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Matthews K, Cavagnaro T, Weinstein P, Stanhope J. Health by design; optimising our urban environmental microbiomes for human health. ENVIRONMENTAL RESEARCH 2024; 257:119226. [PMID: 38797467 DOI: 10.1016/j.envres.2024.119226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
Humans have evolved in direct and intimate contact with their environment and the microbes that it contains, over a period of 2 million years. As a result, human physiology has become intrinsically linked to environmental microbiota. Urbanisation has reduced our exposure to harmful pathogens, however there is now increasing evidence that these same health-protective improvements in our environment may also be contributing to a hidden disease burden: immune dysregulation. Thoughtful and purposeful design has the potential to ameliorate these health concerns by providing sources of microbial diversity for human exposure. In this narrative review, we highlight the role of environmental microbiota in human health and provide insights into how we can optimise human health through well-designed cities, urban landscapes and buildings. The World Health Organization recommends there should be at least one public green space of least 0.5 ha in size within 300m of a place of residence. We argue that these larger green spaces are more likely to permit functioning ecosystems that deliver ecosystem services, including the provision of diverse aerobiomes. Urban planning must consider the conservation and addition of large public green spaces, while landscape design needs to consider how to maximise environmental, social and public health outcomes, which may include rewilding. Landscape designers need to consider how people use these spaces, and how to optimise utilisation, including for those who may experience challenges in access (e.g. those living with disabilities, people in residential care). There are also opportunities to improve health via building design that improves access to diverse environmental microbiota. Considerations include having windows that open, indoor plants, and the relationship between function, form and organization. We emphasise possibilities for re-introducing potentially health-giving microbial exposures into urban environments, particularly where the benefits of exposure to biodiverse environments may have been lost.
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Affiliation(s)
- Kate Matthews
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia; School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Timothy Cavagnaro
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia; School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia; Environment Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Philip Weinstein
- Environment Institute, The University of Adelaide, Adelaide, SA, Australia; School of Public Health, The University of Adelaide, Adelaide, SA, Australia; South Australian Museum, Adelaide, SA, Australia
| | - Jessica Stanhope
- Environment Institute, The University of Adelaide, Adelaide, SA, Australia; School of Allied Health Science and Practice, The University of Adelaide, Adelaide, SA, Australia.
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Mészárošová L, Kuťáková E, Kohout P, Münzbergová Z, Baldrian P. Plant effects on microbiome composition are constrained by environmental conditions in a successional grassland. ENVIRONMENTAL MICROBIOME 2024; 19:8. [PMID: 38268048 PMCID: PMC10809484 DOI: 10.1186/s40793-024-00550-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
BACKGROUND Below-ground microbes mediate key ecosystem processes and play a vital role in plant nutrition and health. Understanding the composition of the belowground microbiome is therefore important for maintaining ecosystem stability. The structure of the belowground microbiome is largely determined by individual plants, but it is not clear how far their influence extends and, conversely, what the influence of other plants growing nearby is. RESULTS To determine the extent to which a focal host plant influences its soil and root microbiome when growing in a diverse community, we sampled the belowground bacterial and fungal communities of three plant species across a primary successional grassland sequence. The magnitude of the host effect on its belowground microbiome varied among microbial groups, soil and root habitats, and successional stages characterized by different levels of diversity of plant neighbours. Soil microbial communities were most strongly structured by sampling site and showed significant spatial patterns that were partially driven by soil chemistry. The influence of focal plant on soil microbiome was low but tended to increase with succession and increasing plant diversity. In contrast, root communities, particularly bacterial, were strongly structured by the focal plant species. Importantly, we also detected a significant effect of neighbouring plant community composition on bacteria and fungi associating with roots of the focal plants. The host influence on root microbiome varied across the successional grassland sequence and was highest in the most diverse site. CONCLUSIONS Our results show that in a species rich natural grassland, focal plant influence on the belowground microbiome depends on environmental context and is modulated by surrounding plant community. The influence of plant neighbours is particularly pronounced in root communities which may have multiple consequences for plant community productivity and stability, stressing the importance of plant diversity for ecosystem functioning.
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Affiliation(s)
- Lenka Mészárošová
- Institute of Microbiology of the CAS, v. v. i., Vídeňská 1083, Prague 4, 142 20, Czech Republic.
- University of Chemistry and Technology, Technická 5, Praha 6, 166 28, Czech Republic.
| | - Eliška Kuťáková
- Institute of Botany of the CAS, v. v. i., Zámek 1, Průhonice, 252 43, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague 2, 128 01, Czech Republic
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Skogsmarksgränd 17, Umeå, 901 83, Sweden
| | - Petr Kohout
- Institute of Microbiology of the CAS, v. v. i., Vídeňská 1083, Prague 4, 142 20, Czech Republic
| | - Zuzana Münzbergová
- Institute of Botany of the CAS, v. v. i., Zámek 1, Průhonice, 252 43, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague 2, 128 01, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the CAS, v. v. i., Vídeňská 1083, Prague 4, 142 20, Czech Republic
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Centenaro G, de-Miguel S, Bonet JA, Martínez Peña F, De Gomez REG, Ponce Á, Dashevskaya S, Alday JG. Spatially-explicit effects of small-scale clear-cutting on soil fungal communities in Pinus sylvestris stands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168628. [PMID: 37979846 DOI: 10.1016/j.scitotenv.2023.168628] [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: 06/26/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 11/20/2023]
Abstract
Clear-cutting is a common silvicultural practice. Although temporal changes in the soil fungal community after clear-cutting have been widely investigated, little is known about stand-level variations in the spatial distribution of soil fungi, particularly at the clear-cut edge. We performed spatial soil sampling in three clear-cuts (0.5 ha), edge habitats, and surrounding forests 8 years after clear-cutting to examine the impact of clear-cutting on the soil fungal community (diversity, composition, guilds, and biomass) and soil properties in a managed Pinus sylvestris forest in northern Spain. Our analyses showed small differences in the composition of the soil fungal community between edge, forest, and clear-cut zones, with <4 % of the species strictly associated with one or two zones. The richness, diversity, and evenness of the fungal community in the edge zone was not significantly different to that in the forest or clear-cut zones, although the clear-cut core had approximately a third fewer ectomycorrhizal species than the edge or the forest. Saprotrophic fungi were widespread across the clear-cut-forest gradient. Soil fungal biomass varied significantly between zones, ranging from 4 to 5 mg g-1 dry soil in the forest and at the forest edge to 1.7 mg g-1 dry soil in the clear-cut area. Soil organic matter, pH, nitrogen, and phosphorus did not differ significantly between edge, forest, and clear-cutting zones and were not significantly related to the fungal community composition. Overall, our study showed that small-scale clear-cut treatments are optimal to guarantee, in the medium-term, soil fungal communities within harvested areas and at the forest edge that are comparable to soil fungal communities in the forest, even though the amount of fungal biomass in the clear-cut zone is lower than at the forest edge or in the forest.
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Affiliation(s)
- Giada Centenaro
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain; Joint Research Unit CTFC - AGROTECNIO - CERCA, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain.
| | - Sergio de-Miguel
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain; Joint Research Unit CTFC - AGROTECNIO - CERCA, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain
| | - José Antonio Bonet
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain; Joint Research Unit CTFC - AGROTECNIO - CERCA, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain
| | - Fernando Martínez Peña
- Agrifood Research and Technology Centre of Aragon CITA, Avda Montañana 930, E-50059 Zaragoza, Spain; European Mycological Institute EGTC-EMI, E-42003 Soria, Spain
| | | | - Ángel Ponce
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain; Joint Research Unit CTFC - AGROTECNIO - CERCA, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain
| | - Svetlana Dashevskaya
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain; Joint Research Unit CTFC - AGROTECNIO - CERCA, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain
| | - Josu G Alday
- Department of Agricultural and Forest Sciences and Engineering, University of Lleida, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain; Joint Research Unit CTFC - AGROTECNIO - CERCA, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain
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Hodgson LM, Rakshit S, Lopez-Ruiz FJ, Gibberd MR, Thomas GJ, Zerihun A. Spatial Dependency in Stubble-Borne Pyrenophora teres f. teres and Influence of Sample Support Size on DNA Concentration and Fungicide Resistance Frequency. PHYTOPATHOLOGY 2024; 114:269-281. [PMID: 37505095 DOI: 10.1094/phyto-02-23-0062-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Fungicide resistance in foliar fungal pathogens is an increasing challenge to crop production. Yield impacts due to loss of fungicide efficacy may be reduced through effective surveillance and appropriate management intervention. For stubble-borne pathogens, off-season crop residues may be used to monitor fungicide resistance to inform pre-planting decisions; however, appropriate sampling strategies and support sizes for crop residues have not previously been considered. Here, we used Pyrenophora teres f. teres (Ptt) with resistance to demethylase inhibitor fungicides as a model system to assess spatial dependency and to compare the effects of different sampling strategies and support sizes on pathogen density (Ptt DNA concentration) and the frequency of fungicide resistance mutation. The results showed that sampling strategies (hand-picked versus raked) did not affect estimates of pathogen density or fungicide resistance frequency; however, sample variances were lower from raked samples. The effects of differing sample support size, as the size of the collection area (1.2, 8.6, or 60 m2), on fungicide resistance frequency were not evident (P > 0.05). However, measures of pathogen density increased with area size (P < 0.05); the 60 m2 area yielded the highest Ptt DNA concentration and produced the lowest number of pathogen-absent samples. Sample variances for pathogen density and fungicide resistance frequency were generally homogeneous between area sizes. The pattern of pathogen density was spatially independent; however, spatial dependency was identified for fungicide resistance frequency, with a range of 110 m, in one of the two fields surveyed. Collectively, the results inform designs for monitoring of fungicide resistance in stubble-borne pathogens.
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Affiliation(s)
- Leon M Hodgson
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Suman Rakshit
- Curtin Biometry and Agriculture Data Analytics, Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
- School of Electrical Engineering, Computing and Mathematical Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Francisco J Lopez-Ruiz
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Mark R Gibberd
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Geoff J Thomas
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia
| | - Ayalsew Zerihun
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
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Cheng M, Song J, Li W, Zhao Y, Zhang G, Chen Y, Gao H. Potentilla parvifolia strongly influenced soil microbial community and environmental effect along an altitudinal gradient in central Qilian Mountains in western China. Ecol Evol 2023; 13:e10685. [PMID: 38020704 PMCID: PMC10645544 DOI: 10.1002/ece3.10685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
The Qilian Mountains (QLMs) form an important ecological security barrier in western China and a priority area for biodiversity conservation. Potentilla parvifolia is a widespread species in the mid-high altitudes of the QLMs and has continuously migrated to higher altitudes in recent years. Understanding the effects of P. parvifolia on microbial community characteristics is important for exploring future changes in soil biogeochemical processes in the QLMs. This study found that P. parvifolia has profound effects on the community structure and ecological functions of soil microorganisms. The stability and complexity of the root zone microbial co-occurrence network were significantly higher than those of bare soils. There was a distinct altitudinal gradient in the effect of P. parvifolia on soil microbial community characteristics. At an elevation of 3204 m, P. parvifolia promoted the accumulation of carbon, nitrogen, and phosphorus and increased sucrase activity and soil C/N while significantly improving the community richness index of fungi (p < .05) compared with that of bacteria and the relative abundance of Ascomycota. The alpha diversity of fungi in the root zone soil of P. parvifolia was also significantly increased at 3550 m altitude. Furthermore, the community similarity distance matrix of fungi showed an evident separation at 3204 m. However, at an altitude of 3750 m, P. parvifolia mainly affected the bacterial community. Potentilla parvifolia increased the bacterial community richness. This is in agreement with the findings based on the functional prediction that P. parvifolia favors the growth and enrichment of denitrifying communities at 3550 and 3750 m. The results provide a scientific basis for predicting the evolutionary trends of the effects of P. parvifolia on soil microbial communities and functions and have important implications for ecological governance in the QLMs.
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Affiliation(s)
- Miaomiao Cheng
- College of Life Sciences and Engineering, Hexi University, Key Laboratory of the Hexi Corridor Resources Utilization of GansuZhangyeChina
- School of Life SciencesLanzhou UniversityLanzhouChina
| | - Jinge Song
- School of StomatologyLanzhou UniversityLanzhouChina
| | - Weikun Li
- School of Life SciencesLanzhou UniversityLanzhouChina
| | - Yiming Zhao
- School of Life SciencesLanzhou UniversityLanzhouChina
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and EngineeringLanzhouChina
| | - Yong Chen
- School of Life SciencesLanzhou UniversityLanzhouChina
| | - Haining Gao
- College of Life Sciences and Engineering, Hexi University, Key Laboratory of the Hexi Corridor Resources Utilization of GansuZhangyeChina
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Nobarinezhad MH, Wallace LE. Fine-scale genetic structure in rhizosphere microbial communities associated with Chamaecrista fasciculata (Fabaceae). Ecol Evol 2023; 13:e10570. [PMID: 37753306 PMCID: PMC10518841 DOI: 10.1002/ece3.10570] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/27/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
Soil microbiota of the rhizosphere are an important extension of the plant phenotype because they impact the health and fitness of host plants. The composition of these communities is expected to differ among host plants due to influence by host genotype. Given that many plant populations exhibit fine-scale genetic structure (SGS), associated microbial communities may also exhibit SGS. In this study, we tested this hypothesis using Chamaecrista fasciculata, a legume species that has previously been determined to have significant SGS. We collected genetic data from prokaryotic and fungal rhizosphere communities in association with 70 plants in an area of ~400 square meters to investigate the presence of SGS in microbial communities. Bacteria of Acidobacteria, Protobacteria, and Bacteroidetes and fungi of Basidiomycota, Ascomycota, and Mortierellomycota were dominant members of the rhizosphere. Although microbial alpha diversity did not differ significantly among plants hosts, we detected significant compositional differences among the microbial communities as well as isolation by distance. The strongest factor associated with microbial distance was genetic distance of the other microbial community, followed by geographic distance, but there was not a significant association with plant genetic distance for either microbial community. This study further demonstrates the strong potential for spatial structuring of soil microbial communities at the smallest spatial scales and provides further insight into the complexity of factors that influence microbial composition in soils and in association with host plants.
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Affiliation(s)
| | - Lisa E. Wallace
- Department of Biological SciencesOld Dominion UniversityNorfolkVirginiaUSA
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7
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Barbour KM, Barrón-Sandoval A, Walters KE, Martiny JBH. Towards quantifying microbial dispersal in the environment. Environ Microbiol 2023; 25:137-142. [PMID: 36308707 PMCID: PMC10100412 DOI: 10.1111/1462-2920.16270] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Kristin M Barbour
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, California, USA
| | - Alberto Barrón-Sandoval
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, California, USA
| | | | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, California, USA
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8
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Li W, Tan L, Peng M, Chen H, Tan C, Zhao E, Zhang L, Peng H, Liang Y. The spatial distribution of phytoliths and phytolith-occluded carbon in wheat (Triticum aestivum L.) ecosystem in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:158005. [PMID: 35964741 DOI: 10.1016/j.scitotenv.2022.158005] [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: 06/25/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Phytolith is a form of SiO2 in plants. Carbon can be sequestrated as phytolith-occluded carbon (PhytOC) during the formation of phytoliths. PhytOC is characterized by its high resistance to temperature, oxidation and decomposition under protection of phytoliths and can be stored in the soil for thousands of years. Soil also is a huge PhytOC sink; however, most studies focus on PhytOC storage in straw and other residues. Wheat is a major staple food crop accumulating high content of Si and distributed widely, while its potential for PhytOC is not clear. At present, PhytOC storage only considers on the average value, but not on the relationship between ecological factors and the spatial distribution of PhytOC sequestration. Climatic factors and soil physiochemical properties together affect the formation process and stability of phytoliths. In our study, we collected wheat straw and soil samples from 95 sites among five provinces to extract phytolith and PhytOC. We constructed XGBoost model to predict the spatial distribution of phytolith and PhytOC across the country using the national soil testing and formula fertilization nutrient dataset and climate data. As a result, soil physiochemical factors such as available silicon (Siavail), total carbon (Ctot) and total nitrogen (Ntot) and climate factors related to temperature and precipitation have a great positive impact on the production of phytoliths and PhytOC. Meanwhile, PhytOC storage in wheat ecosystems was estimated to be 7.59 × 106 t, which is equivalent to 27.83 Tg of CO2. In China, the distribution characteristics of phytoliths and PhytOC in wheat straw and soil display a trend of decrease from south to north. He'nan Province is the largest wheat production area, producing approximately 1.59 × 106 t PhytOC per year. Therefore, PhytOC is a stable CO2 sink pathway in the agricultural ecosystems, which is of great importance for mitigating climate warming.
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Affiliation(s)
- Wenjuan Li
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Li Tan
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Miao Peng
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hao Chen
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Che Tan
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Enqiang Zhao
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lei Zhang
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongyun Peng
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Liang
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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Ji G, Hu G, Liu G, Bai Z, Li B, Li D, L H, Cui G. Response of soil microbes to Carex meyeriana meadow degeneration caused by overgrazing in inner Mongolia. ACTA OECOLOGICA 2022. [DOI: 10.1016/j.actao.2022.103860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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10
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Kageyama T, Toju H. Effects of source sample amount on biodiversity surveys of bacteria, fungi, and nematodes in soil ecosystems. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.959945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bacteria, fungi, and nematodes are major components of soil ecosystems, playing pivotal roles in belowground material cycles and biological community processes. A number of studies have recently uncovered the diversity and community structure of those organisms in various types of soil ecosystems based on DNA metabarcoding (amplicon sequencing). However, because most previous studies examined only one or two of the three organismal groups, it remains an important challenge to reveal the entire picture of soil community structure. We examined how we could standardize DNA extraction protocols for simultaneous DNA metabarcoding of bacteria, fungi, and nematodes. Specifically, in an Illumina sequencing analysis of forest and farmland soil samples, we performed DNA extraction at five levels of soil-amount (0.5, 2, 5, 10, and 20 g). We then found that DNA extraction with the 0.5 g soil setting, which had been applied as default in many commercial DNA extraction kits, could lead to underestimation of α-diversity in nematode community. We also found that dissimilarity (β-diversity) estimates of community structure among replicate samples could be affected by soil sample amount. Based on the assays, we conclude that DNA extraction from at least 20 g of soil is a standard for comparing biodiversity patterns among bacteria, fungi and nematodes.
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Berry JC, Qi M, Sonawane BV, Sheflin A, Cousins A, Prenni J, Schachtman DP, Liu P, Bart RS. Increased signal-to-noise ratios within experimental field trials by regressing spatially distributed soil properties as principal components. eLife 2022; 11:70056. [PMID: 35819140 PMCID: PMC9275819 DOI: 10.7554/elife.70056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/29/2022] [Indexed: 12/11/2022] Open
Abstract
Environmental variability poses a major challenge to any field study. Researchers attempt to mitigate this challenge through replication. Thus, the ability to detect experimental signals is determined by the degree of replication and the amount of environmental variation, noise, within the experimental system. A major source of noise in field studies comes from the natural heterogeneity of soil properties which create microtreatments throughout the field. In addition, the variation within different soil properties is often nonrandomly distributed across a field. We explore this challenge through a sorghum field trial dataset with accompanying plant, microbiome, and soil property data. Diverse sorghum genotypes and two watering regimes were applied in a split-plot design. We describe a process of identifying, estimating, and controlling for the effects of spatially distributed soil properties on plant traits and microbial communities using minimal degrees of freedom. Importantly, this process provides a method with which sources of environmental variation in field data can be identified and adjusted, improving our ability to resolve effects of interest and to quantify subtle phenotypes.
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Affiliation(s)
- Jeffrey C Berry
- Donald Danforth Plant Science Center, St. Louis, United States
| | - Mingsheng Qi
- Donald Danforth Plant Science Center, St. Louis, United States
| | - Balasaheb V Sonawane
- School of Biological Sciences, Washington State University, Pullman, United States
| | - Amy Sheflin
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Asaph Cousins
- School of Biological Sciences, Washington State University, Pullman, United States
| | - Jessica Prenni
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Daniel P Schachtman
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, United States
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, United States
| | - Rebecca S Bart
- Donald Danforth Plant Science Center, St. Louis, United States
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Abstract
In order to accommodate the empirical fact that population structures are rarely simple, modern studies of evolutionary dynamics allow for complicated and highly heterogeneous spatial structures. As a result, one of the most difficult obstacles lies in making analytical deductions, either qualitative or quantitative, about the long-term outcomes of evolution. The "structure-coefficient" theorem is a well-known approach to this problem for mutation-selection processes under weak selection, but a general method of evaluating the terms it comprises is lacking. Here, we provide such a method for populations of fixed (but arbitrary) size and structure, using easily interpretable demographic measures. This method encompasses a large family of evolutionary update mechanisms and extends the theorem to allow for asymmetric contests to provide a better understanding of the mutation-selection balance under more realistic circumstances. We apply the method to study social goods produced and distributed among individuals in spatially heterogeneous populations, where asymmetric interactions emerge naturally and the outcome of selection varies dramatically, depending on the nature of the social good, the spatial topology, and the frequency with which mutations arise.
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Soil Microbial Community Varied with Vegetation Types on a Small Regional Scale of the Qilian Mountains. SUSTAINABILITY 2022. [DOI: 10.3390/su14137910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Clarifying the response of soil microbial communities to the change of different vegetation types on a small regional scale is of great significance for understanding the sustainability of grassland development. However, the distribution patterns and driving factors of the microbial community are not well understood in the Qilian Mountains. Therefore, we characterized and compared the soil microbial communities underlying the four vegetation types in a national natural reserve (reseeded grassland, swamp meadow, steppe meadow, and cultivated grassland) using high-throughput sequencing of the 16S rRNA and ITS. Meanwhile, the plant community and soil physicochemical characteristics were also determined. The results showed that bacterial and fungal communities in all vegetation types had the same dominant species, but the relative abundance differed substantially, which caused significant spatial heterogeneities on the small regional scale. Specifically, bacteria showed higher variability among different vegetation types than fungi, among which the bacterial and fungal communities were more sensitive to the changes in soil than to plant characteristics. Furthermore, soil organic carbon affected the widest portion of the microbial community, nitrate-nitrogen was the main factor affecting bacteria, and aboveground plant biomass was the main factor affecting fungi. Collectively, these results demonstrate the value of considering multiple small regional spatial scales when studying the relationship between the soil microbial community and environmental characteristics. Our study may have important implications for grassland management following natural disturbances or human alterations.
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Meena M, Yadav G, Sonigra P, Nagda A, Mehta T, Swapnil P, Marwal A, Kumar S. Multifarious Responses of Forest Soil Microbial Community Toward Climate Change. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02051-3. [PMID: 35657425 DOI: 10.1007/s00248-022-02051-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Forest soils are a pressing subject of worldwide research owing to the several roles of forests such as carbon sinks. Currently, the living soil ecosystem has become dreadful as a consequence of several anthropogenic activities including climate change. Climate change continues to transform the living soil ecosystem as well as the soil microbiome of planet Earth. The majority of studies have aimed to decipher the role of forest soil bacteria and fungi to understand and predict the impact of climate change on soil microbiome community structure and their ecosystem in the environment. In forest soils, microorganisms live in diverse habitats with specific behavior, comprising bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are influenced by biotic interactions and nutrient accessibility. Soil microbiome also drives multiple crucial steps in the nutrient biogeochemical cycles (carbon, nitrogen, phosphorous, and sulfur cycles). Soil microbes help in the nitrogen cycle through nitrogen fixation during the nitrogen cycle and maintain the concentration of nitrogen in the atmosphere. Soil microorganisms in forest soils respond to various effects of climate change, for instance, global warming, elevated level of CO2, drought, anthropogenic nitrogen deposition, increased precipitation, and flood. As the major burning issue of the globe, researchers are facing the major challenges to study soil microbiome. This review sheds light on the current scenario of knowledge about the effect of climate change on living soil ecosystems in various climate-sensitive soil ecosystems and the consequences for vegetation-soil-climate feedbacks.
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Affiliation(s)
- Mukesh Meena
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India.
| | - Garima Yadav
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Priyankaraj Sonigra
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Adhishree Nagda
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Tushar Mehta
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Prashant Swapnil
- Department of Botany, School of Biological Science, Central University of Punjab, Bhatinda, Punjab, 151401, India
| | - Avinash Marwal
- Department of Biotechnology, Vigyan Bhawan - Block B, New Campus, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Sumit Kumar
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India
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Zhao N, Zhang X, Hu L, Liu H, Ma L, Xu T, Han X, Kang S, Wang X, Zhao X, Xu S. Cropping practices manipulate soil bacterial structure and functions on the Qinghai-Tibet Plateau. JOURNAL OF PLANT PHYSIOLOGY 2022; 271:153666. [PMID: 35303514 DOI: 10.1016/j.jplph.2022.153666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 03/06/2022] [Accepted: 03/06/2022] [Indexed: 06/14/2023]
Abstract
There is an increasing awareness of the adverse environmental effects of the intensive practices used in modern crop farming, such as those that cause greenhouse gas emissions and nutrient leaching. Harnessing beneficial microbes by changing planting practices presents a promising strategy for optimizing plant growth and agricultural sustainability. However, the characteristics of soil microorganisms under different planting patterns remain uncertain. We conducted a study of soil bacterial structure and function under monoculture vs. polyculture planting regimes using 16S rRNA gene sequencing on the Qinghai-Tibet Plateau. We observed substantial variations in bacterial richness, diversity, and relative abundances of taxa between gramineous and leguminous monocultures, as well as between gramineae-legume polycultures. The number of operational taxonomic units and alpha and beta diversity were markedly higher in the leguminous monocultures than in the gramineous monocultures; conversely, network analysis revealed that the interactions among the bacterial genera in the gramineous monocultures were more complex than those in the other two planting regimes. Moreover, nitrogen fixation, soil detoxification, and productivity were increased under the gramineous monocultures; more importantly, low soil-borne diseases (e.g., animals parasitic or symbiont) also facilitated strongly suppressive effects toward soil-borne pathogens. Nevertheless, the gramineae-legume polycultures were prone to nitrate seepage contamination, and leguminous monocultures exhibited strong denitrification effects. These results revealed that the gramineous monoculture is a more promising cropping pattern on the Qinghai-Tibetan Plateau. Understanding the bacterial distribution patterns and interactions of crop-sensitive microbes presents a basis for developing microbial management strategies for smart farming.
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Affiliation(s)
- Na Zhao
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China; Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining, China
| | - XiaoLing Zhang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - LinYong Hu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China
| | - HongJin Liu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China
| | - Li Ma
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - TianWei Xu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China
| | - XuePing Han
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - ShengPing Kang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - XunGang Wang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - XinQuan Zhao
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China.
| | - ShiXiao Xu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China.
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Qin C, Bartelme R, Chung YA, Fairbanks D, Lin Y, Liptzin D, Muscarella C, Naithani K, Peay K, Pellitier P, St. Rose A, Stanish L, Werbin Z, Zhu K. From DNA sequences to microbial ecology: Wrangling NEON soil microbe data with the
neonMicrobe
R package. Ecosphere 2021. [DOI: 10.1002/ecs2.3842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Clara Qin
- Department of Environmental Studies University of California Santa Cruz Santa Cruz California USA
| | - Ryan Bartelme
- BIO5 Institute University of Arizona Tucson Arizona USA
- CyVerse.org Tucson Arizona USA
| | - Y. Anny Chung
- Department of Plant Biology and Department of Plant Pathology University of Georgia Athens Georgia USA
| | - Dawson Fairbanks
- Department of Environmental Science University of Arizona Tucson Arizona USA
| | - Yang Lin
- Department of Soil and Water Sciences University of Florida Gainesville Florida USA
| | | | - Chance Muscarella
- Department of Environmental Science University of Arizona Tucson Arizona USA
| | - Kusum Naithani
- Department of Biological Sciences University of Arkansas Fayetteville Fayetteville Arkansas USA
| | - Kabir Peay
- Department of Biology Stanford University Stanford California USA
| | - Peter Pellitier
- Department of Biology Stanford University Stanford California USA
| | - Ayanna St. Rose
- Department of Biological Sciences University of Arkansas Fayetteville Fayetteville Arkansas USA
| | - Lee Stanish
- Institute of Arctic and Alpine Research University of Colorado Boulder USA
| | - Zoey Werbin
- Department of Biology Boston University Boston Massachusetts USA
| | - Kai Zhu
- Department of Environmental Studies University of California Santa Cruz Santa Cruz California USA
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17
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Jurkevitch E, Pasternak Z. A walk on the dirt: soil microbial forensics from ecological theory to the crime lab. FEMS Microbiol Rev 2021; 45:5937428. [PMID: 33098291 DOI: 10.1093/femsre/fuaa053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Forensics aims at using physical evidence to solve investigations with science-based principles, thus operating within a theoretical framework. This however is often rather weak, the exception being DNA-based human forensics that is well anchored in theory. Soil is a most commonly encountered, easily and unknowingly transferred evidence but it is seldom employed as soil analyses require extensive expertise. In contrast, comparative analyses of soil bacterial communities using nucleic acid technologies can efficiently and precisely locate the origin of forensic soil traces. However, this application is still in its infancy, and is very rarely used. We posit that understanding the theoretical bases and limitations of their uses is essential for soil microbial forensics to be judiciously implemented. Accordingly, we review the ecological theory and experimental evidence explaining differences between soil microbial communities, i.e. the generation of beta diversity, and propose to integrate a bottom-up approach of interactions at the microscale, reflecting historical contingencies with top-down mechanisms driven by the geographic template, providing a potential explanation as to why bacterial communities map according to soil types. Finally, we delimit the use of soil microbial forensics based on the present technologies and ecological knowledge, and propose possible venues to remove existing bottlenecks.
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Affiliation(s)
- Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Zohar Pasternak
- Division of Identification and Forensic Science, Israel Police
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18
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Hugoni M, Nunan N, Thioulouse J, Dubost A, Abrouk D, Martins JMF, Goffner D, Prigent-Combaret C, Grundmann G. Small-Scale Variability in Bacterial Community Structure in Different Soil Types. MICROBIAL ECOLOGY 2021; 82:470-483. [PMID: 33443587 DOI: 10.1007/s00248-020-01660-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Microbial spatial distribution has mostly been studied at field to global scales (i.e., ecosystem scales). However, the spatial organization at small scales (i.e., centimeter to millimeter scales), which can help improve our understanding of the impacts of spatial communities structure on microbial functioning, has received comparatively little attention. Previous work has shown that small-scale spatial structure exists in soil microbial communities, but these studies have not compared soils from geographically distant locations, nor have they utilized community ecology approaches, such as the core and satellite hypothesis and/or abundance-occupancy relationships, often used in macro-ecology, to improve the description of the spatial organization of communities. In the present work, we focused on bacterial diversity (i.e., 16S rRNA gene sequencing) occurring in micro-samples from a variety of locations with different pedo-climatic histories (i.e., from semi-arid, alpine, and temperate climates) and physicochemical properties. The forms of ecological spatial relationships in bacterial communities (i.e., occupancy-frequency and abundance-occupancy) and taxa distributions (i.e., habitat generalists and specialists) were investigated. The results showed that bacterial composition differed in the four soils at the small scale. Moreover, one soil presented a satellite mode distribution, whereas the three others presented bimodal distributions. Interestingly, numerous core taxa were present in the four soils among which 8 OTUs were common to the four sites. These results confirm that analyses of the small-scale spatial distribution are necessary to understand consequent functional processes taking place in soils, affecting thus ecosystem functioning.
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Affiliation(s)
- Mylène Hugoni
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France.
| | - Naoise Nunan
- Institute of Ecology and Environmental Sciences - Paris, CNRS - Sorbonne Université, 4 place Jussieu, 75005, Paris, France
- Department of Soil and Environment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Jean Thioulouse
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Audrey Dubost
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France
| | - Danis Abrouk
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France
| | - Jean M F Martins
- Université Grenoble Alpes, CNRS, IRD, IGE UMR 5001, 38000, Grenoble, France
| | - Deborah Goffner
- Unité Mixte Internationale CNRS 3189 « Environment, Health and Societies », Faculté de Médecine, 51 Bd Pierre Dramard, 13344, Marseille, France
| | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France
| | - Geneviève Grundmann
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France
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19
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Liu L, Chen X, Hu S, Zhan Q, Peng W. Genetic diversity and distribution of rhizobia associated with soybean in red soil in Hunan Province. Arch Microbiol 2021; 203:1971-1980. [PMID: 33394081 DOI: 10.1007/s00203-020-02120-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/03/2020] [Accepted: 11/13/2020] [Indexed: 10/22/2022]
Abstract
To explore the genetic diversity and distribution of rhizobia in the rhizosphere of soybean grown in red soil, we have collected 21 soil samples from soybean fields across seven counties in Hunan province, China. MiSeq sequencing of rpoB gene was used to determine the intra-species diversity of rhizobia existing in soybean rhizospheres. Soil chemical properties were determined by routine methods. The Principal Coordinates Analysis (PCoA) plot indicated a clear biogeographical pattern characterizing the soybean rhizosphere across different sites. The Mantel test demonstrated that biogeographical pattern was significantly correlated with the geographical distance (Mantel statistic R 0.385, p < 0.001). There were obvious differences in the rhizobial communities among northeastern eco-region, southeastern eco-region and western eco-region. In general, Bradyrhizobium diazoefficiens was the most abundant rhizobial species in the soybean rhizosphere. At an intermediate (10-400 km) spatial scale, the biogeographical pattern of rhizobial communities in soybean rhizosphere is associated with both soil properties and geographical distance. Redundancy analysis (RDA) showed that total potassium (TK), available potassium (AK), soil organic carbon (SOC), and available nitrogen (AN) were the main factors that influenced the α-diversity of rhizobial communities. Canonical correspondence analysis (CCA) showed that pH and exchangeable Ca and Mg had the greatest influence on the β-diversity of the rhizobial communities in the soybean rhizosphere. These findings characterize the distribution pattern and its influencing factors of soybean rhizobia in rhizosphere in Hunan province, which may be helpful in selecting suitable strains or species as inoculants for soybeans in red soil regions.
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Affiliation(s)
- Lu Liu
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, No.892 Yuanda Road, Furong District, Changsha City, 410125, Hunan Province, People's Republic of China
| | - Xi Chen
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, No.892 Yuanda Road, Furong District, Changsha City, 410125, Hunan Province, People's Republic of China
| | - Shujuan Hu
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, No.892 Yuanda Road, Furong District, Changsha City, 410125, Hunan Province, People's Republic of China
- Longping Branch of Graduate School, Hunan University, Changsha, People's Republic of China
| | - Qingcai Zhan
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, No.892 Yuanda Road, Furong District, Changsha City, 410125, Hunan Province, People's Republic of China
| | - Weizheng Peng
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, No.892 Yuanda Road, Furong District, Changsha City, 410125, Hunan Province, People's Republic of China.
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20
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Lebre PH, Bottos E, Makhalanyane TP, Hogg I, Cowan DA. Islands in the sand: are all hypolithic microbial communities the same? FEMS Microbiol Ecol 2021; 97:5928546. [PMID: 33068395 DOI: 10.1093/femsec/fiaa216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/16/2020] [Indexed: 01/04/2023] Open
Abstract
Hypolithic microbial communities (hypolithons) are complex assemblages of phototrophic and heterotrophic organisms associated with the ventral surfaces of translucent minerals embedded in soil surfaces. Past studies on the assembly, structure and function of hypolithic communities have tended to use composite samples (i.e. bulked hypolithic biomass) with the underlying assumption that samples collected from within a 'homogeneous' locality are phylogenetically homogeneous. In this study, we question this assumption by analysing the prokaryote phylogenetic diversity of multiple individual hypolithons: i.e. asking the seemingly simple question of 'Are all hypolithons the same'? Using 16S rRNA gene-based phylogenetic analysis of hypolithons recovered for a localized moraine region in the Taylor Valley, McMurdo Dry Valleys, Antarctica, we demonstrate that these communities are heterogeneous at very small spatial scales (<5 m). Using null models of phylogenetic turnover, we showed that this heterogeneity between hypolithons is probably due to stochastic effects such as dispersal limitations, which is entirely consistent with the physically isolated nature of the hypolithic communities ('islands in the sand') and the almost complete absence of a liquid continuum as a mode of microbial transport between communities.
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Affiliation(s)
- Pedro H Lebre
- Centre for Microbial Ecology and Genomic, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynwood Road, Hatfield, Pretoria, 0028, South Africa
| | - Eric Bottos
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, British Colombia, BC V2C 0C8, Canada
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomic, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynwood Road, Hatfield, Pretoria, 0028, South Africa
| | - Ian Hogg
- Canadian High Arctic Research Station, rue Uvajuq place, Cambridge Bay, Nunavut, CP 2150, Canada
| | - Don A Cowan
- Centre for Microbial Ecology and Genomic, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynwood Road, Hatfield, Pretoria, 0028, South Africa
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21
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Abstract
Bacterial community composition is largely influenced by environmental factors, and this applies to the Arctic region. However, little is known about the role of spatial factors in structuring such communities. In this study, we evaluated the influence of spatial scale on bacterial community structure across an Arctic landscape. Our results showed that spatial factors accounted for approximately 10% of the variation at the landscape scale, equivalent to observations across the whole Arctic region, suggesting that while the role and magnitude of other processes involved in community structure may vary, the role of dispersal may be stable globally in the region. We assessed dispersal limitation by identifying the spatial autocorrelation distance, standing at approximately 60 m, which would be required in order to obtain fully independent samples and may inform future sampling strategies in the region. Finally, indicator taxa with strong statistical correlations with environment variables were identified. However, we showed that these strong taxa-environment associations may not always be reflected in the geographical distribution of these taxa.IMPORTANCE The significance of this study is threefold. It investigated the influence of spatial scale on the soil bacterial community composition across a typical Arctic landscape and demonstrated that conclusions reached when examining the influence of specific environmental variables on bacterial community composition are dependent upon the spatial scales over which they are investigated. This study identified a dispersal limitation (spatial autocorrelation) distance of approximately 60 m, required to obtain samples with fully independent bacterial communities, and therefore, should serve to inform future sampling strategies in the region and potentially elsewhere. The work also showed that strong taxa-environment statistical associations may not be reflected in the observed landscape distribution of the indicator taxa.
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22
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Fang K, Chen L, Zhang H. Evaluation of foliar fungus-mediated interactions with below and aboveground enemies of the invasive plant Ageratina adenophora. Ecol Evol 2021; 11:526-535. [PMID: 33437448 PMCID: PMC7790651 DOI: 10.1002/ece3.7072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 11/29/2022] Open
Abstract
Plant-fungal associations are frequently key drivers of plant invasion success. Foliar fungi can benefit their invasive hosts by enhancing growth promotion, disease resistance and environmental stress tolerance. However, the roles of foliar fungi may vary when a given invasive plant faces different stresses. In this study, we designed three independent experiments to evaluate the effects of a foliar fungus, Colletotrichum sp., on the growth performance of the invasive plant Ageratina adenophora under different soil conditions, as well as the responses of A. adenophora to the foliar fungal pathogen Diaporthe helianthi and to herbivory. We found that the soil type was the most influential factor for the growth of A. adenophora. The role of the foliar fungus Colletotrichum sp. varied in the different soil types but generally adversely affected leaf development in A. adenophora. Colletotrichum sp. may be a weak latent foliar pathogen that can enhance the pathogenicity of D. helianthi on leaves of A. adenophora and marginally reduce signs of herbivory by natural insects in the wild on A. adenophora seedlings. In general, the benefits of the foliar fungus Colletotrichum to the fitness of A. adenophora are not significant in the context of this experimental design. However, our data highlight the need to consider both aboveground and belowground biota in different soil habitats when evaluating the effects of foliar fungi.
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Affiliation(s)
- Kai Fang
- School of Ecology and Environmental ScienceYunnan UniversityKunmingChina
- State Key Laboratory for Conservation and Utilization of Bio‐Resources in YunnanYunnan UniversityKunmingChina
| | - Li‐Min Chen
- Sichuan Academy of Grassland SciencesChengduChina
| | - Han‐Bo Zhang
- School of Ecology and Environmental ScienceYunnan UniversityKunmingChina
- State Key Laboratory for Conservation and Utilization of Bio‐Resources in YunnanYunnan UniversityKunmingChina
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23
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Zhang T, Wang Z, Lv X, Dang H, Zhuang L. Variation of rhizosphere bacterial community diversity in the desert ephemeral plant Ferula sinkiangensis across environmental gradients. Sci Rep 2020; 10:18442. [PMID: 33116202 PMCID: PMC7595108 DOI: 10.1038/s41598-020-75591-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/15/2020] [Indexed: 11/18/2022] Open
Abstract
Ferula sinkiangensis (F. sinkiangensis) is a desert short-lived medicinal plant, and its number is rapidly decreasing. Rhizosphere microbial community plays an important role in plant growth and adaptability. However, F. sinkiangensis rhizosphere bacterial communities and the soil physicochemical factors that drive the bacterial community distribution are currently unclear. On this study, based on high-throughput sequencing, we explored the diversity, structure and composition of F. sinkiangensis rhizosphere bacterial communities at different slope positions and soil depths and their correlation with soil physicochemical properties. Our results revealed the heterogeneity and changed trend of F. sinkiangensis rhizosphere bacterial community diversity and abundance on slope position and soil depth and found Actinobacteria (25.5%), Acidobacteria (16.9%), Proteobacteria (16.6%), Gemmatimonadetes (11.5%) and Bacteroidetes (5.8%) were the dominant bacterial phyla in F. sinkiangensis rhizosphere soil. Among all soil physicochemical variables shown in this study, there was a strong positive correlation between phosphorus (AP) and the diversity of rhizosphere bacterial community in F. sinkiangensis. In addition, Soil physicochemical factors jointly explained 24.28% of variation in F. sinkiangensis rhizosphere bacterial community structure. Among them, pH largely explained the variation of F. sinkiangensis rhizosphere bacterial community structure (5.58%), followed by total salt (TS, 5.21%) and phosphorus (TP, 4.90%).
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Affiliation(s)
- Tao Zhang
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource Utilization, Ministry of Education, Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Zhongke Wang
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource Utilization, Ministry of Education, Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Xinhua Lv
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource Utilization, Ministry of Education, Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Hanli Dang
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource Utilization, Ministry of Education, Shihezi University, Shihezi, 832003, Xinjiang, China.
| | - Li Zhuang
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource Utilization, Ministry of Education, Shihezi University, Shihezi, 832003, Xinjiang, China.
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Sathyamoorthy R, Kushmaro Y, Rotem O, Matan O, Kadouri DE, Huppert A, Jurkevitch E. To hunt or to rest: prey depletion induces a novel starvation survival strategy in bacterial predators. ISME JOURNAL 2020; 15:109-123. [PMID: 32884113 DOI: 10.1038/s41396-020-00764-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/12/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
Abstract
The small size of bacterial cells necessitates rapid adaption to sudden environmental changes. In Bdellovibrio bacteriovorus, an obligate predator of bacteria common in oligotrophic environments, the non-replicative, highly motile attack phase (AP) cell must invade a prey to ensure replication. AP cells swim fast and respire at high rates, rapidly consuming their own contents. How the predator survives in the absence of prey is unknown. We show that starvation for prey significantly alters swimming patterns and causes exponential decay in prey-searching cells over hours, until population-wide swim-arrest. Swim-arrest is accompanied by changes in energy metabolism, enabling rapid swim-reactivation upon introduction of prey or nutrients, and a sweeping change in gene expression and gene regulation that largely differs from those of the paradigmatic stationary phase. Swim-arrest is costly as it imposes a fitness penalty in the form of delayed growth. We track the control of the swim arrest-reactivation process to cyclic-di-GMP (CdG) effectors, including two motility brakes. CRISPRi transcriptional inactivation, and in situ localization of the brakes to the cell pole, demonstrated their essential role for effective survival under prey-induced starvation. Thus, obligate predators evolved a unique CdG-controlled survival strategy, enabling them to sustain their uncommon lifestyle under fluctuating prey supply.
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Affiliation(s)
- Rajesh Sathyamoorthy
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
| | - Yuval Kushmaro
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
| | - Or Rotem
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel.,Seed-x., Magshimim, Israel
| | - Ofra Matan
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
| | - Daniel E Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - Amit Huppert
- Bio-statistical Unit, The Gertner Institute for Epidemiology and Health Policy Research, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel.
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Aas AB, Andrew CJ, Blaalid R, Vik U, Kauserud H, Davey ML. Fine-scale diversity patterns in belowground microbial communities are consistent across kingdoms. FEMS Microbiol Ecol 2020; 95:5484836. [PMID: 31049552 DOI: 10.1093/femsec/fiz058] [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: 10/12/2018] [Accepted: 04/30/2019] [Indexed: 11/12/2022] Open
Abstract
The belowground environment is heterogeneous and complex at fine spatial scales. Physical structures, biotic components and abiotic conditions create a patchwork mosaic of potential niches for microbes. Questions remain about mechanisms and patterns of community assembly belowground, including: Do fungal and bacterial communities assemble differently? How do microbes reach the roots of host plants? Within a 4 m2 plot in alpine vegetation, high throughput sequencing of the 16S (bacteria) and ITS1 (fungal) ribosomal RNA genes was used to characterise microbial community composition in roots and adjacent soil of a viviparous host plant (Bistorta vivipara). At fine spatial scales, beta-diversity patterns in belowground bacterial and fungal communities were consistent, although compositional change was greater in bacteria than fungi. Spatial structure and distance-decay relationships were also similar for bacteria and fungi, with significant spatial structure detected at <50 cm among root- but not soil-associated microbes. Recruitment of root microbes from the soil community appeared limited at this sampling and sequencing depth. Possible explanations for this include recruitment from low-abundance populations of soil microbes, active recruitment from neighbouring plants and/or vertical transmission of symbionts to new clones, suggesting varied methods of microbial community assembly for viviparous plants. Our results suggest that even at relatively small spatial scales, deterministic processes play a significant role in belowground microbial community structure and assembly.
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Affiliation(s)
- Anders Bjørnsgaard Aas
- Section of Genetic and Evolution Department of Biosciences, University of Oslo, Oslo, Norway
| | - Carrie J Andrew
- Section of Genetic and Evolution Department of Biosciences, University of Oslo, Oslo, Norway
| | - Rakel Blaalid
- Norwegian Institute for Nature Research, Bergen, Norway
| | - Unni Vik
- Section of Genetic and Evolution Department of Biosciences, University of Oslo, Oslo, Norway
| | - Håvard Kauserud
- Section of Genetic and Evolution Department of Biosciences, University of Oslo, Oslo, Norway
| | - Marie L Davey
- Section of Genetic and Evolution Department of Biosciences, University of Oslo, Oslo, Norway.,Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research, NO-1431 Ås, Norway
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26
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Community-level signatures of ecological succession in natural bacterial communities. Nat Commun 2020; 11:2386. [PMID: 32404904 PMCID: PMC7220908 DOI: 10.1038/s41467-020-16011-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 03/24/2020] [Indexed: 11/08/2022] Open
Abstract
A central goal in microbial ecology is to simplify the extraordinary biodiversity that inhabits natural environments into ecologically coherent units. We profiled (16S rRNA sequencing) > 700 semi-aquatic bacterial communities while measuring their functional capacity when grown in laboratory conditions. This approach allowed us to investigate the relationship between composition and function excluding confounding environmental factors. Simulated data allowed us to reject the hypothesis that stochastic processes were responsible for community assembly, suggesting that niche effects prevailed. Consistent with this idea we identified six distinct community classes that contained samples collected from distant locations. Structural equation models showed there was a functional signature associated with each community class. We obtained a more mechanistic understanding of the classes using metagenomic predictions (PiCRUST). This approach allowed us to show that the classes contained distinct genetic repertoires reflecting community-level ecological strategies. The ecological strategies resemble the classical distinction between r- and K-strategists, suggesting that bacterial community assembly may be explained by simple ecological mechanisms.
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Gamalero E, Bona E, Novello G, Boatti L, Mignone F, Massa N, Cesaro P, Berta G, Lingua G. Discovering the bacteriome of Vitis vinifera cv. Pinot Noir in a conventionally managed vineyard. Sci Rep 2020; 10:6453. [PMID: 32296119 PMCID: PMC7160115 DOI: 10.1038/s41598-020-63154-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/16/2020] [Indexed: 01/22/2023] Open
Abstract
The structure of the bacteriome associated with grapevine roots can affect plant development, health and grape quality. We previously investigated the bacterial biodiversity of the Vitis vinifera cv. Pinot Noir rhizosphere in a vineyard subjected to integrated pest management. The aim of this work is to characterize the bacteriome of V. vinifera cv. Pinot Noir in a conventionally managed vineyard using a metabarcoding approach. Comparisons between the microbial community structure in bulk soil and rhizosphere (variable space) were performed and shifts of bacteriome according to two sampling times (variable time) were characterized. Bacterial biodiversity was higher at the second than at the first sampling and did not differ according to the variable space. Actinobacteria was the dominant class, with Gaiella as the most represented genus in all the samples. Among Proteobacteria, the most represented classes were Alpha, Beta and Gamma-Proteobacteria, with higher abundance at the second than at the first sampling time. Bradyrhizobium was the most frequent genus among Alpha-Proteobacteria, while Burkholderia was the predominant Beta-Proteobacteria. Among Firmicutes, the frequency of Staphylococcus was higher than 60% in bulk soil and rhizosphere. Finally, the sampling time can be considered as one of the drivers responsible for the bacteriome variations assessed.
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Affiliation(s)
- Elisa Gamalero
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Elisa Bona
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Piazza San Eusebio 5, 13100, Vercelli, Italy
| | - Giorgia Novello
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Lara Boatti
- SmartSeq s.r.l., spin-off of the Università del Piemonte Orientale, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Flavio Mignone
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy.,SmartSeq s.r.l., spin-off of the Università del Piemonte Orientale, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Nadia Massa
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Patrizia Cesaro
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy.
| | - Graziella Berta
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Guido Lingua
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
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Cao MW, Jia T, Mi J, Jing JH, Chai BF. Relative roles of niche and neutral processes on turnover of plant, fungal and bacterial communities in arid and semi-arid areas at the regional scale. Basic Appl Ecol 2019. [DOI: 10.1016/j.baae.2019.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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Borg Dahl M, Brejnrod AD, Russel J, Sørensen SJ, Schnittler M. Different Degrees of Niche Differentiation for Bacteria, Fungi, and Myxomycetes Within an Elevational Transect in the German Alps. MICROBIAL ECOLOGY 2019; 78:764-780. [PMID: 30903202 DOI: 10.1007/s00248-019-01347-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
We used direct DNA amplification from soil extracts to analyze microbial communities from an elevational transect in the German Alps by parallel metabarcoding of bacteria (16S rRNA), fungi (ITS2), and myxomycetes (18S rRNA). For the three microbial groups, 5710, 6133, and 261 operational taxonomic units (OTU) were found. For the latter group, we can relate OTUs to barcodes from fruit bodies sampled over a 4-year period. The alpha diversity of myxomycetes was positively correlated with that of bacteria. Vegetation type was found to be the main explanatory parameter for the community composition of all three groups and a substantial species turnover with elevation was observed. Bacteria and fungi display similar community responses, driven by symbiont species and plant substrate quality. Myxamoebae show a more patchy distribution, though still clearly stratified between taxa, which seems to be a response to both structural properties of the habitat and interaction with specific bacterial and fungal taxa. Finally, we report a high number of myxomycete OTUs not represented in a reference database from fructifications, which might represent novel species.
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Affiliation(s)
- Mathilde Borg Dahl
- Institute of Botany and Landscape Ecology, University of Greifswald, Soldmannstrasse 15, 17487, Greifswald, Mecklenburg-Vorpommern, Germany.
| | - Asker Daniel Brejnrod
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Russel
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, University of Greifswald, Soldmannstrasse 15, 17487, Greifswald, Mecklenburg-Vorpommern, Germany
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30
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Castle SC, Samac DA, Sadowsky MJ, Rosen CJ, Gutknecht JLM, Kinkel LL. Impacts of Sampling Design on Estimates of Microbial Community Diversity and Composition in Agricultural Soils. MICROBIAL ECOLOGY 2019; 78:753-763. [PMID: 30852638 DOI: 10.1007/s00248-019-01318-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 01/03/2019] [Indexed: 06/09/2023]
Abstract
Soil microbiota play important and diverse roles in agricultural crop nutrition and productivity. Yet, despite increasing efforts to characterize soil bacterial and fungal assemblages, it is challenging to disentangle the influences of sampling design on assessments of communities. Here, we sought to determine whether composite samples-often analyzed as a low cost and effort alternative to replicated individual samples-provide representative summary estimates of microbial communities. At three Minnesota agricultural research sites planted with an oat cover crop, we conducted amplicon sequencing for soil bacterial and fungal communities (16SV4 and ITS2) of replicated individual or homogenized composite soil samples. We compared soil microbiota from within and among plots and then among agricultural sites using both sampling strategies. Results indicated that single or multiple replicated individual samples, or a composite sample from each plot, were sufficient for distinguishing broad site-level macroecological differences among bacterial and fungal communities. Analysis of a single sample per plot captured only a small fraction of the distinct OTUs, diversity, and compositional variability detected in the analysis of multiple individual samples or a single composite sample. Likewise, composite samples captured only a fraction of the diversity represented by the six individual samples from which they were formed, and, on average, analysis of two or three individual samples offered greater compositional coverage (i.e., greater number of OTUs) than a single composite sample. We conclude that sampling design significantly impacts estimates of bacterial and fungal communities even in homogeneously managed agricultural soils, and our findings indicate that while either strategy may be sufficient for broad macroecological investigations, composites may be a poor substitute for replicated samples at finer spatial scales.
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Affiliation(s)
- Sarah C Castle
- Department of Plant Pathology, University of Minnesota, Minneapolis, USA.
| | - Deborah A Samac
- Department of Plant Pathology, University of Minnesota, Minneapolis, USA
- USDA-ARS, Plant Science Research Unit, Saint Paul, MN, USA
| | - Michael J Sadowsky
- Department of Soil, Water, and Climate, University of Minnesota, Minneapolis, MN, USA
- Biotechnology Institute, University of Minnesota, Minneapolis, MN, USA
| | - Carl J Rosen
- Department of Soil, Water, and Climate, University of Minnesota, Minneapolis, MN, USA
| | - Jessica L M Gutknecht
- Department of Soil, Water, and Climate, University of Minnesota, Minneapolis, MN, USA
| | - Linda L Kinkel
- Department of Plant Pathology, University of Minnesota, Minneapolis, USA
- Biotechnology Institute, University of Minnesota, Minneapolis, MN, USA
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31
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Martínez-Olivas MA, Jiménez-Bueno NG, Hernández-García JA, Fusaro C, Luna-Guido M, Navarro-Noya YE, Dendooven L. Bacterial and archaeal spatial distribution and its environmental drivers in an extremely haloalkaline soil at the landscape scale. PeerJ 2019; 7:e6127. [PMID: 31249729 PMCID: PMC6587938 DOI: 10.7717/peerj.6127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 11/17/2018] [Indexed: 11/20/2022] Open
Abstract
Background A great number of studies have shown that the distribution of microorganisms in the soil is not random, but that their abundance changes along environmental gradients (spatial patterns). The present study examined the spatial variability of the physicochemical characteristics of an extreme alkaline saline soil and how they controlled the archaeal and bacterial communities so as to determine the main spatial community drivers. Methods The archaeal and bacterial community structure, and soil characteristics were determined at 13 points along a 211 m transect in the former lake Texcoco. Geostatistical techniques were used to describe spatial patterns of the microbial community and soil characteristics and determine soil properties that defined the prokaryotic community structure. Results A high variability in electrolytic conductivity (EC) and water content (WC) was found. Euryarchaeota dominated Archaea, except when the EC was low. Proteobacteria, Bacteroidetes and Actinobacteria were the dominant bacterial phyla independent of large variations in certain soil characteristics. Multivariate analysis showed that soil WC affected the archaeal community structure and a geostatistical analysis found that variation in the relative abundance of Euryarchaeota was controlled by EC. The bacterial alpha diversity was less controlled by soil characteristics at the scale of this study than the archaeal alpha diversity. Discussion Results indicated that WC and EC played a major role in driving the microbial communities distribution and scale and sampling strategies were important to define spatial patterns.
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Affiliation(s)
| | | | - Juan Alfredo Hernández-García
- Laboratory of Biological Variation and Evolution, Department of Zoology, Escuela Nacional de Ciencias Biológicas, Instituto Politecnico Nacional, Mexico City, Mexico
| | - Carmine Fusaro
- Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Tlaxcala, Mexico
| | | | | | - Luc Dendooven
- Laboratory of Soil Ecology, Cinvestav, Mexico City, Mexico
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32
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Langenheder S, Lindström ES. Factors influencing aquatic and terrestrial bacterial community assembly. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:306-315. [PMID: 30618071 DOI: 10.1111/1758-2229.12731] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/26/2018] [Indexed: 05/12/2023]
Abstract
During recent years, many studies have shown that different processes including drift, environmental selection and dispersal can be important for the assembly of bacterial communities in aquatic and terrestrial ecosystems. However, we lack a conceptual overview about the ecological context and factors that influence the relative importance of the different assembly mechanisms and determine their dynamics in time and space. Focusing on free-living, i.e., nonhost associated, bacterial communities, this minireview, therefore, summarizes and conceptualizes findings from empirical studies about how (i) environmental factors, such as environmental heterogeneity, disturbances, productivity and trophic interactions; (ii) connectivity and dispersal rates (iii) spatial scale, (iv) community properties and traits and (v) the use of taxonomic/phylogenetic or functional metrics influence the relative importance of different community assembly processes. We find that there is to-date little consistency among studies and suggest that future studies should now address how (i)-(v) differ between habitats and organisms and how this, in turn, influences the temporal and spatial-scale dependency of community assembly processes in microorganisms.
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Affiliation(s)
- Silke Langenheder
- Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Eva S Lindström
- Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
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33
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Zhang B, Xue K, Zhou S, Che R, Du J, Tang L, Pang Z, Wang F, Wang D, Cui X, Hao Y, Wang Y. Phosphorus mediates soil prokaryote distribution pattern along a small-scale elevation gradient in Noijin Kangsang Peak, Tibetan Plateau. FEMS Microbiol Ecol 2019; 95:5499016. [DOI: 10.1093/femsec/fiz076] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/24/2019] [Indexed: 01/12/2023] Open
Affiliation(s)
- Biao Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Xue
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Environmental Biotechnology, Chinese Academy of Sciences (CAS), Beijing 100085, China
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Shutong Zhou
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongxiao Che
- Institute of International Rivers and Eco-security, Yunnan University, Kunming 650091, China
| | - Jianqing Du
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Tang
- University of Chinese Academy of Sciences, Beijing 100049, China
- Environmental Futures Research Institute, School of Environment and Science, Griffith University, Nathan QLD 4111, Australia
| | - Zhe Pang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Wang
- University of Chinese Academy of Sciences, Beijing 100049, China
- Environmental Futures Research Institute, School of Environment and Science, Griffith University, Nathan QLD 4111, Australia
| | - Di Wang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyong Cui
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Yanbin Hao
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Yanfen Wang
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences (CAS), Beijing 100101, China
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Averill C, Cates LL, Dietze MC, Bhatnagar JM. Spatial vs. temporal controls over soil fungal community similarity at continental and global scales. ISME JOURNAL 2019; 13:2082-2093. [PMID: 31019271 DOI: 10.1038/s41396-019-0420-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/21/2019] [Accepted: 03/20/2019] [Indexed: 11/09/2022]
Abstract
Large-scale environmental sequencing efforts have transformed our understanding of the spatial controls over soil microbial community composition and turnover. Yet, our knowledge of temporal controls is comparatively limited. This is a major uncertainty in microbial ecology, as there is increasing evidence that microbial community composition is important for predicting microbial community function in the future. Here, we use continental- and global-scale soil fungal community surveys, focused within northern temperate latitudes, to estimate the relative contribution of time and space to soil fungal community turnover. We detected large intra-annual temporal differences in soil fungal community similarity, where fungal communities differed most among seasons, equivalent to the community turnover observed over thousands of kilometers in space. inter-annual community turnover was comparatively smaller than intra-annual turnover. Certain environmental covariates, particularly climate covariates, explained some spatial-temporal effects, though it is unlikely the same mechanisms drive spatial vs. temporal turnover. However, these commonly measured environmental covariates could not fully explain relationships between space, time and community composition. These baseline estimates of fungal community turnover in time provide a starting point to estimate the potential duration of legacies in microbial community composition and function.
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Affiliation(s)
- Colin Averill
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, USA. .,Department of Earth & Environment, Boston University, Boston, MA, USA.
| | - LeAnna L Cates
- Department of Biology, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Michael C Dietze
- Department of Earth & Environment, Boston University, Boston, MA, USA
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Harrison E, Hall JPJ, Brockhurst MA. Migration promotes plasmid stability under spatially heterogeneous positive selection. Proc Biol Sci 2019; 285:rspb.2018.0324. [PMID: 29794045 DOI: 10.1098/rspb.2018.0324] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/25/2018] [Indexed: 01/01/2023] Open
Abstract
Bacteria-plasmid associations can be mutualistic or antagonistic depending on the strength of positive selection for plasmid-encoded genes, with contrasting outcomes for plasmid stability. In mutualistic environments, plasmids are swept to high frequency by positive selection, increasing the likelihood of compensatory evolution to ameliorate the plasmid cost, which promotes long-term stability. In antagonistic environments, plasmids are purged by negative selection, reducing the probability of compensatory evolution and driving their extinction. Here we show, using experimental evolution of Pseudomonas fluorescens and the mercury-resistance plasmid, pQBR103, that migration promotes plasmid stability in spatially heterogeneous selection environments. Specifically, migration from mutualistic environments, by increasing both the frequency of the plasmid and the supply of compensatory mutations, stabilized plasmids in antagonistic environments where, without migration, they approached extinction. These data suggest that spatially heterogeneous positive selection, which is common in natural environments, coupled with migration helps to explain the stability of plasmids and the ecologically important genes that they encode.
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Affiliation(s)
- Ellie Harrison
- P3 Institute, Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 1AE, UK
| | - James P J Hall
- Department of Animal and Plant Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Science, University of Sheffield, Sheffield S10 2TN, UK
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Yu S, Chen Z, Zhao K, Ye Z, Zhang L, Dong J, Shao Y, Zhang C, Fu W. Spatial Patterns of Potentially Hazardous Metals in Soils of Lin'an City, Southeastern China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16020246. [PMID: 30654530 PMCID: PMC6352076 DOI: 10.3390/ijerph16020246] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 12/29/2018] [Accepted: 01/11/2019] [Indexed: 12/02/2022]
Abstract
Urban soils are strongly related to human health. In this study, Lin’an city was chosen as a typical small-scale city with which to study the spatial variation of potentially hazardous metals (PHMs) in urban soils and their potential ecological risks using multivariate analysis, geostatistics and GIS techniques. A total of 62 soil samples were collected from the study area. The results showed that the average concentrations of total soil Mn, Cu, Zn, Pb, Cr, Cd were 439.42, 42.23, 196.80, 62.55, 63.65, 0.22 mg·kg−1, respectively. Compared with the background values and the environmental quality standards, these PHMs were accumulated in urban soils to some extent. The single potential ecological risk indices of PHMs indicated that Pb and Cd had relatively high ecological risks. The pH and most of the PHMs had significant correlations (p < 0.05). The principle components analysis (PCA) showed that Pb, Zn and Cu had similar pollution sources related to the vehicles’ exhaust emission; Mn and Cr were mainly from the parent materials; while Cd was from the emission of industrial manufactories. The spatial structures and distributions of PHMs and their corresponding available fractions had strong/moderate spatial autocorrelation, which were influenced by human activities.
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Affiliation(s)
- Shiying Yu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an 311300, China.
| | - Zhoulun Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an 311300, China.
| | - Keli Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an 311300, China.
| | - Zhengqian Ye
- Key Laboratory of Soil Contamination Bioremediation of Zhejiang Province, School of Environmental Sciences and Resources, Zhejiang A & F University, Lin'an 311300, China.
| | - Luyao Zhang
- Key Laboratory of Soil Contamination Bioremediation of Zhejiang Province, School of Environmental Sciences and Resources, Zhejiang A & F University, Lin'an 311300, China.
| | - Jiaqi Dong
- Key Laboratory of Soil Contamination Bioremediation of Zhejiang Province, School of Environmental Sciences and Resources, Zhejiang A & F University, Lin'an 311300, China.
| | - Yangfeng Shao
- Technology Promotion Center of Agriculture and Forestry in Lin'an City, Hangzhou 311300, China.
| | - Chaosheng Zhang
- International Network for Environment and Health, School of Geography and Archaeology & Ryan Institute, National University of Ireland, Galway, Ireland.
| | - Weijun Fu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an 311300, China.
- Key Laboratory of Soil Contamination Bioremediation of Zhejiang Province, School of Environmental Sciences and Resources, Zhejiang A & F University, Lin'an 311300, China.
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Meng Q, Xu X, Zhang W, Cheng L, Men M, Xu B, Deng L, Sun X. Diversity and abundance of denitrifiers during cow manure composting. Rev Argent Microbiol 2018; 51:191-200. [PMID: 30467018 DOI: 10.1016/j.ram.2018.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 07/17/2018] [Accepted: 08/06/2018] [Indexed: 10/27/2022] Open
Abstract
Diversity and abundance of the denitrifying genes nirK, nirS and nosZ were investigated in cow manure compost using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time quantitative PCR (qPCR), respectively. These three genes were detected in all the stages of the composting process. Phylogenetic analysis showed that the nirK gene was closely related to Rhizobiales, Burkholderiales, the nirS gene was closely related to Pseudomonadales and Burkholderiales, and the nosZ gene was closely related to Rhodospirillales, Rhizobiales, Pseudomonadales, and Alteromonadales. qPCR results showed that the abundance of these three genes (nirK, nirS and nosZ) reached the peak value in the late thermophilic stage of composting and abundance of the nirK gene was higher than that of the nosZ gene and the nirS gene. Redundancy analysis (RDA) showed that the diversity of the nirK and nirS genes was significantly correlated with ammonium (p<0.05), the diversity of the nosZ gene was significantly correlated with pH (p<0.05) and the abundance of the nirK nirS and nosZ genes was significantly correlated with temperature (p<0.05).
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Affiliation(s)
- Qingxin Meng
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xiuhong Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China.
| | - Wenhao Zhang
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Lijun Cheng
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Mengqi Men
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Benshu Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Liting Deng
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xuewei Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
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38
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Darcy JL, Gendron EMS, Sommers P, Porazinska DL, Schmidt SK. Island Biogeography of Cryoconite Hole Bacteria in Antarctica's Taylor Valley and Around the World. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00180] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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Teurlincx S, Heijboer A, Veraart AJ, Kowalchuk GA, Declerck SAJ. Local Functioning, Landscape Structuring: Drivers of Soil Microbial Community Structure and Function in Peatlands. Front Microbiol 2018; 9:2060. [PMID: 30233537 PMCID: PMC6129579 DOI: 10.3389/fmicb.2018.02060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/13/2018] [Indexed: 12/04/2022] Open
Abstract
Agricultural peatlands are essential for a myriad of ecosystem functions and play an important role in the global carbon (C) cycle through C sequestration. Management of these agricultural peatlands takes place at different spatial scales, ranging from local to landscape management, and drivers of soil microbial community structure and function may be scale-dependent. Effective management for an optimal biogeochemical functioning thus requires knowledge of the drivers on soil microbial community structure and functioning, as well as the spatial scales upon which they are influenced. During two field campaigns, we examined the importance of different drivers (i.e., soil characteristics, nutrient management, vegetation composition) at two spatial scales (local vs. landscape) for, respectively, the soil microbial community structure (determined by PLFA) and soil microbial community functional capacity (as assessed by CLPP) in agricultural peatlands. First, we show by an analysis of PLFA profiles that the total microbial biomass changes with soil moisture and relative C:P nutrient availability. Secondly, we showed that soil communities are controlled by a distinct set of drivers at the local, as opposed to landscape, scale. Community structure was found to be markedly different between areas, in contrast to community function which showed high variability within areas. We further found that microbial structure appears to be controlled more at a landscape scale by nutrient-related variables, whereas microbial functional capacity is driven locally through plant community feedbacks. Optimal management strategies within such peatlands should therefore consider the scale-dependent action of soil microbial community drivers, for example by first optimizing microbial structure at the landscape scale by targeted areal management, and then optimizing soil microbial function by local vegetation management.
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Affiliation(s)
- Sven Teurlincx
- Department of Aquatic Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Amber Heijboer
- Biometris, Wageningen University, Wageningen, Netherlands.,Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Radboud University Nijmegen, Nijmegen, Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - George A Kowalchuk
- Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
| | - Steven A J Declerck
- Department of Aquatic Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
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40
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Deakin G, Tilston EL, Bennett J, Passey T, Harrison N, Fernández-Fernández F, Xu X. Spatial structuring of soil microbial communities in commercial apple orchards. APPLIED SOIL ECOLOGY : A SECTION OF AGRICULTURE, ECOSYSTEMS & ENVIRONMENT 2018; 130:1-12. [PMID: 30177867 PMCID: PMC6102658 DOI: 10.1016/j.apsoil.2018.05.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 05/09/2018] [Accepted: 05/20/2018] [Indexed: 05/07/2023]
Abstract
Characterising spatial microbial community structure is important to understand and explain the consequences of continuous plantation of one crop species on the performance of subsequent crops, especially where this leads to reduced growth vigour and crop yield. We investigated the spatial structure, specifically distance-decay of similarity, of soil bacterial and fungal communities in two long-established orchards with contrasting agronomic characteristics. A spatially explicit sampling strategy was used to collect soil from under recently grubbed rows of apple trees and under the grassed aisles. Amplicon-based metabarcoding technology was used to characterise the soil microbial communities. The results suggested that (1) most of the differences in soil microbial community structure were due to large-scale differences (i.e. between orchards), (2) within-orchard, small-scale (1-5 m) spatial variability was also present, but spatial relationships in microbial community structure differed between orchards and were not predictable, and (3) vegetation type (i.e. trees or grass and their associated management) can significantly alter the structure of soil microbial communities, affecting a large proportion of microbial groups. The discontinuous nature of soil microbial community structure in the tree stations and neighbouring grass aisles within an orchard illustrate the importance of vegetation type and allied weed and nutrient management on soil microbial community structure.
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Affiliation(s)
| | | | | | | | | | | | - Xiangming Xu
- NIAB EMR, East Malling, West Malling, Kent ME19 6BJ, UK
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41
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Pershina EV, Ivanova EA, Korvigo IO, Chirak EL, Sergaliev NH, Abakumov EV, Provorov NA, Andronov EE. Investigation of the core microbiome in main soil types from the East European plain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 631-632:1421-1430. [PMID: 29727966 DOI: 10.1016/j.scitotenv.2018.03.136] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 03/12/2018] [Accepted: 03/12/2018] [Indexed: 05/12/2023]
Abstract
The main goal of modern microbial ecology is to determine the key factors influencing the global diversity of microorganisms. Because of their complexity, soil communities are largely underexplored in this context. We studied soil genesis (combination of various soil-forming processes, specific to a particular soil type) that is driven by microbial activity. To investigate the interrelation between soil type and microbial diversity, we analyzed six soil types that are common in Russia, the Crimea, and Kazakhstan using 16S rDNA pyrosequencing. Soils of different types varied in the taxonomic composition of microbial communities. Their core microbiomes comprised 47 taxa within the orders Solirubrobacteriales and Hyphomicrobiaceae and the Gaiellaceae family. Two species from Bradyrhizobiaceae and Solirubrobactriaceae were present in all samples, whereas most other taxa were soil-type specific. Multiple resampling analysis revealed that two random soil samples from the same soil type shared more taxa than two samples from different types. The differences in community composition were mostly affected by the variation in pH values and exchangeable potassium content. The results show that data on the soil microbiome could be used for soil identification and clarification of their taxonomic position.
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Affiliation(s)
- Elizaveta V Pershina
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia; Department of Microbiology, Saint-Petersburg State University, Saint-Petersburg, Russia.
| | - Ekaterina A Ivanova
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia; Saint-Petersburg State University, Saint-Petersburg, Russia; Laboratory of Biology and Biochemistry of Soils, V.V. Dokuchaev Soil Science Institute, Moscow, Russia
| | - Ilia O Korvigo
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Evgeny L Chirak
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Nurlan H Sergaliev
- West Kazakhstan Agrarian Technical University, Zhangir Khan, Uralsk, Kazakhstan
| | | | - Nikolai A Provorov
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Evgeny E Andronov
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia; Saint-Petersburg State University, Saint-Petersburg, Russia; Laboratory of Biology and Biochemistry of Soils, V.V. Dokuchaev Soil Science Institute, Moscow, Russia
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42
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Meyer KM, Memiaghe H, Korte L, Kenfack D, Alonso A, Bohannan BJM. Why do microbes exhibit weak biogeographic patterns? ISME JOURNAL 2018; 12:1404-1413. [PMID: 29662146 DOI: 10.1038/s41396-018-0103-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/25/2017] [Accepted: 11/20/2017] [Indexed: 11/09/2022]
Abstract
Analysis of patterns in the distribution of taxa can provide important insights into ecological and evolutionary processes. Microbial biogeographic patterns almost always appear to be weaker than those reported for plant and animal taxa. It is as yet unclear why this is the case. Some argue that microbial diversity scales differently over space because microbial taxa are fundamentally different in their abundance, longevity and dispersal abilities. Others have argued that differences in scaling are an artifact of how we assess microbial biogeography, driven, for example, by differences in taxonomic resolution, spatial scale, sampling effort or community activity/dormancy. We tested these alternative explanations by comparing bacterial biogeographic patterns in soil to those of trees found in a forest in Gabon. Altering taxonomic resolution, excluding inactive individuals, or adjusting for differences in spatial scale were insufficient to change the rate of microbial taxonomic turnover. In contrast, we account for the differences in spatial turnover between these groups by equalizing sampling extent. Our results suggest that spatial scaling differences between microbial and plant diversity are likely not due to fundamental differences in biology, and that sampling extent should be taken into account when comparing the biogeographic patterns of microorganisms and larger organisms.
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Affiliation(s)
- Kyle M Meyer
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA.
| | - Hervé Memiaghe
- Department of Landscape Architecture, University of Oregon, Eugene, OR, USA.,Institut de Recherche en Écologie Tropicale (IRET), Libreville, Gabon, USA
| | - Lisa Korte
- Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - David Kenfack
- Smithsonian Tropical Research Institute, Washington, DC, USA
| | - Alfonso Alonso
- Smithsonian Conservation Biology Institute, Washington, DC, USA
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43
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Shi Y, Li Y, Xiang X, Sun R, Yang T, He D, Zhang K, Ni Y, Zhu YG, Adams JM, Chu H. Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain. MICROBIOME 2018; 6:27. [PMID: 29402331 PMCID: PMC5799910 DOI: 10.1186/s40168-018-0409-4] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/19/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND The relative importance of stochasticity versus determinism in soil bacterial communities is unclear, as are the possible influences that alter the balance between these. Here, we investigated the influence of spatial scale on the relative role of stochasticity and determinism in agricultural monocultures consisting only of wheat, thereby minimizing the influence of differences in plant species cover and in cultivation/disturbance regime, extending across a wide range of soils and climates of the North China Plain (NCP). We sampled 243 sites across 1092 km and sequenced the 16S rRNA bacterial gene using MiSeq. We hypothesized that determinism would play a relatively stronger role at the broadest scales, due to the strong influence of climate and soil differences in selecting many distinct OTUs of bacteria adapted to the different environments. In order to test the more general applicability of the hypothesis, we also compared with a natural ecosystem on the Tibetan Plateau. RESULTS Our results revealed that the relative importance of stochasticity vs. determinism did vary with spatial scale, in the direction predicted. On the North China Plain, stochasticity played a dominant role from 150 to 900 km (separation between pairs of sites) and determinism dominated at more than 900 km (broad scale). On the Tibetan Plateau, determinism played a dominant role from 130 to 1200 km and stochasticity dominated at less than 130 km. Among the identifiable deterministic factors, soil pH showed the strongest influence on soil bacterial community structure and diversity across the North China Plain. Together, 23.9% of variation in soil microbial community composition could be explained, with environmental factors accounting for 19.7% and spatial parameters 4.1%. CONCLUSIONS Our findings revealed that (1) stochastic processes are relatively more important on the North China Plain, while deterministic processes are more important on the Tibetan Plateau; (2) soil pH was the major factor in shaping soil bacterial community structure of the North China Plain; and (3) most variation in soil microbial community composition could not be explained with existing environmental and spatial factors. Further studies are needed to dissect the influence of stochastic factors (e.g., mutations or extinctions) on soil microbial community distribution, which might make it easier to predictably manipulate the microbial community to produce better yield and soil sustainability outcomes.
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Affiliation(s)
- Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Yuntao Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Xingjia Xiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Ruibo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Dan He
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Kaoping Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Yingying Ni
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
| | - Jonathan M. Adams
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK46 0AL UK
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
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44
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Damaso N, Mendel J, Mendoza M, von Wettberg EJ, Narasimhan G, Mills D. Bioinformatics Approach to Assess the Biogeographical Patterns of Soil Communities: The Utility for Soil Provenance. J Forensic Sci 2018; 63:1033-1042. [PMID: 29357400 DOI: 10.1111/1556-4029.13741] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 12/26/2017] [Accepted: 12/28/2017] [Indexed: 01/23/2023]
Abstract
Soil DNA profiling has potential as a forensic tool to establish a link between soil collected at a crime scene and soil recovered from a suspect. However, a quantitative measure is needed to investigate the spatial/temporal variability across multiple scales prior to their application in forensic science. In this study, soil DNA profiles across Miami-Dade, FL, were generated using length heterogeneity PCR to target four taxa. The objectives of this study were to (i) assess the biogeographical patterns of soils to determine whether soil biota is spatially correlated with geographic location and (ii) evaluate five machine learning algorithms for their predictive ability to recognize biotic patterns which could accurately classify soils at different spatial scales regardless of seasonal collection. Results demonstrate that soil communities have unique patterns and are spatially autocorrelated. Bioinformatic algorithms could accurately classify soils across all scales with Random Forest significantly outperforming all other algorithms regardless of spatial level.
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Affiliation(s)
- Natalie Damaso
- Department of Biological Sciences, Florida International University, 11200 SW 8th Street, OE 167, Miami, FL 33199.,International Forensic Research Institute, Florida International University, 11200 SW 8th Street, OE 116, Miami, FL 33199
| | - Julian Mendel
- Department of Biological Sciences, Florida International University, 11200 SW 8th Street, OE 167, Miami, FL 33199.,International Forensic Research Institute, Florida International University, 11200 SW 8th Street, OE 116, Miami, FL 33199
| | - Maria Mendoza
- Department of Biological Sciences, Florida International University, 11200 SW 8th Street, OE 167, Miami, FL 33199.,International Forensic Research Institute, Florida International University, 11200 SW 8th Street, OE 116, Miami, FL 33199
| | - Eric J von Wettberg
- Department of Biological Sciences, Florida International University, 11200 SW 8th Street, OE 167, Miami, FL 33199.,International Center for Tropical Botany, Florida International University, 4013 South Douglas Road, Miami, FL 33133
| | - Giri Narasimhan
- Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL 33199
| | - DeEtta Mills
- Department of Biological Sciences, Florida International University, 11200 SW 8th Street, OE 167, Miami, FL 33199.,International Forensic Research Institute, Florida International University, 11200 SW 8th Street, OE 116, Miami, FL 33199
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45
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Gentry DM, Amador ES, Cable ML, Chaudry N, Cullen T, Jacobsen MB, Murukesan G, Schwieterman EW, Stevens AH, Stockton A, Tan G, Yin C, Cullen DC, Geppert W. Correlations Between Life-Detection Techniques and Implications for Sampling Site Selection in Planetary Analog Missions. ASTROBIOLOGY 2017; 17:1009-1021. [PMID: 29048222 PMCID: PMC5686451 DOI: 10.1089/ast.2016.1575] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 06/29/2017] [Indexed: 05/26/2023]
Abstract
We conducted an analog sampling expedition under simulated mission constraints to areas dominated by basaltic tephra of the Eldfell and Fimmvörðuháls lava fields (Iceland). Sites were selected to be "homogeneous" at a coarse remote sensing resolution (10-100 m) in apparent color, morphology, moisture, and grain size, with best-effort realism in numbers of locations and replicates. Three different biomarker assays (counting of nucleic-acid-stained cells via fluorescent microscopy, a luciferin/luciferase assay for adenosine triphosphate, and quantitative polymerase chain reaction (qPCR) to detect DNA associated with bacteria, archaea, and fungi) were characterized at four nested spatial scales (1 m, 10 m, 100 m, and >1 km) by using five common metrics for sample site representativeness (sample mean variance, group F tests, pairwise t tests, and the distribution-free rank sum H and u tests). Correlations between all assays were characterized with Spearman's rank test. The bioluminescence assay showed the most variance across the sites, followed by qPCR for bacterial and archaeal DNA; these results could not be considered representative at the finest resolution tested (1 m). Cell concentration and fungal DNA also had significant local variation, but they were homogeneous over scales of >1 km. These results show that the selection of life detection assays and the number, distribution, and location of sampling sites in a low biomass environment with limited a priori characterization can yield both contrasting and complementary results, and that their interdependence must be given due consideration to maximize science return in future biomarker sampling expeditions. Key Words: Astrobiology-Biodiversity-Microbiology-Iceland-Planetary exploration-Mars mission simulation-Biomarker. Astrobiology 17, 1009-1021.
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Affiliation(s)
- Diana M. Gentry
- Biospheric Science, NASA Ames Research Center, Moffett Field, California
| | - Elena S. Amador
- Astrobiology Program, University of Washington, Seattle, Washington
| | - Morgan L. Cable
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Nosheen Chaudry
- School of Engineering, Cranfield University, Cranfield, United Kingdom
| | - Thomas Cullen
- School of Engineering, Cranfield University, Cranfield, United Kingdom
| | | | - Gayathri Murukesan
- Department of Biochemistry/Biochemistry, University of Turku, Turku, Finland
| | | | - Adam H. Stevens
- UK Centre for Astrobiology, School of Physics and Astronomy, The University of Edinburgh, Edinburgh, United Kingdom
| | - Amanda Stockton
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - George Tan
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - Chang Yin
- Stockholm University Astrobiology Centre, Stockholm University, Stockholm, Sweden
| | - David C. Cullen
- School of Engineering, Cranfield University, Cranfield, United Kingdom
| | - Wolf Geppert
- Stockholm University Astrobiology Centre, Stockholm University, Stockholm, Sweden
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46
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Tecon R, Or D. Biophysical processes supporting the diversity of microbial life in soil. FEMS Microbiol Rev 2017; 41:599-623. [PMID: 28961933 PMCID: PMC5812502 DOI: 10.1093/femsre/fux039] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 07/10/2017] [Indexed: 12/13/2022] Open
Abstract
Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure-the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning.
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Affiliation(s)
- Robin Tecon
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Dani Or
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
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47
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Kaleita AL, Schott LR, Hargreaves SK, Hofmockel KS. Differences in soil biological activity by terrain types at the sub-field scale in central Iowa US. PLoS One 2017; 12:e0180596. [PMID: 28686652 PMCID: PMC5501568 DOI: 10.1371/journal.pone.0180596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/16/2017] [Indexed: 11/29/2022] Open
Abstract
Soil microbial communities are structured by biogeochemical processes that occur at many different spatial scales, which makes soil sampling difficult. Because soil microbial communities are important in nutrient cycling and soil fertility, it is important to understand how microbial communities function within the heterogeneous soil landscape. In this study, a self-organizing map was used to determine whether landscape data can be used to characterize the distribution of microbial biomass and activity in order to provide an improved understanding of soil microbial community function. Points within a row crop field in south-central Iowa were clustered via a self-organizing map using six landscape properties into three separate landscape clusters. Twelve sampling locations per cluster were chosen for a total of 36 locations. After the soil samples were collected, the samples were then analysed for various metabolic indicators, such as nitrogen and carbon mineralization, extractable organic carbon, microbial biomass, etc. It was found that sampling locations located in the potholes and toe slope positions had significantly greater microbial biomass nitrogen and carbon, total carbon, total nitrogen and extractable organic carbon than the other two landscape position clusters, while locations located on the upslope did not differ significantly from the other landscape clusters. However, factors such as nitrate, ammonia, and nitrogen and carbon mineralization did not differ significantly across the landscape. Overall, this research demonstrates the effectiveness of a terrain-based clustering method for guiding soil sampling of microbial communities.
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Affiliation(s)
- Amy L. Kaleita
- Agricultural & Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
| | - Linda R. Schott
- Biological Systems Engineering, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Sarah K. Hargreaves
- Ecological Farmers Association of Ontario, Guelph, Ontario, Canada
- Formerly: Ecology, Evolutionary and Organismal Biology, Iowa State University, Ames, Iowa, United States of America
| | - Kirsten S. Hofmockel
- Formerly: Ecology, Evolutionary and Organismal Biology, Iowa State University, Ames, Iowa, United States of America
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
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48
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Gutleben J, Chaib De Mares M, van Elsas JD, Smidt H, Overmann J, Sipkema D. The multi-omics promise in context: from sequence to microbial isolate. Crit Rev Microbiol 2017; 44:212-229. [PMID: 28562180 DOI: 10.1080/1040841x.2017.1332003] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The numbers and diversity of microbes in ecosystems within and around us is unmatched, yet most of these microorganisms remain recalcitrant to in vitro cultivation. Various high-throughput molecular techniques, collectively termed multi-omics, provide insights into the genomic structure and metabolic potential as well as activity of complex microbial communities. Nonetheless, pure or defined cultures are needed to (1) decipher microbial physiology and thus test multi-omics-based ecological hypotheses, (2) curate and improve database annotations and (3) realize novel applications in biotechnology. Cultivation thus provides context. In turn, we here argue that multi-omics information awaits integration into the development of novel cultivation strategies. This can build the foundation for a new era of omics information-guided microbial cultivation technology and reduce the inherent trial-and-error search space. This review discusses how information that can be extracted from multi-omics data can be applied for the cultivation of hitherto uncultured microorganisms. Furthermore, we summarize groundbreaking studies that successfully translated information derived from multi-omics into specific media formulations, screening techniques and selective enrichments in order to obtain novel targeted microbial isolates. By integrating these examples, we conclude with a proposed workflow to facilitate future omics-aided cultivation strategies that are inspired by the microbial complexity of the environment.
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Affiliation(s)
- Johanna Gutleben
- a Laboratory of Microbiology , Wageningen University & Research , Wageningen , The Netherlands
| | - Maryam Chaib De Mares
- b Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences (GELIFES) , Rijksuniversiteit Groningen , Groningen , The Netherlands
| | - Jan Dirk van Elsas
- b Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences (GELIFES) , Rijksuniversiteit Groningen , Groningen , The Netherlands
| | - Hauke Smidt
- a Laboratory of Microbiology , Wageningen University & Research , Wageningen , The Netherlands
| | - Jörg Overmann
- c Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen , Braunschweig , Germany
| | - Detmer Sipkema
- a Laboratory of Microbiology , Wageningen University & Research , Wageningen , The Netherlands
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Spatial and Temporal Variability of Soil Respiration between Soybean Crop Rows as Measured Continuously over a Growing Season. SUSTAINABILITY 2017. [DOI: 10.3390/su9030436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Jumpponen A, Johnson LC. Can rDNA analyses of diverse fungal communities in soil and roots detect effects of environmental manipulations—a case study from tallgrass prairie. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
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