populations by changing a soil's physical, chemical and biological properties. However, the impact of these practices on the microbiota associated with economically important crops such as oilseed rape, are still understudied. In this work we investigated the impact of two contrasting crop establishment practices, conventional (plow based) and conservation (strip-tillage) systems, on the microbiota inhabiting different plant microhabitats, namely rhizosphere, root and shoot, of winter oilseed rape under Irish agronomic conditions. Illumina 16S rRNA gene sequence profiling showed that the plant associated microhabitats (root and shoot), are dominated by members of the bacterial phyla Proteobacteria, Actinobacteria and Bacteroidetes. The root and shoot associated bacterial communities displayed markedly distinct profiles as a result of tillage practices. We observed a very limited 'rhizosphere effect' in the root zone of WOSR, i.e., there was little or no increase in bacterial community richness and abundance in the WOSR rhizosphere compared to the bulk soil. The two tillage systems investigated did not appear to lead to any major long term differences on the bulk soil or rhizosphere bacterial communities. Our data suggests that the WOSR root and shoot microbiota can be impacted by management practices and is an important mechanism that could allow us to understand how plants respond to different management practices and environments.
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Affiliation(s)
- Ridhdhi Rathore
- Envirocore, Dargan Research Centre, Institute of TechnologyCarlow, Ireland
| | - David N Dowling
- Envirocore, Dargan Research Centre, Institute of TechnologyCarlow, Ireland
| | | | - John Spink
- Teagasc Crops Research CentreCarlow, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, and the APC Microbiome InstituteCork, Ireland
| | - Davide Bulgarelli
- Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton InstituteInvergowrie, Scotland
| | - Kieran J Germaine
- Envirocore, Dargan Research Centre, Institute of TechnologyCarlow, Ireland
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19
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Hill P, Heberlig GW, Boddy CN. Sampling Terrestrial Environments for Bacterial Polyketides. Molecules 2017; 22:E707. [PMID: 28468277 PMCID: PMC6154731 DOI: 10.3390/molecules22050707] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 04/14/2017] [Accepted: 04/18/2017] [Indexed: 12/17/2022] Open
Abstract
Bacterial polyketides are highly biologically active molecules that are frequently used as drugs, particularly as antibiotics and anticancer agents, thus the discovery of new polyketides is of major interest. Since the 1980s discovery of polyketides has slowed dramatically due in large part to the repeated rediscovery of known compounds. While recent scientific and technical advances have improved our ability to discover new polyketides, one key area has been under addressed, namely the distribution of polyketide-producing bacteria in the environment. Identifying environments where producing bacteria are abundant and diverse should improve our ability to discover (bioprospect) new polyketides. This review summarizes for the bioprospector the state-of-the-field in terrestrial microbial ecology. It provides insight into the scientific and technical challenges limiting the application of microbial ecology discoveries for bioprospecting and summarizes key developments in the field that will enable more effective bioprospecting. The major recent efforts by researchers to sample new environments for polyketide discovery is also reviewed and key emerging environments such as insect associated bacteria, desert soils, disease suppressive soils, and caves are highlighted. Finally strategies for taking and characterizing terrestrial samples to help maximize discovery efforts are proposed and the inclusion of non-actinomycetal bacteria in any terrestrial discovery strategy is recommended.
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Affiliation(s)
- Patrick Hill
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| | - Graham W Heberlig
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| | - Christopher N Boddy
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
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20
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Castañeda LE, Barbosa O. Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests. PeerJ 2017; 5:e3098. [PMID: 28382231 PMCID: PMC5376117 DOI: 10.7717/peerj.3098] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 02/15/2017] [Indexed: 11/20/2022] Open
Abstract
Mediterranean biomes are biodiversity hotspots, and vineyards are important components of the Mediterranean landscape. Over the last few decades, the amount of land occupied by vineyards has augmented rapidly, thereby increasing threats to Mediterranean ecosystems. Land use change and agricultural management have important effects on soil biodiversity, because they change the physical and chemical properties of soil. These changes may also have consequences on wine production considering that soil is a key component of terroir. Here, we describe the taxonomic diversity and metabolic functions of bacterial and fungal communities present in forest and vineyard soils in Chile. To accomplish this goal, we collected soil samples from organic vineyards in central Chile and employed a shotgun metagenomic approach to sequence the microbial DNA. Additionally, we studied the surrounding native forest to obtain a baseline of the soil conditions in the area prior to the establishment of the vineyard. Our metagenomic analyses revealed that both habitats shared most of the soil microbial species. The most abundant genera in the two habitats were the bacteria Candidatus Solibacter and Bradyrhizobium and the fungus Gibberella. Our results suggest that the soil microbial communities are similar in these forests and vineyards. Therefore, we hypothesize that native forests surrounding the vineyards may be acting as a microbial reservoir buffering the effects of the land conversion. Regarding the metabolic diversity, we found that genes pertaining to the metabolism of amino acids, fatty acids, and nucleotides as well as genes involved in secondary metabolism were enriched in forest soils. On the other hand, genes related to miscellaneous functions were more abundant in vineyard soils. These results suggest that the metabolic function of microbes found in these habitats differs, though differences are not related to taxonomy. Finally, we propose that the implementation of environmentally friendly practices by the wine industry may help to maintain the microbial diversity and ecosystem functions associated with natural habitats.
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Affiliation(s)
- Luis E Castañeda
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile , Valdivia , Chile
| | - Olga Barbosa
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Instituto de Ecología y Biodiversidad (IEB-Chile), Santiago, Chile
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21
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Characterization of bacterial communities from Masseiras, a unique Portuguese greenhouse agricultural system. Antonie van Leeuwenhoek 2017; 110:665-676. [DOI: 10.1007/s10482-017-0833-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/18/2017] [Indexed: 11/30/2022]
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22
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Lupatini M, Korthals GW, de Hollander M, Janssens TKS, Kuramae EE. Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System. Front Microbiol 2017; 7:2064. [PMID: 28101080 PMCID: PMC5209367 DOI: 10.3389/fmicb.2016.02064] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/07/2016] [Indexed: 11/17/2022] Open
Abstract
Organic farming system and sustainable management of soil pathogens aim at reducing the use of agricultural chemicals in order to improve ecosystem health. Despite the essential role of microbial communities in agro-ecosystems, we still have limited understanding of the complex response of microbial diversity and composition to organic and conventional farming systems and to alternative methods for controlling plant pathogens. In this study we assessed the microbial community structure, diversity and richness using 16S rRNA gene next generation sequences and report that conventional and organic farming systems had major influence on soil microbial diversity and community composition while the effects of the soil health treatments (sustainable alternatives for chemical control) in both farming systems were of smaller magnitude. Organically managed system increased taxonomic and phylogenetic richness, diversity and heterogeneity of the soil microbiota when compared with conventional farming system. The composition of microbial communities, but not the diversity nor heterogeneity, were altered by soil health treatments. Soil health treatments exhibited an overrepresentation of specific microbial taxa which are known to be involved in soil suppressiveness to pathogens (plant-parasitic nematodes and soil-borne fungi). Our results provide a comprehensive survey on the response of microbial communities to different agricultural systems and to soil treatments for controlling plant pathogens and give novel insights to improve the sustainability of agro-ecosystems by means of beneficial microorganisms.
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Affiliation(s)
- Manoeli Lupatini
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
| | - Gerard W. Korthals
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
| | - Thierry K. S. Janssens
- MicroLife SolutionsAmsterdam, Netherlands
- Department of Ecological Science, Vrije Universiteit AmsterdamAmsterdam, Netherlands
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, Netherlands
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23
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Zhou YJ, Li JH, Ross Friedman C, Wang HF. Variation of Soil Bacterial Communities in a Chronosequence of Rubber Tree ( Hevea brasiliensis) Plantations. FRONTIERS IN PLANT SCIENCE 2017; 8:849. [PMID: 28611794 PMCID: PMC5447074 DOI: 10.3389/fpls.2017.00849] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/08/2017] [Indexed: 05/19/2023]
Abstract
Regarding rubber tree plantations, researchers lack a basic understanding of soil microbial communities; specifically, little is known about whether or not soil microbial variation is correlated with succession in these plantations. In this paper, we used high-throughput sequencing of the 16S rRNA gene to investigate the diversity and composition of the soil bacterial communities in a chronosequence of rubber tree plantations that were 5, 10, 13, 18, 25, and 30 years old. We determined that: (1) Soil bacterial diversity and composition show changes over the succession stages of rubber tree plantations. The diversity of soil bacteria were highest in 10, 13, and 18 year-old rubber tree plantations, followed by 30 year-old rubber tree plantations, whereas 5 and 25 year-old rubber tree plantations had the lowest values for diversity. A total of 438,870 16S rDNA sequences were detected in 18 soil samples from six rubber tree plantations, found in 28 phyla, 66 classes, 139 orders, 245 families, 355 genera, and 645 species, with 1.01% sequences from unclassified bacteria. The dominant phyla were Acidobacteria, Proteobacteria, Chloroflexi, Actinobacteria, and Verrucomicrobia (relative abundance large than 3%). There were differences in soil bacterial communities among different succession stages of rubber tree plantation. (2) Soil bacteria diversity and composition in the different stages was closely related to pH, vegetation, soil nutrient, and altitude, of which pH, and vegetation were the main drivers.
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Affiliation(s)
- Yu-Jie Zhou
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan UniversityHaikou, China
- Hainan Agricultural Reclamation Academy of SciencesHaikou, China
- Agricultural Science Research Institute of Hainan ReclamationHaikou, China
| | - Jian-Hua Li
- Hainan Agricultural Reclamation Academy of SciencesHaikou, China
| | | | - Hua-Feng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan UniversityHaikou, China
- *Correspondence: Hua-Feng Wang
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24
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Wolińska A, Kuźniar A, Zielenkiewicz U, Banach A, Izak D, Stępniewska Z, Błaszczyk M. Metagenomic Analysis of Some Potential Nitrogen-Fixing Bacteria in Arable Soils at Different Formation Processes. MICROBIAL ECOLOGY 2017; 73:162-176. [PMID: 27581036 PMCID: PMC5209426 DOI: 10.1007/s00248-016-0837-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/14/2016] [Indexed: 05/08/2023]
Abstract
The main goal of the study was to determine the diversity of the potential nitrogen-fixing (PNF) bacteria inhabiting agricultural (A) soils versus wastelands serving as controls (C). The soils were classified into three groups based on the formation process: autogenic soils (Albic Luvisols, Brunic Arenosols, Haplic Phaeozem) formed on loess material, hydrogenic soils (Mollic Gleysols, Eutric Fluvisol, Eutric Histosol) formed under the effect of stagnant water and lithogenic soils (Rendzina Leptosols) formed on limestone. In order to determine the preferable conditions for PNF bacteria, the relationships between the soil chemical features and bacterial operational taxonomic units (OTUs) were tested. Additionally, the nitrogen content and fertilisation requirement of the lithogenic (LG), autogenic (AG) and hydrogenic (HG) soils were discussed. The composition of the bacterial communities was analysed with the next-generation sequencing (NGS) by the Ion Torrent™ technology. The sequences were clustered into OTU based on a 99 % similarity threshold. The arable soils tested were distinctly dominated by β-Proteobacteria representatives of PNF bacteria belonging to the genus Burkholderia. Bacteria from the α-Proteobacteria class and Devosia genus were subdominants. A free-living Cyanobacteria population dominated in A rather than in C soils. We have found that both soil agricultural management and soil formation processes are the most conducive factors for PNF bacteria, as a majority of these microorganisms inhabit the AG group of soils, whilst the LG soils with the lowest abundance of PNF bacteria revealed the need for additional mineral fertilisation. Our studies have also indicated that there are close relationships between soil classification with respect to soil formation processes and PNF bacteria preference for occupation of soil niches.
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Affiliation(s)
- Agnieszka Wolińska
- Department of Biochemistry and Environmental Chemistry, Institute of Biotechnology, The John Paul II Catholic University of Lublin, 1 I Konstantynów Str, 20-708, Lublin, Poland.
| | - Agnieszka Kuźniar
- Department of Biochemistry and Environmental Chemistry, Institute of Biotechnology, The John Paul II Catholic University of Lublin, 1 I Konstantynów Str, 20-708, Lublin, Poland
| | - Urszula Zielenkiewicz
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, 5a Pawińskiego Str, 02-206, Warsaw, Poland
| | - Artur Banach
- Department of Biochemistry and Environmental Chemistry, Institute of Biotechnology, The John Paul II Catholic University of Lublin, 1 I Konstantynów Str, 20-708, Lublin, Poland
| | - Dariusz Izak
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, 5a Pawińskiego Str, 02-206, Warsaw, Poland
| | - Zofia Stępniewska
- Department of Biochemistry and Environmental Chemistry, Institute of Biotechnology, The John Paul II Catholic University of Lublin, 1 I Konstantynów Str, 20-708, Lublin, Poland
| | - Mieczysław Błaszczyk
- Department of Microbial Biology, Warsaw University of Life Sciences, Nowoursynowska 159 Str, 02-776, Warsaw, Poland
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25
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Postma A, Slabbert E, Postma F, Jacobs K. Soil bacterial communities associated with natural and commercialCyclopiaspp. FEMS Microbiol Ecol 2016; 92:fiw016. [DOI: 10.1093/femsec/fiw016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2016] [Indexed: 12/16/2022] Open
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Pii Y, Borruso L, Brusetti L, Crecchio C, Cesco S, Mimmo T. The interaction between iron nutrition, plant species and soil type shapes the rhizosphere microbiome. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 99:39-48. [PMID: 26713550 DOI: 10.1016/j.plaphy.2015.12.002] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/30/2015] [Accepted: 12/01/2015] [Indexed: 05/07/2023]
Abstract
Plant-associated microorganisms can stimulate plants growth and influence both crops yield and quality by nutrient mobilization and transport. Therefore, rhizosphere microbiome appears to be one of the key determinants of plant health and productivity. The roots of plants have the ability to influence its surrounding microbiology, the rhizosphere microbiome, through the creation of specific chemical niches in the soil mediated by the release of phytochemicals (i.e. root exudates) that depends on several factors, such as plants genotype, soil properties, plant nutritional status, climatic conditions. In the present research, two different crop species, namely barley and tomato, characterized by different strategies for Fe acquisition, have been grown in the RHIZOtest system using either complete or Fe-free nutrient solution to induce Fe starvation. Afterward, plants were cultivated for 6 days on two different calcareous soils. Total DNA was extracted from rhizosphere and bulk soil and 454 pyrosequencing technology was applied to V1-V3 16S rRNA gene region. Approximately 5000 sequences were obtained for each sample. The analysis of the bacterial population confirmed that the two bulk soils showed a different microbial community. The presence of the two plant species, as well as the nutritional status (Fe-deficiency and Fe-sufficiency), could promote a differentiation of the rhizosphere microbiome, as highlighted by non-metric multidimensional scaling (NMDS) analysis. Alphaproteobacteria, Actinobacteria, Chloracidobacteria, Thermoleophilia, Betaproteobacteria, Saprospirae, Gemmatimonadetes, Gammaproteobacteria, Acidobacteria were the most represented classes in all the samples analyzed even though their relative abundance changed as a function of the soil, plant species and nutritional status. To our knowledge, this research demonstrate for the first time that different plants species with a diverse nutritional status can promote the development of a peculiar rhizosphere microbiome, depending on the growth substrate.
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Affiliation(s)
- Youry Pii
- Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, I-39100 Bolzano, Italy.
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, I-39100 Bolzano, Italy
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, I-39100 Bolzano, Italy
| | - Carmine Crecchio
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", via Amendola 165/A, I-70126 Bari, Italy
| | - Stefano Cesco
- Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, I-39100 Bolzano, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, I-39100 Bolzano, Italy
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Miranda-Sánchez F, Rivera J, Vinuesa P. Diversity patterns ofRhizobiaceaecommunities inhabiting soils, root surfaces and nodules reveal a strong selection of rhizobial partners by legumes. Environ Microbiol 2015; 18:2375-91. [DOI: 10.1111/1462-2920.13061] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/17/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Fabiola Miranda-Sánchez
- Programa de Ingeniería Genómica; Centro de Ciencias Genómicas; Universidad Nacional Autónoma de México; Cuernavaca Morelos 62210 Mexico
| | - Javier Rivera
- Programa de Ingeniería Genómica; Centro de Ciencias Genómicas; Universidad Nacional Autónoma de México; Cuernavaca Morelos 62210 Mexico
| | - Pablo Vinuesa
- Programa de Ingeniería Genómica; Centro de Ciencias Genómicas; Universidad Nacional Autónoma de México; Cuernavaca Morelos 62210 Mexico
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28
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Ranjan K, Paula FS, Mueller RC, Jesus EDC, Cenciani K, Bohannan BJM, Nüsslein K, Rodrigues JLM. Forest-to-pasture conversion increases the diversity of the phylum Verrucomicrobia in Amazon rainforest soils. Front Microbiol 2015; 6:779. [PMID: 26284056 PMCID: PMC4519759 DOI: 10.3389/fmicb.2015.00779] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 07/15/2015] [Indexed: 11/13/2022] Open
Abstract
The Amazon rainforest is well known for its rich plant and animal diversity, but its bacterial diversity is virtually unexplored. Due to ongoing and widespread deforestation followed by conversion to agriculture, there is an urgent need to quantify the soil biological diversity within this tropical ecosystem. Given the abundance of the phylum Verrucomicrobia in soils, we targeted this group to examine its response to forest-to-pasture conversion. Both taxonomic and phylogenetic diversities were higher for pasture in comparison to primary and secondary forests. The community composition of Verrucomicrobia in pasture soils was significantly different from those of forests, with a 11.6% increase in the number of sequences belonging to subphylum 3 and a proportional decrease in sequences belonging to the class Spartobacteria. Based on 99% operational taxonomic unit identity, 40% of the sequences have not been detected in previous studies, underscoring the limited knowledge regarding the diversity of microorganisms in tropical ecosystems. The abundance of Verrucomicrobia, measured with quantitative PCR, was strongly correlated with soil C content (r = 0.80, P = 0.0016), indicating their importance in metabolizing plant-derived carbon compounds in soils.
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Affiliation(s)
- Kshitij Ranjan
- Department of Biology, The University of Texas at Arlington Arlington, TX, USA
| | - Fabiana S Paula
- Department of Biology, The University of Texas at Arlington Arlington, TX, USA
| | - Rebecca C Mueller
- Institute of Ecology and Evolution, University of Oregon Eugene, OR, USA
| | | | - Karina Cenciani
- Centro de Energia Nuclear na Agricultura, University of Sao Paulo Piracicaba, Brazil
| | | | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Jorge L M Rodrigues
- Department of Land, Air and Water Resources, University of California, Davis Davis, CA, USA
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