1
|
Jiang A, Dong Y, Asitaiken J, Zhou S, Nie T, Wu Y, Liu Z, An S, Yang K. Response of soil fungal communities and their co-occurrence patterns to grazing exclusion in different grassland types. Front Microbiol 2024; 15:1404633. [PMID: 39027108 PMCID: PMC11256198 DOI: 10.3389/fmicb.2024.1404633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
Overgrazing and climate change are the main causes of grassland degradation, and grazing exclusion is one of the most common measures for restoring degraded grasslands worldwide. Soil fungi can respond rapidly to environmental stresses, but the response of different grassland types to grazing control has not been uniformly determined. Three grassland types (temperate desert, temperate steppe grassland, and mountain meadow) that were closed for grazing exclusion for 9 years were used to study the effects of grazing exclusion on soil nutrients as well as fungal community structure in the three grassland types. The results showed that (1) in the 0-5 cm soil layer, grazing exclusion significantly affected the soil water content of the three grassland types (P < 0.05), and the pH, total phosphorous (TP), and nitrogen-to-phosphorous ratio (N/P) changed significantly in all three grassland types (P < 0.05). Significant changes in soil nutrients in the 5-10 cm soil layer after grazing exclusion occurred in the mountain meadow grasslands (P < 0.05), but not in the temperate desert and temperate steppe grasslands. (2) For the different grassland types, Archaeorhizomycetes was most abundant in the montane meadows, and Dothideomycetes was most abundant in the temperate desert grasslands and was significantly more abundant than in the remaining two grassland types (P < 0.05). Grazing exclusion led to insignificant changes in the dominant soil fungal phyla and α diversity, but significant changes in the β diversity of soil fungi (P < 0.05). (3) Grazing exclusion areas have higher mean clustering coefficients and modularity classes than grazing areas. In particular, the highest modularity class is found in temperate steppe grassland grazing exclusion areas. (4) We also found that pH is the main driving factor affecting soil fungal community structure, that plant coverage is a key environmental factor affecting soil community composition, and that grazing exclusion indirectly affects soil fungal communities by affecting soil nutrients. The above results suggest that grazing exclusion may regulate microbial ecological processes by changing the soil fungal β diversity in the three grassland types. Grazing exclusion is not conducive to the recovery of soil nutrients in areas with mountain grassland but improves the stability of soil fungi in temperate steppe grassland. Therefore, the type of degraded grassland should be considered when formulating suitable restoration programmes when grazing exclusion measures are implemented. The results of this study provide new insights into the response of soil fungal communities to grazing exclusion, providing a theoretical basis for the management of degraded grassland restoration.
Collapse
Affiliation(s)
- Anjing Jiang
- College of Grassland Science, Xinjiang Agricultural University, Ürümqi, China
| | - Yiqiang Dong
- College of Grassland Science, Xinjiang Agricultural University, Ürümqi, China
- Xinjiang Key Laboratory of Grassland Resources and Ecology, Ürümqi, Xinjiang, China
- Key Laboratory of Grassland Resources and Ecology of Western Arid Region, Ministry of Education, Ürümqi, China
- Postdoctoral Mobile Station of Xinjiang Agricultural University, Ürümqi, China
| | - Julihaiti Asitaiken
- College of Grassland Science, Xinjiang Agricultural University, Ürümqi, China
| | - Shijie Zhou
- College of Grassland Science, Xinjiang Agricultural University, Ürümqi, China
| | - Tingting Nie
- College of Grassland Science, Xinjiang Agricultural University, Ürümqi, China
| | - Yue Wu
- College of Grassland Science, Xinjiang Agricultural University, Ürümqi, China
| | - Zeyu Liu
- College of Grassland Science, Xinjiang Agricultural University, Ürümqi, China
| | - Shazhou An
- College of Grassland Science, Xinjiang Agricultural University, Ürümqi, China
- Xinjiang Key Laboratory of Grassland Resources and Ecology, Ürümqi, Xinjiang, China
- Key Laboratory of Grassland Resources and Ecology of Western Arid Region, Ministry of Education, Ürümqi, China
| | - Kailun Yang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| |
Collapse
|
2
|
Cantarel AAM, Signoret A, Gervaix J, Beligon C, Béraud C, Boisselet C, Creuzé des Châtelliers C, Defour P, Delort A, Lacroix E, Lobreau C, Louvez E, Marais C, Simonin M, Piola F. Biological inhibition of denitrification (BDI): an early plant strategy for Fallopia × bohemica seedling development. ANNALS OF BOTANY 2024; 133:533-546. [PMID: 37970962 PMCID: PMC11037488 DOI: 10.1093/aob/mcad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND AND AIMS The successful plant Fallopia × bohemica presents interesting capacities for control of the soil nitrogen cycle at the adult stage, termed biological inhibition of denitrification (BDI). The BDI strategy allows the plant, via the production of secondary metabolites (procyanidins), to compete with the denitrifying microbial community and to divert nitrate from the soil for its benefit. In this study, we analysed whether seedlings of F. × bohemica can implement BDI at the seedling stage. We also determined whether soil nitrogen availability influences the implementation of BDI and seedling growth. METHODS We sowed achenes of F. × bohemica in soils representing a nitrogen gradient (six treatments) and harvested seedlings after 20 or 40 days of growth. The denitrification and related microbial communities (i.e. functional gene abundances of nirK and nirS), soil parameters (nitrate content and humidity) and plant performance (biomass, growth and root morphology) were determined. KEY RESULTS On soil without addition of nitrogen, BDI was observed after 20 days of growth, whereas a stimulation of denitrification was found after 40 days. The increase of soil N content had few effects on the activity and structure of the soil denitrifying community and on the plant biomasses or the relative growth rates. Correlations between plant and microbial parameters were observed after 20 days of growth, reflecting early and strong chemical interactions between plants and the denitrifying community, which decreased with plant growth after 40 days. CONCLUSIONS This study shows that an early BDI enhances the efficiency of nitrogen acquisition in the first weeks of growth, allowing for a conservative root strategy after 40 days. This switch to a conservative strategy involved resource storage, an altered allocation to above- and below-ground parts and an investment in fine roots. It now seems clear that this storage strategy starts at a very young age with early establishment of BDI, giving this clonal plant exceptional capacities for storage and multiplication.
Collapse
Affiliation(s)
- Amélie A M Cantarel
- Université Claude Bernard Lyon 1, Laboratoire d’Ecologie Microbienne LEM, UMR 5557 CNRS, UMR 1418 INRAE, VetAgro Sup, 69622 Villeurbanne, France
| | - Aymeric Signoret
- Université Claude Bernard Lyon 1, Laboratoire d’Ecologie Microbienne LEM, UMR 5557 CNRS, UMR 1418 INRAE, VetAgro Sup, 69622 Villeurbanne, France
- Université Claude Bernard Lyon 1, Laboratoire des Ecosystèmes et Hydosystèmes Naturels et Anthropisés LEHNA, ENTPE, UMR 5023 CNRS, 69622 Villeurbanne, France
| | - Jonathan Gervaix
- Université Claude Bernard Lyon 1, Laboratoire d’Ecologie Microbienne LEM, UMR 5557 CNRS, UMR 1418 INRAE, VetAgro Sup, 69622 Villeurbanne, France
| | - Chiquitta Beligon
- Université Claude Bernard Lyon 1, Laboratoire des Ecosystèmes et Hydosystèmes Naturels et Anthropisés LEHNA, ENTPE, UMR 5023 CNRS, 69622 Villeurbanne, France
| | - Cédric Béraud
- Université Claude Bernard Lyon 1, Laboratoire d’Ecologie Microbienne LEM, UMR 5557 CNRS, UMR 1418 INRAE, VetAgro Sup, 69622 Villeurbanne, France
- Université Claude Bernard Lyon 1, Laboratoire des Ecosystèmes et Hydosystèmes Naturels et Anthropisés LEHNA, ENTPE, UMR 5023 CNRS, 69622 Villeurbanne, France
| | - Christelle Boisselet
- Université Claude Bernard Lyon 1, Laboratoire des Ecosystèmes et Hydosystèmes Naturels et Anthropisés LEHNA, ENTPE, UMR 5023 CNRS, 69622 Villeurbanne, France
| | - Charline Creuzé des Châtelliers
- Université Claude Bernard Lyon 1, Laboratoire d’Ecologie Microbienne LEM, UMR 5557 CNRS, UMR 1418 INRAE, VetAgro Sup, 69622 Villeurbanne, France
| | - Pauline Defour
- Université Claude Bernard Lyon 1, Laboratoire d’Ecologie Microbienne LEM, UMR 5557 CNRS, UMR 1418 INRAE, VetAgro Sup, 69622 Villeurbanne, France
| | - Abigaïl Delort
- Université Claude Bernard Lyon 1, Laboratoire d’Ecologie Microbienne LEM, UMR 5557 CNRS, UMR 1418 INRAE, VetAgro Sup, 69622 Villeurbanne, France
| | - Elise Lacroix
- Université Claude Bernard Lyon 1, Plateforme ‘Serre et Chambres Climatiques’, FR BioEEnVis, Domaine scientifique de la DOUA, 69622 Villeurbanne, France
| | - Clément Lobreau
- Université Claude Bernard Lyon 1, Laboratoire d’Ecologie Microbienne LEM, UMR 5557 CNRS, UMR 1418 INRAE, VetAgro Sup, 69622 Villeurbanne, France
- Université Claude Bernard Lyon 1, Laboratoire des Ecosystèmes et Hydosystèmes Naturels et Anthropisés LEHNA, ENTPE, UMR 5023 CNRS, 69622 Villeurbanne, France
| | - Enzo Louvez
- Université Claude Bernard Lyon 1, Laboratoire d’Ecologie Microbienne LEM, UMR 5557 CNRS, UMR 1418 INRAE, VetAgro Sup, 69622 Villeurbanne, France
| | - Coralie Marais
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Marie Simonin
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Florence Piola
- Université Claude Bernard Lyon 1, Laboratoire des Ecosystèmes et Hydosystèmes Naturels et Anthropisés LEHNA, ENTPE, UMR 5023 CNRS, 69622 Villeurbanne, France
| |
Collapse
|
3
|
Yu T, Nie J, Zang H, Zeng Z, Yang Y. Peanut-based Rotation Stabilized Diazotrophic Communities and Increased Subsequent Wheat Yield. MICROBIAL ECOLOGY 2023; 86:2447-2460. [PMID: 37296336 DOI: 10.1007/s00248-023-02254-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/05/2023] [Indexed: 06/12/2023]
Abstract
The introduction of legumes into rotations can improve nitrogen use efficiency and crop yield; however, its microbial mechanism involved remains unclear. This study aimed to explore the temporal impact of peanut introduction on microorganisms related to nitrogen metabolism in rotation systems. In this study, the dynamics of diazotrophic communities in two crop seasons and wheat yields of two rotation systems: winter wheat - summer maize (WM) and spring peanut → winter wheat - summer maize (PWM) in the North China Plain were investigated. Our results showed that peanut introduction increased wheat yield and biomass by 11.6% (p < 0.05) and 8.9%, respectively. Lower Chao1 and Shannon indexes of the diazotrophic communities were detected in soils that sampling in June compared with those sampling in September, although no difference was found between WM and PWM. Principal co-ordinates analysis (PCoA) showed that rotation system significantly changed the diazotrophic community structures (PERMANOVA; p < 0.05). Compared with WM, the genera of Azotobacter, Skermanella, Azohydromonas, Rhodomicrobium, Azospirillum, Unclassified_f_Opitutaceae, and Unclassified_f_Rhodospirillaceae were significantly enriched (p < 0.05) in PWM. Furthermore, rotation system and sampling time significantly influenced soil properties, which significantly correlated with the top 15 genera in relative abundance. Partial least squares path modeling (PLS-PM) analysis further showed that the diazotrophic community diversity (alpha- and beta-diversity) and soil properties (pH, SOC and TN) significantly affected wheat yield. In conclusion, legume inclusion has the potential to stabilize diazotrophic community structure at the temporal scales and increase subsequent crop yield.
Collapse
Affiliation(s)
- Taobing Yu
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Jiangwen Nie
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Huadong Zang
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Zhaohai Zeng
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yadong Yang
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
| |
Collapse
|
4
|
Zaman T, Asad SA, Irshad M, Faridullah, Shahzad M, Nazir R, Arefeen A, Iqbal A, Hafeez F. Unraveling the impact of human perturbation on nitrogen cycling in terrestrial ecosystems of lower Himalaya, Pakistan. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:1324. [PMID: 37845391 DOI: 10.1007/s10661-023-11964-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/06/2023] [Indexed: 10/18/2023]
Abstract
Terrestrial ecosystems are under the enormous pressure of land use management regimes through human disturbances, resulting in the disruption of biogeochemical cycles and associated ecosystem services. Nitrogen (N) in soil ecosystems is of vital importance for primary productivity, hence estimating the extent of these human interventions on N-cycling processes becomes imperative from economic and environmental perspectives. This work investigated the impacts of variable anthropogenic activities on N cycling in three different terrestrial ecosystems (arable, grassland, and forest) in three regions of lower Himalaya, Pakistan. Potential nitrification (PNA) and denitrification (DEA) enzyme activities, relative distribution of inorganic N species (NH4, NO3), and the role of inherent edaphic factors were assessed. Results revealed high nitrification potentials and increased nitrous oxide (N2O) emissions in the incubated soil microcosms, in the order as arable > grassland > forest ecosystems. Notably, higher rates of both studied processes (~ 30-50%) and elevated soil mineral nitrogen pool were observed in arable ecosystems. Forest soils, assumed as pristine ecosystems relying mainly on natural N fixation, produced (de)nitrification rates relatively lower than grasslands, followed by arable soils which were moderately disturbed through long-term fertilization and intensive land-use regimes. Linear regression modeling revealed that the inorganic N species (particularly NO3), and inherent edaphic factors were the key determinants of high (de)nitrification rates, hence warn of accelerated N losses in these ecosystems. The study highlights that elevated PNA and DEA being proxies for the altered N cycling in the studied terrestrial ecosystems are of great ecological relevance in view of predicted N2O budget in the lower Himalaya.
Collapse
Affiliation(s)
- Tahir Zaman
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan
| | - Saeed Ahmad Asad
- Department of Bio Sciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
| | - Muhammad Irshad
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan
| | - Faridullah
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan
| | - Muhammad Shahzad
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan
| | - Rashid Nazir
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan
| | - Awais Arefeen
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan
| | - Akhtar Iqbal
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan.
| | - Farhan Hafeez
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan.
| |
Collapse
|
5
|
Malard LA, Guisan A. Into the microbial niche. Trends Ecol Evol 2023; 38:936-945. [PMID: 37236880 DOI: 10.1016/j.tree.2023.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023]
Abstract
The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.
Collapse
Affiliation(s)
- Lucie A Malard
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland; Institute of Earth Surface Dynamics, University of Lausanne, 1015 Lausanne, Switzerland
| |
Collapse
|
6
|
Xu Z, Zuo L, Zhang Y, Huang R, Li L. Is allelochemical synthesis in Casuarina equisetifolia plantation related to litter microorganisms? FRONTIERS IN PLANT SCIENCE 2022; 13:1022984. [PMID: 36407626 PMCID: PMC9666782 DOI: 10.3389/fpls.2022.1022984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Productivity decline of Casuarina equisetifolia plantation and difficulty in natural regeneration remains a serious problem because of allelopathy. Previous studies have confirmed that 2,4-di-tert-butylphenol (2,4-DTBP) are the major allelochemicals of the C. equisetifolia litter exudates. The production of these allelochemicals may derive from decomposition of litter or from the litter endophyte and microorganisms adhering to litter surfaces. In the present study, we aimed to evaluate the correlation between allelochemicals in litter and endophytic and epiphytic fungi and bacteria from litter. A total of 100 fungi and 116 bacteria were isolated from the interior and surface of litter of different forest ages (young, half-mature, and mature plantation). Results showed that the fermentation broth of fungal genera Mycosphaerella sp. and Pestalotiopsis sp., and bacterial genera Bacillus amyloliquefaciens, Burkholderia-Paraburkholderia, and Pantoea ananatis had the strongest allelopathic effect on C. equisetifolia seeds. Allelochemicals, such as 2,4-DTBP and its analogs were identified in the fermentation broths of these microorganisms using GC/MS analysis. These results indicate that endophytic and epiphytic fungi and bacteria in litters are involved in the synthesis of allelochemicals of C. equisetifolia. To further determine the abundance of the allelopathic fungi and bacteria, Illumina MiSeq high-throughput sequencing was performed. The results showed that bacterial genera with strong allelopathic potential were mainly distributed in the young and half-mature plantation with low abundance, while the abundance of fungal genera Mycosphaerella sp. and Pestalotiopsis sp. were higher in the young and mature plantations. In particular, the abundance of Mycosphaerella sp. in the young and mature plantations were 501.20% and 192.63% higher than in the half-mature plantation, respectively. Overall, our study demonstrates that the litter fungi with higher abundance in the young and mature plantation were involved in the synthesis of the allelochemical 2,4-DTBP of C. equisetifolia. This finding may be important for understanding the relationship between autotoxicity and microorganism and clarifying the natural regeneration problem of C. equisetifolia.
Collapse
|
7
|
Dong J, Cui X, Niu H, Zhang J, Zhu C, Li L, Pang Z, Wang S. Effects of Nitrogen Addition on Plant Properties and Microbiomes Under High Phosphorus Addition Level in the Alpine Steppe. FRONTIERS IN PLANT SCIENCE 2022; 13:894365. [PMID: 35795351 PMCID: PMC9251499 DOI: 10.3389/fpls.2022.894365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/13/2022] [Indexed: 05/28/2023]
Abstract
Nitrogen (N) addition can increase the vegetative growth, improve the plant production, and restore the degraded terrestrial ecosystems. But, it simultaneously aggravates the soil phosphorus (P) limitation for plant growth, thus affecting its positive effects on ecosystems. However, how plants and soil microorganisms will change under conditions of high P content in soil is still unknown. In this study, we explored the effects of three levels of N addition (0, 7.5, and 15 g.N.m-2.year-1) on plants and microorganisms at the high P addition level (13.09 g.P.m-2.year-1) in the alpine steppe. We found that the soil microbial community composition had no significant difference between different N addition levels, and the soil AN and AP had a significant effect on the phospholipid fatty acid (PLFA) composition. The abundance of the core PLFAs (i.e., 16:1ω7c, 16:0, a17:1, i17:0, 18:1ω9c, and 18:1ω7c) also remained unchanged after N addition, and microbes at individual, population, and community levels were all correlated with SOM, AK, AN, and pH. Conversely, plant biomass and nutrient content showed linear trends with increasing N addition, especially the dominant functional groups. Specifically, the biomass and plant tissue N content of Gramineae, and the total N content of aboveground biomass were all improved by N addition. They were correlated with soil ammonium and AP. The structural equation modeling (SEM) demonstrated that N addition had a direct negative effect on soil microbial biomass, but an indirect positive effect on aboveground biomass via soil ammonium. These findings clarify the importance of N-amendment in regulating plants and microorganisms under high P conditions and provide a better understanding of the N-added effects in the alpine steppe.
Collapse
Affiliation(s)
- Junfu Dong
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyong Cui
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Haishan Niu
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Zhang
- College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Chuanlu Zhu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Linfeng Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhe Pang
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shiping Wang
- Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
8
|
Mafa‐Attoye TG, Borden KA, Alvarez DO, Thevathasan N, Isaac ME, Dunfield KE. Roots alter soil microbial diversity and interkingdom interactions in diversified agricultural landscapes. OIKOS 2022. [DOI: 10.1111/oik.08717] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
| | - Kira A. Borden
- Faculty of Land and Food Systems, Univ. of British Columbia Vancouver BC Canada
| | | | | | - Marney E. Isaac
- Dept of Physical&Environmental Sciences, Univ. of Toronto Scarborough Toronto ON Canada
| | - Kari E. Dunfield
- School of Environmental Sciences, Univ. of Guelph Guelph ON Canada
| |
Collapse
|
9
|
Kiesewetter KN, Afkhami ME. Microbiome-mediated effects of habitat fragmentation on native plant performance. THE NEW PHYTOLOGIST 2021; 232:1823-1838. [PMID: 34213774 DOI: 10.1111/nph.17595] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
Habitat fragmentation is a leading cause of biodiversity and ecosystem function loss in the Anthropocene. Despite the importance of plant-microbiome interactions to ecosystem productivity, we have limited knowledge of how fragmentation affects microbiomes and even less knowledge of its consequences for microbial interactions with plants. Combining field surveys, microbiome sequencing, manipulative experiments, and random forest models, we investigated fragmentation legacy effects on soil microbiomes in imperiled pine rocklands, tested how compositional shifts across 14 fragmentation-altered soil microbiomes affected performance and resource allocation of three native plant species, and identified fragmentation-responding microbial families underpinning plant performance. Legacies of habitat fragmentation were associated with significant changes in microbial diversity and composition (across three of four community axes). Experiments showed plants often strongly benefited from the microbiome's presence, but fragmentation-associated changes in microbiome composition also significantly affected plant performance and resource allocation across all seven metrics examined. Finally, random forest models identified ten fungal and six bacterial families important for plant performance that changed significantly with fragmentation. Our findings not only support the existence of significant fragmentation effects on natural microbiomes, but also demonstrate for the first time that fragmentation-associated changes in microbiomes can have meaningful consequences for native plant performance and investment.
Collapse
Affiliation(s)
| | - Michelle E Afkhami
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| |
Collapse
|
10
|
Cao C, Tao S, Cui Z, Zhang Y. Response of Soil Properties and Microbial Communities to Increasing Salinization in the Meadow Grassland of Northeast China. MICROBIAL ECOLOGY 2021; 82:722-735. [PMID: 33511437 DOI: 10.1007/s00248-021-01695-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/17/2021] [Indexed: 05/20/2023]
Abstract
Secondary salinization is a serious environmental issue and a major threat to the sustainable use of grasslands. Information about the response of microbial communities and soil properties in already saline soils to increasing salinity is lacking. We investigated soil properties and the structures of soil bacterial and fungal communities across a gradient of salinization in the Horqin Grassland, China. Three sites with relatively lightly (average soluble salt content = 0.11%), relatively moderately (average soluble salt content = 0.44%), and heavily (average soluble salt content = 1.07%) degraded grassland, were selected as experimental sites. We examined variations in the composition and structure of the soil bacterial and fungal communities by using high-throughput sequencing of the 16S and 18S rRNA genes, respectively. We found degrading effects of salinization on soil properties, i.e., decreased soil moisture, organic matter, total N, NH4-N, and NO3-N and increased soil bulk density, pH, and electrical conductivity. The bacterial and fungal community structures changed with increasing salinity. However, dominant microbial taxa (including phylum, genus, and operational taxonomic unit levels) were similar among experimental sites, indicating that increasing salinization slightly affected the basic compositions of microbial communities in already saline grasslands. Furthermore, the relative abundances of most dominant taxa sensitively responded to the soil salt content. Acidobacteria, Actinobacteria, Chloroflexi, RB4, Rubrobacter, Blastocatella, H16, Glomeromycota, and Aspergillus linearly increased with increasing salinization, suggesting that they could be used as bioindicators for salt-tolerant communities. Overall, the changes in the structures of soil bacterial and fungal communities were determined by the relative quantities of dominant taxa rather than community composition. The structures of soil bacterial and fungal communities were linked to soil properties and vegetation. Increasing soil salt content, and thereby varied pH and organic matter, were likely the direct influencing factors of microbial communities in these saline grasslands.
Collapse
Affiliation(s)
- Chengyou Cao
- College of Life and Health Sciences, Northeastern University, 3 Wenhua Road, Shenyang, 110169, People's Republic of China.
| | - Shuang Tao
- College of Life and Health Sciences, Northeastern University, 3 Wenhua Road, Shenyang, 110169, People's Republic of China
| | - Zhenbo Cui
- College of Life and Health Sciences, Northeastern University, 3 Wenhua Road, Shenyang, 110169, People's Republic of China
| | - Ying Zhang
- College of Life and Health Sciences, Northeastern University, 3 Wenhua Road, Shenyang, 110169, People's Republic of China.
| |
Collapse
|
11
|
Borden KA, Mafa-Attoye TG, Dunfield KE, Thevathasan NV, Gordon AM, Isaac ME. Root Functional Trait and Soil Microbial Coordination: Implications for Soil Respiration in Riparian Agroecosystems. FRONTIERS IN PLANT SCIENCE 2021; 12:681113. [PMID: 34305979 PMCID: PMC8296843 DOI: 10.3389/fpls.2021.681113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
Predicting respiration from roots and soil microbes is important in agricultural landscapes where net flux of carbon from the soil to the atmosphere is of large concern. Yet, in riparian agroecosystems that buffer aquatic environments from agricultural fields, little is known on the differential contribution of CO2 sources nor the systematic patterns in root and microbial communities that relate to these emissions. We deployed a field-based root exclusion experiment to measure heterotrophic and autotrophic-rhizospheric respiration across riparian buffer types in an agricultural landscape in southern Ontario, Canada. We paired bi-weekly measurements of in-field CO2 flux with analysis of soil properties and fine root functional traits. We quantified soil microbial community structure using qPCR to estimate bacterial and fungal abundance and characterized microbial diversity using high-throughput sequencing. Mean daytime total soil respiration rates in the growing season were 186.1 ± 26.7, 188.7 ± 23.0, 278.6 ± 30.0, and 503.4 ± 31.3 mg CO2-C m-2 h-1 in remnant coniferous and mixed forest, and rehabilitated forest and grass buffers, respectively. Contributions of autotrophic-rhizospheric respiration to total soil CO2 fluxes ranged widely between 14 and 63% across the buffers. Covariation in root traits aligned roots of higher specific root length and nitrogen content with higher specific root respiration rates, while microbial abundance in rhizosphere soil coorindated with roots that were thicker in diameter and higher in carbon to nitrogen ratio. Variation in autotrophic-rhizospheric respiration on a soil area basis was explained by soil temperature, fine root length density, and covariation in root traits. Heterotrophic respiration was strongly explained by soil moisture, temperature, and soil carbon, while multiple factor analysis revealed a positive correlation with soil microbial diversity. This is a first in-field study to quantify root and soil respiration in relation to trade-offs in root trait expression and to determine interactions between root traits and soil microbial community structure to predict soil respiration.
Collapse
Affiliation(s)
- Kira A. Borden
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
- Centre for Sustainable Food Systems, The University of British Columbia, Vancouver, BC, Canada
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | | | - Kari E. Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | | | - Andrew M. Gordon
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Marney E. Isaac
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| |
Collapse
|
12
|
Cantarel AAM, Allard V, Andrieu B, Barot S, Enjalbert J, Gervaix J, Goldringer I, Pommier T, Saint-Jean S, Le Roux X. Plant functional trait variability and trait syndromes among wheat varieties: the footprint of artificial selection. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1166-1180. [PMID: 33080022 DOI: 10.1093/jxb/eraa491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
Although widely used in ecology, trait-based approaches are seldom used to study agroecosystems. In particular, there is a need to evaluate how functional trait variability among varieties of a crop species compares to the variability among wild plant species and how variety selection can modify trait syndromes. Here, we quantified 18 above- and below-ground functional traits for 57 varieties of common wheat representative of different modern selection histories. We compared trait variability among varieties and among Pooideae species, and analyzed the effect of selection histories on trait values and trait syndromes. For traits under strong selection, trait variability among varieties was less than 10% of the variability observed among Pooideae species. However, for traits not directly selected, such as root N uptake capacity, the variability was up to 75% of the variability among Pooideae species. Ammonium absorption capacity by roots was counter-selected for conventional varieties compared with organic varieties and landraces. Artificial selection also altered some trait syndromes classically reported for Pooideae. Identifying traits that have high or low variability among varieties and characterizing the hidden effects of selection on trait values and syndromes will benefit the selection of varieties to be used especially for lower N input agroecosystems.
Collapse
Affiliation(s)
- Amélie A M Cantarel
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne, France
| | - Vincent Allard
- UMR Génétique, Diversité et Ecophysiologie des Céréales, INRAE, Clermont-Ferrand, France
| | - Bruno Andrieu
- UMR ECOSYS, INRAE, AgroParisTech, Université Paris-Saclay, Thieverval-Grignon, France
| | - Sébastien Barot
- IEES-Paris (CNRS, IRD, UPMC, INRA, UPEC, UP7), UPMC, 4 place Jussieu, cedex 05 Paris, France
| | - Jérôme Enjalbert
- UMR Génétique Quantitative et Evolution Le Moulon INRAE, CNRS, UPS, Gif-sur-Yvette, France
| | - Jonathan Gervaix
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne, France
| | - Isabelle Goldringer
- UMR Génétique Quantitative et Evolution Le Moulon INRAE, CNRS, UPS, Gif-sur-Yvette, France
| | - Thomas Pommier
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne, France
| | - Sébastien Saint-Jean
- UMR ECOSYS, INRAE, AgroParisTech, Université Paris-Saclay, Thieverval-Grignon, France
| | - Xavier Le Roux
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne, France
| |
Collapse
|
13
|
Abalos D, De Deyn GB, Philippot L, Oram NJ, Oudová B, Pantelis I, Clark C, Fiorini A, Bru D, Mariscal‐Sancho I, Groenigen JW. Manipulating plant community composition to steer efficient N‐cycling in intensively managed grasslands. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13788] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Diego Abalos
- Soil Biology Group Wageningen University Wageningen The Netherlands
- Department of Agroecology Aarhus University Tjele Denmark
| | | | - Laurent Philippot
- Université Bourgogne Franche‐ComtéINRAAgroSup DijonAgroécologie Dijon France
| | - Natalie J. Oram
- Soil Biology Group Wageningen University Wageningen The Netherlands
| | - Barbora Oudová
- Soil Biology Group Wageningen University Wageningen The Netherlands
- School of Biological Sciences University of East Anglia Norwich UK
| | - Ioannis Pantelis
- Soil Biology Group Wageningen University Wageningen The Netherlands
| | - Callum Clark
- Soil Biology Group Wageningen University Wageningen The Netherlands
| | - Andrea Fiorini
- Department of Sustainable Crop Production Università Cattolica del Sacro Cuore Piacenza Italy
| | - David Bru
- Université Bourgogne Franche‐ComtéINRAAgroSup DijonAgroécologie Dijon France
| | - Ignacio Mariscal‐Sancho
- Departamento de Producción Agraria ETS Ingeniería Agronómica Alimentaria y de Biosistemas Universidad Politécnica de Madrid Madrid Spain
| | | |
Collapse
|
14
|
Uqab B, Nazir R, Ahmad Ganai B, Rahi P, Rehman S, Farooq S, Dar R, Parray JA, Fahad Al-Arjani Al-Arjani AB, Tabassum B, Fathi Abd Allah E. MALDI-TOF-MS and 16S rRNA characterization of lead tolerant metallophile bacteria isolated from saffron soils of Kashmir for their sequestration potential. Saudi J Biol Sci 2020; 27:2047-2053. [PMID: 32714029 PMCID: PMC7376117 DOI: 10.1016/j.sjbs.2020.04.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 04/11/2020] [Accepted: 04/12/2020] [Indexed: 11/25/2022] Open
Abstract
Toxic metal contamination in soils due industrialization is nowadays a concern to the scientists worldwide. The current study deals with the evaluation of response and tolerance by isolated metallophilic bacteria in different lead concentrations (100 ppm to 1000 ppm). By taking optical densities of the isolates, the minimum inhibitory concentration (MIC) of Pb2+ were determined.16S rRNA and MALDI-TOF MS were used for the identification of the bacteria. Total of 37 isolates were observed, among them 04 (Staphylococcus equorum, Staphylococcus warneri, Bacillus safensis and Bacillus thuringiensis), isolated were detected having efficacy of Pb2+tolerance and sequestration at varying MIC. Furthermore, B. thuringiensis was observed to have highest (900 ppm) tolerance for lead and lowest (500 ppm) for Staphylococcus warneri. Moreover, the highest (65.3%) sequestration potential has been observed for B. thuringiensis and least (52.8%) for S. warneri. The tolerance and sequestration potential properties of these isolated species can be utilised to exterminate heavy metals and reduce their toxicity from the contaminated environment.
Collapse
Affiliation(s)
- Baba Uqab
- Department of Environmental Science, University of Kashmir, 190006 Jammu & Kashmir, India
| | - Ruqeya Nazir
- Centre of Research for Development (CORD), University of Kashmir, 190006 Jammu & Kashmir, India
| | - Bashir Ahmad Ganai
- Centre of Research for Development (CORD), University of Kashmir, 190006 Jammu & Kashmir, India
| | - Praveen Rahi
- National Centre For Microbial Research (NCMR), Pune, India
| | - Sabeehah Rehman
- Centre of Research for Development (CORD), University of Kashmir, 190006 Jammu & Kashmir, India
| | - Saleem Farooq
- Department of Environmental Science, University of Kashmir, 190006 Jammu & Kashmir, India
| | - Rubiya Dar
- Centre of Research for Development (CORD), University of Kashmir, 190006 Jammu & Kashmir, India
| | - Javid A Parray
- Centre of Research for Development (CORD), University of Kashmir, 190006 Jammu & Kashmir, India.,Govt SAM Degree College Budgam, JK 191111, India
| | | | - Baby Tabassum
- Toxicology Laboratory, Department of Zoology, Govt. Raza P.G. College Rampur, 244901 U.P., India
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia
| |
Collapse
|
15
|
Raes EJ, Karsh K, Kessler AJ, Cook PLM, Holmes BH, van de Kamp J, Bodrossy L, Bissett A. Can We Use Functional Genetics to Predict the Fate of Nitrogen in Estuaries? Front Microbiol 2020; 11:1261. [PMID: 32655525 PMCID: PMC7325967 DOI: 10.3389/fmicb.2020.01261] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/18/2020] [Indexed: 11/13/2022] Open
Abstract
Increasing nitrogen (N) loads present a threat to estuaries, which are among the most heavily populated and perturbed parts of the world. N removal is largely mediated by the sediment microbial process of denitrification, in direct competition to dissimilatory nitrate reduction to ammonium (DNRA), which recycles nitrate to ammonium. Molecular proxies for N pathways are increasingly measured and analyzed, a major question in microbial ecology, however, is whether these proxies can add predictive power around the fate of N. We analyzed the diversity and community composition of sediment nirS and nrfA genes in 11 temperate estuaries, covering four types of land use in Australia, and analyzed how these might be used to predict N removal. Our data suggest that sediment microbiomes play a central role in controlling the magnitude of the individual N removal rates in the 11 estuaries. Inclusion, however, of relative gene abundances of 16S, nirS, nrfA, including their ratios did not improve physicochemical measurement-based regression models to predict rates of denitrification or DNRA. Co-occurrence network analyses of nirS showed a greater modularity and a lower number of keystone OTUs in pristine sites compared to urban estuaries, suggesting a higher degree of niche partitioning in pristine estuaries. The distinctive differences between the urban and pristine network structures suggest that the nirS gene could be a likely gene candidate to understand the mechanisms by which these denitrifying communities form and respond to anthropogenic pressures.
Collapse
Affiliation(s)
- Eric J Raes
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, TAS, Australia
| | - Kristen Karsh
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, TAS, Australia
| | - Adam J Kessler
- School of Earth, Atmosphere and Environment, Monash University, Melbourne, VIC, Australia
| | - Perran L M Cook
- Water Studies Centre, School of Chemistry, Monash University, Melbourne, VIC, Australia
| | - Bronwyn H Holmes
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, TAS, Australia
| | - Jodie van de Kamp
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, TAS, Australia
| | - Levente Bodrossy
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, TAS, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, TAS, Australia
| |
Collapse
|
16
|
Hanisch M, Schweiger O, Cord AF, Volk M, Knapp S. Plant functional traits shape multiple ecosystem services, their trade‐offs and synergies in grasslands. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13644] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mario Hanisch
- Department of Community Ecology UFZ—Helmholtz Centre for Environmental Research Halle Germany
| | - Oliver Schweiger
- Department of Community Ecology UFZ—Helmholtz Centre for Environmental Research Halle Germany
| | - Anna F. Cord
- Department of Computational Landscape Ecology UFZ—Helmholtz Centre for Environmental Research Leipzig Germany
- Chair of Computational Landscape Ecology Institute of Geography Technische Universität Dresden Dresden Germany
| | - Martin Volk
- Department of Computational Landscape Ecology UFZ—Helmholtz Centre for Environmental Research Leipzig Germany
| | - Sonja Knapp
- Department of Community Ecology UFZ—Helmholtz Centre for Environmental Research Halle Germany
| |
Collapse
|
17
|
Ecosystem Service Loss in Response to Agricultural Expansion in the Small Sanjiang Plain, Northeast China: Process, Driver and Management. SUSTAINABILITY 2020. [DOI: 10.3390/su12062430] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Converting natural ecosystems to cultivated land, driven by human activities, has been considered a significant driver of limiting the delivery of ecosystem services (ES). The ES loss in the past was mainly caused by agricultural activities that have been taken to meet people’s needs in Northeast China. Quantifying historical declining ecosystem service values is essential to facilitate sustainable development. In this study, remote sensing images were used to investigate the history of cultivated land expansion over the last five decades. Additionally, ES variations caused by agricultural expansion since 1965 were quantified in the Small Sanjiang Plain (SSP), Northeast China. From the results, cultivated land expanded from 3.97% of the total SSP area to 66.40% from 1965 to 2015 (approximately 898.23 million ha), of which paddy field expanded drastically from 0% to 55.93%. Variations in cultivated land resulted in a loss of ecosystem service values by 11,893.85 million dollars, of which 62.98 million dollars were caused by the internal conversion between cultivation during 1965–2015. Agricultural expansion accelerated the export of agricultural products function, while it decreased almost all other functions, especially hydrological regulation and freshwater supply function. For future sustainability of the SSP, some suggestions, such as restoring natural ecosystems, planting trees between cultivated land, coculture systems, and winter-flooding of paddy rice were provided in our study.
Collapse
|
18
|
Manzella M, Geiss R, Hall EK. Evaluating the stoichiometric trait distributions of cultured bacterial populations and uncultured microbial communities. Environ Microbiol 2019; 21:3613-3626. [PMID: 31090973 DOI: 10.1111/1462-2920.14684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 10/26/2022]
Abstract
We measured the stoichiometric trait distribution of cultured freshwater bacterial populations under different resource conditions and compared them to natural microbial communities sampled from three lakes. Trait distributions showed population differences among growth phases and community differences among lakes that would have been masked by only reporting the mean biomass value. The stoichiometric trait distribution of the environmental isolates changed with P availability, growth phase and genotype, with P availability having the strongest effect. The distribution of biomass ratios within each isolate growth experiment were the most constrained during the stages of rapid growth and commonly had unimodal distributions. In contrast to the population distributions, the distribution of N:P and C:P for a similar number of cells from each of the lake communities had narrower stoichiometric distributions and more commonly exhibited multiple modes. © 2019 Society for Applied Microbiology and John Wiley & Sons Ltd.
Collapse
Affiliation(s)
- Michael Manzella
- Department of Ecosystem Science and Sustainability, Colorado State University, Fort Collins, CO, 80523, USA.,Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Roy Geiss
- Central Instrument Facility, Department of Chemistry, Colorado State University, Fort Collins, CO, 80523, USA
| | - Ed K Hall
- Department of Ecosystem Science and Sustainability, Colorado State University, Fort Collins, CO, 80523, USA.,Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO, 80523, USA
| |
Collapse
|
19
|
Jones MS, Fu Z, Reganold JP, Karp DS, Besser TE, Tylianakis JM, Snyder WE. Organic farming promotes biotic resistance to foodborne human pathogens. J Appl Ecol 2019. [DOI: 10.1111/1365-2664.13365] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Matthew S. Jones
- Department of EntomologyWashington State University Pullman Washington
- Tree Fruit Research and Extension CenterWashington State University Wenatchee Washington
| | - Zhen Fu
- Department of EntomologyWashington State University Pullman Washington
| | - John P. Reganold
- Department of Crop and Soil SciencesWashington State University Pullman Washington
| | - Daniel S. Karp
- Department of Wildlife, Fish, and Conservation BiologyUniversity of California at Davis Davis California
| | - Thomas E. Besser
- School of Veterinary MedicineWashington State University Pullman Washington
| | - Jason M. Tylianakis
- Bio‐Protection Research CentreSchool of Biological SciencesUniversity of Canterbury Christchurch New Zealand
- Department of Life SciencesImperial College London Berkshire UK
| | - William E. Snyder
- Department of EntomologyWashington State University Pullman Washington
| |
Collapse
|
20
|
Simonin M, Cantarel AAM, Crouzet A, Gervaix J, Martins JMF, Richaume A. Negative Effects of Copper Oxide Nanoparticles on Carbon and Nitrogen Cycle Microbial Activities in Contrasting Agricultural Soils and in Presence of Plants. Front Microbiol 2018; 9:3102. [PMID: 30619181 PMCID: PMC6301197 DOI: 10.3389/fmicb.2018.03102] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/30/2018] [Indexed: 12/28/2022] Open
Abstract
Metal-oxide nanoparticles (NPs) such as copper oxide (CuO) NPs offer promising perspectives for the development of novel agro-chemical formulations of pesticides and fertilizers. However, their potential impact on agro-ecosystem functioning still remains to be investigated. Here, we assessed the impact of CuO-NPs (0.1, 1, and 100 mg/kg dry soil) on soil microbial activities involved in the carbon and nitrogen cycles in five contrasting agricultural soils in a microcosm experiment over 90 days. Additionally, in a pot experiment, we evaluated the influence of plant presence on the toxicity of CuO-NPs on soil microbial activities. CuO-NPs caused significant reductions of the three microbial activities measured (denitrification, nitrification, and soil respiration) at 100 mg/kg dry soil, but the low concentrations (0.1 and 1 mg/kg) had limited effects. We observed that denitrification was the most sensitive microbial activity to CuO-NPs in most soil types, while soil respiration and nitrification were mainly impacted in coarse soils with low organic matter content. Additionally, large decreases in heterotrophic microbial activities were observed in soils planted with wheat, even at 1 mg/kg for soil substrate-induced respiration, indicating that plant presence did not mitigate or compensate CuO-NP toxicity for microorganisms. These two experiments show that CuO-NPs can have detrimental effects on microbial activities in soils with contrasting physicochemical properties and previously exposed to various agricultural practices. Moreover, we observed that the negative effects of CuO-NPs increased over time, indicating that short-term studies (hours, days) may underestimate the risks posed by these contaminants in soils.
Collapse
Affiliation(s)
- Marie Simonin
- Université de Lyon, Lyon, France.,Université Claude Bernard Lyon 1, Villeurbanne, France.,CNRS, UMR 5557, Microbial Ecology Centre, Université Lyon 1, Villeurbanne, France
| | - Amélie A M Cantarel
- Université de Lyon, Lyon, France.,Université Claude Bernard Lyon 1, Villeurbanne, France.,CNRS, UMR 5557, Microbial Ecology Centre, Université Lyon 1, Villeurbanne, France
| | - Armelle Crouzet
- Université de Lyon, Lyon, France.,Université Claude Bernard Lyon 1, Villeurbanne, France.,CNRS, UMR 5557, Microbial Ecology Centre, Université Lyon 1, Villeurbanne, France
| | - Jonathan Gervaix
- Université de Lyon, Lyon, France.,Université Claude Bernard Lyon 1, Villeurbanne, France.,CNRS, UMR 5557, Microbial Ecology Centre, Université Lyon 1, Villeurbanne, France
| | | | - Agnès Richaume
- Université de Lyon, Lyon, France.,Université Claude Bernard Lyon 1, Villeurbanne, France.,CNRS, UMR 5557, Microbial Ecology Centre, Université Lyon 1, Villeurbanne, France
| |
Collapse
|
21
|
Wang B, Adachi Y, Sugiyama S. Soil productivity and structure of bacterial and fungal communities in unfertilized arable soil. PLoS One 2018; 13:e0204085. [PMID: 30248134 PMCID: PMC6152964 DOI: 10.1371/journal.pone.0204085] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 09/04/2018] [Indexed: 01/22/2023] Open
Abstract
Soil productivity is strongly influenced by the activities of microbial communities. However, it is not well understood how community structure, including its richness, mass, and composition, influences soil functions. We investigated the relationships between soil productivity and microbial communities in unfertilized arable soils extending over 1000 km in eastern Japan. Soil properties, including C turnover rate, N mineralization rate, microbial C, and various soil chemical properties, were measured. Soil bacterial and fungal communities were analyzed by Illumina's MiSeq using 16S rRNA and ITS regions. In addition, root microbial communities from maize grown in each soil were also investigated. Soil bacterial communities shared many operational taxonomic units (OTUs) among farms. An ordination plot based on correspondence analysis revealed convergent distribution of soil bacterial communities across the farms, which seemed to be a result of similar agricultural management practices. Although fungal communities showed lower richness and a lower proportion of shared OTUs than bacterial communities, community structure between the farms tended to be convergent. On the other hand, root communities had lower richness and a higher abundance of specific taxa than the soil communities. Two soil functions, decomposition activity and soil productivity, were extracted by principal component analysis (PCA) based on eight soil properties. Soil productivity correlated with N mineralization rate, P2O5, and maize growth, but not with decomposition activity, which is characterized by C turnover rate, soil organic C, and microbial mass. Soil productivity showed a significant association with community composition, but not with richness and mass of soil microbial communities. Soil productivity also correlated with the abundance of several specific taxa, both in bacteria and fungi. Root communities did not show any clear correlations with soil productivity. These results demonstrate that community composition and abundance of soil microbial communities play important roles in determining soil productivity.
Collapse
Affiliation(s)
- Boxi Wang
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, Japan
| | - Yoichi Adachi
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
| | - Shuichi Sugiyama
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
- * E-mail:
| |
Collapse
|
22
|
Martin AR, Isaac ME. Functional traits in agroecology: Advancing description and prediction in agroecosystems. J Appl Ecol 2017. [DOI: 10.1111/1365-2664.13039] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Adam R. Martin
- Department of Physical and Environmental Sciences; and the Centre for Critical Development of Toronto Scarborough; Toronto Ontario Canada
| | - Marney E. Isaac
- Department of Physical and Environmental Sciences; and the Centre for Critical Development of Toronto Scarborough; Toronto Ontario Canada
- Department of Geography; University of Toronto; Toronto Ontario Canada
| |
Collapse
|
23
|
Pommier T, Cantarel AAM, Grigulis K, Lavorel S, Legay N, Baxendale C, Bardgett RD, Bahn M, Poly F, Clément JC. The added value of including key microbial traits to determine nitrogen-related ecosystem services in managed grasslands. J Appl Ecol 2017. [DOI: 10.1111/1365-2664.13010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas Pommier
- Ecologie Microbienne Lyon; INRA UMR 1418, CNRS UMR 5557; Université Lyon I; Villeurbanne France
| | - Amélie A. M. Cantarel
- Ecologie Microbienne Lyon; INRA UMR 1418, CNRS UMR 5557; Université Lyon I; Villeurbanne France
| | - Karl Grigulis
- Laboratoire d'Ecologie Alpine; CNRS UMR 5553 - Université Joseph Fourier; Grenoble France
| | - Sandra Lavorel
- Laboratoire d'Ecologie Alpine; CNRS UMR 5553 - Université Joseph Fourier; Grenoble France
| | - Nicolas Legay
- Laboratoire d'Ecologie Alpine; CNRS UMR 5553 - Université Joseph Fourier; Grenoble France
- Ecole de la Nature et du Paysage; INSA CVL; Blois France
- CNRS, CITERES, UMR 7324; Tours France
| | | | - Richard D. Bardgett
- School of Earth and Environmental Sciences; The University of Manchester; Manchester UK
| | - Michael Bahn
- Institute of Ecology; University of Innsbruck; Innsbruck Austria
| | - Franck Poly
- Ecologie Microbienne Lyon; INRA UMR 1418, CNRS UMR 5557; Université Lyon I; Villeurbanne France
| | - Jean-Christophe Clément
- Laboratoire d'Ecologie Alpine; CNRS UMR 5553 - Université Joseph Fourier; Grenoble France
- CARRTEL; INRA UMR 0042 - Université Savoie Mont Blanc; Thonon-les-Bains France
| |
Collapse
|