1
|
Zhang F, Gu Z, Wang H, Wang R, Qing J, Xu X, Baoyin T, Zhong L, Rui Y, Li FY. Short term grazing increased growing-season N 2O production and decreased its reduction potential by reducing the abundance and expression of nosZ clade II gene in a semi-arid steppe. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168361. [PMID: 37944603 DOI: 10.1016/j.scitotenv.2023.168361] [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: 05/20/2023] [Revised: 10/23/2023] [Accepted: 11/04/2023] [Indexed: 11/12/2023]
Abstract
Understanding nitrous oxide (N2O) production as well as reduction in response to grazing and mowing is essential for designing better management strategies to improve sustainability of grassland ecosystems. We evaluated how four years of grazing or mowing altered N2O production and reduction potential, gene abundance, and expression of microbial functional groups pertinent to N2O production in situ on a typical grassland in Inner Mongolia. In our study, we found that grazing dramatically raised soil ammonium (NH4+-N) and nitrate (NO3--N) concentrations, AOB gene abundance and potential of N2O production through nitrification (NN2O) and denitrification (DN2O) in summer, but lessened the expression of nosZ clade II gene in all seasons. Mowing had minor effect on soil inorganic nitrogen (N) concentrations. Mowing diminished the quantity of denitrification genes (narG and nosZ), expression of nosZ and nosZ clade II genes, and DN2O concentration. The expression and abundance of nosZ clade II gene were related to DN2. These results suggested that short-term grazing could enhance N2O production potential in peak growing season, while the reduction in abundance and expression of nosZ calde II gene might be an important contributor to the enhanced N2O production of semi-arid typical steppe grasslands.
Collapse
Affiliation(s)
- Feifan Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Zhibin Gu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Hongyue Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Ruying Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Jinwu Qing
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Xingliang Xu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources, Chinese Academy of Sciences, Beijing 100101, China
| | - Taogetao Baoyin
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology & Environment, Inner Mongolia University, Hohhot 010021, China
| | - Lei Zhong
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China.
| | - Yichao Rui
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Frank Yonghong Li
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology & Environment, Inner Mongolia University, Hohhot 010021, China
| |
Collapse
|
2
|
Liu C, Yue Y, Zheng S, Liu X, Pang L, Yang Z. Impacts of substrate properties and aquatic nutrient concentrations on the relative abundance of nitrifying/denitrifying genes and the associated microbes in epilithic biofilms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:120930-120944. [PMID: 37945964 DOI: 10.1007/s11356-023-30818-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 10/29/2023] [Indexed: 11/12/2023]
Abstract
Substrates like sand or gravels and aquatic nutrient concentrations of rivers are highly heterogeneous, influencing the abundance of functional genes in epilithic biofilms where nitrification-denitrification processes take place. To analyze how the relative abundance of nitrifying/denitrifying genes and the associated microbes changes with the physical properties of substrates and aquatic concentrations of nutrients, this paper utilized metagenomics to comprehensively characterize these functional genes (i.e., amoA, hao, and nxrB involved in nitrification, and napA, narG, nirS, norB, and nosZ associated with denitrification) from epilithic biofilms collected along the Shitingjiang River in Southwest China and further obtained the relative abundance of major nitrifiers and denitrifiers. The results show that substrate size most significantly affects the relative abundance of hao and norB by altering the hydrodynamic conditions. In sampling sites with high heterogeneity in substrate size distribution, the relative abundance of most denitrifying genes is also higher. The carbon-nitrogen ratio negatively correlates with the relative abundance of all the nitrifying genes, while ammonium, total inorganic carbon, and total organic carbon concentrations positively affect the relative abundance of amoA and nxrB. As to the relative abundance of nitrifiers and denitrifiers, mainly belonging to phyla Proteobacteria and Actinobacteria, substrate heterogeneity and the aquatic concentrations of nutrients have greater influences than substrate size. Also, the substrate heterogeneity exerted positive influence on functional species of Pseudogemmobacter bohemicus and Paracoccus zhejiangensis. Considering the genes' functions and the dominant species linked to denitrification, nitrous oxide is more likely to occur in rivers with higher heterogeneity and larger substrates.
Collapse
Affiliation(s)
- Caiqiong Liu
- State Key Laboratory of Water Resources Engineering and Management, Wuhan University, Wuhan, 430072, China
| | - Yao Yue
- State Key Laboratory of Water Resources Engineering and Management, Wuhan University, Wuhan, 430072, China
- Institute for Water-Carbon Cycles and Carbon Neutrality, Wuhan University, Wuhan, 430072, China
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Shan Zheng
- State Key Laboratory of Water Resources Engineering and Management, Wuhan University, Wuhan, 430072, China
| | - Xuna Liu
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, China
| | - Lina Pang
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, China
| | - Zhonghua Yang
- State Key Laboratory of Water Resources Engineering and Management, Wuhan University, Wuhan, 430072, China.
| |
Collapse
|
3
|
The Contribution of Nitrate Dissimilation to Nitrate Consumption in narG- and napA-Containing Nitrate Reducers with Various Oxygen and Nitrate Supplies. Microbiol Spectr 2022; 10:e0069522. [PMID: 36453888 PMCID: PMC9769761 DOI: 10.1128/spectrum.00695-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Nitrate reducers containing narG or napA play an important role in the nitrogen cycle, but little is known about their functional differentiations in relation to environmental changes. In this study, three types of nitrate reducers in the genus Pseudomonas, including strains containing narG (G type), napA (A type) and both narG and napA (GA type), were selected to explore their functional performances under varied nitrate and oxygen concentrations. Their growth characteristics, nitrate consumption, and dissimilatory nitrate-reducing activity were investigated. Growth and nitrate consumption of all three types of strains were generally promoted with increasing oxygen and nitrate concentrations. However, their dissimilatory nitrate-reducing activities were restricted by oxygen supply. When supplied with 0.25 mM KNO3, A-type strains showed a higher growth rate but lower activity of dissimilatory nitrate reduction (DNR) than G-type strains, regardless of oxygen concentration. However, when nitrate concentration increased to 0.75 mM or 5 mM, G-type strains displayed stronger capability of nitrate consumption and DNR than A-type strains under anaerobic conditions, whereas under oxygenated conditions, A-type strains exhibited higher growth and nitrate consumption but weaker DNR than G-type strains. The GA-type strains appeared similar to G type under anaerobic conditions but performed more similarly to A type in aerobic environments. In summary, the nitrate consumption of narG-containing nitrate reducers is mainly caused by DNR in both anaerobic and aerobic environments, while the large proportion of nitrate consumption in A-type nitrate reducers under the aerobic condition is attributed to the assimilation by cell growth. IMPORTANCE Nitrate reducers containing narG or napA are ubiquitous, but little is known about their functional performance in various environments. Our study provides an important clue that the nitrate consumption of narG-containing strains is mainly caused by dissimilatory reduction in the environments, while that of napA-containing nitrate reducers under anaerobic conditions is ascribed to nitrate dissimilation but under the aerobic condition is attributed to the assimilation by cell growth. This finding broadens the understanding of aerobic nitrate reduction in the nitrogen cycle and highlights the important role of narG-containing bacteria in nitrate reduction under aerobic conditions.
Collapse
|
4
|
Abrahão A, Marhan S, Boeddinghaus RS, Nawaz A, Wubet T, Hölzel N, Klaus VH, Kleinebecker T, Freitag M, Hamer U, Oliveira RS, Lambers H, Kandeler E. Microbial drivers of plant richness and productivity in a grassland restoration experiment along a gradient of land-use intensity. THE NEW PHYTOLOGIST 2022; 236:1936-1950. [PMID: 36128644 DOI: 10.1111/nph.18503] [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: 02/21/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Plant-soil feedbacks (PSFs) underlying grassland plant richness and productivity are typically coupled with nutrient availability; however, we lack understanding of how restoration measures to increase plant diversity might affect PSFs. We examined the roles of sward disturbance, seed addition and land-use intensity (LUI) on PSFs. We conducted a disturbance and seed addition experiment in 10 grasslands along a LUI gradient and characterized plant biomass and richness, soil microbial biomass, community composition and enzyme activities. Greater plant biomass at high LUI was related to a decrease in the fungal to bacterial ratios, indicating highly productive grasslands to be dominated by bacteria. Lower enzyme activity per microbial biomass at high plant species richness indicated a slower carbon (C) cycling. The relative abundance of fungal saprotrophs decreased, while pathogens increased with LUI and disturbance. Both fungal guilds were negatively associated with plant richness, indicating the mechanisms underlying PSFs depended on LUI. We show that LUI and disturbance affect fungal functional composition, which may feedback on plant species richness by impeding the establishment of pathogen-sensitive species. Therefore, we highlight the need to integrate LUI including its effects on PSFs when planning for practices that aim to optimize plant diversity and productivity.
Collapse
Affiliation(s)
- Anna Abrahão
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, 70599, Stuttgart, Germany
- Department of Biology, Science Center, Federal University of Ceará - UFC, Fortaleza, CE, 60440-900, Brazil
| | - Sven Marhan
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, 70599, Stuttgart, Germany
| | - Runa S Boeddinghaus
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, 70599, Stuttgart, Germany
- Landwirtschaftliches Technologiezentrum Augustenberg, 76227, Karlsruhe, Germany
| | - Ali Nawaz
- Department of Community Ecology, UFZ - Helmholtz Center for Environmental Research, 06120, Halle (Saale), Germany
- Department of Civil, Geo and Environmental Engineering, Technical University of Munich, Am Coulombwall 3, 85748, Garching, Germany
| | - Tesfaye Wubet
- Department of Community Ecology, UFZ - Helmholtz Center for Environmental Research, 06120, Halle (Saale), Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Norbert Hölzel
- Institute of Landscape Ecology, University of Münster, Heisenbergstr. 2, D-48149, Münster, Germany
| | - Valentin H Klaus
- Institute of Agricultural Sciences, ETH Zürich, Universitätstr. 2, 8092, Zürich, Switzerland
| | - Till Kleinebecker
- Institute of Landscape Ecology and Resources Management, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 26-32, D-35392, Gießen, Germany
- Center for International Development and Environmental Research (ZEU), Justus Liebig University Giessen, Senckenbergstrasse 3, 35390, Giessen, Germany
| | - Martin Freitag
- Institute of Landscape Ecology, University of Münster, Heisenbergstr. 2, D-48149, Münster, Germany
| | - Ute Hamer
- Institute of Landscape Ecology, University of Münster, Heisenbergstr. 2, D-48149, Münster, Germany
| | - Rafael S Oliveira
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, 13083-970, Campinas, Brazil
| | - Hans Lambers
- School of Biological Sciences, University of Western Australia, Crawley, Perth, WA, 6009, Australia
| | - Ellen Kandeler
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, 70599, Stuttgart, Germany
| |
Collapse
|
5
|
Indigenous microbial populations of abandoned mining sites and their role in natural attenuation. Arch Microbiol 2022; 204:251. [PMID: 35411412 DOI: 10.1007/s00203-022-02861-6] [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: 07/23/2021] [Revised: 03/17/2022] [Accepted: 03/20/2022] [Indexed: 11/02/2022]
Abstract
Environmental contamination by toxic effluents discharged by anthropogenic activities including the mining industries has increased extensively in the recent past. Microbial communities and their biofilms inhabiting these extreme habitats have developed different adaptive strategies in metabolizing and transforming the persistent pollutants. They also play a crucial role in natural attenuation of these abandoned mining sites and act as a major driver of many biogeochemical processes, which helps in ecological rehabilitation and is a viable approach for restoration of wide stretches of land. In this review, the types of mine wastes including the overburden and mine drainage and the types of microbial communities thriving in such environments were probed in detail. The types of biofilms formed along with their possible role in metal bioremediation were also reviewed. This review also provides an overview of the shift in microbial communities in natural reclamation process and also provides an insight into the restoration of the enzyme activities of the soils which may help in further revegetation of abundant mining areas in a sustainable manner. Moreover, the role of indigenous microbiota in bioremediation of heavy metals and their plant growth-promoting activity weres discussed to assess their role in phytoremedial processes.
Collapse
|
6
|
Yang X, You L, Hu H, Chen Y. Conversion of grassland to cropland altered soil nitrogen-related microbial communities at large scales. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151645. [PMID: 34774635 DOI: 10.1016/j.scitotenv.2021.151645] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/18/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Land-use changes may dramatically disturb underground microbial biodiversity, especially in the fragile ecological areas. However, the impact of conversion of grassland to cropland on soil nitrogen (N)-related microbial communities is not fully understood in the farming-pastoral ecotone of northern China. Therefore, 24 paired grassland and cropland soil samples were collected in this region to investigate the community structure and assembly processes of soil N-related microorganisms via amplicon sequencing of nifH, archaeal and bacterial amoA, and nxrB genes. The results showed higher ammonia-oxidizing bacteria (AOB) alpha diversity but a lower nitrite-oxidizing bacteria (NOB) diversity in cropland soil compared to grassland soil. Non-metric multidimensional scaling ordinations revealed that diazotroph, AOB and NOB communities differed considerably between grassland and cropland soil. Soil microbial co-occurrence networks showed that conversion of grassland to cropland significantly lowered the average degree, average clustering coefficient, total nodes and links, resulting in less complex microbial networks in cropland soil. Land-use change altered AOB community assembly processes, resulting from a stochasticity-dominated process in grassland soil to a determinism-dominated process in cropland soil. In contrast, deterministic processes were dominant in diazotroph community assembly, whereas stochastic processes were dominant in constructing ammonia-oxidizing archaea and NOB communities in both grassland and cropland soil. These results provide novel evidence that the conversion of grassland to cropland altered the diversity and assembly processes of soil microbial communities involved in soil N-cycling processes, which has important implications for the potential changes in soil functions under land-use changes.
Collapse
Affiliation(s)
- Xue Yang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Luncheng You
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Hangwei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Yongliang Chen
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
7
|
Effects of Plastic versus Straw Mulching Systems on Soil Microbial Community Structure and Enzymes in Strawberry Cultivation. SOIL SYSTEMS 2022. [DOI: 10.3390/soilsystems6010021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This study aimed to evaluate changes in abundance, structure, and enzyme activity of the soil microbiome in response to 4 years of mulching using either black polyethylene plastic film (PM) or wheat straw (SM). Soil samples (depth 0–5 and 5–10 cm) were collected from conventional strawberry plots, in two samplings: 1 week prior (S1) and 7 weeks after straw application (S2). Selected soil properties were monitored in each system and the abundance and structure of microbial communities were characterized via phospholipid fatty acid (PLFA) analysis. The investigation of soil microbial functions included activities of the enzymes chitinase, leucine aminopeptidase, and acid phosphatase, as well as function genes involved in nitrogen transformation. Each mulch system resulted in distinct physicochemical properties. In particular, a pH value higher by one-unit under PM (7.6 ± 0.3) compared to SM (6.5 ± 0.3) was observed. Values for SOC, DOC, and total-N were 15%, 22%, and 16% higher in PM than in SM. The microbial biomass (total PLFAs) was 1.5-fold higher in SM compared to PM. The abundance of soil fungi (F) and bacteria (B) increased by 37% and 44% after straw incorporation compared to PM (S2). In particular, Gram-negative bacteria (gr–) increased by twofold in SM. Consequently, wider F:B and gr+:gr– ratios were observed in PM. According to the shifts in microbial abundance, the activity of the enzyme chitinase was lower by 27% in PM, while the activity of the acid phosphatase increased by 32%. Denitrification genes were not affected by the mulching systems. In conclusion, the abundance and structure of the investigated microbial groups and the enzyme activities were strongly influenced by the mulching system. In detail, effects on microbiota were primarily attributed to the altered soil pH and probably the input of degradable organic matter with straw mulching in SM. This resulted in higher abundance of soil microorganisms in SM, although measures within this cultivation system such as fungicide application may have exerted adverse effects on the microbiota.
Collapse
|
8
|
Community Composition and Spatial Distribution of N-Removing Microorganisms Optimized by Fe-Modified Biochar in a Constructed Wetland. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18062938. [PMID: 33805608 PMCID: PMC8000742 DOI: 10.3390/ijerph18062938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 11/17/2022]
Abstract
Microbial nitrogen (N) removal capability can be significantly enhanced in a horizontal subsurface flow constructed wetland (HSCW) amended by Fe-modified biochar (FeB). To further explore the microbiological mechanism of FeB enhancing N removal, nirS- and nirK-denitrifier community diversities, as well as spatial distributions of denitrifiers and anaerobic ammonium oxidation (anammox) bacteria, were investigated in HSCWs (C-HSCW: without biochar and FeB; B-HSCW: amended by biochar; FeB-HSCW: amended by FeB) treating tailwater from a wastewater treatment plant, with C-HSCW without biochar and FeB and B-HSCW amended by biochar as control. The community structures of nirS- and nirK-denitrifiers in FeB-HSCW were significantly optimized for improved N removal compared with the two other HSCWs, although no significant differences in their richness and diversity were detected among the HSCWs. The spatial distributions of the relative abundance of genes involved in denitrification and anammox were more heterogeneous and complex in FeB-HSCW than those in other HSCWs. More and larger high-value patches were observed in FeB-HSCW. These revealed that FeB provides more appropriate habitats for N-removing microorganisms, which can prompt the bacteria to use the habitats more differentially, without competitive exclusion. Overall, the Fe-modified biochar enhancement of the microbial N-removal capability of HSCWs was a result of optimized microbial community structures, higher functional gene abundance, and improved spatial distribution of N-removing microorganisms.
Collapse
|
9
|
Capstaff NM, Domoney C, Miller AJ. Real-time monitoring of rhizosphere nitrate fluctuations under crops following defoliation. PLANT METHODS 2021; 17:11. [PMID: 33516255 PMCID: PMC7847023 DOI: 10.1186/s13007-021-00713-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Management regime can hugely influence the efficiency of crop production but measuring real-time below-ground responses is difficult. The combination of fertiliser application and mowing or grazing may have a major impact on roots and on the soil nutrient profile and leaching. RESULTS A novel approach was developed using low-cost ion-selective sensors to track nitrate (NO3-) movement through soil column profiles sown with the forage crops, Lolium perenne and Medicago sativa. Applications of fertiliser, defoliation of crops and intercropping of the grass and the legume were tested. Sensor measurements were compared with conventional testing of lysimeter and leachate samples. There was little leaching of NO3- through soil profiles with current management practices, as monitored by both methods. After defoliation, the measurements detected a striking increase in soil NO3- in the middle of the column where the greatest density of roots was found. This phenomenon was not detected when no NO3- was applied, and when there was no defoliation, or during intercropping with Medicago. CONCLUSION Mowing or grazing may increase rhizodeposition of carbon that stimulates soil mineralization to release NO3- that is acquired by roots without leaching from the profile. The soil columns and sensors provided a dynamic insight into rhizosphere responses to changes in above-ground management practices.
Collapse
Affiliation(s)
- Nicola M Capstaff
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Claire Domoney
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Anthony J Miller
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| |
Collapse
|
10
|
Fiore-Donno AM, Richter-Heitmann T, Bonkowski M. Contrasting Responses of Protistan Plant Parasites and Phagotrophs to Ecosystems, Land Management and Soil Properties. Front Microbiol 2020; 11:1823. [PMID: 32849427 PMCID: PMC7422690 DOI: 10.3389/fmicb.2020.01823] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/10/2020] [Indexed: 11/13/2022] Open
Abstract
Functional traits are increasingly used in ecology to link the structure of microbial communities to ecosystem processes. We investigated two important protistan lineages, Cercozoa and Endomyxa (Rhizaria) in soil using Illumina sequencing and analyzed their diversity and functional traits along with their responses to environmental factors in grassland and forest across Germany. From 600 soil samples, we obtained 2,101 Operational Taxonomic Units representing ∼18 million Illumina reads (region V4, 18S rRNA gene). All major taxonomic and functional groups were present, dominated by small bacterivorous flagellates (Glissomonadida). Endomyxan plant parasites were absent from forests. In grassland, Cercozoa and Endomyxa were promoted by more intensive land use management. Grassland and forest strikingly differed in community composition. Relative abundances of bacterivores and eukaryvores were inversely influenced by environmental factors. These patterns provide new insights into the functional organization of soil biota and indications for a more sustainable land-use management.
Collapse
Affiliation(s)
- Anna Maria Fiore-Donno
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Cologne, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Michael Bonkowski
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Cologne, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| |
Collapse
|
11
|
Richter-Heitmann T, Hofner B, Krah FS, Sikorski J, Wüst PK, Bunk B, Huang S, Regan KM, Berner D, Boeddinghaus RS, Marhan S, Prati D, Kandeler E, Overmann J, Friedrich MW. Stochastic Dispersal Rather Than Deterministic Selection Explains the Spatio-Temporal Distribution of Soil Bacteria in a Temperate Grassland. Front Microbiol 2020; 11:1391. [PMID: 32695081 PMCID: PMC7338559 DOI: 10.3389/fmicb.2020.01391] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/29/2020] [Indexed: 01/15/2023] Open
Abstract
Spatial and temporal processes shaping microbial communities are inseparably linked but rarely studied together. By Illumina 16S rRNA sequencing, we monitored soil bacteria in 360 stations on a 100 square meter plot distributed across six intra-annual samplings in a rarely managed, temperate grassland. Using a multi-tiered approach, we tested the extent to which stochastic or deterministic processes influenced the composition of local communities. A combination of phylogenetic turnover analysis and null modeling demonstrated that either homogenization by unlimited stochastic dispersal or scenarios, in which neither stochastic processes nor deterministic forces dominated, explained local assembly processes. Thus, the majority of all sampled communities (82%) was rather homogeneous with no significant changes in abundance-weighted composition. However, we detected strong and uniform taxonomic shifts within just nine samples in early summer. Thus, community snapshots sampled from single points in time or space do not necessarily reflect a representative community state. The potential for change despite the overall homogeneity was further demonstrated when the focus shifted to the rare biosphere. Rare OTU turnover, rather than nestedness, characterized abundance-independent β-diversity. Accordingly, boosted generalized additive models encompassing spatial, temporal and environmental variables revealed strong and highly diverse effects of space on OTU abundance, even within the same genus. This pure spatial effect increased with decreasing OTU abundance and frequency, whereas soil moisture – the most important environmental variable – had an opposite effect by impacting abundant OTUs more than the rare ones. These results indicate that – despite considerable oscillation in space and time – the abundant and resident OTUs provide a community backbone that supports much higher β-diversity of a dynamic rare biosphere. Our findings reveal complex interactions among space, time, and environmental filters within bacterial communities in a long-established temperate grassland.
Collapse
Affiliation(s)
- Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,International Max Planck Research School of Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Benjamin Hofner
- Institut für Medizininformatik, Biometrie und Epidemiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Franz-Sebastian Krah
- Biodiversity Conservation, Institute for Ecology, Evolution and Diversity, Biologicum, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johannes Sikorski
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Pia K Wüst
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sixing Huang
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Kathleen M Regan
- Institute of Soil Science and Land Evaluation, Soil Biology Department, University of Hohenheim, Stuttgart, Germany
| | - Doreen Berner
- Institute of Soil Science and Land Evaluation, Soil Biology Department, University of Hohenheim, Stuttgart, Germany
| | - Runa S Boeddinghaus
- Institute of Soil Science and Land Evaluation, Soil Biology Department, University of Hohenheim, Stuttgart, Germany
| | - Sven Marhan
- Institute of Soil Science and Land Evaluation, Soil Biology Department, University of Hohenheim, Stuttgart, Germany
| | - Daniel Prati
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation, Soil Biology Department, University of Hohenheim, Stuttgart, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| |
Collapse
|
12
|
Nelson WC, Graham EB, Crump AR, Fansler SJ, Arntzen EV, Kennedy DW, Stegen JC. Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome. PLoS One 2020; 15:e0228165. [PMID: 31986180 PMCID: PMC6984685 DOI: 10.1371/journal.pone.0228165] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/08/2020] [Indexed: 11/29/2022] Open
Abstract
Biodiversity is thought to prevent decline in community function in response to changing environmental conditions through replacement of organisms with similar functional capacity but different optimal growth characteristics. We examined how this concept translates to the within-gene level by exploring seasonal dynamics of within-gene diversity for genes involved in nitrogen cycling in hyporheic zone communities. Nitrification genes displayed low richness—defined as the number of unique within-gene phylotypes—across seasons. Conversely, denitrification genes varied in both richness and the degree to which phylotypes were recruited or lost. These results demonstrate that there is not a universal mechanism for maintaining community functional potential for nitrogen cycling activities, even across seasonal environmental shifts to which communities would be expected to be well adapted. As such, extreme environmental changes could have very different effects on the stability of the different nitrogen cycle activities. These outcomes suggest a need to modify existing conceptual models that link biodiversity to microbiome function to incorporate within-gene diversity. Specifically, we suggest an expanded conceptualization that 1) recognizes component steps (genes) with low diversity as potential bottlenecks influencing pathway-level function, and 2) includes variation in both the number of entities (e.g. species, phylotypes) that can contribute to a given process and the turnover of those entities in response to shifting conditions. Building these concepts into process-based ecosystem models represents an exciting opportunity to connect within-gene-scale ecological dynamics to ecosystem-scale services.
Collapse
Affiliation(s)
- William C. Nelson
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail:
| | - Emily B. Graham
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Alex R. Crump
- Department of Soil and Water Systems, University of Idaho, Moscow, Idaho, United States of America
| | - Sarah J. Fansler
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Evan V. Arntzen
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - David W. Kennedy
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - James C. Stegen
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| |
Collapse
|
13
|
Beule L, Corre MD, Schmidt M, Göbel L, Veldkamp E, Karlovsky P. Conversion of monoculture cropland and open grassland to agroforestry alters the abundance of soil bacteria, fungi and soil-N-cycling genes. PLoS One 2019; 14:e0218779. [PMID: 31246995 PMCID: PMC6597161 DOI: 10.1371/journal.pone.0218779] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 06/10/2019] [Indexed: 01/15/2023] Open
Abstract
Integration of trees in agroforestry systems can increase the system sustainability compared to monocultures. The resulting increase in system complexity is likely to affect soil-N cycling by altering soil microbial community structure and functions. Our study aimed to assess the abundance of genes encoding enzymes involved in soil-N cycling in paired monoculture and agroforestry cropland in a Phaeozem soil, and paired open grassland and agroforestry grassland in Histosol and Anthrosol soils. The soil fungi-to-bacteria ratio was greater in the tree row than in the crop or grass rows of the monoculture cropland and open grassland in all soil types, possibly due to increased input of tree residues and the absence of tillage in the Phaeozem (cropland) soil. In the Phaeozem (cropland) soil, gene abundances of amoA indicated a niche differentiation between archaeal and bacterial ammonia oxidizers that distinctly separated the influence of the tree row from the crop row and monoculture system. Abundances of nitrate (napA and narG), nitrite (nirK and nirS) and nitrous oxide reductase genes (nosZ clade I) were largely influenced by soil type rather than management system. The soil types’ effects were associated with their differences in soil organic C, total N and pH. Our findings show that in temperate regions, conversion of monoculture cropland and open grassland to agroforestry systems can alter the abundance of soil bacteria and fungi and soil-N-cycling genes, particularly genes involved in ammonium oxidation.
Collapse
Affiliation(s)
- Lukas Beule
- Molecular Phytopathology and Mycotoxin Research, Faculty of Agricultural Sciences, University of Goettingen, Goettingen, Germany
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Goettingen, Germany
- * E-mail:
| | - Marife D. Corre
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Goettingen, Germany
| | - Marcus Schmidt
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Goettingen, Germany
| | - Leonie Göbel
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Goettingen, Germany
| | - Edzo Veldkamp
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Goettingen, Germany
| | - Petr Karlovsky
- Molecular Phytopathology and Mycotoxin Research, Faculty of Agricultural Sciences, University of Goettingen, Goettingen, Germany
| |
Collapse
|
14
|
Sun S, Sun H, Zhang D, Zhang J, Cai Z, Qin G, Song Y. Response of Soil Microbes to Vegetation Restoration in Coal Mining Subsidence Areas at Huaibei Coal Mine, China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16101757. [PMID: 31108967 PMCID: PMC6572236 DOI: 10.3390/ijerph16101757] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/10/2019] [Accepted: 05/15/2019] [Indexed: 12/26/2022]
Abstract
Vegetation restoration is an available way to ameliorate degraded lands. In order to study the response of soil microbes to vegetation restoration in coal mining subsidence areas, the composition and distribution of soil microbes were discussed through three plots: unsubsided area (CA), new subsided area (NSA), and old subsided area (OSA) with different vegetation restoration time in Huabei coal mine. Meanwhile, changes in soil catalase and urease activity were explored and the correlation between soil bacteria, fungi, and environmental factors was analysed. The results demonstrated that Nitrospira was the dominant bacteria in all areas sampled. Microorganisms in the 0–20 cm and 40–60 cm soil layers of OSA had the highest Simpson index, whereas the index in NSA was lowest (at all soil depths). The catalase activity in NSA was significantly higher than that in CA, and there was no significant difference in catalase activity with soil depth, while the urease activity declined gradually with increasing soil depth. The urease activity in the 20–60 cm soil layer of NSA and OSA was significantly higher than that of CA. Furthermore, the distribution of bacteria was mainly affected by soil organic matter, available potassium, available phosphorus, and alkali-hydrolyzable nitrogen, whereas pH and catalase activity mainly affected fungal distribution. These results implied that soil catalase activity in NSA and urease activity in the 20–40 cm soil layer of NSA and OSA were significantly enhanced after vegetation restoration, and that long-term plant restoration could improve soil fertility and soil microbial community diversity in coal mining areas.
Collapse
Affiliation(s)
- Shiyong Sun
- Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang 311400, China.
| | - Hui Sun
- Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang 311400, China.
- Institute of Timber Forests and Bamboos, Anhui Academy of Forestry Sciences, Hefei 230031, China.
| | - Deshun Zhang
- College of Architecture and Urban Planning, Tongji University, Shanghai 200092, China.
| | - Jianfeng Zhang
- Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang 311400, China.
| | - Zeyu Cai
- Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang 311400, China.
| | - Guanghua Qin
- Institute of Forest Breeding & Cultivation, Shandong Academy of Forestry, Jinan 250014, China.
| | - Yumin Song
- Institute of Forest Breeding & Cultivation, Shandong Academy of Forestry, Jinan 250014, China.
| |
Collapse
|
15
|
Szukics U, Grigulis K, Legay N, Kastl EM, Baxendale C, Bardgett RD, Clément JC, Lavorel S, Schloter M, Bahn M. Management versus site effects on the abundance of nitrifiers and denitrifiers in European mountain grasslands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 648:745-753. [PMID: 30134212 DOI: 10.1016/j.scitotenv.2018.08.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 08/03/2018] [Accepted: 08/03/2018] [Indexed: 06/08/2023]
Abstract
It is well established that the abundances of nitrogen (N) transforming microbes are strongly influenced by land-use intensity in lowland grasslands. However, their responses to management change in less productive and less fertilized mountain grasslands are largely unknown. We studied eight mountain grasslands, positioned along gradients of management intensity in Austria, the UK, and France, which differed in their historical management trajectories. We measured the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) as well as nitrite-reducing bacteria using specific marker genes. We found that management affected the abundance of these microbial groups along each transect, though the specific responses differed between sites, due to different management histories and resulting variations in environmental parameters. In Austria, cessation of management caused an increase in nirK and nirS gene abundances. In the UK, intensification of grassland management led to 10-fold increases in the abundances of AOA and AOB and doubling of nirK gene abundance. In France, ploughing of previously mown grassland caused a 20-fold increase in AOA abundance. Across sites the abundance of AOB was most strongly related to soil NO3--N availability, and AOA were favored by higher soil pH. Among the nitrite reducers, nirS abundance correlated most strongly with N parameters, such as soil NO3--N, microbial N, leachate NH4+-N, while the abundance of nirK-denitrifiers was affected by soil total N, organic matter (SOM) and water content. We conclude that alteration of soil environmental conditions is the dominant mechanism by which land management practices influence the abundance of each group of ammonia oxidizers and nitrite reducers.
Collapse
Affiliation(s)
- Ute Szukics
- Universität Innsbruck, Institut für Ökologie, Sternwartestr. 15, Innsbruck, Austria
| | - Karl Grigulis
- Laboratoire d'Ecologie Alpine, UMR 5553 CNRS, Université Joseph Fourier, Grenoble, France
| | - Nicolas Legay
- École de la Nature et du Paysage, INSA Centre Val de Loire, 9 Rue Chocolaterie, 41000 Blois, France; CNRS, CITERES, UMR 7324, 37200 Tours, France
| | - Eva-Maria Kastl
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, 85758 Oberschleissheim, Germany
| | | | - Richard D Bardgett
- School of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | | | - Sandra Lavorel
- Laboratoire d'Ecologie Alpine, UMR 5553 CNRS, Université Joseph Fourier, Grenoble, France
| | - Michael Schloter
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, 85758 Oberschleissheim, Germany
| | - Michael Bahn
- Universität Innsbruck, Institut für Ökologie, Sternwartestr. 15, Innsbruck, Austria.
| |
Collapse
|
16
|
Sun X, Zhou Y, Tan Y, Wu Z, Lu P, Zhang G, Yu F. Restoration with pioneer plants changes soil properties and remodels the diversity and structure of bacterial communities in rhizosphere and bulk soil of copper mine tailings in Jiangxi Province, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:22106-22119. [PMID: 29802615 DOI: 10.1007/s11356-018-2244-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/06/2018] [Indexed: 06/08/2023]
Abstract
To unravel the ecological function played by pioneer plants in the practical restoration of mine tailings, it is vital to explore changes of soil characteristics and microbial communities in rhizosphere and bulk soil following the adaptation and survival of plants. In the present study, the diversity and structure of rhizospheric bacterial communities of three pioneer plants in copper mine tailings were investigated by Illumina MiSeq sequencing, and the effects of pioneer plants on soil properties were also evaluated. Significant soil improvement was detected in rhizospheric samples, and Alnus cremastogyne showed higher total organic matter, total nitrogen, and available phosphorus than two other herbaceous plants. Microbial diversity indices in rhizosphere and bulk soil of reclaimed tailings were significantly higher than bare tailings, even the soil properties of bulk soil in reclaimed tailings were not significantly different from those of bare tailings. A detailed taxonomic composition analysis demonstrated that Alphaproteobacteria and Deltaproteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes showed significantly higher relative abundance in rhizosphere and bulk soil. In contrast, Gammaproteobacteria and Firmicutes were abundant in bare tailings, in which Bacillus, Pseudomonas, and Lactococcus made up the majority of the bacterial community (63.04%). Many species within known heavy metal resistance and nutrient regulatory microorganism were identified in reclaimed tailings, and were more abundant among rhizospheric microbes. Hierarchical clustering and principal coordinate analysis (PCoA) analysis demonstrated that the bacterial profiles in the rhizosphere clustered strictly together according to plant types, and were distinguishable from bulk soil. However, we also identified a large shared OTUs that occurred repeatedly and was unaffected by highly diverse soil properties in rhizosphere and bulk samples. Redundancy analysis indicated that water content and Cu and As concentrations were the main environmental regulators of microbial composition. These results suggest that the interactive effect of pioneer plants and harsh soil environmental conditions remodel the specific bacterial communities in rhizosphere and bulk soil in mine tailings. And A. cremastogyne might be approximate candidate for phytoremediation of mine tailings for better soil amelioration effect and relative higher diversity of bacterial community in rhizosphere.
Collapse
Affiliation(s)
- Xiaoyan Sun
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China.
| | - Yanling Zhou
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Yinjing Tan
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Zhaoxiang Wu
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Ping Lu
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Guohua Zhang
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Faxin Yu
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| |
Collapse
|
17
|
Wang H, Deng N, Wu D, Hu S, Kou M. Long-term net transformation and quantitative molecular mechanisms of soil nitrogen during natural vegetation recovery of abandoned farmland on the Loess Plateau of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 607-608:152-159. [PMID: 28689119 DOI: 10.1016/j.scitotenv.2017.07.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/30/2017] [Accepted: 07/02/2017] [Indexed: 06/07/2023]
Abstract
The availability of nitrogen (N) can alter vegetation species composition and diversity in degraded ecosystems. A comprehensive understanding of the dynamic fate of ammonium (NH4+-N) and nitrate (NO3--N) processing and the underlying mechanisms are still lacking, particularly in arid to semi-arid degraded ecosystems. We compared and quantified the changes in the rates of net ammonification (Ra), nitrification (Rn) and total mineralization (Rm) and the abundance of bacteria, archaea, and microbial genes related to N transformation on the northern Loess Plateau of China across a 40-year chronosequence of farmland undergoing spontaneous restoration. We found that Ra, Rn, and Rm decreased in grassland soils (0-30-y sites) of different ages and exhibited significant increases at the 40-y sites. The capabilities of the soil to deliver NH4+-N and NO3--N were not a limiting factor during the growing season after 40years of vegetation recovery. Soil mineral nitrogen may be not suitable for predicting and assessing the long-term (approximately 40years) restoration success and progress. The abundance of functional N genes showed differences in sensitivity to natural vegetation recovery of abandoned farmland, which likely reflects the fact that the multi-pathways driven by N functional microbial communities had a large influence on the dynamic fate of NH4+-N and NO3--N. Quantitative response relationships between net N transformation rates and microbial genes related to N transformation were established, and these relationships confirmed that different N transformation processes were strongly linked with certain N functional genes, and collaboratively contributed to N transformation as vegetation recovery progressed. Specifically, Ra was controlled by AOA-amoA, AOB-amoA, and nxrA; Rn was governed by napA, narG, nirK, nirS, and nosZ; and Rm was controlled by nifH, apr, AOA-amoA, AOB-amoA, nirS, and nirK.
Collapse
Affiliation(s)
- Honglei Wang
- State Key Laboratory of Soil Erosion and Dry Land Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A & F University, Yangling 712100, Shaanxi, China.
| | - Na Deng
- State Key Laboratory of Soil Erosion and Dry Land Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A & F University, Yangling 712100, Shaanxi, China
| | - Duoyang Wu
- State Key Laboratory of Soil Erosion and Dry Land Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A & F University, Yangling 712100, Shaanxi, China
| | - Shu Hu
- State Key Laboratory of Soil Erosion and Dry Land Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A & F University, Yangling 712100, Shaanxi, China
| | - Meng Kou
- College of Natural Resources & Environment and History & Culture, Xianyang Normal University, Shaanxi, Xianyang 712000, China
| |
Collapse
|
18
|
Schulz S, Kölbl A, Ebli M, Buegger F, Schloter M, Fiedler S. Field-Scale Pattern of Denitrifying Microorganisms and N 2O Emission Rates Indicate a High Potential for Complete Denitrification in an Agriculturally Used Organic Soil. MICROBIAL ECOLOGY 2017; 74:765-770. [PMID: 28492990 DOI: 10.1007/s00248-017-0991-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 04/27/2017] [Indexed: 06/07/2023]
Abstract
More than 50% of all anthropogenic N2O emissions come from the soil. Drained Histosols that are used for agricultural purposes are particularly potent sources of denitrification due to higher stocks of organic matter and fertiliser application. However, conditions that favour denitrification can vary considerably across a field and change significantly throughout the year. Spatial and temporal denitrifier dynamics were assessed in a drained, intensely managed Histosol by focusing on the genetic nitrite and N2O reduction potential derived from the abundance of nirK, nirS and nosZ genes. These data were correlated with soil properties at two different points in time in 2013. N2O emissions were measured every 2 weeks over three vegetation periods (2012-2014). Very low N2O emission rates were measured throughout the entire period of investigation in accordance with the geostatistical data that revealed an abundance of microbes carrying the N2O reductase gene nosZ. This, along with neutral soil pH values, is indicative of high microbial denitrification potential. While the distribution of the microbial communities was strongly influenced by total organic carbon and nitrogen pools in March, the spatial distribution pattern was not related to the distribution of soil properties in October, when higher nutrient availability was observed. Different nitrite reducer groups prevailed in spring and autumn. While nirS, followed by nosZ and nirK, was most abundant in March, the latter was the dominant nitrite reductase in October.
Collapse
Affiliation(s)
- Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Angelika Kölbl
- Department of Ecology and Ecosystem Management, Technical University of Munich, Emil-Ramann-Straße 2, 85354, Freising, Germany
| | - Martin Ebli
- Institute for Geography, Soil Science, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 21, 55099, Mainz, Germany
| | - Franz Buegger
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Sabine Fiedler
- Institute for Geography, Soil Science, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 21, 55099, Mainz, Germany.
| |
Collapse
|
19
|
Tecon R, Or D. Biophysical processes supporting the diversity of microbial life in soil. FEMS Microbiol Rev 2017; 41:599-623. [PMID: 28961933 PMCID: PMC5812502 DOI: 10.1093/femsre/fux039] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 07/10/2017] [Indexed: 12/13/2022] Open
Abstract
Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure-the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning.
Collapse
Affiliation(s)
- Robin Tecon
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Dani Or
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
| |
Collapse
|
20
|
Quantitative response relationships between net nitrogen transformation rates and nitrogen functional genes during artificial vegetation restoration following agricultural abandonment. Sci Rep 2017; 7:7752. [PMID: 28798309 PMCID: PMC5552692 DOI: 10.1038/s41598-017-08016-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/03/2017] [Indexed: 11/09/2022] Open
Abstract
A comprehensive understanding of how microbial associated with nitrogen (N) cycling respond to artificial vegetation restoration is still lacking, particularly in arid to semi-arid degraded ecosystems. We compared soil net N mineralization rates and the abundance of bacteria, archaea, and eleven N microbial genes on the northern Loess Plateau of China during the process of artificial vegetation restoration. The quantitative relationships between net N mineralization rates and N microbial genes were determined. We observed a significant difference of net transformation rates of NH4+-N (Ra), NO3--N (Rd), and total mineralization (Rm), which rapidly decreased in 10-year soils and steadily increased in the 10-30-year soils. Different N functional microbial groups responded to artificial vegetation restoration distinctly and differentially, especially for denitrifying bacteria. Stepwise regression analysis suggested that Ra was collectively controlled by AOA-amoA and Archaea; Rd was jointly governed by narG, napA, nxrA, and bacreria; and Rm was jointly controlled by napA, narG, nirK, nirS, norB, nosZ, and nxrA.
Collapse
|
21
|
Identification of the Core Set of Carbon-Associated Genes in a Bioenergy Grassland Soil. PLoS One 2016; 11:e0166578. [PMID: 27855202 PMCID: PMC5113961 DOI: 10.1371/journal.pone.0166578] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/31/2016] [Indexed: 01/30/2023] Open
Abstract
Despite the central role of soil microbial communities in global carbon (C) cycling, little is known about soil microbial community structure and even less about their metabolic pathways. Efforts to characterize soil communities often focus on identifying differences in gene content across environmental gradients, but an alternative question is what genes are similar in soils. These genes may indicate critical species or potential functions that are required in all soils. Here we identified the "core" set of C cycling sequences widely present in multiple soil metagenomes from a fertilized prairie (FP). Of 226,887 sequences associated with known enzymes involved in the synthesis, metabolism, and transport of carbohydrates, 843 were identified to be consistently prevalent across four replicate soil metagenomes. This core metagenome was functionally and taxonomically diverse, representing five enzyme classes and 99 enzyme families within the CAZy database. Though it only comprised 0.4% of all CAZy-associated genes identified in FP metagenomes, the core was found to be comprised of functions similar to those within cumulative soils. The FP CAZy-associated core sequences were present in multiple publicly available soil metagenomes and most similar to soils sharing geographic proximity. In soil ecosystems, where high diversity remains a key challenge for metagenomic investigations, these core genes represent a subset of critical functions necessary for carbohydrate metabolism, which can be targeted to evaluate important C fluxes in these and other similar soils.
Collapse
|
22
|
Nguyen NL, Kim YJ, Hoang VA, Subramaniyam S, Kang JP, Kang CH, Yang DC. Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time. PLoS One 2016; 11:e0155055. [PMID: 27187071 PMCID: PMC4871511 DOI: 10.1371/journal.pone.0155055] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 04/24/2016] [Indexed: 12/12/2022] Open
Abstract
Traditional molecular methods have been used to examine bacterial communities in ginseng-cultivated soil samples in a time-dependent manner. Despite these efforts, our understanding of the bacterial community is still inadequate. Therefore, in this study, a high-throughput sequencing approach was employed to investigate bacterial diversity in various ginseng field soil samples over cultivation times of 2, 4, and 6 years in the first and second rounds of cultivation. We used non-cultivated soil samples to perform a comparative study. Moreover, this study assessed changes in the bacterial community associated with soil depth and the health state of the ginseng. Bacterial richness decreased through years of cultivation. This study detected differences in relative abundance of bacterial populations between the first and second rounds of cultivation, years of cultivation, and health states of ginseng. These bacterial populations were mainly distributed in the classes Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Sphingobacteria. In addition, we found that pH, available phosphorus, and exchangeable Ca+ seemed to have high correlations with bacterial class in ginseng cultivated soil.
Collapse
Affiliation(s)
- Ngoc-Lan Nguyen
- Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung-Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Yeon-Ju Kim
- Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung-Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
- * E-mail: (D-CY); (Y-JK)
| | - Van-An Hoang
- Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung-Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Sathiyamoorthy Subramaniyam
- Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung-Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Jong-Pyo Kang
- Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung-Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Chang Ho Kang
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, JinJu-si, Gyeongsangnam-do, Republic of Korea
| | - Deok-Chun Yang
- Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung-Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
- Graduation of Biotechnology, Kyung-Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
- * E-mail: (D-CY); (Y-JK)
| |
Collapse
|
23
|
O'Brien SL, Gibbons SM, Owens SM, Hampton-Marcell J, Johnston ER, Jastrow JD, Gilbert JA, Meyer F, Antonopoulos DA. Spatial scale drives patterns in soil bacterial diversity. Environ Microbiol 2016; 18:2039-51. [PMID: 26914164 DOI: 10.1111/1462-2920.13231] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 01/17/2016] [Indexed: 01/16/2023]
Abstract
Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high microbial diversity and large spatial variability of most soil characteristics. We investigated soil bacterial community structure in a switchgrass stand planted on soil with a history of grassland vegetation at high spatial resolution to determine whether biogeographic trends occurred at the centimeter scale. Moreover, we tested whether such heterogeneity, if present, influenced community structure within or among ecosystems. Pronounced heterogeneity was observed at centimeter scales, with abrupt changes in relative abundance of phyla from sample to sample. At the ecosystem scale (> 10 m), however, bacterial community composition and structure were subtly, but significantly, altered by fertilization, with higher alpha diversity in fertilized plots. Moreover, by comparing these data with data from 1772 soils from the Earth Microbiome Project, it was found that 20% of bacterial taxa were shared between their site and diverse globally sourced soil samples, while grassland soils shared approximately 40% of their operational taxonomic units with the current study. By spanning several orders of magnitude, the analysis suggested that extreme patchiness characterized community structure at smaller scales but that coherent patterns emerged at larger length scales.
Collapse
Affiliation(s)
- Sarah L O'Brien
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA
| | - Sean M Gibbons
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA.,Graduate Program in Biophysical Sciences, University of Chicago, 929 E. 57th St., Chicago, IL, 60637, USA
| | - Sarah M Owens
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA.,Computation Institute, University of Chicago, Chicago, IL, 60637, USA
| | - Jarrad Hampton-Marcell
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA.,Department of Ecology and Evolution, Department of Surgery, University of Chicago, 1101 E. 57th St., Chicago, IL, 606037, USA
| | - Eric R Johnston
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA
| | - Julie D Jastrow
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA
| | - Jack A Gilbert
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA.,Department of Ecology and Evolution, Department of Surgery, University of Chicago, 1101 E. 57th St., Chicago, IL, 606037, USA.,Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA.,College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Folker Meyer
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL, 60439, USA.,Computation Institute, University of Chicago, Chicago, IL, 60637, USA
| | | |
Collapse
|
24
|
Stempfhuber B, Richter-Heitmann T, Regan KM, Kölbl A, Wüst PK, Marhan S, Sikorski J, Overmann J, Friedrich MW, Kandeler E, Schloter M. Spatial Interaction of Archaeal Ammonia-Oxidizers and Nitrite-Oxidizing Bacteria in an Unfertilized Grassland Soil. Front Microbiol 2016; 6:1567. [PMID: 26834718 PMCID: PMC4722141 DOI: 10.3389/fmicb.2015.01567] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/27/2015] [Indexed: 12/18/2022] Open
Abstract
Interrelated successive transformation steps of nitrification are performed by distinct microbial groups - the ammonia-oxidizers, comprising ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizers such as Nitrobacter and Nitrospira, which are the dominant genera in the investigated soils. Hence, not only their presence and activity in the investigated habitat is required for nitrification, but also their temporal and spatial interactions. To demonstrate the interdependence of both groups and to address factors promoting putative niche differentiation within each group, temporal and spatial changes in nitrifying organisms were monitored in an unfertilized grassland site over an entire vegetation period at the plot scale of 10 m(2). Nitrifying organisms were assessed by measuring the abundance of marker genes (amoA for AOA and AOB, nxrA for Nitrobacter, 16S rRNA gene for Nitrospira) selected for the respective sub-processes. A positive correlation between numerically dominant AOA and Nitrospira, and their co-occurrence at the same spatial scale in August and October, suggests that the nitrification process is predominantly performed by these groups and is restricted to a limited timeframe. Amongst nitrite-oxidizers, niche differentiation was evident in observed seasonally varying patterns of co-occurrence and spatial separation. While their distributions were most likely driven by substrate concentrations, oxygen availability may also have played a role under substrate-limited conditions. Phylogenetic analysis revealed temporal shifts in Nitrospira community composition with an increasing relative abundance of OTU03 assigned to sublineage V from August onward, indicating its important role in nitrite oxidation.
Collapse
Affiliation(s)
- Barbara Stempfhuber
- Environmental Genomics, Helmholtz Zentrum München, German Research Centre for Environmental Health Neuherberg, Germany
| | | | - Kathleen M Regan
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart-Hohenheim, Germany
| | - Angelika Kölbl
- Lehrstuhl für Bodenkunde, Technische Universität München Freising, Germany
| | - Pia K Wüst
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Sven Marhan
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart-Hohenheim, Germany
| | - Johannes Sikorski
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | | | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart-Hohenheim, Germany
| | - Michael Schloter
- Environmental Genomics, Helmholtz Zentrum München, German Research Centre for Environmental Health Neuherberg, Germany
| |
Collapse
|
25
|
Glaser K, Kuppardt A, Boenigk J, Harms H, Fetzer I, Chatzinotas A. The influence of environmental factors on protistan microorganisms in grassland soils along a land-use gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 537:33-42. [PMID: 26282737 DOI: 10.1016/j.scitotenv.2015.07.158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/30/2015] [Accepted: 07/31/2015] [Indexed: 06/04/2023]
Abstract
In this study, we investigated the effect of land use intensity, soil parameters and vegetation on protistan communities in grassland soils. We performed qualitative (T-RFLP) and quantitative (qPCR) analyses using primers specifically targeting the 18S rRNA gene for all Eukarya and for two common flagellate groups, i.e. the Chrysophyceae and the Kinetoplastea. Both approaches were applied to extracted soil DNA and RNA, in order to distinguish between the potentially active protists (i.e. RNA pool) and the total protistan communities, including potentially inactive and encysted cells (i.e. DNA pool). Several environmental determinants such as site, soil parameters and vegetation had an impact on the T-RFLP community profiles and the abundance of the quantified 18S rRNA genes. Correlating factors often differed between quantitative (qPCR) and qualitative (T-RFLP) approaches. For instance the Chrysophyceae/Eukarya 18S rDNA ratio as determined by qPCR correlated with the C/N ratio, whereas the community composition based on T-RLFP analysis was not affected indicating that both methods taken together provide a more complete picture of the parameters driving protist diversity. Moreover, distinct T-RFs were obtained, which could serve as potential indicators for either active organisms or environmental conditions like water content. While site was the main determinant across all investigated exploratories, land use seemed to be of minor importance for structuring protist communities. The impact of other parameters differed between the target groups, e.g. Kinetoplastea reacted on changes to water content on all sites, whereas Chrysophyceae were only affected in the Schorfheide. Finally, in most cases different responses were observed on RNA- and DNA-level, respectively. Vegetation for instance influenced the two flagellate groups only at the DNA-level across all sites. Future studies should thus include different protistan groups and also distinguish between active and inactive cells, in order to reveal causal shifts in community composition and abundance in agriculturally used systems.
Collapse
Affiliation(s)
- Karin Glaser
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Anke Kuppardt
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Jens Boenigk
- Department of Biodiversity, University Duisburg-Essen, 45117 Essen, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Ingo Fetzer
- Stockholm Resilience Centre, Stockholm University, Sweden
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Deutscher Platz 5e, 04103 Leipzig, Germany.
| |
Collapse
|
26
|
Lee SH, Kang H. The activity and community structure of total bacteria and denitrifying bacteria across soil depths and biological gradients in estuary ecosystem. Appl Microbiol Biotechnol 2015; 100:1999-2010. [PMID: 26526456 DOI: 10.1007/s00253-015-7111-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 10/14/2015] [Accepted: 10/16/2015] [Indexed: 11/25/2022]
Abstract
The distribution of soil microorganisms often shows variations along soil depth, and even in the same soil layer, each microbial group has a specific niche. In particular, the estuary soil is intermittently flooded, and the characteristics of the surface soil layer are different from those of other terrestrial soils. We investigated the microbial community structure and activity across soil depths and biological gradients composed of invasive and native plants in the shallow surface layer of an estuary ecosystem by using molecular approaches. Our results showed that the total and denitrifying bacterial community structures of the estuarine wetland soil differed according to the short depth gradient. In growing season, gene copy number of 16S rRNA were 1.52(±0.23) × 10(11), 1.10(±0.06) × 10(11), and 4.33(±0.16) × 10(10) g(-1) soil; nirS were 5.41(±1.25) × 10(8), 4.93(±0.94) × 10(8), and 2.61(±0.28) × 10(8) g(-1) soil; and nirK were 9.67(±2.37) × 10(6), 3.42(±0.55) × 10(6), and 2.12(±0.19) × 10(6) g(-1) soil in 0 cm, 5 cm, and 10 cm depth layer, respectively. The depth-based difference was distinct in the vegetated sample and in the growing season, evidencing the important role of plants in structuring the microbial community. In comparison with other studies, we observed differences in the microbial community and functions even across very short depth gradients. In conclusion, our results suggested that (i) in the estuary ecosystem, the denitrifying bacterial community could maintain its abundance and function within shallow surface soil layers through facultative anaerobiosis, while the total bacterial community would be both quantitatively and qualitatively affected by the soil depth, (ii) the nirS gene community, rather than the nirK one, should be the first candidate used as an indicator of the microbial denitrification process in the estuary system, and (iii) as the microbial community is distributed and plays a certain niche role according to biogeochemical factors, the study of the microbial community even in surface soil should be performed in detail by considering the soil depth.
Collapse
Affiliation(s)
- Seung-Hoon Lee
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 120-749, South Korea.,Geobiotech Corporation, Seoul, 120-749, South Korea
| | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 120-749, South Korea.
| |
Collapse
|
27
|
Keil D, Niklaus PA, von Riedmatten LR, Boeddinghaus RS, Dormann CF, Scherer-Lorenzen M, Kandeler E, Marhan S. Effects of warming and drought on potential N2O emissions and denitrifying bacteria abundance in grasslands with different land-use. FEMS Microbiol Ecol 2015; 91:fiv066. [PMID: 26092950 DOI: 10.1093/femsec/fiv066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2015] [Indexed: 11/13/2022] Open
Abstract
Increased warming in spring and prolonged summer drought may alter soil microbial denitrification. We measured potential denitrification activity and denitrifier marker gene abundances (nirK, nirS, nosZ) in grasslands soils in three geographic regions characterized by site-specific land-use indices (LUI) after warming in spring, at an intermediate sampling and after summer drought. Potential denitrification was significantly increased by warming, but did not persist over the intermediate sampling. At the intermediate sampling, the relevance of grassland land-use intensity was reflected by increased potential N2O production at sites with higher LUI. Abundances of total bacteria did not respond to experimental warming or drought treatments, displaying resilience to minor and short-term effects of climate change. In contrast, nirS- and nirK-type denitrifiers were more influenced by drought in combination with LUI and pH, while the nosZ abundance responded to the summer drought manipulation. Land-use was a strong driver for potential denitrification as grasslands with higher LUI also had greater potentials for N2O emissions. We conclude that both warming and drought affected the denitrifying communities and the potential denitrification in grassland soils. However, these effects are overruled by regional and site-specific differences in soil chemical and physical properties which are also related to grassland land-use intensity.
Collapse
Affiliation(s)
- Daniel Keil
- Institute of Soil Science and Land Evaluation, Soil Biology Section, University of Hohenheim, 70599 Stuttgart, Germany
| | - Pascal A Niklaus
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Lars R von Riedmatten
- Computational Landscape Ecology, Helmholtz-Centre for Environmental Research, Permoser Str. 15, 04318 Leipzig, Germany Department of Biometry and Environmental System Analysis, University of Freiburg, 79106 Freiburg, Germany
| | - Runa S Boeddinghaus
- Institute of Soil Science and Land Evaluation, Soil Biology Section, University of Hohenheim, 70599 Stuttgart, Germany
| | - Carsten F Dormann
- Department of Biometry and Environmental System Analysis, University of Freiburg, 79106 Freiburg, Germany
| | | | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation, Soil Biology Section, University of Hohenheim, 70599 Stuttgart, Germany
| | - Sven Marhan
- Institute of Soil Science and Land Evaluation, Soil Biology Section, University of Hohenheim, 70599 Stuttgart, Germany
| |
Collapse
|
28
|
Changes in the composition and diversity of bacterial communities 13 years after soil reclamation of abandoned mine land in eastern China. Ecol Res 2014. [DOI: 10.1007/s11284-014-1230-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
29
|
Succession of bacterial community structure and diversity in soil along a chronosequence of reclamation and re-vegetation on coal mine spoils in China. PLoS One 2014; 9:e115024. [PMID: 25502754 PMCID: PMC4263735 DOI: 10.1371/journal.pone.0115024] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 11/17/2014] [Indexed: 11/19/2022] Open
Abstract
The growing concern about the effectiveness of reclamation strategies has motivated the evaluation of soil properties following reclamation. Recovery of belowground microbial community is important for reclamation success, however, the response of soil bacterial communities to reclamation has not been well understood. In this study, PCR-based 454 pyrosequencing was applied to compare bacterial communities in undisturbed soils with those in reclaimed soils using chronosequences ranging in time following reclamation from 1 to 20 year. Bacteria from the Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Planctomycetes and Bacteroidetes were abundant in all soils, while the composition of predominant phyla differed greatly across all sites. Long-term reclamation strongly affected microbial community structure and diversity. Initial effects of reclamation resulted in significant declines in bacterial diversity indices in younger reclaimed sites (1, 8-year-old) compared to the undisturbed site. However, bacterial diversity indices tended to be higher in older reclaimed sites (15, 20-year-old) as recovery time increased, and were more similar to predisturbance levels nearly 20 years after reclamation. Bacterial communities are highly responsive to soil physicochemical properties (pH, soil organic matter, Total N and P), in terms of both their diversity and community composition. Our results suggest that the response of soil microorganisms to reclamation is likely governed by soil characteristics and, indirectly, by the effects of vegetation restoration. Mixture sowing of gramineae and leguminosae herbage largely promoted soil geochemical conditions and bacterial diversity that recovered to those of undisturbed soil, representing an adequate solution for soil remediation and sustainable utilization for agriculture. These results confirm the positive impacts of reclamation and vegetation restoration on soil microbial diversity and suggest that the most important phase of microbial community recovery occurs between 15 and 20 years after reclamation.
Collapse
|
30
|
Olivares J, Bedmar EJ, Sanjuán J. Biological nitrogen fixation in the context of global change. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:486-494. [PMID: 23360457 DOI: 10.1094/mpmi-12-12-0293-cr] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The intensive application of fertilizers during agricultural practices has led to an unprecedented perturbation of the nitrogen cycle, illustrated by the growing accumulation of nitrates in soils and waters and of nitrogen oxides in the atmosphere. Besides increasing use efficiency of current N fertilizers, priority should be given to value the process of biological nitrogen fixation (BNF) through more sustainable technologies that reduce the undesired effects of chemical N fertilization of agricultural crops. Wider legume adoption, supported by coordinated legume breeding and inoculation programs are approaches at hand. Also available are biofertilizers based on microbes that help to reduce the needs of N fertilization in important crops like cereals. Engineering the capacity to fix nitrogen in cereals, either by themselves or in symbiosis with nitrogen-fixing microbes, are attractive future options that, nevertheless, require more intensive and internationally coordinated research efforts. Although nitrogen-fixing plants may be less productive, at some point, agriculture must significantly reduce the use of warming (chemically synthesized) N and give priority to BNF if it is to sustain both food production and environmental health for a continuously growing human population.
Collapse
Affiliation(s)
- José Olivares
- Dpto. Microbiologia del Suelo y Sistemas Simbioticos, Estacion Experimental del Zaidin, Granada, Spain
| | | | | |
Collapse
|
31
|
Effects of drought and N-fertilization on N cycling in two grassland soils. Oecologia 2013; 171:705-17. [PMID: 23297047 DOI: 10.1007/s00442-012-2578-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 12/18/2012] [Indexed: 10/27/2022]
Abstract
Changes in frequency and intensity of drought events are anticipated in many areas of the world. In pasture, drought effects on soil nitrogen (N) cycling are spatially and temporally heterogeneous due to N redistribution by grazers. We studied soil N cycling responses to simulated summer drought and N deposition by grazers in a 3-year field experiment replicated in two grasslands differing in climate and management. Cattle urine and NH4NO3 application increased soil NH4(+) and NO3(-) concentrations, and more so under drought due to reduced plant uptake and reduced nitrification and denitrification. Drought effects were, however, reflected to a minor extent only in potential nitrification, denitrifying enzyme activity (DEA), and the abundance of functional genes characteristic of nitrifying (bacterial and archaeal amoA) and denitrifying (narG, nirS, nirK, nosZ) micro-organisms. N2O emissions, however, were much reduced under drought, suggesting that this effect was driven by environmental limitations rather than by changes in the activity potential or the size of the respective microbial communities. Cattle urine stimulated nitrification and, to a lesser extent, also DEA, but more so in the absence of drought. In contrast, NH4NO3 reduced the activity of nitrifiers and denitrifiers due to top-soil acidification. In summary, our data demonstrate that complex interactions between drought, mineral N availability, soil acidification, and plant nutrient uptake control soil N cycling and associated N2O emissions. These interactive effects differed between processes of the soil N cycle, suggesting that the spatial heterogeneity in pastures needs to be taken into account when predicting changes in N cycling and associated N2O emissions in a changing climate.
Collapse
|
32
|
Giles M, Morley N, Baggs EM, Daniell TJ. Soil nitrate reducing processes - drivers, mechanisms for spatial variation, and significance for nitrous oxide production. Front Microbiol 2012; 3:407. [PMID: 23264770 PMCID: PMC3524552 DOI: 10.3389/fmicb.2012.00407] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 11/12/2012] [Indexed: 11/13/2022] Open
Abstract
The microbial processes of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two important nitrate reducing mechanisms in soil, which are responsible for the loss of nitrate ([Formula: see text]) and production of the potent greenhouse gas, nitrous oxide (N(2)O). A number of factors are known to control these processes, including O(2) concentrations and moisture content, N, C, pH, and the size and community structure of nitrate reducing organisms responsible for the processes. There is an increasing understanding associated with many of these controls on flux through the nitrogen cycle in soil systems. However, there remains uncertainty about how the nitrate reducing communities are linked to environmental variables and the flux of products from these processes. The high spatial variability of environmental controls and microbial communities across small sub centimeter areas of soil may prove to be critical in determining why an understanding of the links between biotic and abiotic controls has proved elusive. This spatial effect is often overlooked as a driver of nitrate reducing processes. An increased knowledge of the effects of spatial heterogeneity in soil on nitrate reduction processes will be fundamental in understanding the drivers, location, and potential for N(2)O production from soils.
Collapse
Affiliation(s)
- Madeline Giles
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen Aberdeen, UK ; Ecological Sciences, The James Hutton Institute Dundee, UK
| | | | | | | |
Collapse
|
33
|
Correa-Galeote D, Marco DE, Tortosa G, Bru D, Philippot L, Bedmar EJ. Spatial distribution of N-cycling microbial communities showed complex patterns in constructed wetland sediments. FEMS Microbiol Ecol 2012; 83:340-51. [DOI: 10.1111/j.1574-6941.2012.01479.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 07/30/2012] [Accepted: 08/14/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
- David Correa-Galeote
- Department of Soil Microbiology and Symbiotic Systems; Estación Experimental del Zaidín; Agencia CSIC; Granada; Spain
| | | | - Germán Tortosa
- Department of Soil Microbiology and Symbiotic Systems; Estación Experimental del Zaidín; Agencia CSIC; Granada; Spain
| | - David Bru
- INRA-Université de Bourgogne; UMR 1229; Microbiologie et Géochimie des Sols; Dijon Cedex; France
| | - Laurent Philippot
- INRA-Université de Bourgogne; UMR 1229; Microbiologie et Géochimie des Sols; Dijon Cedex; France
| | - Eulogio J. Bedmar
- Department of Soil Microbiology and Symbiotic Systems; Estación Experimental del Zaidín; Agencia CSIC; Granada; Spain
| |
Collapse
|
34
|
Banerjee S, Siciliano SD. Spatially tripartite interactions of denitrifiers in arctic ecosystems: activities, functional groups and soil resources. Environ Microbiol 2012; 14:2601-13. [DOI: 10.1111/j.1462-2920.2012.02814.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
35
|
Actinobacterial nitrate reducers and proteobacterial denitrifiers are abundant in N2O-metabolizing palsa peat. Appl Environ Microbiol 2012; 78:5584-96. [PMID: 22660709 DOI: 10.1128/aem.00810-12] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Palsa peats are characterized by elevated, circular frost heaves (peat soil on top of a permanently frozen ice lens) and are strong to moderate sources or even temporary sinks for the greenhouse gas nitrous oxide (N(2)O). Palsa peats are predicted to react sensitively to global warming. The acidic palsa peat Skalluvaara (approximate pH 4.4) is located in the discontinuous permafrost zone in northwestern Finnish Lapland. In situ N(2)O fluxes were spatially variable, ranging from 0.01 to -0.02 μmol of N(2)O m(-2) h(-1). Fertilization with nitrate stimulated in situ N(2)O emissions and N(2)O production in anoxic microcosms without apparent delay. N(2)O was subsequently consumed in microcosms. Maximal reaction velocities (v(max)) of nitrate-dependent denitrification approximated 3 and 1 nmol of N(2)O per h per gram (dry weight [g(DW)]) in soil from 0 to 20 cm and below 20 cm of depth, respectively. v(max) values of nitrite-dependent denitrification were 2- to 5-fold higher than the v(max) nitrate-dependent denitrification, and v(max) of N(2)O consumption was 1- to 6-fold higher than that of nitrite-dependent denitrification, highlighting a high N(2)O consumption potential. Up to 12 species-level operational taxonomic units (OTUs) of narG, nirK and nirS, and nosZ were retrieved. Detected OTUs suggested the presence of diverse uncultured soil denitrifiers and dissimilatory nitrate reducers, hitherto undetected species, as well as Actino-, Alpha-, and Betaproteobacteria. Copy numbers of nirS always outnumbered those of nirK by 2 orders of magnitude. Copy numbers of nirS tended to be higher, while copy numbers of narG and nosZ tended to be lower in 0- to 20-cm soil than in soil below 20 cm. The collective data suggest that (i) the source and sink functions of palsa peat soils for N(2)O are associated with denitrification, (ii) actinobacterial nitrate reducers and nirS-type and nosZ-harboring proteobacterial denitrifiers are important players, and (iii) acidic soils like palsa peats represent reservoirs of diverse acid-tolerant denitrifiers associated with N(2)O fluxes.
Collapse
|