1
|
Yang S, Zhao X, Wang Q, Tian P. Greater influences of nitrogen addition on priming effect in forest subsoil than topsoil regardless of incubation warming. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174308. [PMID: 38936708 DOI: 10.1016/j.scitotenv.2024.174308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/24/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
Subsoil (below 20 cm), storing over 50 % of soil organics carbon (SOC) within the 1 m depth, plays a critical role in regulating climate and ecosystem function. However, little was known on the changes in SOC decomposition induced by exogenous C input (i.e., priming effect) across the whole soil profile under nitrogen (N) enrichment and climate warming. We designed an incubation system of soil columns with minor physical disturbance, which allows the manual additions of exogenous C and N and incubation under ambient or elevated temperature. A negative priming effect by glucose was observed in all layers of ambient soil, while the negative priming effect was enhanced by soil depth but inhibited by warming. Nitrogen addition shifted the priming effect from negative to positive under ambient temperature, and decreased the magnitude of negative priming effect under elevated temperature. Nitrogen uplift effect on priming effect was more pronounced in subsoil compared to topsoil, while this effect diminished with rising temperature. Soil microbial activity (e.g., the CO2 production within 3 days) and acid phosphatase activity had important roles in regulating the variations in priming effect across the soil profile. Our results indicated that increase in labile substrate (e.g., exogenous C input) input would not lead to native SOC destabilization in subsoil, N addition shifted the priming effect from negative to positive, increasing the SOC decomposition under ambient temperature, while labile C input together with N addition benefited SOC sequestration by inducing negative priming effects in forest soil under warming climate.
Collapse
Affiliation(s)
- Shaobo Yang
- Anhui Province Key Laboratory of Forest Resources and Silviculture, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Xuechao Zhao
- Anhui Province Key Laboratory of Forest Resources and Silviculture, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China
| | - Qingkui Wang
- Anhui Province Key Laboratory of Forest Resources and Silviculture, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China; Huitong Experimental Station of Forest Ecology, CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Shenyang 110016, China.
| | - Peng Tian
- Anhui Province Key Laboratory of Forest Resources and Silviculture, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China.
| |
Collapse
|
2
|
Yang S, Sun J, Wang C, Li S, Li Z, Luo W, Wei G, Chen W. Residue quality drives SOC sequestration by altering microbial taxonomic composition and ecophysiological function in desert ecosystem. ENVIRONMENTAL RESEARCH 2024; 250:118518. [PMID: 38382662 DOI: 10.1016/j.envres.2024.118518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Plant residues are important sources of soil organic carbon in terrestrial ecosystems. The degradation of plant residue by microbes can influence the soil carbon cycle and sequestration. However, little is known about the microbial composition and function, as well as the accumulation of soil organic carbon (SOC) in response to the inputs of different quality plant residues in the desert environment. The present study evaluated the effects of plant residue addition from Pinus sylvestris var. mongolica (Pi), Artemisia desertorum (Ar) and Amorpha fruticosa (Am) on desert soil microbial community composition and function in a field experiment in the Mu Us Desert. The results showed that the addition of the three plant residues with different C/N ratios induced significant variation in soil microbial communities. The Am treatment (low C/N ratio) improved microbial diversity compared with the Ar and Pi treatments (medium and high C/N ratios). The variations in the taxonomic and functional compositions of the dominant phyla Actinobacteria and Proteobacteria were higher than those of the other phyla among the different treatments. Moreover, the network links between Proteobacteria and other phyla and the CAZyme genes abundances from Proteobacteria increased with increasing residue C/N, whereas those decreased for Actinobacteria. The SOC content of the Am, Ar and Pi treatments increased by 45.73%, 66.54% and 107.99%, respectively, as compared to the original soil. The net SOC accumulation was positively correlated with Proteobacteria abundance and negatively correlated with Actinobacteria abundance. These findings showed that changing the initial quality of plant residue from low C/N to high C/N can result in shifts in taxonomic and functional composition from Actinobacteria to Proteobacteria, which favors SOC accumulation. This study elucidates the ecophysiological roles of Actinobacteria and Proteobacteria in the desert carbon cycle, expands our understanding of the potential microbial-mediated mechanisms by which plant residue inputs affect SOC sequestration in desert soils, and provides valuable guidance for species selection in desert vegetation reconstruction.
Collapse
Affiliation(s)
- Shanshan Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Jieyu Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Chang Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Shuyue Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Zubing Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Wen Luo
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China.
| |
Collapse
|
3
|
Wang C, Kuzyakov Y. Soil organic matter priming: The pH effects. GLOBAL CHANGE BIOLOGY 2024; 30:e17349. [PMID: 38822665 DOI: 10.1111/gcb.17349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/30/2024] [Accepted: 05/10/2024] [Indexed: 06/03/2024]
Abstract
Priming of soil organic matter (SOM) decomposition by microorganisms is a key phenomenon of global carbon (C) cycling. Soil pH is a main factor defining priming effects (PEs) because it (i) controls microbial community composition and activities, including enzyme activities, (ii) defines SOM stabilization and destabilization mechanisms, and (iii) regulates intensities of many biogeochemical processes. In this critical review, we focus on prerequisites and mechanisms of PE depending on pH and assess the global change consequences for PE. The highest PEs were common in soils with pH between 5.5 and 7.5, whereas low molecular weight organic compounds triggered PE mainly in slightly acidic soils. Positive PEs up to 20 times of SOM decomposition before C input were common at pH around 6.5. Negative PEs were common at soil pH below 4.5 or above 7 reflecting a suboptimal environment for microorganisms and specific SOM stabilization mechanisms at low and high pH. Short-term soil acidification (in rhizosphere, after fertilizer application) affects PE by: mineral-SOM complexation, SOM oxidation by iron reduction, enzymatic depolymerization, and pH-dependent changes in nutrient availability. Biological processes of microbial metabolism shift over the short-term, whereas long-term microbial community adaptations to slow acidification are common. The nitrogen fertilization induced soil acidification and land use intensification strongly decrease pH and thus boost the PE. Concluding, soil pH is one of the strongest but up to now disregarded factors of PE, defining SOM decomposition through short-term metabolic adaptation of microbial groups and long-term shift of microbial communities.
Collapse
Affiliation(s)
- Chaoqun Wang
- Biogeochemistry of Agroecosystems, University of Göttingen, Göttingen, Germany
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
- Key Laboratory of Low-carbon Green Agriculture in Tropical region of China, Ministry of Agriculture and Rural Affairs; Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen, Germany
- Peoples Friendship University of Russia (RUDN University), Moscow, Russia
| |
Collapse
|
4
|
Zhu QZ, Yin X, Taubner H, Wendt J, Friedrich MW, Elvert M, Hinrichs KU, Middelburg JJ. Secondary production and priming reshape the organic matter composition in marine sediments. SCIENCE ADVANCES 2024; 10:eadm8096. [PMID: 38758798 PMCID: PMC11100564 DOI: 10.1126/sciadv.adm8096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/11/2024] [Indexed: 05/19/2024]
Abstract
Organic matter (OM) transformations in marine sediments play a crucial role in the global carbon cycle. However, secondary production and priming have been ignored in marine biogeochemistry. By incubating shelf sediments with various 13C-labeled algal substrates for 400 days, we show that ~65% of the lipids and ~20% of the proteins were mineralized by numerically minor heterotrophic bacteria as revealed by RNA stable isotope probing. Up to 11% of carbon from the algal lipids was transformed into the biomass of secondary producers as indicated by 13C incorporation in amino acids. This biomass turned over throughout the experiment, corresponding to dynamic microbial shifts. Algal lipid addition accelerated indigenous OM degradation by 2.5 to 6 times. This priming was driven by diverse heterotrophic bacteria and sulfur- and iron-cycling bacteria and, in turn, resulted in extra secondary production, which exceeded that stimulated by added substrates. These interactions between degradation, secondary production, and priming govern the eventual fate of OM in marine sediments.
Collapse
Affiliation(s)
- Qing-Zeng Zhu
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Xiuran Yin
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Heidi Taubner
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Jenny Wendt
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W. Friedrich
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Jack J. Middelburg
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
5
|
Deng W, Lu Y, Lyu M, Deng C, Li X, Jiang Y, Zhu H, Yang Y, Xie J. Chemical composition of soil carbon is governed by microbial diversity during understory fern removal in subtropical pine forests. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169904. [PMID: 38185157 DOI: 10.1016/j.scitotenv.2024.169904] [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: 10/12/2023] [Revised: 12/26/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
Understory vegetation has an important impact on soil organic carbon (SOC) accumulation. However, little is known about how understory vegetation alters soil microbial community composition and how microbial diversity contributes to SOC chemical composition and persistence during subtropical forest restoration. In this study, removal treatments of an understory fern (Dicranopteris dichotoma) were carried out within pine (Pinus massoniana) plantations restored in different years in subtropical China. Soil microbial community composition and microbial diversity were measured using phospholipid fatty acids (PLFAs) biomarkers and high-throughput sequencing, respectively. The chemical composition of SOC was also measured via solid-state 13C nuclear magnetic resonance (13C NMR). Our results showed that fern removal decreased alkyl C by 4.2 % but increased O-alkyl C by 15.6 % on average, leading to a decline of alkyl C/O-alkyl C ratio, suggesting altered chemical composition of SOC and lowered SOC recalcitrance without fern. Fern removal significantly lowered the fungi-to-bacteria ratio, and it also reduced fungal and bacterial diversity. Partial correlation analysis revealed that soil nitrogen availability was a key factor influencing microbial diversity. Bacterial diversity showed a close relationship with the Alkyl C/O-alkyl C ratio following fern removal. Furthermore, the microbial community structure and bacterial diversity were responsible for 18 % and 55 % of the explained variance in the chemical composition of SOC, respectively. Taken together, these analyses jointly suggest that bacterial diversity exerts a greater role than microbial community structure in supporting SOC persistence during understory fern removal. Our study emphasizes the significance of understory ferns in supporting microbial abundance and diversity as a means of altering SOC persistence during subtropical forest restoration.
Collapse
Affiliation(s)
- Wei Deng
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou 350117, China
| | - Yuming Lu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou 350117, China
| | - Maokui Lyu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou 350117, China; Sanming Forest Ecosystem National Observation and Research Station, Fujian Normal University, Sanming 365002, China.
| | - Cui Deng
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou 350117, China
| | - Xiaojie Li
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou 350117, China
| | - Yongmeng Jiang
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou 350117, China
| | - Hongru Zhu
- Fujian Province Forestry Survey and Planning Institute, Fuzhou 350003, China
| | - Yusheng Yang
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou 350117, China; Sanming Forest Ecosystem National Observation and Research Station, Fujian Normal University, Sanming 365002, China
| | - Jinsheng Xie
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou 350117, China; Sanming Forest Ecosystem National Observation and Research Station, Fujian Normal University, Sanming 365002, China.
| |
Collapse
|
6
|
Ren K, Yang X, Li J, Jin H, Gu K, Chen Y, Liu M, Luo Y, Jiang Y. Alleviating the adverse effects of Cd-Pb contamination through the application of silicon fertilizer: Enhancing soil microbial diversity and mitigating heavy metal contamination. CHEMOSPHERE 2024; 352:141414. [PMID: 38336042 DOI: 10.1016/j.chemosphere.2024.141414] [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: 11/19/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
The use of silicon fertilizer (SF) as a means of remediating cadmium (Cd) and lead (Pb) pollution has proven to be beneficial. However, the mechanism via which SF enhances soil quality and crop productivity under Cd- and Pb-contaminated soil (S) remains unclear. This study investigated the impacts of chemical fertilizer, mineral SF (MSF), and organic SF (OSF) on microbial community structure, activity of nutrient acquisition enzymes, and growth of tobacco in the presence of S condition. SF significantly reduced the contents of Cd and Pb in soil under S condition by 6.92-42.43% and increased plant height and leaf area by 15.27-81.77%. Moreover, the use of SF was observed to increase the efficiency of soil carbon and phosphorus cycling under S condition by 6.88-23.08%. Concurrently, SF was found to play a crucial role in facilitating the establishment of a complex, efficient, and interdependent molecular ecological network among soil microorganisms. In this context, Actinobacteriota, Bacteroidota, Ascomycota, and Basidiomycota were observed to be integral components of this network. SF was found to have a substantial positive impact on the metabolic functions and organismal systems of soil microorganisms. Moreover, the combined utilization of the Mantel test and partial least squares path model provided empirical evidence supporting the assertion that the administration of SF had a positive impact on both soil nutrient acquisition enzyme activity and tobacco growth, which was attributed to the enhancement of soil microbial diversity resulting from the application of SF. Furthermore, compared with MSF, OSF has advantages in reducing soil Pb and Cd content, promoting tobacco agronomic traits, increasing the number of key microbial communities, and maintaining the structural stability of microbial networks. The aforementioned findings, therefore, suggest that the OSF played a pivotal role in alleviating the adverse impacts of S, thereby demonstrating its efficacy in this particular process.
Collapse
Affiliation(s)
- Ke Ren
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China; College of Agronomy and Biotechnology, Southwest University / Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China
| | - Xiongwei Yang
- College of Landscape Architecture, Southwest Forestry University, Kunming, 650224, China
| | - Jian Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Hongyan Jin
- College of Landscape Architecture, Southwest Forestry University, Kunming, 650224, China
| | - Kaiyuan Gu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China; College of Agronomy and Biotechnology, Southwest University / Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China
| | - Yi Chen
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Ming Liu
- College of Agronomy and Biotechnology, Southwest University / Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China
| | - Yigui Luo
- College of Tobacco Science, Yunnan Agricultural University, Kunming, 650031, China.
| | - Yonglei Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China.
| |
Collapse
|
7
|
Stuij TM, Cleary DFR, Rocha RJM, Polónia ARM, Silva DAM, Louvado A, de Voogd NJ, Gomes NCM. Impacts of humic substances, elevated temperature, and UVB radiation on bacterial communities of the marine sponge Chondrilla sp. FEMS Microbiol Ecol 2024; 100:fiae022. [PMID: 38366951 PMCID: PMC10939426 DOI: 10.1093/femsec/fiae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 02/19/2024] Open
Abstract
Sponges are abundant components of coral reefs known for their filtration capabilities and intricate interactions with microbes. They play a crucial role in maintaining the ecological balance of coral reefs. Humic substances (HS) affect bacterial communities across terrestrial, freshwater, and marine ecosystems. However, the specific effects of HS on sponge-associated microbial symbionts have largely been neglected. Here, we used a randomized-controlled microcosm setup to investigate the independent and interactive effects of HS, elevated temperature, and UVB radiation on bacterial communities associated with the sponge Chondrilla sp. Our results indicated the presence of a core bacterial community consisting of relatively abundant members, apparently resilient to the tested environmental perturbations, alongside a variable bacterial community. Elevated temperature positively affected the relative abundances of ASVs related to Planctomycetales and members of the families Pseudohongiellaceae and Hyphomonadaceae. HS increased the relative abundances of several ASVs potentially involved in recalcitrant organic matter degradation (e.g., the BD2-11 terrestrial group, Saccharimonadales, and SAR202 clade). There was no significant independent effect of UVB and there were no significant interactive effects of HS, heat, and UVB on bacterial diversity and composition. The significant, independent impact of HS on the composition of sponge bacterial communities suggests that alterations to HS inputs may have cascading effects on adjacent marine ecosystems.
Collapse
Affiliation(s)
- Tamara M Stuij
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Daniel F R Cleary
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Rui J M Rocha
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Ana R M Polónia
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Davide A M Silva
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Antonio Louvado
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, the Netherlands
- Institute of Biology (IBL), Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
| | - Newton C M Gomes
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| |
Collapse
|
8
|
Jaeger ACH, Hartmann M, Conz RF, Six J, Solly EF. Prolonged water limitation shifts the soil microbiome from copiotrophic to oligotrophic lifestyles in Scots pine mesocosms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13211. [PMID: 37991154 PMCID: PMC10866073 DOI: 10.1111/1758-2229.13211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023]
Abstract
Reductions in soil moisture due to prolonged episodes of drought can potentially affect whole forest ecosystems, including soil microorganisms and their functions. We investigated how the composition of soil microbial communities is affected by prolonged episodes of water limitation. In a mesocosm experiment with Scots pine saplings and natural forest soil maintained at different levels of soil water content over 2 years, we assessed shifts in prokaryotic and fungal communities and related these to changes in plant development and soil properties. Prolonged water limitation induced progressive changes in soil microbial community composition. The dissimilarity between prokaryotic communities at different levels of water limitation increased over time regardless of the recurrent seasons, while fungal communities were less affected by prolonged water limitation. Under low soil water contents, desiccation-tolerant groups outcompeted less adapted, and the lifestyle of prokaryotic taxa shifted from copiotrophic to oligotrophic. While the abundance of saprotrophic and ligninolytic groups increased alongside an accumulation of dead plant material, the abundance of symbiotic and nutrient-cycling taxa decreased, likely impairing the development of the trees. Overall, prolonged episodes of drought appeared to continuously alter the structure of microbial communities, pointing to a potential loss of critical functions provided by the soil microbiome.
Collapse
Affiliation(s)
- Astrid C. H. Jaeger
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Martin Hartmann
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Rafaela Feola Conz
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Johan Six
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Emily F. Solly
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
- Helmholtz Centre for Environmental Research—UFZLeipzigGermany
| |
Collapse
|
9
|
Rzehak T, Praeg N, Zink H, Simon A, Geitner C, Illmer P. Microbial perspective of inhibited carbon turnover in Tangel humus of the Northern Limestone Alps. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13215. [PMID: 38062558 PMCID: PMC10866079 DOI: 10.1111/1758-2229.13215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/01/2023] [Indexed: 02/15/2024]
Abstract
Tangel humus primarily occurs in montane and subalpine zones of the calcareous Alps that exhibit low temperatures and high precipitation sums. This humus form is characterized by inhibited carbon turnover and accumulated organic matter, leading to the typical thick organic layers. However, the reason for this accumulation of organic matter is still unclear, and knowledge about the microbial community within Tangel humus is lacking. Therefore, we investigated the prokaryotic and fungal communities along with the physical and chemical properties within a depth gradient (0-10, 10-20, 20-30, 30-40, 40-50 cm) of a Tangel humus located in the Northern Limestone Alps. We hypothesized that humus properties and microbial activity, biomass, and diversity differ along the depth gradient and that microbial key players refer to certain humus depths. Our results give the first comprehensive information about microbiota within the Tangel humus and establish a microbial zonation of the humus. Microbial activity, biomass, as well as microbial alpha diversity significantly decreased with increasing depths. We identified microbial biomarkers for both, the top and the deepest depth, indicating different, microbial habitats. The microbial characterization together with the established nutrient deficiencies in the deeper depths might explain reduced C-turnover and Tangel humus formation.
Collapse
Affiliation(s)
- Theresa Rzehak
- Department of MicrobiologyUniversität InnsbruckInnsbruckAustria
| | - Nadine Praeg
- Department of MicrobiologyUniversität InnsbruckInnsbruckAustria
| | - Harald Zink
- Department of GeographyUniversität InnsbruckInnsbruckAustria
| | - Alois Simon
- Department of Forest PlanningOffice of the Tyrolean GovernmentInnsbruckAustria
| | - Clemens Geitner
- Department of GeographyUniversität InnsbruckInnsbruckAustria
| | - Paul Illmer
- Department of MicrobiologyUniversität InnsbruckInnsbruckAustria
| |
Collapse
|
10
|
Zhang Y, Mo C, Pan Y, Yang P, Ding X, Lei Q, Kang P. Responses of Soil Microbial Survival Strategies and Functional Changes to Wet-Dry Cycle Events. Microorganisms 2023; 11:2783. [PMID: 38004794 PMCID: PMC10672765 DOI: 10.3390/microorganisms11112783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Soil microbial taxa have different functional ecological characteristics that influence the direction and intensity of plant-soil feedback responses to changes in the soil environment. However, the responses of soil microbial survival strategies to wet and dry events are poorly understood. In this study, soil physicochemical properties, enzyme activity, and high-throughput sequencing results were comprehensively anal0079zed in the irrigated cropland ecological zone of the northern plains of the Yellow River floodplain of China, where Oryza sativa was grown for a long period of time, converted to Zea mays after a year, and then Glycine max was planted. The results showed that different plant cultivations in a paddy-dryland rotation system affected soil physicochemical properties and enzyme activity, and G. max field cultivation resulted in higher total carbon, total nitrogen, soil total organic carbon, and available nitrogen content while significantly increasing α-glucosidase, β-glucosidase, and alkaline phosphatase activities in the soil. In addition, crop rotation altered the r/K-strategist bacteria, and the soil environment was the main factor affecting the community structure of r/K-strategist bacteria. The co-occurrence network revealed the inter-relationship between r/K-strategist bacteria and fungi, and with the succession of land rotation, the G. max sample plot exhibited more stable network relationships. Random forest analysis further indicated the importance of soil electrical conductivity, total carbon, total nitrogen, soil total organic carbon, available nitrogen, and α-glucosidase in the composition of soil microbial communities under wet-dry events and revealed significant correlations with r/K-strategist bacteria. Based on the functional predictions of microorganisms, wet-dry conversion altered the functions of bacteria and fungi and led to a more significant correlation between soil nutrient cycling taxa and environmental changes. This study contributes to a deeper understanding of microbial functional groups while helping to further our understanding of the potential functions of soil microbial functional groups in soil ecosystems.
Collapse
Affiliation(s)
- Yaqi Zhang
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (C.M.); (P.Y.); (X.D.)
| | - Chunyi Mo
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (C.M.); (P.Y.); (X.D.)
| | - Yaqing Pan
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco–Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China;
| | - Pengbin Yang
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (C.M.); (P.Y.); (X.D.)
| | - Xiaodong Ding
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (C.M.); (P.Y.); (X.D.)
| | - Qian Lei
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (C.M.); (P.Y.); (X.D.)
| | - Peng Kang
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (Y.Z.); (C.M.); (P.Y.); (X.D.)
| |
Collapse
|
11
|
Singh S, Singh S, Lukas SB, Machado S, Nouri A, Calderon F, Rieke ER, Cappellazzi SB. Long-term agro-management strategies shape soil bacterial community structure in dryland wheat systems. Sci Rep 2023; 13:13929. [PMID: 37626146 PMCID: PMC10457325 DOI: 10.1038/s41598-023-41216-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 08/23/2023] [Indexed: 08/27/2023] Open
Abstract
Soil microbes play a crucial role in soil organic matter decomposition and nutrient cycling and are influenced by management practices. Therefore, quantifying the impacts of various agricultural management practices on soil microbiomes and their activity is crucial for making informed management decisions. This study aimed to assess the impact of various management systems on soil bacterial abundance and diversity, soil enzyme activities and carbon mineralization potential in wheat-based systems. To accomplish this, soil samples from 0 to 15 cm depth were collected from ongoing long-term field trials in eastern Oregon region under wheat (Triticum aestivum L.)-fallow (WF), WF with different tillage (WT), wheat-pea (Pisum sativum L.) (WP), WF under different crop residue management (CR) and natural undisturbed/unmanaged grassland pasture (GP). These trials consisted of an array of treatments like tillage intensities, nitrogen rates, organic amendments, and seasonal residue burning. This study was a part of the Soil Health Institute's North American Project to Evaluate Soil Health measurements (NAPESHM). Bacterial community structure was determined using amplicon sequencing of the V4 region of 16SrRNA genes and followed the protocols of the Earth Microbiome Project. In addition, extracellular enzyme activities, and carbon mineralization potential (1d-CO2) were measured. Among different trials, 1d-CO2 in WT, WP, and CR studies averaged 53%, 51% and 87% lower than GP systems, respectively. Enzyme activities were significantly greater in GP compared to the other managements and followed similar trend as respiration. We observed higher evenness in GP and higher richness in spring residue burning treatment of CR study. Our results indicated that species evenness is perhaps a better indicator of soil health in comparison to other indices in dryland wheat systems.
Collapse
Affiliation(s)
- Shikha Singh
- Hermiston Agricultural Research and Extension Center, Oregon State University, 2121 S 1St, Hermiston, OR, 97838, USA
| | - Surendra Singh
- Columbia Basin Agricultural Research Center, Oregon State University, 48037 Tubbs Ranch Rd., Adams, OR, 97810, USA
| | - Scott B Lukas
- Hermiston Agricultural Research and Extension Center, Oregon State University, 2121 S 1St, Hermiston, OR, 97838, USA.
| | - Stephen Machado
- Columbia Basin Agricultural Research Center, Oregon State University, 48037 Tubbs Ranch Rd., Adams, OR, 97810, USA
| | - Amin Nouri
- Hermiston Agricultural Research and Extension Center, Oregon State University, 2121 S 1St, Hermiston, OR, 97838, USA
| | - Francisco Calderon
- Columbia Basin Agricultural Research Center, Oregon State University, 48037 Tubbs Ranch Rd., Adams, OR, 97810, USA
| | | | | |
Collapse
|
12
|
Christel A, Dequiedt S, Chemidlin-Prevost-Bouré N, Mercier F, Tripied J, Comment G, Djemiel C, Bargeot L, Matagne E, Fougeron A, Mina Passi JB, Ranjard L, Maron PA. Urban land uses shape soil microbial abundance and diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 883:163455. [PMID: 37062324 DOI: 10.1016/j.scitotenv.2023.163455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 06/03/2023]
Abstract
Soil microbial biodiversity provides many useful services in cities. However, the ecology of microbial communities in urban soils remains poorly documented, and studies are required to better predict the impact of urban land use. We characterized microbial communities (archea/bacteria and fungi) in urban soils in Dijon (Burgundy, France). Three main land uses were considered - public leisure, traffic, and urban agriculture - sub-categorized in sub-land uses according to urban indexes and management practices. Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA. Variation partitioning analysis was used to rank soil physicochemical characteristics and land uses according to their relative contribution to the variation of soil microbial communities. Urban soils in Dijon harbored high levels of microbial biomass and diversity that varied according to land uses. Microbial biomass was 1.8 times higher in public leisure and traffic sites than in urban agriculture sites. Fungal richness increased by 25 % in urban agriculture soils, and bacterial richness was lower (by 20 %) in public leisure soils. Partitioning models explained 25.7 %, 46.2 % and 75.6 % of the variance of fungal richness, bacterial richness and microbial biomass, respectively. The organic carbon content and the C/N ratio were the best predictors of microbial biomass, whereas soil bacterial diversity was mainly explained by soil texture and land use. Neither metal trace elements nor polycyclic aromatic hydrocarbons contents explained variations of microbial communities, probably due to their very low concentration in the soils. The microbial composition results highlighted that leisure sites represented a stabilized habitat favoring specialized microbial groups and microbial plant symbionts, as opposed to urban agriculture sites that stimulated opportunistic populations able to face the impact of agricultural practices. Altogether, our results provide evidence that there is scope for urban planners to drive soil microbial diversity through sustainable urban land use and associated management practices.
Collapse
Affiliation(s)
- Amélie Christel
- AgroParisTech, 75732 Paris, France; Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Samuel Dequiedt
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Florian Mercier
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Julie Tripied
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Gwendoline Comment
- Platforme GenoSol, INRAE-Université de Bourgogne, CMSE, 21000 Dijon, France
| | - Christophe Djemiel
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Eric Matagne
- AGARIC-IG, 144 Rue Rambuteau, 71000 Macon, France
| | - Agnès Fougeron
- Jardin de l'Arquebuse Mairie de Dijon, CS 73310, 21033 Dijon Cedex, France
| | | | - Lionel Ranjard
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Pierre-Alain Maron
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France.
| |
Collapse
|
13
|
Acharya SM, Yee MO, Diamond S, Andeer PF, Baig NF, Aladesanmi OT, Northen TR, Banfield JF, Chakraborty R. Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots. ISME COMMUNICATIONS 2023; 3:54. [PMID: 37280433 PMCID: PMC10244434 DOI: 10.1038/s43705-023-00265-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/08/2023]
Abstract
For a deeper and comprehensive understanding of the composition and function of rhizosphere microbiomes, we need to focus at the scale of individual roots in standardized growth containers. Root exudation patterns are known to vary along distinct parts of the root even in juvenile plants giving rise to spatially distinct microbial niches. To address this, we analyzed the microbial community from two spatially distinct zones of the developing primary root (tip and base) in young Brachypodium distachyon grown in natural soil using standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and tubes. 16S rRNA based community analysis showed a strong rhizosphere effect resulting in significant enrichment of several OTUs belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. However, microbial community composition did not differ between root tips and root base or across different growth containers. Functional analysis of bulk metagenomics revealed significant differences between root tips and bulk soil. The genes associated with different metabolic pathways and root colonization were enriched in root tips. On the other hand, genes associated with nutrient-limitation and environmental stress were prominent in the bulk soil compared to root tips, implying the absence of easily available, labile carbon and nutrients in bulk soil relative to roots. Such insights into the relationships between developing root and microbial communities are critical for judicious understanding of plant-microbe interactions in early developmental stages of plants.
Collapse
Affiliation(s)
- Shwetha M Acharya
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mon Oo Yee
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Spencer Diamond
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA
| | - Peter F Andeer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nameera F Baig
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Omolara T Aladesanmi
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA
| | - Romy Chakraborty
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| |
Collapse
|
14
|
Li Y, Hou Y, Hou Q, Long M, Yang Y, Wang Z, Liao Y. Long-term plastic mulching decreases rhizoplane soil carbon sequestration by decreasing microbial anabolism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161713. [PMID: 36682553 DOI: 10.1016/j.scitotenv.2023.161713] [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: 10/01/2022] [Revised: 01/12/2023] [Accepted: 01/15/2023] [Indexed: 06/17/2023]
Abstract
Ridge-furrow with plastic mulching (RFPM) is a widely used agricultural practice in rain-fed farmlands. However, the impact of microbial related metabolism on soil organic carbon (SOC) is not fully understood. Amino sugar analysis, high-throughput sequencing, and high-throughput qPCR approaches are combined to investigate this topic, based on a long-term experiment. Treatments include flat planting without mulching (FP), ridge-furrow without mulching (RF), and RFPM. RFPM significantly decreases rhizoplane SOC contents, while bulk SOC contents change insignificantly across treatments. In terms of microbial metabolic pathways, RFPM decreases indicators of the in vivo metabolic pathway, whereas those of the ex vivo pathway are increased. In terms of microbial community features, core taxa module #1 is dominated by Sphingomonadaceae. These are putative high yield (Y) strategists, according to the microbial life-history strategy framework. They are closely related to the in vivo pathway and are most predictive for SOC; their abundance is highest under FP and lowest under RFPM. Core taxa module #2 is dominated by Chitinophagaceae, putative resource acquisition (A) strategists, that are closely related to the ex vivo pathway. Their abundance in the rhizoplane is highest under RFPM and lowest under FP. The RFPM-induced decline in SOC occurs simultaneously with the abundance of A-strategists with in vivo pathway but not the Y-strategists with ex vivo pathway. Overall, the result of this study shows a trade-off. In RFPM practice, the ex vivo microbial pathway is enhanced along with the abundance of A-strategists. This is not the case for the in vivo pathway and associated abundance of Y-strategists, which are closely associated with SOC. Our findings underlined the impact of rhizoplane microbial metabolic pathways on SOC status is key to agricultural practices in drylands such as RFPM, and advanced our understanding of how microbes affect the carbon cycling in dryland farming.
Collapse
Affiliation(s)
- Yüze Li
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Yuting Hou
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Quanming Hou
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Mei Long
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Yali Yang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, Liaoning, PR China
| | - Ziting Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China; College of Agronomy, Guangxi University, Nanning, 530004, Guangxi, PR China; Guangxi Key Laboratory of Sugarcane Biology, Nanning, 530004, Guangxi, PR China.
| | - Yuncheng Liao
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China.
| |
Collapse
|
15
|
Stone BWG, Dijkstra P, Finley BK, Fitzpatrick R, Foley MM, Hayer M, Hofmockel KS, Koch BJ, Li J, Liu XJA, Martinez A, Mau RL, Marks J, Monsaint-Queeney V, Morrissey EM, Propster J, Pett-Ridge J, Purcell AM, Schwartz E, Hungate BA. Life history strategies among soil bacteria-dichotomy for few, continuum for many. THE ISME JOURNAL 2023; 17:611-619. [PMID: 36732614 PMCID: PMC10030646 DOI: 10.1038/s41396-022-01354-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 02/04/2023]
Abstract
Study of life history strategies may help predict the performance of microorganisms in nature by organizing the complexity of microbial communities into groups of organisms with similar strategies. Here, we tested the extent that one common application of life history theory, the copiotroph-oligotroph framework, could predict the relative population growth rate of bacterial taxa in soils from four different ecosystems. We measured the change of in situ relative growth rate to added glucose and ammonium using both 18O-H2O and 13C quantitative stable isotope probing to test whether bacterial taxa sorted into copiotrophic and oligotrophic groups. We saw considerable overlap in nutrient responses across most bacteria regardless of phyla, with many taxa growing slowly and few taxa that grew quickly. To define plausible life history boundaries based on in situ relative growth rates, we applied Gaussian mixture models to organisms' joint 18O-13C signatures and found that across experimental replicates, few taxa could consistently be assigned as copiotrophs, despite their potential for fast growth. When life history classifications were assigned based on average relative growth rate at varying taxonomic levels, finer resolutions (e.g., genus level) were significantly more effective in capturing changes in nutrient response than broad taxonomic resolution (e.g., phylum level). Our results demonstrate the difficulty in generalizing bacterial life history strategies to broad lineages, and even to single organisms across a range of soils and experimental conditions. We conclude that there is a continued need for the direct measurement of microbial communities in soil to advance ecologically realistic frameworks.
Collapse
Affiliation(s)
- Bram W G Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA.
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Brianna K Finley
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Raina Fitzpatrick
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Megan M Foley
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Junhui Li
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Xiao Jun A Liu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Ayla Martinez
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Jane Marks
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Jeffrey Propster
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, USA
- Life and Environmental Sciences Department, University of California Merced, Merced, CA, USA
| | - Alicia M Purcell
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| |
Collapse
|
16
|
Qi JY, Yao XB, Lu J, He LX, Cao JL, Kan ZR, Wang X, Pan SG, Tang XR. A 40 % paddy surface soil organic carbon increase after 5-year no-tillage is linked with shifts in soil bacterial composition and functions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160206. [PMID: 36400297 DOI: 10.1016/j.scitotenv.2022.160206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/26/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
Soil organic carbon (SOC) is related to soil fertility, crop yield, and climate change mitigation. Paddy soil is a significant carbon (C) sink, but its C sequestration potential has not been realized as the various driving factors are still not fully understood. We performed a 5-year paddy field experiment in southern China to estimate tillage effects on SOC accumulation and its relation with soil bacteria. The C input from rice residue, SOC content, CO2 flux, soil bacterial community composition, and predicted functions were analyzed. No-tillage (NT) increased (p < 0.05) rice residue C inputs (by 12.6 %-15.9 %), SOC (by 40 % at the surface soil layer compared with conventional tillage, CT), and CO2 fluxes compared with reduced tillage (RT) and CT. Also, NT significantly altered the soil bacterial community. The random forest model showed that the predicted bacterial functions of "Degradation/Utilization/Assimilation Other", "C1 Compound Assimilation", and "Amin and Polyamine Degradation" were the most important functions associated with SOC accumulation. Analysis of metabolic pathway differences indicated that NT significantly decreased the BENZCOA-PWY (anaerobic aromatic compound degradation) and the AST-PWY (L-arginine degradation II). Therefore, the rapid paddy SOC increase is associated with both residue C input (from higher rice yields) and the degradation functions regulated by soil bacteria.
Collapse
Affiliation(s)
- Jian-Ying Qi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Xiang-Bin Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Jian Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Long-Xin He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Jun-Li Cao
- Shanxi Center for Testing of Functional Agro⁃Products, Shanxi Agricultural University, Taiyuan 030031, China
| | - Zheng-Rong Kan
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xing Wang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Sheng-Gang Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Xiang-Ru Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; Guangzhou Key Laboratory for Science and Technology of Fragrant Rice, Guangzhou 510642, China.
| |
Collapse
|
17
|
Cheng H, Zhou X, Dong R, Wang X, Liu G, Li Q. Priming of soil organic carbon mineralization and its temperature sensitivity in response to vegetation restoration in a karst area of Southwest China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158400. [PMID: 36049694 DOI: 10.1016/j.scitotenv.2022.158400] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Plant residue input alters native soil organic carbon (SOC) mineralization through the priming effect, which strongly controls C sequestration during vegetation restoration. However, the effects of different vegetation types on SOC priming and the underlying microbial mechanisms due to global warming are poorly understood. To elucidate these unknowns, the current study quantified soil priming effects using 13C-labeled maize residue amendments and analyzed the community structure and abundances in the soils of a vegetation succession gradient (maize field (MF), grassland (GL), and secondary forest (SF)) from a karst region under two incubation temperatures (15 °C and 25 °C). Results revealed that after 120 d of incubation, vegetation restoration increased the soil priming effects. Compared to MF, the priming effects of SF at 15 °C and 25 °C increased by 142.36 % and 161.09 %, respectively. This may be attributed to a high C/N ratio and low-N availability (NO3-), which supports the "microbial nitrogen mining" theory. Variations in soil priming were linked to changes in microbial properties. Moreover, with vegetation restoration, the relative abundance of Actinobacteria (copiotrophs) increased, while Ascomycota (oligotrophs) decreased, which accelerated native SOC decomposition. Co-occurrence network analysis indicated that the cooperative interactions of co-existing keystone taxa may facilitate SOC priming. Furthermore, structural equation modeling (SEM) indicated that changes in the priming effects were directly related to the fungal Shannon index and microbial biomass C (MBC), which were affected by soil C/N and NO3-. Warming significantly decreased soil priming, which may be attributed to the increase in microbial respiration (qCO2) and decreased MBC. The temperature sensitivity (Q10) of SOC mineralization was higher after residue amendment, but significant differences were not detected among the vegetation types. Collectively, our results indicated that the intensity of priming effects was dependent on vegetation type and temperature. Microbial community alterations and physicochemical interactions played important roles in SOC decomposition and sequestration.
Collapse
Affiliation(s)
- Hanting Cheng
- Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; Hainan Provincial Key Laboratory of Tropical Eco-cycle Agriculture, Haikou, Hainan, China; Agricultural Environmental Science Observation and Experiment Station, Ministry of Agriculture, Danzhou, Hainan, China
| | - Xiaohui Zhou
- Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; Hainan Provincial Key Laboratory of Tropical Eco-cycle Agriculture, Haikou, Hainan, China; Agricultural Environmental Science Observation and Experiment Station, Ministry of Agriculture, Danzhou, Hainan, China
| | - Rongshu Dong
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xiaomin Wang
- Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xingyi, Guizhou 562400, China
| | - Guodao Liu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Qinfen Li
- Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; Hainan Provincial Key Laboratory of Tropical Eco-cycle Agriculture, Haikou, Hainan, China; Agricultural Environmental Science Observation and Experiment Station, Ministry of Agriculture, Danzhou, Hainan, China.
| |
Collapse
|
18
|
Wei X, Wu F, Heděnec P, Yue K, Peng Y, Yang J, Zhang X, Ni X. Changes in soil faunal density and microbial community under altered litter input in forests and grasslands. FUNDAMENTAL RESEARCH 2022; 2:954-963. [PMID: 38933376 PMCID: PMC11197608 DOI: 10.1016/j.fmre.2022.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 01/07/2022] [Accepted: 01/19/2022] [Indexed: 11/21/2022] Open
Abstract
Root and foliar litter inputs are the primary sources of carbon and nutrients for soil fauna and microorganisms, yet we still lack a quantitative assessment to evaluate the effects of root and foliar litter on various groups of soil organisms across terrestrial ecosystems. Here, we compiled 978 paired observations from 68 experimental sites to assess the directions and magnitudes of adding and removing foliar and root litter on the soil faunal density and microbial biomass that was evaluated by phospholipid fatty acids (PLFAs) across forests and grasslands worldwide. We found that litter addition had only a marginal effect on soil faunal density but significantly increased the soil total microbial-, fungal- and bacterial-PLFAs by 13%, 14%, and 10%, respectively, across ecosystems, suggesting that the soil microbial community is more sensitive to carbon source addition than soil fauna, particularly in soils with low carbon to nitrogen ratios. In contrast, removing litter significantly decreased the soil faunal density by 17% but had few effects on soil microorganisms. Compared with foliar litter, root litter input had a more positive effect on the development of soil fungal taxa. The effect of both litter addition and removal on soil faunal density and microbial biomass did not differ between humid and arid regions, but a greater influence was observed in grasslands than in forests for soil microbial community. Our results highlight that the increasing litter production under a global greening scenario would stimulate microbial activity in grasslands more than in forests, and this stimulation would be greater for soil microbes than soil fauna.
Collapse
Affiliation(s)
- Xinyu Wei
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Fuzhong Wu
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Petr Heděnec
- Agritec Plant Research Ltd., Zemědělská 16, Šumperk 78701, Czech Republic
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Kai Yue
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Yan Peng
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Jing Yang
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Xiaoyue Zhang
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Xiangyin Ni
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| |
Collapse
|
19
|
Du M, Zhang J, Wang G, Liu C, Wang Z. Response of bacterial community composition and co-occurrence network to straw and straw biochar incorporation. Front Microbiol 2022; 13:999399. [PMID: 36246223 PMCID: PMC9563622 DOI: 10.3389/fmicb.2022.999399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/30/2022] [Indexed: 11/22/2022] Open
Abstract
Microbial decomposition plays a crucial role in the incorporation of straw and straw biochar (SSB) into soil. Lime concretion black soil (LCBS) is a typical low-medium crop yield soil, and it is also one of the main soil types for grain production in China. However, the link between SSB additions and soil bacterial communities in LCBS remains unclear. This study explored the effects of SSB incorporation on bacterial community composition, structure and co-occurrence network patterns at different soil depths and maize growth stages. The results showed that soil PH, soil organic matter and total nitrogen significantly affected the seasonality and stratification of the soil bacterial community. The composition and diversity of bacterial communities were significantly affected by growth period and treatment rather than soil depth. Specifically, the bacterial community diversity increased significantly with crop growth at 0–20 cm, decreased the relative abundance of Actinobacteria, and increased the relative abundance of Proteobacteria and Acidobacteria. SF (straw with fertilizer) and BF (straw biochar with fertilizer) treatments decreased bacterial community diversity. Co-occurrence networks are more complex in BF, S (straw), and SF treatments, and the number of edge network patterns is increased by 92.5, 40, and 60% at the maturity stage compared with F (fertilizer) treatment, respectively. Moreover, the positive effect of straw biochar on the bacterial network pattern increased with time, while the effect of straw weakened. Notably, we found that rare species inside keystone taxa (Gemmatimonadetes and Nitrospirae) play an indispensable role in maintaining bacterial network construction in LCBS. This study offers a comprehensive understanding of the response of soil bacterial communities to SSB addition in LCBS areas, and provides a reference for further improvement of LCBS productivity.
Collapse
Affiliation(s)
- Mingcheng Du
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, China
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing, China
- Yangtze Institute for Conservation and Development, Nanjing, China
- Research Center for Climate Change, Nanjing, China
| | - Jianyun Zhang
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, China
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing, China
- Yangtze Institute for Conservation and Development, Nanjing, China
- Research Center for Climate Change, Nanjing, China
| | - Guoqing Wang
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing, China
- Yangtze Institute for Conservation and Development, Nanjing, China
- Research Center for Climate Change, Nanjing, China
- *Correspondence: Guoqing Wang,
| | - Cuishan Liu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing, China
- Yangtze Institute for Conservation and Development, Nanjing, China
- Research Center for Climate Change, Nanjing, China
| | - Zhenlong Wang
- Wudaogou Experimental Station for Hydrology and Water Resources, Bengbu, China
- Anhui Hydraulic Research Institute, Huai River Commission, Bengbu, China
| |
Collapse
|
20
|
Wang L, Wang M, Li Q, Zhang J, Li C, Yuan Y, Tan P, Liu H. Dynamics of soil properties and bacterial community structure by mulched fertigation system in semi-arid area of Northeast China. PeerJ 2022; 10:e14044. [PMID: 36168430 PMCID: PMC9509672 DOI: 10.7717/peerj.14044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/21/2022] [Indexed: 01/19/2023] Open
Abstract
The agricultural irrigation and fertigation systems have a non-negligible impact on the soil microenvironment in arid and semi-arid areas. Therefore, studying the processes and changes of soil microenvironment under different plastic mulch drip irrigation systems can reveal the "soil-microbe" mechanism and provide a theoretical support for the optimal irrigation and nutrition management of maize in the semi-arid area of Northeast China. Three treatments were used for this study in the semi-arid area of northeast China, namely; mulched fertigation system (MF), drip irrigation system (DI), and farmers' practices system (FP). We used high-throughput sequencing to study the soil bacterial community structure targeting the 16S rRNA gene. The agricultural irrigation and fertigation systems significantly affected soil properties. MF significantly increased bacterial abundance and bacterial diversity and richness. Moreover, MF and DI markedly increased some relative abundance of beneficial bacterial. The bacterial network in MF was more conducive to the health and stability of the agroecosystem and the relationships among species in MF bacterial network were more complex. The agricultural irrigation and fertigation systems had indirect effects on community composition and bacterial diversity through soil organic carbon (SOC), ammonium nitrogen ( NH 4 + -N), nitrate nitrogen ( NO 3 - -N), pH, moisture, NH 4 + -N and NO 3 - -N had indirect effects on yield through bacterial community composition, bacterial diversity and bacterial abundance. These findings suggested that MF was the most effective treatment to improve soil bacterial abundance and diversity, and stabilize the functional quality of soil biological processes.
Collapse
Affiliation(s)
- Ling Wang
- Key Laboratory of Soil Resource Sustainable Utilization for Commodity Grain Bases of Jilin Province, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Meng Wang
- Institute of Agricultural Environment and Resources Research, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Qian Li
- Institute of Agricultural Environment and Resources Research, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jinjing Zhang
- Key Laboratory of Soil Resource Sustainable Utilization for Commodity Grain Bases of Jilin Province, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Cuilan Li
- Key Laboratory of Soil Resource Sustainable Utilization for Commodity Grain Bases of Jilin Province, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yuhan Yuan
- Key Laboratory of Soil Resource Sustainable Utilization for Commodity Grain Bases of Jilin Province, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Pan Tan
- Key Laboratory of Soil Resource Sustainable Utilization for Commodity Grain Bases of Jilin Province, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Hang Liu
- Key Laboratory of Soil Resource Sustainable Utilization for Commodity Grain Bases of Jilin Province, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, Jilin, China
| |
Collapse
|
21
|
Yu H, Le Roux JJ, Zhao M, Li W. Mikania sesquiterpene lactones enhance soil bacterial diversity and fungal and bacterial activities. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02907-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
22
|
Hafez T, Ortiz-Zarragoitia M, Cagnon C, Cravo-Laureau C, Duran R. Legacy and dispersant influence microbial community dynamics in cold seawater contaminated by crude oil water accommodated fractions. ENVIRONMENTAL RESEARCH 2022; 212:113467. [PMID: 35588780 DOI: 10.1016/j.envres.2022.113467] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/26/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Dispersants, used for combating oil spills, increase hydrocarbon bioavailability promoting their biodegradation. Oil weathering process introduces harmful soluble hydrocarbons, such as polycyclic aromatic hydrocarbons (PAHs), into the water column, resulting in water-accommodated fraction (WAF). The presence of dispersants can influence the weathering process by increasing PAHs solubility, toxicity and biodegradability. However, little is known on how dispersants affect microbial communities and their degradation capacities, especially in cold environment where low temperature decreases microbial activity and thus hydrocarbon degradation. Here, we investigated the microbial community dynamics in cold water contaminated by WAF prepared from crude oil with or without a commercial dispersant (Finasol OSR52). The WAFs, prepared with Naphthenic North Atlantic crude oil, were used to contaminate seawater from Norwegian cold sites, one oil-contaminated and the other pristine. The WAF-contaminated seawaters were maintained in microcosms at 4 °C for 21 days. The content of PAHs and microbial compositions (16S rRNA gene sequencing) were determined at days 0, 7, 14 and 21. In addition, the 96 h toxicity assay with adult Acartia tonsa revealed WAFs toxicity at days 0 and 21. The toxicity of WAF mixtures, with and without dispersant, against Acartia tonsa was reduced during the experiment, but PAHs removal was not increased. The water from the oil-contaminated site showed the highest PAHs removal revealing legacy effect (presence of microorganisms adapted to PAHs). Additionally, our results reveal: i) microbial community plasticity allowing the adaptation to the presence of PAHs and dispersant, ii) specific bacteria taxa probably involved in PAHs degradation, and iii) dispersants shape the microbial communities dynamics by stimulating potential dispersant-degrading taxa, such as Fusibacter. Thus, our results provide valuable insights on the role of microbial community in determining the fate of water-solubilized hydrocarbon in cold environment while questioning the role of dispersant used for fighting oil spill.
Collapse
Affiliation(s)
- Tamer Hafez
- CBET Research Group, Department of Zoology and Cell Biology, Faculty of Science and Technology and Research Center for Marine Biology and Biotechnology (PiE-UPV/EHU) University of the Basque Country, Areatza z/g, 48620, Plentzia, Bizkaia, Basque Country, Spain; Universite de Pau et des Pays de l'Adour, E2S/UPPA, IPREM5254, 64000, Pau, France
| | - Maren Ortiz-Zarragoitia
- CBET Research Group, Department of Zoology and Cell Biology, Faculty of Science and Technology and Research Center for Marine Biology and Biotechnology (PiE-UPV/EHU) University of the Basque Country, Areatza z/g, 48620, Plentzia, Bizkaia, Basque Country, Spain
| | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S/UPPA, IPREM5254, 64000, Pau, France
| | | | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S/UPPA, IPREM5254, 64000, Pau, France.
| |
Collapse
|
23
|
Pan Y, Kang P, Tan M, Hu J, Zhang Y, Zhang J, Song N, Li X. Root exudates and rhizosphere soil bacterial relationships of Nitraria tangutorum are linked to k-strategists bacterial community under salt stress. FRONTIERS IN PLANT SCIENCE 2022; 13:997292. [PMID: 36119572 PMCID: PMC9471988 DOI: 10.3389/fpls.2022.997292] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
When plants are subjected to various biotic and abiotic stresses, the root system responds actively by secreting different types and amounts of bioactive compounds, while affects the structure of rhizosphere soil bacterial community. Therefore, understanding plant-soil-microbial interactions, especially the strength of microbial interactions, mediated by root exudates is essential. A short-term experiment was conducted under drought and salt stress to investigate the interaction between root exudates and Nitraria tangutorum rhizosphere bacterial communities. We found that drought and salt stress increased rhizosphere soil pH (9.32 and 20.6%) and electrical conductivity (1.38 and 11 times), respectively, while decreased organic matter (27.48 and 31.38%), total carbon (34.55 and 29.95%), and total phosphorus (20 and 28.57%) content of N. tangutorum rhizosphere soil. Organic acids, growth hormones, and sugars were the main differential metabolites of N. tangutorum under drought and salt stress. Salt stress further changed the N. tangutorum rhizosphere soil bacterial community structure, markedly decreasing the relative abundance of Bacteroidota as r-strategist while increasing that of Alphaproteobacteria as k-strategists. The co-occurrence network analysis showed that drought and salt stress reduced the connectivity and complexity of the rhizosphere bacterial network. Soil physicochemical properties and root exudates in combination with salt stress affect bacterial strategies and interactions. Our study revealed the mechanism of plant-soil-microbial interactions under the influence of root exudates and provided new insights into the responses of bacterial communities to stressful environments.
Collapse
Affiliation(s)
- Yaqing Pan
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Peng Kang
- College of Biological Sciences and Engineering, North Minzu University, Yinchuan, China
| | - Min Tan
- College of Biological Sciences and Engineering, North Minzu University, Yinchuan, China
| | - Jinpeng Hu
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Yinchuan, China
| | - Yaqi Zhang
- College of Biological Sciences and Engineering, North Minzu University, Yinchuan, China
| | - Jinlin Zhang
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Yinchuan, China
| | - Naiping Song
- Breeding Base for Key Laboratory Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
| | - Xinrong Li
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| |
Collapse
|
24
|
Barnett SE, Youngblut ND, Buckley DH. Bacterial community dynamics explain carbon mineralization and assimilation in soils of different land-use history. Environ Microbiol 2022; 24:5230-5247. [PMID: 35920035 DOI: 10.1111/1462-2920.16146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 11/30/2022]
Abstract
Soil dwelling microorganisms are key players in the terrestrial carbon cycle, driving both the degradation and stabilization of soil organic matter. Bacterial community structure and function vary with respect to land-use, yet the ecological drivers of this variation remain poorly described and difficult to predict. We conducted a multi-substrate DNA-stable isotope probing experiment across cropland, old-field, and forest habitats to link carbon mineralization dynamics with the dynamics of bacterial growth and carbon assimilation. We tracked the movement of 13 C derived from five distinct carbon sources as it was assimilated into bacterial DNA over time. We show that carbon mineralization, community composition, and carbon assimilation dynamics all differed with respect to land-use. We also show that microbial community dynamics affect carbon assimilation dynamics and are associated with soil DNA content. Soil DNA yield is easy to measure and may be useful in predicting microbial community dynamics linked to soil carbon cycling. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Samuel E Barnett
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| |
Collapse
|
25
|
Cui X, He H, Zhu F, Liu X, Ma Y, Xie W, Meng H, Zhang L. Community structure and co-occurrence network analysis of bacteria and fungi in wheat fields vs fruit orchards. Arch Microbiol 2022; 204:453. [PMID: 35786781 DOI: 10.1007/s00203-022-03074-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 11/26/2022]
Abstract
Soil microorganisms play a vital role in biogeochemical processes and nutrient turnover in agricultural ecosystems. However, the information on how the structure and co-occurrence patterns of microbial communities response to the change of planting methods is still limited. In this study, a total of 34 soil samples were collected from 17 different fields of 2 planting types (wheat and orchards) along the Taige Canal in Yangtze River Delta. The structure of bacterial and fungal communities in soil were determined by 16S rRNA gene and ITS gene, respectively. The dominated bacteria were Proteobacteria, Acidobacteriota, Actinobacteriota, Chloroflexi, Bacteroidota, and Firmicutes. The relative abundances of Actinobacteriota and Firmicutes were higher in the orchards, while Chloroflexi and Nitrospirota were more abundant in wheat fields. Ascomycota, Mortierellomycota, and Basidiomycota were the predominant fungus in both soil types. Diversity of bacterial and fungal communities were greater in the wheat fields than in orchards. Statistical analyses showed that pH was the main factor shaping the community structure, and parameters of water content (WC), total organic carbon (TOC) and total nitrogen (TN) had great influences on community structure. Moreover, high co-occurrence patterns of bacterial and fungal were confirmed in both wheat fields and orchards. Network analyses showed that both wheat fields and orchards occurred modular structure, including nodes of Acidobacteriota, Chloroflexi, Gemmatimonadota, Nitrospirota and Ascomycota. In summary, our work showed the co-occurrence network and the convergence/divergence of microbial community structure in wheat fields and orchards, giving a comprehensive understanding of the microbe-microbe interaction during planting methods' changes.
Collapse
Affiliation(s)
- Xinyu Cui
- School of Environment, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Huan He
- School of Environment, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Fengxiao Zhu
- School of Environment, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Xiaobo Liu
- Environmental Science and Engineering Research Group, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, 515063, Guangdong, People's Republic of China
| | - You Ma
- School of Environment, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Wenming Xie
- School of Environment, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Han Meng
- School of Environment, Nanjing Normal University, Nanjing, 210023, People's Republic of China.
| | - Limin Zhang
- School of Environment, Nanjing Normal University, Nanjing, 210023, People's Republic of China
- Green Economy Development Institute, Nanjing University of Finance and Economics, Nanjing, 210023, People's Republic of China
| |
Collapse
|
26
|
Zhou S, Wang J, Chen L, Wang J, Zhao F. Microbial community structure and functional genes drive soil priming effect following afforestation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 825:153925. [PMID: 35218819 DOI: 10.1016/j.scitotenv.2022.153925] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/12/2022] [Accepted: 02/12/2022] [Indexed: 06/14/2023]
Abstract
Afforestation substantially modifies native soil organic carbon (SOC) decomposition via plant carbon inputs (the priming effect), and in turn, triggers vital biogeochemical processes that influence the regulation of soil carbon dynamics. Soil microbes are crucial in regulating the direction and magnitude of the priming effect. In the present study, we performed metagenomic sequencing and 13C-glucose labeling analyses of microbial communities and priming effects across a Robinia pseudoacacia afforestation chronosequence (14-, 20-, 30-, and 45-year-old stands) in the Loess Plateau in China, with adjacent farmland being selected as a control. Our results revealed that the cumulative priming effect across five sites along the afforestation chronosequence initially increased and approached a peak value in the 20-year-old stand, after which it declined. The priming effect was predominantly driven by the microbial community structure (i.e., the fungal-to-bacterial ratios and relative abundances of Proteobacteria and Actinobacteria), and stable C decomposition genes and C-degrading enzymes. Specifically, among the key functional genes correlated with priming effect, which were identified in orders Rhizobiales and Pseudonocardiales, considerably promoted SOC priming. Overall, our findings indicate that afforestation alters soil microbial community structure and function, particularly with respect to enhancing stable soil C decomposition genes, which may promote SOC priming. The findings of the present study could enhance our understanding of fresh C input-induced changes associated with C mineralization in the context of the revegetation of ecologically fragile areas.
Collapse
Affiliation(s)
- Sha Zhou
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi'an, Shaanxi 710127, China; College of Urban and Environmental Sciences, Northwest University, Xi'an, Shaanxi 710127, China
| | - Jieying Wang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi'an, Shaanxi 710127, China; College of Urban and Environmental Sciences, Northwest University, Xi'an, Shaanxi 710127, China
| | - Lan Chen
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi'an, Shaanxi 710127, China; College of Urban and Environmental Sciences, Northwest University, Xi'an, Shaanxi 710127, China
| | - Jun Wang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi'an, Shaanxi 710127, China; College of Urban and Environmental Sciences, Northwest University, Xi'an, Shaanxi 710127, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling 712100, China.
| | - Fazhu Zhao
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi'an, Shaanxi 710127, China; College of Urban and Environmental Sciences, Northwest University, Xi'an, Shaanxi 710127, China
| |
Collapse
|
27
|
Song Z, Sun Y, Liu P, Wang Y, Huang Y, Gao Y, Hu X. Invasion of
Spartina alterniflora
on
Zostera japonica
enhances the abundances of bacteria by absolute quantification sequencing analysis. Ecol Evol 2022; 12:e8939. [PMID: 35600690 PMCID: PMC9120208 DOI: 10.1002/ece3.8939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 04/15/2022] [Accepted: 05/04/2022] [Indexed: 11/26/2022] Open
Abstract
Plant invasion can alter soil organic matter composition and indirectly impact estuary ecology; therefore, it is paramount to understand how plant invasion influences the bacterial community. Here, we present an absolute quantification 16S rRNA gene sequencing to investigate the bacterial communities that were collected from Zostera japonica and Spartina alterniflora covered areas and Z. japonica degradation areas in the Yellow River Estuary. Our data revealed that the absolute quantity of bacteria in the surface layer was significantly (p < .05) higher than that in the bottom and degradation areas. Following the invasion of S. alterniflora, the abundances of Bacteroidia, Acidimicrobiaceae, and Dehalococcoidaceaewere enriched in the S. alterniflora sediment. In addition, variations in the composition of sediment bacterial communities at the phylum level were the most intimately related to total organic carbon (TOC), and the content of heavy metals could reduce the abundance of bacteria. This study provided some information to understand the effects of S. alterniflora invasion on Z. japonica from the perspective of microbiome level.
Collapse
Affiliation(s)
- Zenglei Song
- Key laboratory of Coastal Biology and Bioresource Utilization Yantai Institute of Costal Zone Research Chinese Academy of Sciences Yantai China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- University of Chinese Academy of Sciences Beijing China
| | - Yanyu Sun
- Key laboratory of Coastal Biology and Bioresource Utilization Yantai Institute of Costal Zone Research Chinese Academy of Sciences Yantai China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- University of Chinese Academy of Sciences Beijing China
| | - Pengyuan Liu
- Key laboratory of Coastal Biology and Bioresource Utilization Yantai Institute of Costal Zone Research Chinese Academy of Sciences Yantai China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- University of Chinese Academy of Sciences Beijing China
| | - Yibo Wang
- Key laboratory of Coastal Biology and Bioresource Utilization Yantai Institute of Costal Zone Research Chinese Academy of Sciences Yantai China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- University of Chinese Academy of Sciences Beijing China
| | - Yanyan Huang
- Key laboratory of Coastal Biology and Bioresource Utilization Yantai Institute of Costal Zone Research Chinese Academy of Sciences Yantai China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- University of Chinese Academy of Sciences Beijing China
| | - Yan Gao
- Marine Science Research Institute of Shandong Province National Oceanographic Center of Qingdao Qingdao China
| | - Xiaoke Hu
- Key laboratory of Coastal Biology and Bioresource Utilization Yantai Institute of Costal Zone Research Chinese Academy of Sciences Yantai China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
| |
Collapse
|
28
|
Xiao J, Lan S, Zhang Z, Yang L, Qian L, Xia L, Song S, Farías ME, Torres RM, Wu L. Physical Disturbance Reduces Cyanobacterial Relative Abundance and Substrate Metabolism Potential of Biological Soil Crusts on a Gold Mine Tailing of Central China. Front Microbiol 2022; 13:811039. [PMID: 35464943 PMCID: PMC9019783 DOI: 10.3389/fmicb.2022.811039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/21/2022] [Indexed: 11/19/2022] Open
Abstract
As the critical ecological engineers, biological soil crusts (biocrusts) are considered to play essential roles in improving substrate conditions during ecological rehabilitation processes. Physical disturbance, however, often leads to the degradation of biocrusts, and it remains unclear how the physical disturbance affects biocrust microorganisms and their related metabolism. In this study, the photosynthetic biomass (indicated by chlorophyll a), nutrients, enzyme activities, and bacterial communities of biocrusts were investigated in a gold mine tailing of Central China to evaluate the impact of physical disturbance on biocrusts during the rehabilitation process of gold mine tailings. The results show that physical disturbance significantly reduced the photosynthetic biomass, nutrient contents (organic carbon, ammonium nitrogen, nitrate nitrogen, and total phosphorus), and enzyme activities (β-glucosidase, sucrase, nitrogenase, neutral phosphatase, and urease) of biocrusts in the mine tailings. Furthermore, 16S rDNA sequencing showed that physical disturbance strongly changed the composition, structure, and interactions of the bacterial community, leading to a shift from a cyanobacteria dominated community to a heterotrophic bacteria (proteobacteria, actinobacteria, and acidobacteria) dominated community and a more complex bacterial network (higher complexity, nodes, and edges). Altogether, our results show that the biocrusts dominated by cyanobacteria could also develop in the tailings of humid region, and the dominants (e.g., Microcoleus) were the same as those from dryland biocrusts; nevertheless, physical disturbance significantly reduced cyanobacterial relative abundance in biocrusts. Based on our findings, we propose the future work on cyanobacterial inoculation (e.g., Microcoleus), which is expected to promote substrate metabolism and accumulation, ultimately accelerating the development of biocrusts and the subsequent ecological restoration of tailings.
Collapse
Affiliation(s)
- Jingshang Xiao
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, China
| | - Shubin Lan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zulin Zhang
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, China.,The James Hutton Institute, Aberdeen, United Kingdom
| | - Lie Yang
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, China
| | - Long Qian
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, China
| | - Ling Xia
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, China
| | - Shaoxian Song
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, China
| | - María E Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), Centro Científico Tecnológico (CCT), Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán, Argentina
| | - Rosa María Torres
- CETMIC- CONICET- CCT La Plata, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICBA), La Plata, Argentina
| | - Li Wu
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, China
| |
Collapse
|
29
|
Sennett LB, Goyer C, Burton DL, Zebarth BJ, Whitney S. Chemical fumigation and biofumigation alter soil bacterial community diversity and composition. FEMS Microbiol Ecol 2022; 98:fiac026. [PMID: 35441686 DOI: 10.1093/femsec/fiac026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024] Open
Abstract
Chemical fumigation and biofumigation are used to reduce soil-borne diseases in agricultural production systems; however, non-targeted soil microorganisms may also be affected. This study compared the effects of chemical fumigation, either used alone or combined with an organic amendment, and biofumigation on soil bacterial community diversity and composition under controlled conditions over 160 days. Treatments included: fumigation with chloropicrin (CP), fumigation with metam sodium used alone (MS) or combined with barley plant residues (MSBR); biofumigation with mustard plant residues; addition of barley plant residues; and untreated control. Biofumigation had a greater impact on bacterial diversity at early time points, transiently decreasing species evenness and yielding the most dissimilar β-diversity after 3 days. MS fumigation did not affect bacterial diversity indices; however, MSBR transiently decreased species evenness after 8 days. CP-treated soil had decreased species evenness that did not recover over time and had the most dissimilar β-diversity at the end of the incubation compared to all other treatments. This study demonstrated that CP fumigation had the greatest and most persistent impact on bacterial diversity, whereas MS fumigation and biofumigation led to transient decreases in bacterial diversity.
Collapse
Affiliation(s)
- Louise B Sennett
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - Claudia Goyer
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - David L Burton
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Bernie J Zebarth
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - Sean Whitney
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| |
Collapse
|
30
|
Zhang Y, Heal KV, Shi M, Chen W, Zhou C. Decreasing molecular diversity of soil dissolved organic matter related to microbial community along an alpine elevation gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151823. [PMID: 34808163 DOI: 10.1016/j.scitotenv.2021.151823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Characterization of soil dissolved organic matter (DOM) and understanding of the interactions between soil microbial communities and DOM molecules along elevation gradients in alpine ecosystems are still limited. To unravel these interactions and how they change along alpine elevation gradients, we sampled topsoil in the Sygera Mountains (Tibet, China) at elevations between 3800 and 4600 m. The molecular characteristics of soil DOM were determined using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and soil microbial composition was identified by high-throughput sequencing. Among the seven components of DOM, the lignins/CRAM (carboxyl-rich alicyclic molecules)-like structure dominated at all elevations, followed by tannins, while the relative abundance of unstable substances, including lipids, aliphatic/protein, and carbohydrates, was lower. As elevation increased, the molecular diversity, degree of oxidation, aromaticity, and unsaturation of soil DOM decreased. The abundance and diversity of soil bacteria and fungi also generally decreased with elevation. Both bacteria and fungi play an important role in the degradation of DOM molecules, but bacteria appear to have greater degradation ability. Among them, Proteobacteria and Bacteroidetes mainly promote the degradation of lignins/CRAM-like structure molecules, while Basidiomycota mainly degrade more unstable substrates. Co-occurrence network analysis revealed complex correlations between specific microbial groups and DOM molecules. Our results suggest that more active cycling of soil DOM could occur in alpine ecosystems due to climate warming, as the result of increased vegetation productivity and litter input in response to rising temperature promoting the relative abundance of microbial groups capable of degrading lignins/CRAM-like structures in soil DOM.
Collapse
Affiliation(s)
- Yanlin Zhang
- Forestry College, Fujian Agriculture and Forestry University, National Positioning Observation Research Station of Red Earth Hilly Ecosystem in Changting, Fujian, 350002, Fujian Province, China
| | - Kate V Heal
- School of GeoSciences, The University of Edinburgh, Crew Building, Alexander Crum Brown Road, Edinburgh EH9 3FF, UK
| | - Mengjie Shi
- Forestry College, Fujian Agriculture and Forestry University, National Positioning Observation Research Station of Red Earth Hilly Ecosystem in Changting, Fujian, 350002, Fujian Province, China
| | - Wenxin Chen
- Forestry College, Fujian Agriculture and Forestry University, National Positioning Observation Research Station of Red Earth Hilly Ecosystem in Changting, Fujian, 350002, Fujian Province, China
| | - Chuifan Zhou
- Forestry College, Fujian Agriculture and Forestry University, National Positioning Observation Research Station of Red Earth Hilly Ecosystem in Changting, Fujian, 350002, Fujian Province, China.
| |
Collapse
|
31
|
Yang J, Han M, Zhao Z, Han J, Zhang X, Xie Z, Jiang H. Microbial response to multiple-level addition of grass organic matter in lake sediments with different salinity. FEMS Microbiol Ecol 2022; 98:6568899. [DOI: 10.1093/femsec/fiac046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/05/2022] [Accepted: 04/12/2022] [Indexed: 11/12/2022] Open
Abstract
ABSTRACT
Water surface expansion of saline lakes usually causes the inundation of surrounding grassland, leading to the increase of terrestrial grass organic matter (OM) input to the lakes and the decrease of lake salinity. However, the influence of terrestrial grass OM input increase and salinity decrease on organic carbon mineralization and microbial community composition remains unknown in saline lakes. Here, microbial mineralization of terrestrial grass (Achnatherum splendens) OM at different quantity levels in lake sediments with different salinity was investigated by performing microcosm experiments. The results showed that the CO2 production rates increased with the increase of grass OM supply in the studied sediments with different salinity, which may be driven by certain microbial groups (e.g., Bacteroidota, Firmicutes and Ascomycota). The increase of grass OM supply reduced the richness of prokaryotic community, which will decrease the size and complexity of the studied microbial networks, but increase the interaction between prokaryotic and fungal taxa. Taken together, our results suggest that the increase of terrestrial grass OM input caused by lake expansion would enhance the mineralization of organic carbon and affect the community composition and interactions of related microorganisms in lake sediments with different salinity.
Collapse
Affiliation(s)
- Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Mingxian Han
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Zhuoli Zhao
- School of Ocean Sciences, China University of Geosciences, Beijing, 100083, China
| | - Jinbin Han
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China
| | - Xiying Zhang
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China
| | - Zhanling Xie
- College of Ecology-Environment Engineering, Qinghai University, Xining, 810016, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China
| |
Collapse
|
32
|
Haq IU, Hillmann B, Moran M, Willard S, Knights D, Fixen KR, Schilling JS. Bacterial communities associated with wood rot fungi that use distinct decomposition mechanisms. ISME COMMUNICATIONS 2022; 2:26. [PMID: 37938255 PMCID: PMC9723729 DOI: 10.1038/s43705-022-00108-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 05/11/2023]
Abstract
Wood decomposer fungi are grouped by how they extract sugars from lignocellulose. Brown rot fungi selectively degrade cellulose and hemicellulose, leaving lignin intact, and white rot fungi degrade all components. Many trees are susceptible to both rot types, giving carbon in Earth's woody biomass, specifically lignin, a flexible fate that is affected not only by the fungal decomposition mechanism but also the associated microbial community. However, little is understood about how rot type may influence the microbial community in decaying wood. In this study, we quantified bacterial communities associated with Fomes fomentarius (white rot) and Fomitopsis betulina (brown rot) found on a shared tree host species, birch (Betula papyrifera). We collected 25 wood samples beneath sporocarps of F. fomentarius (n = 13) and F. betulina (n = 12) on standing dead trees, and coupled microbial DNA sequencing with chemical signatures of rot type (pH and lignin removal). We found that bacterial communities for both fungi were dominated by Proteobacteria, a commonly reported association. However, rot type exerted significant influence on less abundant taxa in ways that align logically with fungal traits. Amplicon sequence variants (ASVs) were enriched in Firmicutes in white-rotted wood, and were enriched in Alphaproteobacteria, Actinobacteria and Acidobacteria in lower pH brown rot. Our results suggest that wood decomposer strategies may exert significant selection effects on bacteria, or vice versa, among less-abundant taxa that have been overlooked when using abundance as the only measure of influence.
Collapse
Affiliation(s)
- Irshad Ul Haq
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Molly Moran
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
| | - Samuel Willard
- Department of Life Sciences, Imperial College London, London, UK
| | - Dan Knights
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Kathryn R Fixen
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Jonathan S Schilling
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA.
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA.
| |
Collapse
|
33
|
Chen Z, Kumar A, Brookes PC, Kuzyakov Y, Luo Y, Xu J. Three source-partitioning of CO 2 fluxes based on a dual-isotope approach to investigate interactions between soil organic carbon, glucose and straw. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 811:152163. [PMID: 34875335 DOI: 10.1016/j.scitotenv.2021.152163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 11/23/2021] [Accepted: 11/29/2021] [Indexed: 06/13/2023]
Abstract
Inputs of available organic materials into soil alter the decomposition of soil organic matter (SOM), a process called priming effect. Organic carbon (C) inputs in terrestrial ecosystems are common from various sources (e.g. rhizodeposits, plant residues, microbial necromass) simultaneously, but their interactions as well as mutual effects on SOM decomposition are unknown because multisource partitioning of pools and fluxes was not available. A dual-isotope approach (identical materials except for straw being possessed two 13C abundances) was adopted to partition total CO2 emission from three C sources: SOM, glucose and straw. Cumulative CO2 efflux was quantified into straw-derived (558 μg C g-1), glucose-derived (480 μg C g-1) and SOM-derived (58 μg C g-1) CO2 during the first 7 days of incubation. Glucose or straw addition induced positive SOM priming, whereas glucose combined with straw resulted in higher SOC loss than that induced by single addition of glucose or straw after day 7. The Spearman's correlation showed that the interactions between glucose and straw shifted from increased CO2 evolved during their intensive decomposition (days 1 to 3) to mutual constraint on mineralization during the late stage (days 5 to 7). This study provides evidences for the suitability of the dual-isotope approach to partition multiple sources of CO2 fluxes and C pools, and evaluates their individual or mutual contributions to SOM priming, thus, implicating C sequestration in terrestrial ecosystems.
Collapse
Affiliation(s)
- Zhiyi Chen
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Amit Kumar
- Chair of Ecosystem Functioning and Services, Institute of Ecology, Leuphana University of Lüneburg, Universitätsallee 1, 21335 Lüneburg, Germany
| | - Philip C Brookes
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Goettingen, 37077 Goettingen, Germany; Agro-Technological Institute, RUDN University, 117198 Moscow, Russia
| | - Yu Luo
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China.
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
34
|
Gupta A, Singh UB, Sahu PK, Paul S, Kumar A, Malviya D, Singh S, Kuppusamy P, Singh P, Paul D, Rai JP, Singh HV, Manna MC, Crusberg TC, Kumar A, Saxena AK. Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19053141. [PMID: 35270832 DOI: 10.3390/ijerph190531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 05/28/2023]
Abstract
Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.
Collapse
Affiliation(s)
- Amrita Gupta
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Udai B Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Pramod K Sahu
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Surinder Paul
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Adarsh Kumar
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Deepti Malviya
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Shailendra Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Pandiyan Kuppusamy
- ICAR-Central Institute for Research on Cotton Technology, Ginning Training Centre, Nagpur 440023, India
| | - Prakash Singh
- Department of Plant Breeding and Genetics, Veer Kunwar Singh College of Agriculture, Bihar Agricultural University, Dumraon 802136, India
| | - Diby Paul
- Pilgram Marpeck School of Science, Technology, Engineering and Mathematics, Truett McConnel University, 100 Alumni Dr., Cleveland, GA 30528, USA
| | - Jai P Rai
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Harsh V Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Madhab C Manna
- Soil Biology Division, ICAR-Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal 462038, India
| | - Theodore C Crusberg
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA
| | - Arun Kumar
- Department of Agronomy, Bihar Agricultural University, Sabour, Bhagalpur 813210, India
| | - Anil K Saxena
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| |
Collapse
|
35
|
Gupta A, Singh UB, Sahu PK, Paul S, Kumar A, Malviya D, Singh S, Kuppusamy P, Singh P, Paul D, Rai JP, Singh HV, Manna MC, Crusberg TC, Kumar A, Saxena AK. Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:3141. [PMID: 35270832 PMCID: PMC8910389 DOI: 10.3390/ijerph19053141] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 12/01/2022]
Abstract
Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.
Collapse
Affiliation(s)
- Amrita Gupta
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Udai B. Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Pramod K. Sahu
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Surinder Paul
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Adarsh Kumar
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Deepti Malviya
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Shailendra Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Pandiyan Kuppusamy
- ICAR-Central Institute for Research on Cotton Technology, Ginning Training Centre, Nagpur 440023, India;
| | - Prakash Singh
- Department of Plant Breeding and Genetics, Veer Kunwar Singh College of Agriculture, Bihar Agricultural University, Dumraon 802136, India;
| | - Diby Paul
- Pilgram Marpeck School of Science, Technology, Engineering and Mathematics, Truett McConnel University, 100 Alumni Dr., Cleveland, GA 30528, USA;
| | - Jai P. Rai
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Harsh V. Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Madhab C. Manna
- Soil Biology Division, ICAR-Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal 462038, India;
| | - Theodore C. Crusberg
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA;
| | - Arun Kumar
- Department of Agronomy, Bihar Agricultural University, Sabour, Bhagalpur 813210, India;
| | - Anil K. Saxena
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| |
Collapse
|
36
|
Siles JA, Díaz-López M, Vera A, Eisenhauer N, Guerra CA, Smith LC, Buscot F, Reitz T, Breitkreuz C, van den Hoogen J, Crowther TW, Orgiazzi A, Kuzyakov Y, Delgado-Baquerizo M, Bastida F. Priming effects in soils across Europe. GLOBAL CHANGE BIOLOGY 2022; 28:2146-2157. [PMID: 34984772 DOI: 10.1111/gcb.16062] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Land use is a key factor driving changes in soil carbon (C) cycle and contents worldwide. The priming effect (PE)-CO2 emissions from changed soil organic matter decomposition in response to fresh C inputs-is one of the most unpredictable phenomena associated with C cycling and related nutrient mobilization. Yet, we know very little about the influence of land use on soil PE across contrasting environments. Here, we conducted a continental-scale study to (i) determine the PE induced by 13 C-glucose additions to 126 cropland and seminatural (forests and grasslands) soils from 22 European countries; (ii) compare PE magnitude in soils under various crop types (i.e., cereals, nonpermanent industrial crops, and orchards); and (iii) model the environmental factors influencing PE. On average, PEs were negative in seminatural (with values ranging between -60 and 26 µg C g-1 soil after 35 days of incubation; median = -11) and cropland (from -55 to 27 µC g-1 soil; median = -4.3) soils, meaning that microbial communities preferentially switched from soil organic C decomposition to glucose mineralization. PE was significantly less negative in croplands compared with seminatural ecosystems and not influenced by the crop type. PE was driven by soil basal respiration (reflecting microbial activity), microbial biomass C, and soil organic C, which were all higher in seminatural ecosystems compared with croplands. This cross European experimental and modeling study elucidated that PE intensity is dependent on land use and allowed to clarify the factors regulating this important C cycling process.
Collapse
Affiliation(s)
- José A Siles
- Department of Soil and Water Conservation and Waste Management, CEBAS-CSIC, Murcia, Spain
| | - Marta Díaz-López
- Department of Soil and Water Conservation and Waste Management, CEBAS-CSIC, Murcia, Spain
| | - Alfonso Vera
- Department of Soil and Water Conservation and Waste Management, CEBAS-CSIC, Murcia, Spain
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Carlos A Guerra
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Martin Luther University Halle Wittenberg, Halle (Saale), Germany
| | - Linnea C Smith
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Martin Luther University Halle Wittenberg, Halle (Saale), Germany
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Martin Luther University Halle Wittenberg, Halle (Saale), Germany
- Soil Ecology Department, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
| | - Thomas Reitz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Soil Ecology Department, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
| | - Claudia Breitkreuz
- Soil Ecology Department, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
| | - Johan van den Hoogen
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, Zurich, Switzerland
| | - Thomas W Crowther
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, Zurich, Switzerland
| | | | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems and Department of Agricultural Soil Science, University of Gottingen, Gottingen, Germany
- Agro-Technological Institute, RUDN University, Moscow, Russia
- Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia
| | - Manuel Delgado-Baquerizo
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Sevilla, Spain
| | - Felipe Bastida
- Department of Soil and Water Conservation and Waste Management, CEBAS-CSIC, Murcia, Spain
| |
Collapse
|
37
|
Thomson T, Fusi M, Bennett-Smith MF, Prinz N, Aylagas E, Carvalho S, Lovelock CE, Jones BH, Ellis JI. Contrasting Effects of Local Environmental and Biogeographic Factors on the Composition and Structure of Bacterial Communities in Arid Monospecific Mangrove Soils. Microbiol Spectr 2022; 10:e0090321. [PMID: 34985338 PMCID: PMC8729789 DOI: 10.1128/spectrum.00903-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/11/2021] [Indexed: 12/23/2022] Open
Abstract
Mangrove forests are important biotic sinks of atmospheric CO2 and play an integral role in nutrient-cycling and decontamination of coastal waters, thereby mitigating climatic and anthropogenic stressors. These services are primarily regulated by the activity of the soil microbiome. To understand how environmental changes may affect this vital part of the ecosystem, it is key to understand the patterns that drive microbial community assembly in mangrove forest soils. High-throughput amplicon sequencing (16S rRNA) was applied on samples from arid Avicennia marina forests across different spatial scales from local to regional. Alongside conventional analyses of community ecology, microbial co-occurrence networks were assessed to investigate differences in composition and structure of the bacterial community. The bacterial community composition varied more strongly along an intertidal gradient within each mangrove forest, than between forests in different geographic regions (Australia/Saudi Arabia). In contrast, co-occurrence networks differed primarily between geographic regions, illustrating that the structure of the bacterial community is not necessarily linked to its composition. The local diversity in mangrove forest soils may have important implications for the quantification of biogeochemical processes and is important to consider when planning restoration activities. IMPORTANCE Mangrove ecosystems are increasingly being recognized for their potential to sequester atmospheric carbon, thereby mitigating the effects of anthropogenically driven greenhouse gas emissions. The bacterial community in the soils plays an important role in the breakdown and recycling of carbon and other nutrients. To assess and predict changes in carbon storage, it is important to understand how the bacterial community is shaped by its environment. Here, we compared the bacterial communities of mangrove forests on different spatial scales, from local within-forest to biogeographic comparisons. The bacterial community composition differed more between distinct intertidal zones of the same forest than between forests in distant geographic regions. The calculated network structure of theoretically interacting bacteria, however, differed most between the geographic regions. Our findings highlight the importance of local environmental factors in shaping the microbial soil community in mangroves and highlight a disconnect between community composition and structure in microbial soil assemblages.
Collapse
Affiliation(s)
- T. Thomson
- University of Waikato, School of Science, Tauranga, New Zealand
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - M. Fusi
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - M. F. Bennett-Smith
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - N. Prinz
- University of Waikato, School of Science, Tauranga, New Zealand
| | - E. Aylagas
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - S. Carvalho
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - C. E. Lovelock
- School of Biological Sciences, The University of Queensland, St Lucida, Australia
| | - B. H. Jones
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - J. I. Ellis
- University of Waikato, School of Science, Tauranga, New Zealand
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| |
Collapse
|
38
|
Xue W, Cao S, Zhu J, Li W, Li J, Huang D, Wang R, Gao Y. Stabilization of cadmium in contaminated sediment based on a nanoremediation strategy: Environmental impacts and mechanisms. CHEMOSPHERE 2022; 287:132363. [PMID: 34826961 DOI: 10.1016/j.chemosphere.2021.132363] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/14/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Nanomaterials have great application potential for the remediation of heavy metal contaminated sediments, but their environmental impacts are still limited. Herein, graphene oxide-supported nanoscale zero-valent iron (GNZVI) was synthesized to explore its role in mediating the immobilization of cadmium (Cd) from contaminated river sediments, with the consideration of the potential impacts on sediment enzyme activities and bacterial community. Compared to NZVI and GO, GNZVI could more effectively promote the transformation of mobile Cd into stable speciation with a maximum residual percentage increasing by 64.82% after 56 days of treatment. The activities of urease, catalase and sucrase were gradually increased and stabilized with the prolongation of treatment time, indicating that the metabolic function of sediments was recovered. 16 S rRNA gene sequencing results confirmed that the application of GNZVI increased the abundance of some Fe(III)-reducing bacteria, further stimulating the bioavailability of organic matter. Additionally, the properties of GO were gradually changed via microbial reduction and finally showed similar properties to rGO. The critical role of rGO as an electrical conductor was to promote the electron transfer process of microbial Fe(III) mineral reduction, which redistributes part of the Fe(III) mineral-associated Cd to more stable secondary iron minerals, thereby further improving the stabilization efficiency of r-GNZVI for Cd.
Collapse
Affiliation(s)
- Wenjing Xue
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225009, PR China.
| | - Shan Cao
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225009, PR China
| | - Jing Zhu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225009, PR China
| | - Wanyao Li
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225009, PR China
| | - Jun Li
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225009, PR China
| | - Danlian Huang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China.
| | - Rongzhong Wang
- School of Resource & Environment and Safety Engineering, University of South China, Heng yang, 421001, PR China
| | - Yang Gao
- School of Hydraulic Engineering, Changsha University of Science & Technology, Changsha, 410114, PR China
| |
Collapse
|
39
|
Blagodatskaya E, Tarkka M, Knief C, Koller R, Peth S, Schmidt V, Spielvogel S, Uteau D, Weber M, Razavi BS. Bridging Microbial Functional Traits With Localized Process Rates at Soil Interfaces. Front Microbiol 2021; 12:625697. [PMID: 34777265 PMCID: PMC8581545 DOI: 10.3389/fmicb.2021.625697] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 09/01/2021] [Indexed: 12/30/2022] Open
Abstract
In this review, we introduce microbially-mediated soil processes, players, their functional traits, and their links to processes at biogeochemical interfaces [e.g., rhizosphere, detritusphere, (bio)-pores, and aggregate surfaces]. A conceptual view emphasizes the central role of the rhizosphere in interactions with other biogeochemical interfaces, considering biotic and abiotic dynamic drivers. We discuss the applicability of three groups of traits based on microbial physiology, activity state, and genomic functional traits to reflect microbial growth in soil. The sensitivity and credibility of modern molecular approaches to estimate microbial-specific growth rates require further development. A link between functional traits determined by physiological (e.g., respiration, biomarkers) and genomic (e.g., genome size, number of ribosomal gene copies per genome, expression of catabolic versus biosynthetic genes) approaches is strongly affected by environmental conditions such as carbon, nutrient availability, and ecosystem type. Therefore, we address the role of soil physico-chemical conditions and trophic interactions as drivers of microbially-mediated soil processes at relevant scales for process localization. The strengths and weaknesses of current approaches (destructive, non-destructive, and predictive) for assessing process localization and the corresponding estimates of process rates are linked to the challenges for modeling microbially-mediated processes in heterogeneous soil microhabitats. Finally, we introduce a conceptual self-regulatory mechanism based on the flexible structure of active microbial communities. Microbial taxa best suited to each successional stage of substrate decomposition become dominant and alter the community structure. The rates of decomposition of organic compounds, therefore, are dependent on the functional traits of dominant taxa and microbial strategies, which are selected and driven by the local environment.
Collapse
Affiliation(s)
- Evgenia Blagodatskaya
- Department of Soil Ecology, Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- Agro-Technological Institute, RUDN University, Moscow, Russia
| | - Mika Tarkka
- Department of Soil Ecology, Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research Halle–Jena–Leipzig, Leipzig, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Robert Koller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Stephan Peth
- Institute of Soil Science, University of Hannover, Hanover, Germany
| | | | - Sandra Spielvogel
- Department Soil Science, Institute for Plant Nutrition and Soil Science, Christian-Albrechts University Kiel, Kiel, Germany
| | - Daniel Uteau
- Department of Soil Science, Faculty of Organic Agricultural Sciences, University of Kassel, Kassel, Germany
| | | | - Bahar S. Razavi
- Department of Soil and Plant Microbiome, Institute of Phytopathology, Christian-Albrechts-University of Kiel, Kiel, Germany
| |
Collapse
|
40
|
Yang H, Li Y, Wang S, Zhan J, Ning Z, Han D. The Response of Critical Microbial Taxa to Litter Micro-Nutrients and Macro-Chemistry Determined the Agricultural Soil Priming Intensity After Afforestation. Front Microbiol 2021; 12:730117. [PMID: 34603260 PMCID: PMC8481769 DOI: 10.3389/fmicb.2021.730117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/27/2021] [Indexed: 11/13/2022] Open
Abstract
Afforestation with trees and shrubs around cropland can effectively decrease soil degradation and avoid sand storms, but subsequent modification of litter quality accelerates the degradation of native organic matter via the soil priming effect (PE). Although carbon accumulation in agricultural soils after afforestation was widely studied, little is known about the extent to which soil organic carbon (SOC) mineralization is induced by complex residue input in agro-forest-grass composite ecosystems. Here, we mixed corn field soil and litter of afforestation tree and shrub species together in a micro-environment to quantify the effects of litter-mixture input on farmland soil priming associated with afforestation. Additionally, we studied the responses of bacterial and fungal species to litter chemistry, with the aim to identify the litter and microbial driver of soil priming. The results showed that soil priming was accelerated by different litter addition which varied from 24 to 74% of SOC mineralization, suggesting that priming intensity was relatively flexible and highly affected by litter quality. We also find that the macro-chemistry (including litter carbon, nitrogen, lignin, and cellulose) directly affects priming intensity, while micro-chemistry (including litter soluble sugar, water-soluble phenol, methanol-soluble phenol, and condensed tannin) indirectly influences priming via alteration to dominant bacterial taxa. The stepwise regression analysis suggested that litter nitrogen and cellulose were the critical litter drivers to soil priming (r 2 = 0.279), and the combination of bacterial phylum Proteobacteria, Firmicutes, Bacteroidetes, Acidobacteria, and fungal taxa Eurotiomycetes was a great model to explain the priming intensity (r 2 = 0.407).
Collapse
Affiliation(s)
- Hongling Yang
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yulin Li
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China
| | - Shaokun Wang
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China
- Urat Desert-Grassland Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China
| | - Jin Zhan
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China
| | - Zhiying Ning
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Dan Han
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
41
|
Tian Q, Jiang Y, Tang Y, Wu Y, Tang Z, Liu F. Soil pH and Organic Carbon Properties Drive Soil Bacterial Communities in Surface and Deep Layers Along an Elevational Gradient. Front Microbiol 2021; 12:646124. [PMID: 34394018 PMCID: PMC8363232 DOI: 10.3389/fmicb.2021.646124] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Abstract
Elevational gradients strongly affect the spatial distribution and structure of soil bacterial communities. However, our understanding of the effects and determining factors is still limited, especially in the deep soil layer. Here, we investigated the diversity and composition of soil bacterial communities in different soil layers along a 1,500-m elevational gradient in the Taibai Mountain. The variables associated with climate conditions, plant communities, and soil properties were analyzed to assess their contributions to the variations in bacterial communities. Soil bacterial richness and α-diversity showed a hump-shaped trend with elevation in both surface and deep layers. In the surface layer, pH was the main factor driving the elevational pattern in bacterial diversity, while in the deep layer, pH and soil carbon (C) availability were the two main predictors. Bacterial community composition differed significantly along the elevational gradient in all soil layers. In the surface layer, Acidobacteria, Delta-proteobacteria, and Planctomycetes were significantly more abundant in the lower elevation sites than in the higher elevation sites; and Gemmatimonadetes, Chloroflexi, and Beta-proteobacteria were more abundant in the higher elevation sites. In the deep layer, AD3 was most abundant in the highest elevation site. The elevational pattern of community composition co-varied with mean annual temperature, mean annual precipitation, diversity and basal area of trees, pH, soil C availability, and soil C fractions. Statistical results showed that pH was the main driver of the elevational pattern of the bacterial community composition in the surface soil layer, while soil C fractions contributed more to the variance of the bacterial composition in the deep soil layer. These results indicated that changes in soil bacterial communities along the elevational gradient were driven by soil properties in both surface and deep soil layers, which are critical for predicting ecosystem functions under future climate change scenarios.
Collapse
Affiliation(s)
- Qiuxiang Tian
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Ying Jiang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yanan Tang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu Wu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhiyao Tang
- Key Laboratory for Earth Surface Processes, Department of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Feng Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
42
|
Mesocosm Experiments Reveal Global Warming Accelerates Macrophytes Litter Decomposition and Alters Decomposition-Related Bacteria Community Structure. WATER 2021. [DOI: 10.3390/w13141940] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Global climate change scenarios predict that lake water temperatures will increase up to 4 °C and extreme weather events, such as heat waves and large temperature fluctuations, will occur more frequently. Such changes may result in the increase of aquatic litter decomposition and on shifts in diversity and structure of bacteria communities in this period. We designed a two-month mesocosm experiment to explore how constant (+4 °C than ambient temperature) and variable (randomly +0~8 °C than ambient temperature) warming treatment will affect the submerged macrophyte litter decomposition process. Our data suggests that warming treatments may accelerate the decomposition of submerged macrophyte litter in shallow lake ecosystems, and increase the diversity of decomposition-related bacteria with community composition changed the relative abundance of Proteobacteria, especially members of Alphaproteobacteria increased while that of Firmicutes (mainly Bacillus) decreased.
Collapse
|
43
|
Rocha FI, Ribeiro TG, Fontes MA, Schwab S, Coelho MRR, Lumbreras JF, da Motta PEF, Teixeira WG, Cole J, Borsanelli AC, Dutra IDS, Howe A, de Oliveira AP, Jesus EDC. Land-Use System and Forest Floor Explain Prokaryotic Metacommunity Structuring and Spatial Turnover in Amazonian Forest-to-Pasture Conversion Areas. Front Microbiol 2021; 12:657508. [PMID: 33967996 PMCID: PMC8097146 DOI: 10.3389/fmicb.2021.657508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/29/2021] [Indexed: 01/04/2023] Open
Abstract
Advancing extensive cattle production is a major threat to biodiversity conservation in Amazonia. The dominant vegetation cover has a drastic impact on soil microbial communities, affecting their composition, structure, and ecological services. Herein, we explored relationships between land-use, soil types, and forest floor compartments on the prokaryotic metacommunity structuring in Western Amazonia. Soil samples were taken in sites under high anthropogenic pressure and distributed along a ±800 km gradient. Additionally, the litter and a root layer, characteristic of the forest environment, were sampled. DNA was extracted, and metacommunity composition and structure were assessed through 16S rRNA gene sequencing. Prokaryotic metacommunities in the bulk soil were strongly affected by pH, base and aluminum saturation, Ca + Mg concentration, the sum of bases, and silt percentage, due to land-use management and natural differences among the soil types. Higher alpha, beta, and gamma diversities were observed in sites with higher soil pH and fertility, such as pasture soils or fertile soils of the state of Acre. When taking litter and root layer communities into account, the beta diversity was significantly higher in the forest floor than in pasture bulk soil for all study regions. Our results show that the forest floor's prokaryotic metacommunity performs a spatial turnover hitherto underestimated to the regional scale of diversity.
Collapse
Affiliation(s)
- Fernando Igne Rocha
- Department of Soil, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | | | | | - Stefan Schwab
- National Agrobiology Research Center, Embrapa Agrobiologia, Seropédica, Brazil
| | | | | | | | | | - James Cole
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | | | - Iveraldo dos Santos Dutra
- Department of Support, Production and Animal Health, Universidade Estadual Paulista, Araçatuba, Brazil
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | | | | |
Collapse
|
44
|
Koné AW, Yao MK. Soil microbial functioning and organic carbon storage: can complex timber tree stands mimic natural forests? JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 283:112002. [PMID: 33516096 DOI: 10.1016/j.jenvman.2021.112002] [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: 09/07/2020] [Revised: 01/11/2021] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
Conversion of natural forest to anthropogenic land use systems (LUS) often leads to considerable loss of carbon, however, proper management of these LUS may reverse the trend. A study was conducted in a semi-deciduous forest zone of Côte d'Ivoire to assess soil microbial functioning and soil organic carbon (SOC) stocks in varying tree stands, and to determine whether complex tree stands can mimic the natural forest in terms of these soil attributes. Tree plantations studied were monocultures of teak (Tectona grandis) and full-sun cocoa (Theobroma cacao L.), and a mixture of four tree species (MTS) with Tectona grandis, Gmelina arborea, Terminalia ivoriensis and Terminalia superba. An adjacent natural forest was considered as the reference. Each of these LUS had five replicate stands where soil (0-10 cm depth) samples were taken for physico-chemical parameters and microbial biomass-C (MBC), microbial activities, MBC/SOC ratio and metabolic quotient (qCO2). SOC and total N stocks were also calculated. The C mineralization rate (mg C-CO2 kg-1) and mineral N concentration (mg kg-1) drastically declined in the monocultures of cocoa (154.9 ± 29.3 and 49.8 ± 9.8, respectively) and teak (179.6 ± 27.1 and 54.1 ± 7.3) compared to the natural forest (258.4 ± 21.9 and 108.7 ± 12). However, values in MTS (194.7 ± 24.6 and 105.4 ± 7.4) were not significantly different from those in the natural forest. Similarly, SOC stocks in MTS (28.8 ± 1.9 Mg ha-1) were not significantly different from those recorded in the natural forest (32.9 ± 1.7 Mg ha-1) whereas teak (25.4 ± 1.7 Mg ha-1) and cocoa (23.1 ± 3.4 Mg ha-1) exhibited significantly lower values. Despite the acidic soil and recalcitrant litter conditions, increased MBC/SOC ratio and decreased qCO2 were recorded in the monocrops, suggesting a probable increase in the fungi/bacteria ratio. The complex MTS stand was found to mimic the natural forest in terms of soil microbial activity and organic status, due to the provision of a diversity of litter quality, which may serve as a basis for developing a climate smart timber system in West and Central Africa.
Collapse
Affiliation(s)
- Armand W Koné
- UR Gestion Durable des Sols, Pôle de Recherche Environnement et Développement Durable, UFR Sciences de la Nature, Université Nangui Abrogoua, 02 BP 801, Abidjan 02, Cote d'Ivoire.
| | - Michel K Yao
- UR Gestion Durable des Sols, Pôle de Recherche Environnement et Développement Durable, UFR Sciences et Gestion de l'Environnement, Université Nangui Abrogoua, 02 BP 801, Cote d'Ivoire
| |
Collapse
|
45
|
Delitte M, Caulier S, Bragard C, Desoignies N. Plant Microbiota Beyond Farming Practices: A Review. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.624203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Plants have always grown and evolved surrounded by numerous microorganisms that inhabit their environment, later termed microbiota. To enhance food production, humankind has relied on various farming practices such as irrigation, tilling, fertilization, and pest and disease management. Over the past few years, studies have highlighted the impacts of such practices, not only in terms of plant health or yields but also on the microbial communities associated with plants, which have been investigated through microbiome studies. Because some microorganisms exert beneficial traits that improve plant growth and health, understanding how to modulate microbial communities will help in developing smart farming and favor plant growth-promoting (PGP) microorganisms. With tremendous cost cuts in NGS technologies, metagenomic approaches are now affordable and have been widely used to investigate crop-associated microbiomes. Being able to engineer microbial communities in ways that benefit crop health and growth will help decrease the number of chemical inputs required. Against this background, this review explores the impacts of agricultural practices on soil- and plant-associated microbiomes, focusing on plant growth-promoting microorganisms from a metagenomic perspective.
Collapse
|
46
|
Chiba A, Uchida Y, Kublik S, Vestergaard G, Buegger F, Schloter M, Schulz S. Soil Bacterial Diversity Is Positively Correlated with Decomposition Rates during Early Phases of Maize Litter Decomposition. Microorganisms 2021; 9:microorganisms9020357. [PMID: 33670245 PMCID: PMC7916959 DOI: 10.3390/microorganisms9020357] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/16/2022] Open
Abstract
This study aimed to investigate the effects of different levels of soil- and plant-associated bacterial diversity on the rates of litter decomposition, and bacterial community dynamics during its early phases. We performed an incubation experiment where soil bacterial diversity (but not abundance) was manipulated by autoclaving and reinoculation. Natural or autoclaved maize leaves were applied to the soils and incubated for 6 weeks. Bacterial diversity was assessed before and during litter decomposition using 16S rRNA gene metabarcoding. We found a positive correlation between litter decomposition rates and soil bacterial diversity. The soil with the highest bacterial diversity was dominated by oligotrophic bacteria including Acidobacteria, Nitrospiraceae, and Gaiellaceae, and its community composition did not change during the incubation. In the less diverse soils, those taxa were absent but were replaced by copiotrophic bacteria, such as Caulobacteraceae and Beijerinckiaceae, until the end of the incubation period. SourceTracker analysis revealed that litter-associated bacteria, such as Beijerinckiaceae, only became part of the bacterial communities in the less diverse soils. This suggests a pivotal role of oligotrophic bacteria during the early phases of litter decomposition and the predominance of copiotrophic bacteria at low diversity.
Collapse
Affiliation(s)
- Akane Chiba
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (A.C.); (Y.U.)
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Crop Physiology, TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
| | - Yoshitaka Uchida
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (A.C.); (Y.U.)
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Section of Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Franz Buegger
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany;
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Correspondence: ; Tel.: +49-(0)89-3187-3054
| |
Collapse
|
47
|
Tan B, Li Y, Liu T, Tan X, He Y, You X, Leong KH, Liu C, Li L. Response of Plant Rhizosphere Microenvironment to Water Management in Soil- and Substrate-Based Controlled Environment Agriculture (CEA) Systems: A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:691651. [PMID: 34456936 PMCID: PMC8385539 DOI: 10.3389/fpls.2021.691651] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/16/2021] [Indexed: 05/06/2023]
Abstract
As natural agroecology deteriorates, controlled environment agriculture (CEA) systems become the backup support for coping with future resource consumption and potential food crises. Compared with natural agroecology, most of the environmental parameters of the CEA system rely on manual management. Such a system is dependent and fragile and prone to degradation, which includes harmful bacteria proliferation and productivity decline. Proper water management is significant for constructing a stabilized rhizosphere microenvironment. It has been proved that water is an efficient tool for changing the availability of nutrients, plant physiological processes, and microbial communities within. However, for CEA issues, relevant research is lacking at present. The article reviews the interactive mechanism between water management and rhizosphere microenvironments from the perspectives of physicochemical properties, physiological processes, and microbiology in CEA systems. We presented a synthesis of relevant research on water-root-microbes interplay, which aimed to provide detailed references to the conceptualization, research, diagnosis, and troubleshooting for CEA systems, and attempted to give suggestions for the construction of a high-tech artificial agricultural ecology.
Collapse
Affiliation(s)
- Bo Tan
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Yihan Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Tiegang Liu
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Xiao Tan
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Yuxin He
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Xueji You
- Department of Hydraulic Engineering, College of Civil Engineering, Tongji University, Shanghai, China
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Kah Hon Leong
- Department of Environmental Engineering, Faculty of Engineering and Green Technology, Universiti Tunku Abdul Rahman, Kampar, Malaysia
| | - Chao Liu
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
- *Correspondence: Chao Liu,
| | - Longguo Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
- Longguo Li,
| |
Collapse
|
48
|
Yu J, Pavia MJ, Deem LM, Crow SE, Deenik JL, Penton CR. DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil. Front Microbiol 2020; 11:587972. [PMID: 33329461 PMCID: PMC7717982 DOI: 10.3389/fmicb.2020.587972] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/08/2020] [Indexed: 12/03/2022] Open
Abstract
The functions and interactions of individual microbial populations and their genes in agricultural soils amended with biochar remain elusive but are crucial for a deeper understanding of nutrient cycling and carbon (C) sequestration. In this study, we coupled DNA stable isotope probing (SIP) with shotgun metagenomics in order to target the active community in microcosms which contained soil collected from biochar-amended and control plots under napiergrass cultivation. Our analyses revealed that the active community was composed of high-abundant and low-abundant populations, including Actinobacteria, Proteobacteria, Gemmatimonadetes, and Acidobacteria. Although biochar did not significantly shift the active taxonomic and functional communities, we found that the narG (nitrate reductase) gene was significantly more abundant in the control metagenomes. Interestingly, putative denitrifier genomes generally encoded one gene or a partial denitrification pathway, suggesting denitrification is typically carried out by an assembly of different populations within this Oxisol soil. Altogether, these findings indicate that the impact of biochar on the active soil microbial community are transient in nature. As such, the addition of biochar to soils appears to be a promising strategy for the long-term C sequestration in agricultural soils, does not impart lasting effects on the microbial functional community, and thus mitigates un-intended microbial community shifts that may lead to fertilizer loss through increased N cycling.
Collapse
Affiliation(s)
- Julian Yu
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Michael J Pavia
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States.,Swette Center for Environmental Biotechnology, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Lauren M Deem
- Natural Resources and Environmental Management, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Susan E Crow
- Natural Resources and Environmental Management, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Jonathan L Deenik
- Tropical Plant and Soil Sciences, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Christopher Ryan Penton
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States.,College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, United States
| |
Collapse
|
49
|
Kim N, Zabaloy MC, Riggins CW, Rodríguez-Zas S, Villamil MB. Microbial Shifts Following Five Years of Cover Cropping and Tillage Practices in Fertile Agroecosystems. Microorganisms 2020; 8:E1773. [PMID: 33187276 PMCID: PMC7696634 DOI: 10.3390/microorganisms8111773] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 01/02/2023] Open
Abstract
Metagenomics in agricultural research allows for searching for bioindicators of soil health to characterize changes caused by management practices. Cover cropping (CC) improves soil health by mitigating nutrient losses, yet the benefits depend on the tillage system used. Field studies searching for indicator taxa within these systems are scarce and narrow in their scope. Our goal was to identify bioindicators of soil health from microbes that were responsive to CC (three levels) and tillage (chisel tillage, no-till) treatments after five years under field conditions. We used rRNA gene-based analysis via Illumina HiSeq2500 technology with QIIME 2.0 processing to characterize the microbial communities. Our results indicated that CC and tillage differentially changed the relative abundances (RAs) of the copiotrophic and oligotrophic guilds. Corn-soybean rotations with legume-grass CC increased the RA of copiotrophic decomposers more than rotations with grass CC, whereas rotations with only bare fallows favored stress-tolerant oligotrophs, including nitrifiers and denitrifiers. Unlike bacteria, fewer indicator fungi and archaea were detected; fungi were poorly identified, and their responses were inconsistent, while the archaea RA increased under bare fallow treatments. This is primary information that allows for understanding the potential for managing the soil community compositions using cover crops to reduce nutrient losses to the environment.
Collapse
Affiliation(s)
- Nakian Kim
- Department of Crop Sciences, University of Illinois, Turner Hall, 1102 S. Goodwin Ave., Urbana, IL 61801, USA; (N.K.); (C.W.R.)
| | - María C. Zabaloy
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Ave. de los Constituyentes s/n, Bahía Blanca 8000, Argentina;
| | - Chance W. Riggins
- Department of Crop Sciences, University of Illinois, Turner Hall, 1102 S. Goodwin Ave., Urbana, IL 61801, USA; (N.K.); (C.W.R.)
| | - Sandra Rodríguez-Zas
- Department of Animal Sciences, University of Illinois, 30 ASL, 127 W. Gregory Dr., Urbana, IL 61801, USA;
| | - María B. Villamil
- Department of Crop Sciences, University of Illinois, Turner Hall, 1102 S. Goodwin Ave., Urbana, IL 61801, USA; (N.K.); (C.W.R.)
| |
Collapse
|
50
|
Wang Y, Lian J, Shen H, Ni Y, Zhang R, Guo Y, Ye W. The effects of Bidens alba invasion on soil bacterial communities across different coastal ecosystem land-use types in southern China. PLoS One 2020; 15:e0238478. [PMID: 33112879 PMCID: PMC7592744 DOI: 10.1371/journal.pone.0238478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/17/2020] [Indexed: 12/21/2022] Open
Abstract
Environments in both biotic and abiotic ecosystems have been affected by the colonization of non-native flora. In this study, we examined the effect of Bidens alba invasion on different land-use types along a coastline in southern China. Bacterial communities in each site were determined using 16S rDNA sequencing, and soil physicochemical properties were analyzed using standard methods. Although our results indicated that B. alba invasion did not have a significant effect on the alpha diversity of bacteria, it caused significant differences in soil bacterial community composition between invaded and uninvaded soil across different land-use types. Beta diversity and several physicochemical properties in forest, orchard and waterfront environments were recorded to be more susceptible to B. alba invasion. A high proportion of the variation of bacterial communities can be explained by a combination of environmental variables, indicating that environmental selection rather than plant invasion is a more effective process in coastal microbial assemblages. By comparing topological roles of shared OTUs among invaded and uninvaded soil, keystone taxa in invaded soil were identified. Acidobacteria was the major phyla involved in the invasive process which could be driven by environmental selection. How key phyla react in our experiment should be verified by further studies.
Collapse
Affiliation(s)
- Yue Wang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Juyu Lian
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hao Shen
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yunlong Ni
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruyun Zhang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yun Guo
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wanhui Ye
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| |
Collapse
|