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Zheng J, Shi J, Wang D. Diversity of soil fungi and entomopathogenic fungi in subtropical mountain forest in southwest China. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13267. [PMID: 38943366 PMCID: PMC11213981 DOI: 10.1111/1758-2229.13267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/06/2024] [Indexed: 07/01/2024]
Abstract
Till now, the diversity of entomopathogenic fungi in subtropical mountain forest was less studied. Here, the vertical distribution of forest soil fungi, entomopathogenic fungi, and their environmental influencing factors in a subtropical mountain in western China were investigated. Soil samples were collected from four elevations in a subtropical forest in Shaanxi. The results indicated a greater richness of soil fungi at middle elevations and soil fungi were more even at low elevation. Soil pH, available iron, available potassium, total potassium, and available zinc were the most important influencing factors affecting this vertical distribution of fungi. Interestingly, the Isaria genus was predominant while Metarhizium and Beauveria showed decreasing abundance. The presence of Isaria showed a significant positive correlation with both total phosphorus and available iron, while, available zinc was negatively correlated. Metarhizium was influenced by elevation, pH, available phosphorus, and available copper and Beauveria was influenced by soil organic carbon, total nitrogen, total potassium, available potassium, and available zinc. Overall, as environmental factors affecting soil fungi, elevation, and plant species diversity were less important than soil physical and chemical properties. The virulence of isolated entomopathogenic fungi were tested against larvae of Tenebrio molitor, with mortality ranging from 31.11% to 100%. The above findings provide valuable data to deepen our understanding of the diversity of entomopathogenic fungi in subtropical mountain forests.
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Affiliation(s)
- Jiyang Zheng
- Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingShaanxiChina
| | - Jinduo Shi
- Forest Bureau of Ankang CityAnkangShaanxiChina
| | - Dun Wang
- Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingShaanxiChina
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Wang X, Yang Y, Nan Q, Guo JW, Tan Z, Shao X, Tian C. Barley farmland harbors a highly homogeneous soil bacterial community compared to wild ecosystems in the Qinghai-Xizang Plateau. Front Microbiol 2024; 15:1418161. [PMID: 38979541 PMCID: PMC11228161 DOI: 10.3389/fmicb.2024.1418161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/11/2024] [Indexed: 07/10/2024] Open
Abstract
Introduction Understanding patterns and processes of microbial biogeography in soils is important for monitoring ecological responses to human activities, particularly in ecologically vulnerable areas such as the Qinghai-Xizang Plateau. Highland barley is the staple food of local people and has mainly been cultivated along the Yarlung Zangbo River valley in Xizang. Methods Here we investigated soil bacterial communities from 33 sampling sites of highland barley farmland in this region and compared them to those from wild ecosystems including alpine tundra, meadow, forest, and swamp. Additionally, the effects of environmental factors on bacterial communities, as well as the relative importance of stochastic and deterministic processes in shaping the beta diversity of soil bacterial communities in alpine ecosystems were assessed. Results In contrast to soils of wild ecosystems, these farmland samples harbored a highly homogeneous bacterial community without significant correlations with geographic, elevation, and edaphic distances. Discriminant bacterial taxa identified for farmland samples belong to Acidobacteria, with Acidobacteria Gp4 as the dominant clade. Although Acidobacteria were the most abundant members in all ecosystems, characterized bacterial taxa of meadow and forest were members of other phyla such as Proteobacteria and Verrucomicrobia. pH and organic matter were major edaphic attributes shaping these observed patterns across ecosystems. Null model analyses revealed that the deterministic assembly was dominant in bacterial communities in highland barley farmland and tundra soils, whereas stochastic assembly also contributed a large fraction to the assembly of bacterial communities in forest, meadow and swamp soils. Discussion These findings provide an insight into the consequences of human activities and agricultural intensification on taxonomic homogenization of soil bacterial communities in the Qinghai-Xizang Plateau.
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Affiliation(s)
- Xiaolin Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yibin Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Qiong Nan
- Institute of Environmental Science and Technology, College of Environment and Resource Science, Zhejiang University, Hangzhou, China
| | - Jian-Wei Guo
- College of Agronomy and Life Sciences, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Zhiyuan Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Xiaoming Shao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Changfu Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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Yang Y, Liu H, Chen Y, Wu L, Huang G, Lv J. Soil nitrogen cycling gene abundances in response to organic amendments: A meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:171048. [PMID: 38387590 DOI: 10.1016/j.scitotenv.2024.171048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024]
Abstract
Quantification of nitrogen (N) cycling genes contributes to our best understanding of N transformation processes. The application of organic amendment (OA) is widely recognized as an effective measure to improve N management and soil fertility in various ecosystems. However, our understanding of N-cycling gene abundances in response to OA application remains deficient. We performed a meta-analysis embracing 124 sets of observation data to study the impact of OA application on the main N-cycling gene abundances, including nifH, amoA, nirS, nirK and nosZ. We found that the significantly positive response of N-cycling gene abundances to OA application was attributed to the rotation cropping system (by 6.45 %-104.20 %) in the field experiment (by 19.43 %-52.56 %), OA application alone (by 8.29 %-111.70 %) especially manure addition (by 33.43 %-98.70 %), application dose of OAs within 10-20 t ha-1 (by 45.33 %-381.90 %), fertilization duration <5 years (by 43.69 %-112.63 %), C/N of OA <25 (by 37.87 %-160.90 %), SOC lower than 1.2 % (by 41.44 %-157.89 %) and application to alkaline soil (by 32.24 %-134.40 %). Moreover, soil organic carbon (SOC) and pH were the most essential regulators associated with N-cycling gene abundances with OA application. Identification of key driving factors of the abundance of N-cycling functional genes will help remedy strategies for managing OAs in ecosystems.
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Affiliation(s)
- Yajun Yang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation Chinese Academy of Sciences & College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China.
| | - Hexiang Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation Chinese Academy of Sciences & College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Yi Chen
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation Chinese Academy of Sciences & College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Lijuan Wu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation Chinese Academy of Sciences & College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Guan Huang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation Chinese Academy of Sciences & College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Jialong Lv
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation Chinese Academy of Sciences & College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
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Luo F, Mi W, Liu W, Ma X, Liu K, Ju Z, Li W. Soil microbial community are more sensitive to ecological regions than cropping systems in alpine annual grassland of the Qinghai-Tibet Plateau. Front Microbiol 2024; 15:1345235. [PMID: 38559358 PMCID: PMC10978683 DOI: 10.3389/fmicb.2024.1345235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 03/01/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction Modern agriculture emphasizes the design of cropping systems using ecological function and production services to achieve sustainability. The functional characteristics of plants (grasses vs. legumes) affect changes in soil microbial communities that drive agroecosystem services. Information on the relationship between legume-grass mixtures and soil microorganisms in different ecological zones guides decision-making toward eco-friendly and sustainable forage production. However, it is still poorly understood how cropping patterns affect soil microbial diversity in alpine grasslands and whether this effect varies with altitude. Methods To fill this gap in knowledge, we conducted a field study to investigate the effects of growing oats (Avena sativa L.), forage peas (Pisum sativum L.), common cornflower (Vicia sativa L.), and fava beans (Vicia faba L.) in monocultures and mixtures on the soil microbial communities in three ecological zones of the high alpine zone. Results We found that the fungal and bacterial community structure differed among the cropping patterns, particularly the community structure of the legume mixed cropping pattern was very different from that of monocropped oats. In all ecological zones, mixed cropping significantly (p < 0.05) increased the α-diversity of the soil bacteria and fungi compared to oat monoculture. The α-diversity of the soil bacteria tended to increase with increasing elevation (MY [2,513 m] < HZ [2,661 m] < GN [3,203 m]), while the opposite was true for fungi (except for the Chao1 index in HZ, which was the lowest). Mixed cropping increased the abundance of soil fungi and bacteria across ecological zones, particularly the relative abundances of Nitrospira, Nitrososphaera, Phytophthora, and Acari. Factors affecting the bacterial community structure included the cropping pattern, the ecological zone, water content, nitrate-nitrogen, nitrate reductase, and soil capacity, whereas factors affecting fungal community structure included the cropping pattern, the ecological zone, water content, pH, microbial biomass nitrogen, and catalase. Discussion Our study highlights the variation in soil microbial communities among different in alpine ecological regions and their resilience to cropping systems. Our results also underscore that mixed legume planting is a sustainable and effective forage management practice for the Tibetan Plateau.
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Affiliation(s)
- Feng Luo
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
| | - Wenbo Mi
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
| | - Wenhui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
| | - Xiang Ma
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
| | - KaiQiang Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
| | - Zeliang Ju
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
| | - Wen Li
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
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Chen K, Wang B, Chen C, Zhou G. The relationship between niche breadth and phylogenetic characteristics of eight species of rhubarb on the Qinghai-Tibet Plateau, Asia. Ecol Evol 2024; 14:e11040. [PMID: 38435020 PMCID: PMC10904883 DOI: 10.1002/ece3.11040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/16/2023] [Accepted: 01/23/2024] [Indexed: 03/05/2024] Open
Abstract
The relationship between spatial distribution and phylogeny has been widely debated in recent decades. To understand biogeographic and evolutionary history relationships and to explore the interspecific similarities and phylogenetic correlations of niche characteristics, we collected and recorded all distribution points for eight species of rhubarb on the Qinghai-Tibet Plateau, used different methods to describe the ecological niche, and explored the relationship between phylogeny, ecological niche, and distribution range. The results reveal that: (1) the ranges of optimal environmental variables for species with close kinship are not exactly the same, ecologically similar species are not necessarily sister species, and the overlap of rhubarb has no significant correlation with phylogeny. Therefore, the impact of ecological dimensions on species formation is greater than that of geographical latitude for the eight species of rhubarb. (2) Among the eight species of rhubarb, the breadth of ecological niche is positively correlated with the current suitable habitat area and negatively correlated with fluctuations in future suitable habitat area. In the future, except for Rheum tanguticum and Rheum palmatum, the suitable planting areas for the other six species of rhubarb will decrease as greenhouse gas emissions concentrations and time increase. Therefore, species with smaller ecological niches are at a greater risk of habitat loss compared to species with larger ecological niches. (3) In both existing and future distribution prediction models of rhubarb, we observed that both the widely distributed Rheum spiciforme and the niche narrow Rheum nobile, all eight species of rhubarb are present in the Hengduan Mountains, based on our analysis, we propose that the Hengduan Mountains should be regarded as a priority conservation area for rhubarb, to preserve the species' biodiversity. Our study lays the groundwork for identifying evolutionary trends in ecological specialization.
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Affiliation(s)
- Kaiyang Chen
- Northwest Institute of Plateau Biology, Chinese Academy of ScienceXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Bo Wang
- Northwest Institute of Plateau Biology, Chinese Academy of ScienceXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Chen Chen
- Northwest Institute of Plateau Biology, Chinese Academy of ScienceXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Guoying Zhou
- Northwest Institute of Plateau Biology, Chinese Academy of ScienceXiningChina
- University of Chinese Academy of SciencesBeijingChina
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Aqeel M, Khalid N, Noman A, Ran J, Manan A, Hou Q, Dong L, Sun Y, Deng Y, Lee SS, Hu W, Deng J. Interplay between edaphic and climatic factors unravels plant and microbial diversity along an altitudinal gradient. ENVIRONMENTAL RESEARCH 2024; 242:117711. [PMID: 37995997 DOI: 10.1016/j.envres.2023.117711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/03/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
Altitude influences biodiversity and physiochemical soil attributes in terrestrial ecosystems. It is of immense importance to know the patterns of how interactions among climatic and edaphic factors influence plant and microbial diversity in various ecosystems, particularly along the gradients. We hypothesize that altitudinal variation determines the distribution of plant and microbial species as well as their interactions. To test the hypothesis, different sites with variable altitudes were selected. Analyses of edaphic factors revealed significant (p < 0.001) effects of the altitude. Soil ammonium and nitrate were strongly affected by it contrary to potassium (K), soil organic matter and carbon. The response patterns of individual taxonomic groups differed across the altitudinal gradient. Plant species and soil fungal diversity increased with increasing altitude, while soil archaeal and bacterial diversity decreased with increasing altitude. Plant species richness showed significant positive and negative interactions with edaphic and climatic factors. Fungal species richness was also significantly influenced by the soil ammonium, nitrate, available phosphorus, available potassium, electrical conductivity, and the pH of the soil, but showed non-significant interactions with other edaphic factors. Similarly, soil variables had limited impact on soil bacterial and archaeal species richness along the altitude gradient. Proteobacteria, Ascomycota, and Thaumarchaeota dominate soil bacterial, fungal, and archaeal communities, with relative abundance of 27.4%, 70.56%, and 81.55%, respectively. Additionally, Cynodon dactylon is most abundant plant species, comprising 22.33% of the recorded plant taxa in various study sites. RDA revealed that these communities influenced by certain edaphic and climatic factors, e.g., Actinobacteria strongly respond to MAT, EC, and C/N ratio, Ascomycota and Basidiomycota show strong associations with EC and MAP, respectively. Thaumarcheota are linked to pH, and OM, while Cyperus rotundus are sensitive to AI and EC. In conclusion, the observed variations in microbial as well as plant species richness and changes in soil properties at different elevations provide valuable insights into the factors determining ecosystem stability and multifunctionality in different regions.
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Affiliation(s)
- Muhammad Aqeel
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, 730000, Lanzhou, PR China
| | - Noreen Khalid
- Department of Botany, Government College Women University Sialkot, Pakistan
| | - Ali Noman
- Department of Botany, Government College University Faisalabad, Pakistan
| | - Jinzhi Ran
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, 730000, Lanzhou, PR China
| | - Abdul Manan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, 730000, Lanzhou, PR China
| | - Qingqing Hou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, 730000, Lanzhou, PR China
| | - Longwei Dong
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, 730000, Lanzhou, PR China
| | - Ying Sun
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, 730000, Lanzhou, PR China
| | - Yan Deng
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, 730000, Lanzhou, PR China
| | - Sang Soo Lee
- Department of Environmental and Energy Engineering, Yonsei University, Wonju, 26493, Republic of Korea
| | - Weigang Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, 730000, Lanzhou, PR China.
| | - Jianming Deng
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, 730000, Lanzhou, PR China.
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He C, Harindintwali JD, Cui H, Cui Y, Chen P, Mo C, Zhu Q, Zheng W, Alessi DS, Wang F, Jiang Z, Yang J. Deciphering the dual role of bacterial communities in stabilizing rhizosphere priming effect under intra-annual change of growing seasons. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166777. [PMID: 37660826 DOI: 10.1016/j.scitotenv.2023.166777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/05/2023]
Abstract
The rhizosphere priming effect (RPE) is a widely observed phenomenon affecting carbon (C) turnover in plant-soil systems. While multiple cropping and seasonal changes can have significant impacts on RPE, the mechanisms driving these processes are complex and not yet fully understood. Here, we planted maize in paddy soil during two growing seasons having substantial temperature differences [May-August (warm season, 26.6 °C) and September-November (cool season, 23.1 °C)] within the same calendar year in southern China to examine how seasonal changes affect RPEs and soil C. We identified sources of C emissions by quantifying the natural abundance of 13C and determined microbial metabolic limitations or efficiency and functional genes related to C cycling using an enzyme-based biogeochemical equilibrium model and high-throughput quantitative PCR-based chip technology, respectively. Results showed that microbial metabolism was mainly limited by phosphorus in the warm season, but by C in the cool season, resulting in positive RPEs in both growing seasons, but no significant differences (9.02 vs. 6.27 mg C kg-1 soil day-1). The RPE intensity remained stable as temperature increased (warm season compared to a cool season), which can be largely explained by the simultaneous increase in the abundance of functional genes related to both C degradation and fixation. Our study highlights the simultaneous response and adaptation of microbial communities to seasonal changes and hence contributes to an understanding and prediction of microbially mediated soil C turnover under multiple cropping systems.
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Affiliation(s)
- Chao He
- Institute of Environment Pollution Control and Treatment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Jean Damascene Harindintwali
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Cui
- Institute of Environment Pollution Control and Treatment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yongxing Cui
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Pengfei Chen
- Institute of Environment Pollution Control and Treatment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Chaoyang Mo
- Institute of Environment Pollution Control and Treatment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Qingyang Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Weiwei Zheng
- Institute of Environment Pollution Control and Treatment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Daniel S Alessi
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta T6G 2E3, Canada
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenhui Jiang
- Institute of Environment Pollution Control and Treatment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.
| | - Jingping Yang
- Institute of Environment Pollution Control and Treatment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.
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Ndour PMS, Bargaz A, Rchiad Z, Pawlett M, Clark IM, Mauchline TH, Harris J, Lyamlouli K. Microbial Catabolic Activity: Methods, Pertinence, and Potential Interest for Improving Microbial Inoculant Efficiency. MICROBIAL ECOLOGY 2023; 86:2211-2230. [PMID: 37280438 DOI: 10.1007/s00248-023-02250-6] [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: 04/11/2023] [Accepted: 05/24/2023] [Indexed: 06/08/2023]
Abstract
Microbial catabolic activity (MCA) defined as the degrading activity of microorganisms toward various organic compounds for their growth and energy is commonly used to assess soil microbial function potential. For its measure, several methods are available including multi-substrate-induced respiration (MSIR) measurement which allow to estimate functional diversity using selected carbon substrates targeting specific biochemical pathways. In this review, the techniques used to measure soil MCA are described and compared with respect to their accuracy and practical use. Particularly the efficiency of MSIR-based approaches as soil microbial function indicators was discussed by (i) showing their sensitivity to different agricultural practices including tillage, amendments, and cropping systems and (ii) by investigating their relationship with soil enzyme activities and some soil chemical properties (pH, soil organic carbon, cation exchange capacity). We highlighted the potential of these MSIR-based MCA measurements to improve microbial inoculant composition and to determine their potential effects on soil microbial functions. Finally, we have proposed ideas for improving MCA measurement notably through the use of molecular tools and stable isotope probing which can be combined with classic MSIR methods. Graphical abstract describing the interrelation between the different parts and the concepts developed in the review.
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Affiliation(s)
- Papa Mamadou Sitor Ndour
- College for Sustainable Agriculture and Environmental Sciences, AgroBioSciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco.
- Cranfield Soil and AgriFood Institute, School of Applied Sciences, Cranfield University, Cranfield, MK43 0AL, UK.
| | - Adnane Bargaz
- College for Sustainable Agriculture and Environmental Sciences, AgroBioSciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Zineb Rchiad
- Institute of Biological Sciences (ISSB), Faculty of Medical Sciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Mark Pawlett
- Cranfield Soil and AgriFood Institute, School of Applied Sciences, Cranfield University, Cranfield, MK43 0AL, UK
| | - Ian M Clark
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Tim H Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Jim Harris
- Cranfield Soil and AgriFood Institute, School of Applied Sciences, Cranfield University, Cranfield, MK43 0AL, UK
| | - Karim Lyamlouli
- College for Sustainable Agriculture and Environmental Sciences, AgroBioSciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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Lu M, Luo X, Jiao JJ, Li H, Kuang X, Wang X, Feng Y, Zheng C. Uncovering the processes of microbial community assembly in the near-surface sediments of a climate-sensitive glacier-fed lake. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118714. [PMID: 37542806 DOI: 10.1016/j.jenvman.2023.118714] [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: 03/15/2023] [Revised: 07/09/2023] [Accepted: 07/26/2023] [Indexed: 08/07/2023]
Abstract
Glacier-fed lakes are characterized by cold temperatures, high altitudes, and nutrient-poor conditions. Despite these challenging conditions, near-surface sediments of glacier-fed lakes harbor rich microbial communities that are critical for ecosystem functioning and serve as a bridge between aquatic ecology and the deep subsurface biosphere. However, there is limited knowledge regarding the microbial communities and their assembly processes in these sediments, which are highly vulnerable to climate change. To fill this knowledge gap, this study systematically analyzed environmental variables, microbial communities, diversity, co-occurrence relationships, and community assembly processes in the near-surface sediments of a glacier-fed lake in the Tibetan Plateau. The results revealed distinct vertical gradients in microbial diversity and subcommunities, highlighting the significant influence of selection processes and adaptive abilities on microbial communities. Specifically, specialists played a crucial role within the overall microbial communities. Microbial assembly was primarily driven by homogeneous selection, but its influence declined with increasing depth. In contrast, homogenizing dispersal showed an opposite pattern, and the bottom layer exhibited heterogeneous selection and undominated processes. These patterns of microbial assembly were primarily driven by environmental gradients, with significant contributions from processes associated to ammonium and organic matter deposition, as well as chemical precipitation in response to a warming climate. This study enhances our understanding of the microbial communities and assembly processes in the near-surface sediments of glacier-fed lakes and sheds light on geo-microbiological processes in climate-sensitive lacustrine sediments.
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Affiliation(s)
- Meiqing Lu
- Department of Earth Sciences, The University of Hong Kong, Hong Kong, China; School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xin Luo
- Department of Earth Sciences, The University of Hong Kong, Hong Kong, China
| | - Jiu Jimmy Jiao
- Department of Earth Sciences, The University of Hong Kong, Hong Kong, China.
| | - Hailong Li
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xingxing Kuang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xuejing Wang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuqing Feng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chunmiao Zheng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
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10
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Tang X, Zhang M, Fang Z, Yang Q, Zhang W, Zhou J, Zhao B, Fan T, Wang C, Zhang C, Xia Y, Zheng Y. Changing microbiome community structure and functional potential during permafrost thawing on the Tibetan Plateau. FEMS Microbiol Ecol 2023; 99:fiad117. [PMID: 37766397 DOI: 10.1093/femsec/fiad117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 09/13/2023] [Accepted: 09/27/2023] [Indexed: 09/29/2023] Open
Abstract
Large amounts of carbon sequestered in permafrost on the Tibetan Plateau (TP) are becoming vulnerable to microbial decomposition in a warming world. However, knowledge about how the responsible microbial community responds to warming-induced permafrost thaw on the TP is still limited. This study aimed to conduct a comprehensive comparison of the microbial communities and their functional potential in the active layer of thawing permafrost on the TP. We found that the microbial communities were diverse and varied across soil profiles. The microbial diversity declined and the relative abundance of Chloroflexi, Bacteroidetes, Euryarchaeota, and Bathyarchaeota significantly increased with permafrost thawing. Moreover, warming reduced the similarity and stability of active layer microbial communities. The high-throughput qPCR results showed that the abundance of functional genes involved in liable carbon degradation and methanogenesis increased with permafrost thawing. Notably, the significantly increased mcrA gene abundance and the higher methanogens to methanotrophs ratio implied enhanced methanogenic activities during permafrost thawing. Overall, the composition and functional potentials of the active layer microbial community in the Tibetan permafrost region are susceptible to warming. These changes in the responsible microbial community may accelerate carbon degradation, particularly in the methane releases from alpine permafrost ecosystems on the TP.
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Affiliation(s)
- Xiaotong Tang
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Miao Zhang
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Zhengkun Fang
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Qing Yang
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Wan Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jiaxing Zhou
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Bixi Zhao
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Tongyu Fan
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Congzhen Wang
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yu Xia
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yanhong Zheng
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
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11
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Rui J, Zhao Y, Cong N, Wang F, Li C, Liu X, Hu J, Ling N, Jing X. Elevational distribution and seasonal dynamics of alpine soil prokaryotic communities. Front Microbiol 2023; 14:1280011. [PMID: 37808282 PMCID: PMC10557256 DOI: 10.3389/fmicb.2023.1280011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
The alpine grassland ecosystem is a biodiversity hotspot of plants on the Qinghai-Tibetan Plateau, where rapid climate change is altering the patterns of plant biodiversity along elevational and seasonal gradients of environments. However, how belowground microbial biodiversity changes along elevational gradient during the growing season is not well understood yet. Here, we investigated the elevational distribution of soil prokaryotic communities by using 16S rRNA amplicon sequencing along an elevational gradient between 3,200 and 4,200 m, and a seasonal gradient between June and September in the Qinghai-Tibetan alpine grasslands. First, we found soil prokaryotic diversity and community composition significantly shifted along the elevational gradient, mainly driven by soil temperature and moisture. Species richness did not show consistent elevational trends, while those of evenness declined with elevation. Copiotrophs and symbiotic diazotrophs declined with elevation, while oligotrophs and AOB increased, affected by temperature. Anaerobic or facultatively anaerobic bacteria and AOA were hump-shaped, mainly influenced by moisture. Second, seasonal patterns of community composition were mainly driven by aboveground biomass, precipitation, and soil temperature. The seasonal dynamics of community composition indicated that soil prokaryotic community, particularly Actinobacteria, was sensitive to short-term climate change, such as the monthly precipitation variation. At last, dispersal limitation consistently dominated the assembly process of soil prokaryotic communities along both elevational and seasonal gradients, especially for those of rare species, while the deterministic process of abundant species was relatively higher at drier sites and in drier July. The balance between deterministic and stochastic processes in abundant subcommunities might be strongly influenced by water conditions (precipitation/moisture). Our findings suggest that both elevation and season can alter the patterns of soil prokaryotic biodiversity in alpine grassland ecosystem of Qinghai-Tibetan Plateau, which is a biodiversity hotspot and is experiencing rapid climate change. This work provides new insights into the response of soil prokaryotic communities to changes in elevation and season, and helps us understand the temporal and spatial variations in such climate change-sensitive regions.
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Affiliation(s)
- Junpeng Rui
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuwei Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Nan Cong
- Lhasa Plateau Ecosystem Research Station, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Fuxin Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Chao Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jingjing Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ning Ling
- Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xin Jing
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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12
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Wang M, Sun X, Cao B, Chiariello NR, Docherty KM, Field CB, Gao Q, Gutknecht JLM, Guo X, He G, Hungate BA, Lei J, Niboyet A, Le Roux X, Shi Z, Shu W, Yuan M, Zhou J, Yang Y. Long-term elevated precipitation induces grassland soil carbon loss via microbe-plant-soil interplay. GLOBAL CHANGE BIOLOGY 2023; 29:5429-5444. [PMID: 37317051 DOI: 10.1111/gcb.16811] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/22/2023] [Indexed: 06/16/2023]
Abstract
Global climate models predict that the frequency and intensity of precipitation events will increase in many regions across the world. However, the biosphere-climate feedback to elevated precipitation (eP) remains elusive. Here, we report a study on one of the longest field experiments assessing the effects of eP, alone or in combination with other climate change drivers such as elevated CO2 (eCO2 ), warming and nitrogen deposition. Soil total carbon (C) decreased after a decade of eP treatment, while plant root production decreased after 2 years. To explain this asynchrony, we found that the relative abundances of fungal genes associated with chitin and protein degradation increased and were positively correlated with bacteriophage genes, suggesting a potential viral shunt in C degradation. In addition, eP increased the relative abundances of microbial stress tolerance genes, which are essential for coping with environmental stressors. Microbial responses to eP were phylogenetically conserved. The effects of eP on soil total C, root production, and microbes were interactively affected by eCO2 . Collectively, we demonstrate that long-term eP induces soil C loss, owing to changes in microbial community composition, functional traits, root production, and soil moisture. Our study unveils an important, previously unknown biosphere-climate feedback in Mediterranean-type water-limited ecosystems, namely how eP induces soil C loss via microbe-plant-soil interplay.
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Affiliation(s)
- Mengmeng Wang
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Xin Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Yale Institute for Biospheric Studies, Yale University, New Haven, Connecticut, USA
- Department of Global Ecology, Carnegie Institution for Science, Stanford, California, USA
| | - Baichuan Cao
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Nona R Chiariello
- Jasper Ridge Biological Preserve, Stanford University, Stanford, California, USA
| | - Kathryn M Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, USA
| | - Christopher B Field
- Stanford Woods Institute for the Environment, Stanford University, Stanford, California, USA
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Jessica L M Gutknecht
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, Minnesota, USA
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Genhe He
- School of Life Sciences, Key Laboratory of Agricultural Environmental Pollution Prevention and Control in Red Soil Hilly Region of Jiangxi Province, Jinggangshan University, Ji'an, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jiesi Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Audrey Niboyet
- Institut d'Ecologie et des Sciences de l'Environnement de Paris, CNRS, INRAE, IRD, Sorbonne Université, Université Paris Cité, UPEC, Paris, France
- AgroParisTech, Palaiseau, France
| | - Xavier Le Roux
- Laboratoire d'Ecologie Microbienne, INRAE, CNRS, VetAgroSup, UMR INRAE 1418, UMR CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Zhou Shi
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Wensheng Shu
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Mengting Yuan
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- Earth and Environmental Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma, USA
- School of Computer Science, University of Oklahoma, Norman, Oklahoma, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
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13
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Yang R, Yang Z, Yang S, Chen LL, Xin J, Xu L, Zhang X, Zhai B, Wang Z, Zheng W, Li Z. Nitrogen inhibitors improve soil ecosystem multifunctionality by enhancing soil quality and alleviating microbial nitrogen limitation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 880:163238. [PMID: 37011677 DOI: 10.1016/j.scitotenv.2023.163238] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 05/27/2023]
Abstract
Soil quality (SQI) is a comprehensive indicator reflecting the agricultural productivity of soil, and soil ecosystem multifunctionality (performing multiple functions simultaneously; EMF) can reflect complex biogeochemical processes. However, the effects of enhanced efficiency nitrogen fertilizers (EENFs; urease inhibitors (NBPT), nitrification inhibitors (DCD), and coated controlled-release urea (RCN)) application on the SQI and soil EMF and their relationships are still unclear. Therefore, we conducted a field experiment to study the effects of different EENFs on the SQI, enzyme stoichiometry and soil EMF in semiarid areas of Northwest China (Gansu, Ningxia, Shaanxi, Shanxi). Across the four study sites, DCD and NBPT increased SQI by 7.61-16.80 % and 2.61 %-23.20 % compared to mineral fertilizer, respectively. N fertilizer application (N200 and EENFs) alleviated microbial N limitation, and EENFs alleviated microbial N and C limitations to a greater extent in Gansu and Shanxi. Moreover, nitrogen inhibitors (Nis; DCD and NBPT) improved the soil EMF to a greater extent than N200 and RCN, DCD increased by 205.82-340.00 % and 145.00-215.47 % in Gansu and Shanxi, respectively; NBPT increased by 332.75-778.59 % and 364.44-929.62 % in Ningxia and Shanxi, respectively. A random forest model showed that the microbial biomass carbon (MBC), microbial biomass nitrogen (MBN) and soil water content (SWC) of the SQI factors were the main driving forces of soil EMF. Moreover, SQI improvement could alleviate microbial C and N limitations and promote the improvement of soil EMF. It is worth noting that soil EMF was mainly affected by microbial N limitation rather than C limitation. Overall, NIs application is an effective way to improve the SQI and soil EMF in the semiarid region of Northwest China.
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Affiliation(s)
- Ruizhe Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Ze Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Shilong Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Lan-Lan Chen
- College of Resources and Environmental Sciences, Gansu Agricultural University/Gansu Provincial Key Laboratory of Arid-land Crop Science, Lanzhou 730070, PR China
| | - Jia Xin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Changshu National Agro-Ecosystem Observation and Research Station, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Lingying Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Changshu National Agro-Ecosystem Observation and Research Station, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Xuechen Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Bingnian Zhai
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Zhaohui Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Wei Zheng
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China.
| | - Ziyan Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China.
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14
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Kang Y, Wu H, Zhang Y, Wu Q, Guan Q, Lu K, Lin Y. Differential distribution patterns and assembly processes of soil microbial communities under contrasting vegetation types at distinctive altitudes in the Changbai Mountain. Front Microbiol 2023; 14:1152818. [PMID: 37333641 PMCID: PMC10272400 DOI: 10.3389/fmicb.2023.1152818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 03/29/2023] [Indexed: 06/20/2023] Open
Abstract
Diversity patterns and community assembly of soil microorganisms are essential for understanding soil biodiversity and ecosystem processes. Investigating the impacts of environmental factors on microbial community assembly is crucial for comprehending the functions of microbial biodiversity and ecosystem processes. However, these issues remain insufficiently investigated in related studies despite their fundamental significance. The present study aimed to assess the diversity and assembly of soil bacterial and fungal communities to altitude and soil depth variations in mountain ecosystems by using 16S and ITS rRNA gene sequence analyses. In addition, the major roles of environmental factors in determining soil microbial communities and assembly processes were further investigated. The results showed a U-shaped pattern of the soil bacterial diversity at 0-10 cm soil depth along altitudes, reaching a minimum value at 1800 m, while the fungal diversity exhibited a monotonically decreasing trend with increasing altitude. At 10-20 cm soil depth, the soil bacterial diversity showed no apparent changes along altitudinal gradients, while the fungal Chao1 and phylogenetic diversity (PD) indices exhibited hump-shaped patterns with increasing altitude, reaching a maximum value at 1200 m. Soil bacterial and fungal communities were distinctively distributed with altitude at the same depth of soil, and the spatial turnover rates in fungi was greater than in bacteria. Mantel tests suggested soil physiochemical and climate variables significantly correlated with the β diversity of microbial community at two soil depths, suggesting both soil and climate heterogeneity contributed to the variation of bacterial and fungal community. Correspondingly, a novel phylogenetic null model analysis demonstrated that the community assembly of soil bacterial and fungal communities were dominated by deterministic and stochastic processes, respectively. The assembly processes of bacterial community were significantly related to the soil DOC and C:N ratio, while the fungal community assembly processes were significantly related to the soil C:N ratio. Our results provide a new perspective to assess the responses of soil microbial communities to variations with altitude and soil depth.
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Affiliation(s)
- Yujuan Kang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Haitao Wu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yifan Zhang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Tourism and Geography Sciences, Jilin Normal University, Siping, China
| | - Qiong Wu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Tourism and Geography Sciences, Jilin Normal University, Siping, China
| | - Qiang Guan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Kangle Lu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yiling Lin
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
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15
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Wang Y, Sun J, Lee TM. Altitude dependence of alpine grassland ecosystem multifunctionality across the Tibetan Plateau. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 332:117358. [PMID: 36724595 DOI: 10.1016/j.jenvman.2023.117358] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/17/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
While altitude affects climatic characteristics, terrestrial plant habitats, and species composition, few studies considered the effects of altitude on ecosystem multifunctionality (EMF). Here, we teased apart the EMF at different altitude with a linear piecewise quantile regression and explore ecosystem functions and environmental factors with EMF along the altitudinal gradient across the Tibetan Plateau. Then, we estimated the response of ecosystem functions to environmental factors, and explain the impact of environmental factors on EMF through the structural equation model. Our data revealed an EMF changepoint at an altitude of about 3900 m where the EMF could be segregated into low- and high-altitude patterns. Our results indicate that water availability drives the EMF mainly through improving soil nutrients and microbe cycling functions in low-altitude regions; conversely, water-heat and phenological conditions regulate the EMF through the role of plant productivity and soil nutrients in high-altitude regions. As such, our EMF analysis suggests that to maintain the long-term stability of the grassland ecosystem, it becomes critical to fully consider the differences in the altitudinal patterns and mechanisms, particularly under the ongoing climate change.
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Affiliation(s)
- Yi Wang
- School of Life Sciences and State Key Lab of Biological Control, Sun Yat-sen University, Guangzhou, 510275, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian Sun
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Tien Ming Lee
- School of Life Sciences and State Key Lab of Biological Control, Sun Yat-sen University, Guangzhou, 510275, China; School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
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16
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Xie C, Ma X, Zhao Y, Dai T, Song W, Qi Q, Feng J, Cui X, Zhou J, Huang X, Qi F, Zeng Y, Zhou J, Lin G, Yang Y. Nitrogen addition and warming rapidly alter microbial community compositions in the mangrove sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:157992. [PMID: 35970461 DOI: 10.1016/j.scitotenv.2022.157992] [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: 04/19/2022] [Revised: 07/10/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
The mangrove ecosystem is an important CO2 sink with an extraordinarily high primary productivity. However, it is vulnerable to the impact of climate warming and eutrophication. While there has been extensive research on plant growth and greenhouse gas emission in mangrove ecosystems, microbial communities, the primary biogeochemical cycling drivers, are much less understood. Here, we examined whether short-term experimental treatments: (1) eutrophication with a supplement of 185 g N m-2·year-1 (N), (2) 3°C warming (W), and (3) the dual treatment of N and W (NW) were sufficient to alter microbial communities in the sediment. After 4 months of experiments, most environmental factors remained unchanged. However, N had significant, strong effects on bacterial, fungal, and functional community compositions, while the effects of W on microbial communities were weaker. N increased bacterial richness, phylogenetic diversity, and evenness, owing to stronger stochastic processes induced by eutrophication. There were no interactive effects of N and W on bacterial, fungal, and functional community compositions, suggesting that joint effects of N and W were additive. Concomitant with higher N2O efflux induced by N, the relative abundances of most bacterial nitrogen cycling genes were increased or remained changed by N. In contrast, N decreased or did not change those of most bacterial carbon degradation genes, while W increased or did not change the relative abundances of most of bacterial and fungal carbon degradation genes, implying higher carbon degradation potentials. As the most abundant inorganic nitrogenous species in mangrove sediment, ammonium was a key factor in shaping microbial functional communities. Collectively, our findings showed that microbial community compositions in the mangrove sediment were highly sensitive to short-term N and W treatments, giving rise to ecological consequences such as higher N2O efflux.
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Affiliation(s)
- Changyi Xie
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xingyu Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yan Zhao
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China; Key Laboratory of Stable Isotope and Gulf Ecology, Institute of Ocean Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Tianjiao Dai
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Weimin Song
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China; The Yellow River Delta Ecology Research Station of Coastal Wetland, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Qi Qi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jianxiang Feng
- Key Laboratory of Stable Isotope and Gulf Ecology, Institute of Ocean Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China; School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xiaowei Cui
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China; Key Laboratory of Stable Isotope and Gulf Ecology, Institute of Ocean Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Jian Zhou
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China; Key Laboratory of Stable Isotope and Gulf Ecology, Institute of Ocean Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Xiaofang Huang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Fei Qi
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Yufei Zeng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Guanghui Lin
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China; Key Laboratory of Stable Isotope and Gulf Ecology, Institute of Ocean Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China.
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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17
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Li Y, Fang Z, Yang F, Ji B, Li X, Wang S. Elevational changes in the bacterial community composition and potential functions in a Tibetan grassland. Front Microbiol 2022; 13:1028838. [DOI: 10.3389/fmicb.2022.1028838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/17/2022] [Indexed: 11/11/2022] Open
Abstract
In the Tibetan grasslands, the distribution patterns of the microbial community structure and function along elevation gradients have attracted considerable attention due to the wide distribution of mountain slopes, but the controlling factors of these patterns are still unclear. Here we investigated the taxonomy and potential functions of soil bacteria along an elevation gradient in a Tibetan mountainous grassland in 2 years, aiming to explore the elevation patterns of the bacterial structure and function and the underlying drivers. High-throughput sequencing and environment attribute measurements were conducted to survey the bacterial and environment characters. Furthermore, PICRUSt2 for prediction of bacterial functions, iCAMP for unraveling the drivers controlling community assembly, and HMSC for variance partitioning of bacterial community composition were used. Elevation did not significantly affect the bacterial diversity but changed their composition, driven by both deterministic and stochastic processes. In addition, elevation did not significantly affect the relative importance of deterministic and stochastic processes. Soil carbon, nitrogen, and temperature were important deterministic factors in driving bacterial community structure. The genus Solirubrobacter in Actinobacteriota was identified as most elevation discriminatory. Based on these observations, the bacterial community in the Tibetan mountainous grasslands was more controlled by edaphic factors than temperature, indicating their relative stability under climate change scenarios.
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18
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Liu J, Li C, Ma W, Liu W, Wu W. Molecular Characterization of Distinct Fungal Communities in the Soil of a Rare Earth Mining Area. MICROBIAL ECOLOGY 2022; 84:1212-1223. [PMID: 34839384 DOI: 10.1007/s00248-021-01931-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
The exploitation of ion-absorbed rare earth elements (REEs) has caused serious ecological destruction and environmental pollution. Effects on soil fungal structure and diversity exerted by mining activities are usually ignored, although fungus is one of the most important components in soil ecosystems. In the present research, quantitative polymerase chain reaction (qPCR) and high-throughput Illumina MiSeq sequencing were conducted to characterize fungal community composition and structure in soil of a rare earth mining area after in situ leaching. Statistical analyses, network, and FUNGuild were used to conduct in-depth analyses. Ascomycota, Basidiomycota, and Glomeromycota were the most abundant phyla in the mining soils. Fungal community structures were stable after leaching practice, but nutrition contents (organic matter, TC, and TN) significantly and positively contributed to fungal abundances and diversities. Saprotrophs in phyla Ascomycota and Basidiomycota were the dominant fungal trophic mode, and they played critical roles in nutrient cycling, transformation processes, and reducing REE toxicity. Symbiotrophs of phyla Glomeromycota contributed to soil aggregation and slowing down nutrient losses after in situ leaching practice. In addition, fungi could regulate the interactions between species to resist the harsh environment of REE toxicity or ammonium caused by in situ leaching practice.
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Affiliation(s)
- Jingjing Liu
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, 330013, China.
- Jiangxi Key Laboratory of Mining & Metallurgy Environmental Pollution Control, Ganzhou, 341099, China.
| | - Chun Li
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, 330013, China
| | - Wendan Ma
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, 330013, China
| | - Wei Liu
- College of Chemistry and Environmental Science, Hebei University, Baoding, 071002, China
| | - Weixiang Wu
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, 310030, People's Republic of China
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19
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Li J, Chen L, Wang H, Ouyang S, Liu X, Lu J. Pattern and drivers of soil fungal community along elevation gradient in the Abies georgei forests of Segila mountains, Southeast Tibet. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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20
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Ma T, Zhang X, Wang R, Liu R, Shao X, Li J, Wei Y. Linkages and key factors between soil bacterial and fungal communities along an altitudinal gradient of different slopes on mount Segrila, Tibet, China. Front Microbiol 2022; 13:1024198. [PMID: 36386611 PMCID: PMC9649828 DOI: 10.3389/fmicb.2022.1024198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/11/2022] [Indexed: 12/04/2022] Open
Abstract
Soil microbes are of great significance to many energy flow and material circulation processes in alpine forest ecosystems. The distribution pattern of soil microbial community along altitudinal gradients is an essential research topic for the Tibetan Plateau. Yet our understanding of linkages between soil microbial communities and key factors along an altitudinal gradient of different slopes remains limited. Here, the diversity, composition and interaction of bacterial and fungal communities and in response to environmental factors were compared across five elevation sites (3,500 m, 3,700 m, 3,900 m, 4,100 m, 4,300 m) on the eastern and western slopes of Mount Segrila, by using Illumina MiSeq sequencing. Our results showed that microbial community composition and diversity were distinct at different elevations, being mainly influenced by soil total nitrogen and carbonate. Structural equation models indicated that elevation had a greater influence than slope upon the soil microbial community. Co-occurrence network analysis suggested that fungi were stable but bacteria contributed more to among interactions of bacterial and fungal communities. Ascomycota was identified as a key hub for the internal interactions of microbial community, which might affect the soil microbial co-occurrence network resilience of alpine forest ecosystems on the Tibetan Plateau.
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Affiliation(s)
- Tiantian Ma
- Institute of Tibet Plateau Ecology, Tibet Agricultural and Animal Husbandry University, Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, Tibet, China
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China
| | - Xinjun Zhang
- Institute of Tibet Plateau Ecology, Tibet Agricultural and Animal Husbandry University, Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, Tibet, China
- *Correspondence: Xinjun Zhang,
| | - Ruihong Wang
- Institute of Tibet Plateau Ecology, Tibet Agricultural and Animal Husbandry University, Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, Tibet, China
| | - Rui Liu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China
| | - Xiaoming Shao
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China
| | - Ji Li
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou, China
| | - Yuquan Wei
- Institute of Tibet Plateau Ecology, Tibet Agricultural and Animal Husbandry University, Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education, Nyingchi, Tibet, China
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou, China
- Yuquan Wei,
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21
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Zhu R, Liu C, Xu YD, He W, Liu J, Chen J, An Y, Shi S. Ratio of carbon and nitrogen in fertilizer treatment drives distinct rhizosphere microbial community composition and co-occurrence networks. Front Microbiol 2022; 13:968551. [PMID: 36160210 PMCID: PMC9493311 DOI: 10.3389/fmicb.2022.968551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
Fertilization is the main strategy to accelerate vegetation restoration and improve the rhizosphere microbial community in the northeast China. However, the responses of rhizosphere microbial community structure, specific microbial community and symbiotic pattern to manure fertilization in grassland (alfalfa only) are not well clear. In this study, the variation of bacterial community structures in R_Manure (extracted liquid of fermented cow manure), E_Manure (extracted residue of fermented cow manure), F_Manure (full fermented cow manure), and Control (without fermented cow manure) collected from the rhizosphere microbial community of alfalfa were analyzed by the application of an Illumina HiSeq high-throughput sequencing technique. A total of 62,862 microbial operational taxonomic units (OTUs) were detected and derived from 21 phyla of known bacteria. The dominant bacteria in the rhizosphere include Proteobacteria (70.20%), Acidobacteria (1.24%), Actinobacteria (2.11%), Bacteroidetes (6.15%), Firmicutes (4.21%), and Chlorofexi (2.13%) accounting for 86% of the dominant phyla in all treatments. At the genus level, the dominant genus include NB1-j, Lysobacter, Alphaproteobacteria, Subgroup_6, Actinomarinales, Saccharimonadales, Aneurinibacillus, MO-CFX2, SBR1031, Caldilineaceae, and so on with the average relative abundance (RA) of 1.76%, 1.52%, 1.30%, 1.24%, 1.61%, 2.39%, 1.36%, 1.42%, 1.27%, and 1.03%, respectively. Bacterial diversities and community structures were significantly differentiated by different treatments of fertilization. The results of community structure composition showed that R_Manure treatment significantly increased the population abundance of Firmicutes, Chlorofexi, and Patescibacteria by 34.32%, 6.85%, and 2.70%, and decreased the population abundance of Proteobacteria and Actinobacteria by 16.83% and 1.04%, respectively. In addition, it showed that all treatments significantly resulted in an increase or decrease at the genus level. R_Manure had the higher richness and diversity of the bacterial community, with the greatest topology attributes of the co-occurrence networks. Through the analysis of the molecular ecological network (MENA), the co-occurrence networks had a shorter average path distance and diameter in R_Manure than in others, implying more stability to environmental changes. Redundancy analysis (RDA) showed that the ratio of carbon and nitrogen (C/N) was the main factor affecting rhizosphere microbial community composition while driving distinct rhizosphere bacterial community and its co-occurrence networks. The R_Manure associated with more C/N had relatively complex microbial co-occurrence network with a large number of nodes and edges, while the microbial network of others associated with less C/N had fewer taxa with loose mutual interactions. These results suggested that organic fertilizer with high C/N can regulate the rhizosphere microorganism, while high C/N can determine bacterial community structures, specific bacterial taxa, and their relationships with the nodule size of alfalfa. These significant changes can be used to evaluate soil fertility and fertilizer management in the artificial grassland system, while the potential biological indicators of the rhizosphere microbial community will play an important role in future eco-agriculture.
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Affiliation(s)
- Ruifen Zhu
- Pratacultural College, Gansu Agricultural University, Lanzhou, China
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
- Pratacultural Institute Science, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Chang Liu
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Yuan Dong Xu
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Wei He
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Jielin Liu
- Pratacultural Institute Science, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jishan Chen
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Yajun An
- Gansu Yasheng Agricultural Research Institute Co., Ltd., Lanzhou, China
| | - Shangli Shi
- Pratacultural College, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Shangli Shi
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22
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Ma X, Wang T, Shi Z, Chiariello NR, Docherty K, Field CB, Gutknecht J, Gao Q, Gu Y, Guo X, Hungate BA, Lei J, Niboyet A, Le Roux X, Yuan M, Yuan T, Zhou J, Yang Y. Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity. MICROBIOME 2022; 10:112. [PMID: 35902889 PMCID: PMC9330674 DOI: 10.1186/s40168-022-01309-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Anthropogenic activities have increased the inputs of atmospheric reactive nitrogen (N) into terrestrial ecosystems, affecting soil carbon stability and microbial communities. Previous studies have primarily examined the effects of nitrogen deposition on microbial taxonomy, enzymatic activities, and functional processes. Here, we examined various functional traits of soil microbial communities and how these traits are interrelated in a Mediterranean-type grassland administrated with 14 years of 7 g m-2 year-1 of N amendment, based on estimated atmospheric N deposition in areas within California, USA, by the end of the twenty-first century. RESULTS Soil microbial communities were significantly altered by N deposition. Consistent with higher aboveground plant biomass and litter, fast-growing bacteria, assessed by abundance-weighted average rRNA operon copy number, were favored in N deposited soils. The relative abundances of genes associated with labile carbon (C) degradation (e.g., amyA and cda) were also increased. In contrast, the relative abundances of functional genes associated with the degradation of more recalcitrant C (e.g., mannanase and chitinase) were either unchanged or decreased. Compared with the ambient control, N deposition significantly reduced network complexity, such as average degree and connectedness. The network for N deposited samples contained only genes associated with C degradation, suggesting that C degradation genes became more intensely connected under N deposition. CONCLUSIONS We propose a conceptual model to summarize the mechanisms of how changes in above- and belowground ecosystems by long-term N deposition collectively lead to more soil C accumulation. Video Abstract.
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Affiliation(s)
- Xingyu Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
- China Urban Construction Design & Research Institute Co., Ltd, Beijing, 100120, China
| | - Tengxu Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
- North China Municipal Engineering Design & Research Institute Co., Ltd., the Beijing Branch, Beijing, 100081, China
| | - Zhou Shi
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Nona R Chiariello
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Kathryn Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, 49008, USA
| | - Christopher B Field
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Jessica Gutknecht
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, 06120, Halle, Germany
- Present address: Department of Soil, Water, and Climate, University of Minnesota, Twin Cities, Saint Paul, MN, 55104, USA
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yunfu Gu
- Department of Microbiology, College of Resource, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Jiesi Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Audrey Niboyet
- Sorbonne Université, Université Paris Cité, UPEC, CNRS, INRAE, IRD, Institut d'Ecologie et des Sciences de l'Environnement de Paris, iEES-Paris, Paris, France
- AgroParisTech, Paris, France
| | - Xavier Le Roux
- Microbial Ecology Centre LEM, INRAE, CNRS, University of Lyon, University Lyon 1, VetAgroSup, UMR INRAE 1418, 43 boulevard du 11 novembre 1918, 69622, Villeurbanne, France
| | - Mengting Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Tong Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
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23
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Tian C, Pang J, Bu C, Wu S, Bai H, Li Y, Guo Q, Siddique KHM. The Microbiomes in Lichen and Moss Biocrust Contribute Differently to Carbon and Nitrogen Cycles in Arid Ecosystems. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02077-7. [PMID: 35864173 DOI: 10.1007/s00248-022-02077-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Biological soil crusts (biocrusts) are distributed in arid and semiarid regions across the globe. Microorganisms are an essential component in biocrusts. They add and accelerate critical biochemical processes. However, little is known about the functional genes and metabolic processes of microbiomes in lichen and moss biocrust. This study used shotgun metagenomic sequencing to compare the microbiomes of lichen-dominated and moss-dominated biocrust and reveal the microbial genes and metabolic pathways involved in carbon and nitrogen cycling. The results showed that Actinobacteria, Bacteroidetes, and Acidobacteria were more abundant in moss biocrust than lichen biocrust, while Proteobacteria and Cyanobacteria were more abundant in lichen biocrust than moss biocrust. The relative abundance of carbohydrate-active enzymes and enzymes associated with carbon and nitrogen metabolism differed significantly between microbiomes of the two biocrust types. However, in the microbial communities of both biocrust types, respiration pathways dominated over carbon fixation pathways. The genes encoding carbon monoxide dehydrogenase were more abundant than those encoding ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo) involved in carbon fixation. Similarly, metabolic N-pathway diversity was dominated by nitrogen reduction, followed by denitrification, with nitrogen fixation the lowest proportion. Gene diversity involved in N cycling differed between the microbiomes of the two biocrust types. Assimilatory nitrate reduction genes had higher relative abundance in lichen biocrust, whereas dissimilatory nitrate reduction genes had higher relative abundance in moss biocrust. As dissolved organic carbon and soil organic carbon are considered the main drivers of the community structure in the microbiome of biocrust, these results indicate that biocrust type has a pivotal role in microbial diversity and related biogeochemical cycling.
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Affiliation(s)
- Chang Tian
- Institute of Soil and Water Conservation, Northwest A & F University, Yangling, Shaanxi, 712100, China
- Institute of Soil and Water Conservation, CAS & MWR, Yangling, Shaanxi, 712100, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingwen Pang
- Institute of Soil and Water Conservation, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Chongfeng Bu
- Institute of Soil and Water Conservation, Northwest A & F University, Yangling, Shaanxi, 712100, China.
- Institute of Soil and Water Conservation, CAS & MWR, Yangling, Shaanxi, 712100, China.
| | - Shufang Wu
- College of Water Resources and Architectural Engineering, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Hao Bai
- Sichuan Expressway Construction & Development Group Co., Ltd, Chengdu, Sichuan, 610041, China
| | - Yahong Li
- Institute of Soil and Water Conservation, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Qi Guo
- Institute of Soil and Water Conservation, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, Perth, WA, 6001, Australia
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24
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Elevational Gradient of Climate-Driving Effects on Cropland Ecosystem Net Primary Productivity in Alpine Region of the Southwest China. REMOTE SENSING 2022. [DOI: 10.3390/rs14133069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Investigating elevational gradient of climate driving effects on cropland ecosystem net primary productivity (NPP) plays an important role in food security in alpine region. We simulated cropland NPP by coupling a remote sensing model with an ecosystem process model and explored elevational gradient of climate driving effects on it in an alpine region of the southwest China during 1981–2014. The results showed that cropland NPP increased significantly with a rate of 3.85 gC m−2 year−1 year−1 under significant increasing solar radiation and climate warming and drying, among which the increasing solar radiation was the main driving factor of the increasing NPP. The driving effect of climate warming on cropland NPP shifted from negative at low elevations to positive at high elevations, which was caused by the fragile ecosystem characteristics and frequent drought at low elevations and a higher temperature sensitivity of cropland ecosystem at high elevations. Different effects of climate warming on NPP change at different elevations caused different results when we analyzed the climate-driving effects on cropland NPP at different spatial scales. These results reminded us that we should take the elevational gradient of climate driving effects into account when we manage food security in the alpine region.
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25
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Zhao L, Wang Y, Xing J, Gu S, Wu Y, Li X, Ma J, Mao J. Distinct succession of abundant and rare fungi in fermented grains during Chinese strong-flavor liquor fermentation. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Wang J, Hu A, Meng F, Zhao W, Yang Y, Soininen J, Shen J, Zhou J. Embracing mountain microbiome and ecosystem functions under global change. THE NEW PHYTOLOGIST 2022; 234:1987-2002. [PMID: 35211983 DOI: 10.1111/nph.18051] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Mountains are pivotal to maintaining habitat heterogeneity, global biodiversity, ecosystem functions and services to humans. They have provided classic model natural systems for plant and animal diversity gradient studies for over 250 years. In the recent decade, the exploration of microorganisms on mountainsides has also achieved substantial progress. Here, we review the literature on microbial diversity across taxonomic groups and ecosystem types on global mountains. Microbial community shows climatic zonation with orderly successions along elevational gradients, which are largely consistent with traditional climatic hypotheses. However, elevational patterns are complicated for species richness without general rules in terrestrial and aquatic environments and are driven mainly by deterministic processes caused by abiotic and biotic factors. We see a major shift from documenting patterns of biodiversity towards identifying the mechanisms that shape microbial biogeographical patterns and how these patterns vary under global change by the inclusion of novel ecological theories, frameworks and approaches. We thus propose key questions and cutting-edge perspectives to advance future research in mountain microbial biogeography by focusing on biodiversity hypotheses, incorporating meta-ecosystem framework and novel key drivers, adapting recently developed approaches in trait-based ecology and manipulative field experiments, disentangling biodiversity-ecosystem functioning relationships and finally modelling and predicting their global change responses.
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Affiliation(s)
- Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ang Hu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing, 210008, China
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, China
| | - Fanfan Meng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenqian Zhao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Janne Soininen
- Department of Geosciences and Geography, University of Helsinki, Helsinki, FIN-00014, Finland
| | - Ji Shen
- School of Geography and Ocean Science, Nanjing University, Nanjing, 210023, China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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27
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Liu S, Sun Y, Shi F, Liu Y, Wang F, Dong S, Li M. Composition and Diversity of Soil Microbial Community Associated With Land Use Types in the Agro-Pastoral Area in the Upper Yellow River Basin. FRONTIERS IN PLANT SCIENCE 2022; 13:819661. [PMID: 35548288 PMCID: PMC9082682 DOI: 10.3389/fpls.2022.819661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
The microorganisms of soil are sensitive to their living microenvironment, and their community structure and function will change with the environmental conditions. In the agro-pastoral area on the Qinghai-Tibet Plateau, revealing the diversity of the soil microbial communities and its response to different soil physicochemical properties and environmental factors are important for ecosystem management. The microbial (bacteria and archaea) community composition and diversity under different land use types (cultivated land, grazing grassland and planted forest) were analyzed by 16S rRNA (V4 region) method in a typical agro-pastoral region in the upper Yellow River basin. Also, the soil nutrients were studied and correlated with the microbial community. The results showed that the soil nutrient contents in grassland were low, but the available nutrients were relatively high. There was a great spatial variability under different distances to the river. The microbial community diversity was lower in the grassland than the cultivated land and forest land closer to the river. For all land uses, the dominant phyla of soil microorganisms included Proteobacteria, Actinobacteria, and Bacteroidetes, while the abundance of Clostridia was significantly higher than that of the other groups, indicating that Clostridia dominated the Firmicutes and affected soil microbial community composition. The linear discriminant analysis (LDA) effect size (LefSe) analysis showed different biomarkers were more abundant in grassland than other land use types, suggesting that the structure and diversity of soil microorganisms in grassland were significantly different compared with cultivated land and forest land. The distance-based redundancy analysis (db-RDA) results showed that the total phosphorus (TP) and calcium (Ca) were the key environmental factors affecting the diversity and abundance of the soil microbial community in cultivated land and forestland, respectively. However, the microbial diversity in grassland was more related to spatial distance of the river. These results provided a theoretical basis for the changes in the composition, structure, and function of soil microbial communities in agro-pastoral areas.
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Affiliation(s)
- Shiliang Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Yongxiu Sun
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Fangning Shi
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Yixuan Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Fangfang Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Shikui Dong
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Mingqi Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
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Bacterial Communities of Forest Soils along Different Elevations: Diversity, Structure, and Functional Composition with Potential Impacts on CO 2 Emission. Microorganisms 2022; 10:microorganisms10040766. [PMID: 35456816 PMCID: PMC9032212 DOI: 10.3390/microorganisms10040766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 11/17/2022] Open
Abstract
Soil bacteria are important components of forest ecosystems, there compostion structure and functions are sensitive to environmental conditions along elevation gradients. Using 16S rRNA gene amplicon sequencing followed by FAPROTAX function prediction, we examined the diversity, composition, and functional potentials of soil bacterial communities at three sites at elevations of 1400 m, 1600 m, and 2200 m in a temperate forest. We showed that microbial taxonomic composition did not change with elevation (p = 0.311), though soil bacterial α-diversities did. Proteobacteria, Acidobacteria, Actinobacteria, and Verrucomicrobia were abundant phyla in almost all soil samples, while Nitrospirae, closely associated with soil nitrogen cycling, was the fourth most abundant phylum in soils at 2200 m. Chemoheterotrophy and aerobic chemoheterotrophy were the two most abundant functions performed in soils at 1400 m and 1600 m, while nitrification (25.59% on average) and aerobic nitrite oxidation (19.38% on average) were higher in soils at 2200 m. Soil CO2 effluxes decreased (p < 0.050) with increasing elevation, while they were positively correlated (r = 0.55, p = 0.035) with the abundances of bacterial functional groups associated with carbon degradation. Moreover, bacterial functional composition, rather than taxonomic composition, was significantly associated with soil CO2 effluxes, suggesting a decoupling of taxonomy and function, with the latter being a better predictor of ecosystem functions. Annual temperature, annual precipitation, and pH shaped (p < 0.050) both bacterial taxonomic and functional communities. By establishing linkages between bacterial taxonomic communities, abundances of bacterial functional groups, and soil CO2 fluxes, we provide novel insights into how soil bacterial communities could serve as potential proxies of ecosystem functions.
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Community structure, distribution pattern, and influencing factors of soil Archaea in the construction area of a large-scale photovoltaic power station. Int Microbiol 2022; 25:571-586. [DOI: 10.1007/s10123-022-00244-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/07/2022] [Accepted: 03/23/2022] [Indexed: 11/25/2022]
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Cao PX, Liu Y, Ma HM, Zhao N, Chen ST, Xu GQ, Liu X. Fungal Diversity in the Soil of the Oxytropis glacialis Root System on the Qinghai-Tibet Plateau. Front Microbiol 2022; 13:831783. [PMID: 35283812 PMCID: PMC8907473 DOI: 10.3389/fmicb.2022.831783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/25/2022] [Indexed: 11/17/2022] Open
Abstract
Because of swainonine-producing endophytic fungal, Oxytropis glacialis is one of the main poisonous weeds in the alpine grassland and desert grassland of the Qinghai-Tibet Plateau (QTP). It has a severe impact on grassland degradation on the QTP. In this manuscript, the Internally Transcribed Spacer (ITS) region of fungal communities in the soil of the O. glacialis root system was sequenced by high-throughput sequencing and analyzed by bioinformatics methods. The physical and chemical properties of the soil samples were analyzed in combination with the fungal diversity and its relationship with the soil physical and chemical factors. The results showed that the soil fungal community in the O. glacialis root system are rich in diversity in different ecological environments and are most affected by the soil pH value and organic matter. The swainonine-producing fungal Embellisia oxytropis was first detected in the soil of the O. glacialis root system. This finding provides data to support the next step in demonstrating the horizontal spread of swainone-producing fungal from O. glacialis to soil. In addition, a stable network of core flora has a facilitating effect on the formation of O. glacialis as a dominant species in alpine ecosystems.
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Affiliation(s)
- Peng-Xi Cao
- Ecological Field Station Real-Time Monitoring Center, Research Center for Ecology, Tibet University, Lhasa, China.,Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, China.,College of Life Science, Wuhan University, Wuhan, China
| | - Yixuan Liu
- Ecological Field Station Real-Time Monitoring Center, Research Center for Ecology, Tibet University, Lhasa, China.,Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, China.,College of Life Science, Wuhan University, Wuhan, China
| | - Hong-Mei Ma
- Ecological Field Station Real-Time Monitoring Center, Research Center for Ecology, Tibet University, Lhasa, China.,Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, China
| | - Ning Zhao
- Ecological Field Station Real-Time Monitoring Center, Research Center for Ecology, Tibet University, Lhasa, China.,Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, China
| | - Shu-Ting Chen
- Ecological Field Station Real-Time Monitoring Center, Research Center for Ecology, Tibet University, Lhasa, China.,Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, China
| | - Guo-Qi Xu
- Ecological Field Station Real-Time Monitoring Center, Research Center for Ecology, Tibet University, Lhasa, China.,Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, China
| | - Xing Liu
- Ecological Field Station Real-Time Monitoring Center, Research Center for Ecology, Tibet University, Lhasa, China.,Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, China.,College of Life Science, Wuhan University, Wuhan, China
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31
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Macroecological distributions of gene variants highlight the functional organization of soil microbial systems. THE ISME JOURNAL 2022; 16:726-737. [PMID: 34580430 PMCID: PMC8857198 DOI: 10.1038/s41396-021-01120-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 11/09/2022]
Abstract
The recent application of macroecological tools and concepts has made it possible to identify consistent patterns in the distribution of microbial biodiversity, which greatly improved our understanding of the microbial world at large scales. However, the distribution of microbial functions remains largely uncharted from the macroecological point of view. Here, we used macroecological models to examine how the genes encoding the functional capabilities of microorganisms are distributed within and across soil systems. Models built using functional gene array data from 818 soil microbial communities showed that the occupancy-frequency distributions of genes were bimodal in every studied site, and that their rank-abundance distributions were best described by a lognormal model. In addition, the relationships between gene occupancy and abundance were positive in all sites. This allowed us to identify genes with high abundance and ubiquitous distribution (core) and genes with low abundance and limited spatial distribution (satellites), and to show that they encode different sets of microbial traits. Common genes encode microbial traits related to the main biogeochemical cycles (C, N, P and S) while rare genes encode traits related to adaptation to environmental stresses, such as nutrient limitation, resistance to heavy metals and degradation of xenobiotics. Overall, this study characterized for the first time the distribution of microbial functional genes within soil systems, and highlight the interest of macroecological models for understanding the functional organization of microbial systems across spatial scales.
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Wang Z, Feng K, Lu G, Yu H, Wang S, Wei Z, Dang N, Wang Y, Deng Y. Homogeneous Selection and Dispersal Limitation Dominate the Effect of Soil Strata Under Warming Condition. Front Microbiol 2022; 13:801083. [PMID: 35283849 PMCID: PMC8908236 DOI: 10.3389/fmicb.2022.801083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
Global warming is likely to affect the underground microbial communities in various ecosystems, but the response of soil microbial communities along a vertical depth profile to global warming has been elusive. Herein, we leveraged a warming field experiment in Qinghai-Tibet Plateau grassland and investigated the community structure of prokaryotes and fungi from the upper (0-15 cm) and lower (15-30 cm) strata under ambient and elevated temperature treatments. Three-years continual warming only significantly shifted the prokaryotic community within the upper strata and there was no significant effect observed for the fungal community. Additionally, under ambient temperature, there were significant differences between the two strata in both the prokaryotic and fungal communities, but under warming, this effect was alleviated. Next, the prokaryotic and fungal community assembly processes were measured by a phylogenetic-bin-based null approach (iCAMP). Though deterministic and stochastic processes dominated the assembly of prokaryotic and fungal communities, respectively, the deterministic processes were strengthened under warming for both communities. Specifically, the increased portion of homogeneous selection, contributing to a homogenous state, led to a smaller difference between prokaryotic communities of the two soil strata under warming. The smaller difference in the stochastic process component, i.e., dispersal limitation, contributed to the similar fungal community structures between the two strata under warming. This study deepens our understanding of warming effects on grassland microbial communities and gives greater insights on the underlying mechanisms for microbial assembly between upper and lower soil strata under warming scenarios.
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Affiliation(s)
- Zhujun Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Guangxin Lu
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Hao Yu
- College of Environmental Science and Engineering, Liaoning Technical University, Fuxin, China
| | - Shang Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ziyan Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ning Dang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Yingcheng Wang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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Monteiro MR, Marshall AJ, Hawes I, Lee CK, McDonald IR, Cary SC. Geochemically Defined Space-for-Time Transects Successfully Capture Microbial Dynamics Along Lacustrine Chronosequences in a Polar Desert. Front Microbiol 2022; 12:783767. [PMID: 35173689 PMCID: PMC8841834 DOI: 10.3389/fmicb.2021.783767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/15/2021] [Indexed: 11/15/2022] Open
Abstract
The space-for-time substitution approach provides a valuable empirical assessment to infer temporal effects of disturbance from spatial gradients. Applied to predict the response of different ecosystems under current climate change scenarios, it remains poorly tested in microbial ecology studies, partly due to the trophic complexity of the ecosystems typically studied. The McMurdo Dry Valleys (MDV) of Antarctica represent a trophically simple polar desert projected to experience drastic changes in water availability under current climate change scenarios. We used this ideal model system to develop and validate a microbial space-for-time sampling approach, using the variation of geochemical profiles that follow alterations in water availability and reflect past changes in the system. Our framework measured soil electrical conductivity, pH, and water activity in situ to geochemically define 17 space-for-time transects from the shores of four dynamic and two static Dry Valley lakes. We identified microbial taxa that are consistently responsive to changes in wetness in the soils and reliably associated with long-term dry or wet edaphic conditions. Comparisons between transects defined at static (open-basin) and dynamic (closed-basin) lakes highlighted the capacity for geochemically defined space-for-time gradients to identify lasting deterministic impacts of historical changes in water presence on the structure and diversity of extant microbial communities. We highlight the potential for geochemically defined space-for-time transects to resolve legacy impacts of environmental change when used in conjunction with static and dynamic scenarios, and to inform future environmental scenarios through changes in the microbial community structure, composition, and diversity.
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Affiliation(s)
- Maria R. Monteiro
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Alexis J. Marshall
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Ian Hawes
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Charles K. Lee
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Ian R. McDonald
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Stephen Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
- *Correspondence: Stephen Craig Cary,
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Tuo Y, Rong N, Hu J, Zhao G, Wang Y, Zhang Z, Qi Z, Li Y, Zhang B. Exploring the Relationships between Macrofungi Diversity and Major Environmental Factors in Wunvfeng National Forest Park in Northeast China. J Fungi (Basel) 2022; 8:jof8020098. [PMID: 35205853 PMCID: PMC8880546 DOI: 10.3390/jof8020098] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 01/27/2023] Open
Abstract
In this paper, we analyze the macrofungi communities of five forest types in Wunvfeng National Forest Park (Jilin, China) by collecting fruiting bodies from 2019–2021. Each forest type had three repeats and covered the main habitats of macrofungi. In addition, we evaluate selected environmental variables and macrofungi communities to relate species composition to potential environmental factors. We collected 1235 specimens belonging to 283 species, 116 genera, and 62 families. We found that Amanitaceae, Boletaceae, Russulaceae, and Tricholomataceae were the most diverse family; further, Amanita, Cortinarius, Lactarius, Russula, and Tricholoma were the dominant genera in the area. The macrofungi diversity showed increasing trends from Pinus koraiensis Siebold et Zuccarini forests to Quercus mongolica Fischer ex Ledebour forests. The cumulative species richness was as follows: Q. mongolica forest A > broadleaf mixed forest B > Q. mongolica, P. koraiensis mix forest D (Q. mongolica was the dominant species) > Q. mongolica and P. koraiensis mix forest C (P. koraiensis was the dominant species) > P. koraiensis forest (E). Ectomycorrhizal fungi were the dominant functional group; they were mainly in forest type A and were influenced by soil moisture content and Q. mongolica content (p < 0.05). The wood-rotting fungus showed richer species diversity than other forest types in broadleaf forests A and B. Overall, we concluded that most fungal communities preferred forest types with a relatively high Q. mongolica content. Therefore, the deliberate protection of Q. mongolica forests proves to be a better strategy for maintaining fungal diversity in Wunvfeng National Forest Park.
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Affiliation(s)
| | | | | | | | | | | | | | - Yu Li
- Correspondence: (Y.L.); (B.Z.)
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35
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Liu Y, Chi Q, Cheng H, Ding H, Wen T, Zhao J, Feng X, Zhang J, Cai Z, Liu G. Comparative Microbial Nitrogen Functional Gene Abundances in the Topsoil vs. Subsoil of Three Grassland Habitats in Northern China. FRONTIERS IN PLANT SCIENCE 2022; 12:792002. [PMID: 35095965 PMCID: PMC8798409 DOI: 10.3389/fpls.2021.792002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
The microbial groups of nitrogen fixers, ammonia oxidizers, and denitrifiers play vital roles in driving the nitrogen cycle in grassland ecosystems. However, the understanding of the abundance and distribution of these functional microorganisms as well as their driving factors were limited mainly to topsoil. In this study, the abundances of nitrogen functional genes (NFGs) involved in nitrogen fixation (nifH), ammonia oxidation (amoA), and denitrification (nirK, nirS, and nosZ) were investigated in both topsoil (0-10 cm, soil layer with concentrated root) and subsoil (30-40 cm, soil layer with spare root) of three grassland habitats in northern China. The abundance of NFGs decreased with soil depth except for the archaeal amoA gene and the distribution of nifH, archaeal amoA, nirK, and nirS gene was significantly impacted by grassland habitats. Moreover, the distribution of NFGs was more responsive to the vertical difference than horizontal spatial heterogeneity. Redundancy analysis revealed that the distribution pattern of overall NFGs was regulated by grassland habitats, and these regulations were more obvious in the subsoil than in the topsoil. Variance partitioning analysis further indicated that soil resource supply (e.g., organic matter) may control the vertical distribution of NFGs. Taken together, the findings in this study could fundamentally improve our understanding of the distribution of N cycling-associated microorganisms across a vertical scale, which would be useful for predicting the soil N availability and guiding the soil N management in grassland ecosystems.
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Affiliation(s)
- Yuqing Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences (CAS), Beijing, China
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Qiaodong Chi
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Hui Cheng
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Huanxin Ding
- Suzhou Station of Farmland Quality Protection, Suzhou, China
| | - Teng Wen
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Jun Zhao
- School of Geography, Nanjing Normal University, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
- Zhongke Clean Soil (Guangzhou) Technology Service Co., Ltd., Guangzhou, China
| | - Xiaojuan Feng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences (CAS), Beijing, China
| | - Jinbo Zhang
- School of Geography, Nanjing Normal University, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
- Zhongke Clean Soil (Guangzhou) Technology Service Co., Ltd., Guangzhou, China
| | - Zucong Cai
- School of Geography, Nanjing Normal University, Nanjing, China
- Zhongke Clean Soil (Guangzhou) Technology Service Co., Ltd., Guangzhou, China
- Key Laboratory of Virtual Geographical Environment, Ministry of Education, Nanjing Normal University, Nanjing, China
| | - Guohua Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
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Yang H, Hu C. Soil Chemistry and Nutrients Influence the Distribution of Aerobic Anoxygenic Phototrophic Bacteria and Eukaryotic Phototrophic Microorganisms of Physical Soil Crusts at Different Elevations on the Tibetan Plateau. MICROBIAL ECOLOGY 2022; 83:100-113. [PMID: 33733304 DOI: 10.1007/s00248-021-01734-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
Photosynthetic microorganisms are widely distributed in the soil and play an important role in plant-free soil crusts. However, the distribution and environmental drivers of phototrophic microbial communities in physical soil crusts, where the abundance of cyanobacteria is low, are scarcely understood. Here, we performed high-throughput sequencing of pufM and 18S rRNA genes in soil crusts at different elevations on the Tibetan Plateau and used the data combined with environmental variables to analyze the diversity and structure of phototrophic microbial communities. We found that the dominant taxa of aerobic anoxygenic phototrophic bacteria (AAPB) and eukaryotic phototrophic microorganisms (EPM) were shown to shift with elevation. The phototrophic microbial diversity showed a single-peak pattern, with the lowest diversity of AAPB and highest diversity of EPM at middle elevations. Moreover, the elevation and soil property determined the phototrophic microbial community. Soil salts, especially Cl-, were the most important for AAPB. Likewise, soil nutrients, especially carbon, were the most important for EPM. The relationship between high-abundance taxa and environmental variables showed that Rhizobiales was significantly negatively correlated with salt ions and positively correlated with chlorophyll. Rhodobacterales showed the strongest and significant positive associations with Cl-. Chlorophyceae and Bacillariophyceae were positively correlated with CO32-. These results indicated that salinity and soil nutrients affected the diversity and structure of microbial communities. This study contributes to our understanding of the diversity, composition, and structure of photosynthetic microorganisms in physical soil crusts and helps in developing new approaches for controlling desertification and salinization and improving the desert ecological environment.
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Affiliation(s)
- Haijian Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Pan Y, Kang P, Hu J, Song N. Bacterial community demonstrates stronger network connectivity than fungal community in desert-grassland salt marsh. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149118. [PMID: 34332392 DOI: 10.1016/j.scitotenv.2021.149118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
The diversity of soil bacterial and fungal communities is closely related to the soil characteristics and vegetation types in salt marsh ecosystems, but the biogeographic patterns and driving factors in desert-grassland salt marsh (DGSM) are still unclear. In this study, we divided sample plots according to the dominant species in Jiantan Lake wetland of a typical DGSM in Northwestern China. The effects of different environmental factors and halophytes on the structure of soil bacterial and fungal communities were investigated using soil physicochemical characterization and high-throughput sequencing analysis. The diversity of bacterial communities in bulk soil and three dominant halophytes (Kalidium cuspidatum, Nitraria tangutorum and Sophora alopecuroides) were the main factors affecting soil physicochemical properties and halophyte vegetation coverage. Proteobacteria, Bacteroides and Gemmatimonadetes had the highest abundance in bulk soil and the lowest in Sophora alopecuroides sample soil; the opposite was true for Acidobacteria and Chloroflexi. The abundance of Ascomycota in bulk soil and Sophora alopecuroides sample soil was higher than Kalidium cuspidatum and Nitraria tangutorum sample soils, whereas the Mortierellomycota was the highest in Nitraria tangutorum sample soil. Co-occurrence network analysis showed that halophyte cover increased the connectivity and complexity of the bacterial-fungal interaction network, and the halophytic shrub sample soil had a more stable network relationship than the halophytic herb soil. The key taxa of each plot were identified through network relationships. It was found that the keystone taxa of Proteobacteria, Firmicutes, Ascomycota and Chytridiomycota played important roles in maintaining community functions, and most of them were not significantly influenced by soil physicochemical properties. The results of this study provide new insights for a deeper understanding of the halophytes that drive the multifunctionality and stability of soil ecosystems in DGSM.
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Affiliation(s)
- Yaqing Pan
- College of Agriculture, Ningxia University, Yinchuan 750021, Ningxia, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan 750021, Ningxia, China; Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ministry of Education, Ningxia University, Yinchuan 750021, China
| | - Peng Kang
- College of Biological Sciences and Engineering, North Minzu University, Yinchuan 750021, China; Ningxia Key Laboratory for the Development and Application of Microbial Resources in Extreme Environments, North Minzu University, Yinchuan 750021, China
| | - Jinpeng Hu
- College of Biological Sciences and Engineering, North Minzu University, Yinchuan 750021, China
| | - Naiping Song
- College of Agriculture, Ningxia University, Yinchuan 750021, Ningxia, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan 750021, Ningxia, China; Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ministry of Education, Ningxia University, Yinchuan 750021, China.
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Metagenomic Analyses of Plant Growth-Promoting and Carbon-Cycling Genes in Maize Rhizosphere Soils with Distinct Land-Use and Management Histories. Genes (Basel) 2021; 12:genes12091431. [PMID: 34573413 PMCID: PMC8466292 DOI: 10.3390/genes12091431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/04/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022] Open
Abstract
Many studies have shown that the maize rhizosphere comprises several plant growth-promoting microbes, but there is little or no study on the effects of land-use and management histories on microbial functional gene diversity in the maize rhizosphere soils in Africa. Analyzing microbial genes in the rhizosphere of plants, especially those associated with plant growth promotion and carbon cycling, is important for improving soil fertility and crop productivity. Here, we provide a comparative analysis of microbial genes present in the rhizosphere samples of two maize fields with different agricultural histories using shotgun metagenomics. Genes involved in the nutrient mobilization, including nifA, fixJ, norB, pstA, kefA and B, and ktrB were significantly more abundant (α = 0.05) in former grassland (F1) rhizosphere soils. Among the carbon-cycling genes, the abundance of 12 genes, including all those involved in the degradation of methane were more significant (α = 0.05) in the F1 soils, whereas only five genes were significantly more abundant in the F2 soils. α-diversity indices were different across the samples and significant differences were observed in the β diversity of plant growth-promoting and carbon-cycling genes between the fields (ANOSIM, p = 0.01 and R = 0.52). Nitrate-nitrogen (N-NO3) was the most influential physicochemical parameter (p = 0.05 and contribution = 31.3%) that affected the distribution of the functional genes across the samples. The results indicate that land-use and management histories impact the composition and diversity of plant growth-promoting and carbon-cycling genes in the plant rhizosphere. The study widens our understanding of the effects of anthropogenic activities on plant health and major biogeochemical processes in soils.
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Mu Z, Dong S, Li Y, Li S, Shen H, Zhang J, Han Y, Xu Y, Zhao Z. Soil Bacterial Community Responses to N Application and Warming in a Qinghai-Tibetan Plateau Alpine Steppe. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.709518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nitrogen deposition and climate warming can alter soil bacterial communities. However, the response of soil bacteria in an alpine steppe to these changes is largely unknown. In this study, a field experiment was performed on the northeastern Qinghai-Tibetan Plateau to determine the changes in soil bacterial communities of alpine steppes in response to nitrogen application and warming. The experiment consisted of four treatments, namely no-N application with no-warming (CK), N application (8 kg N ha−1 year−1) with no-warming (N), warming with no-N application (W), and N application (8 kg N ha−1 year−1) with warming (W&N). This study aimed to investigate (1) the changes in soil bacterial diversity and community structure under simulated nitrogen deposition and warming conditions, and (2) the key environmental factors responsible for these changes. Based on the results, soil bacterial diversity and community composition did not change significantly in the short term. Warming had a significant effect on overall bacterial composition, rare species composition, and individual bacterial taxa. Besides, the interaction between nitrogen application and warming had a significant effect on community β-diversity. Above-ground plant variables were highly correlated with bacterial community characteristics. Nitrogen application and warming did not significantly alter the distribution range of the bacterial community. Overall, this study suggests that soil bacterial communities can remain relatively stable at the level of simulated nitrogen application and warming and that short-term climatic changes may have no significant impacts on soil bacterial communities.
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Liu M, Li X, Zhu R, Chen N, Ding L, Chen C. Vegetation richness, species identity and soil nutrients drive the shifts in soil bacterial communities during restoration process. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:411-424. [PMID: 33264476 DOI: 10.1111/1758-2229.12913] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/19/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
Soil bacteria play an essential role in functioning of ecosystems and maintaining of biogeochemical cycles. However, little is known about changes in the compositions and functional groups of soil bacterial communities during different restoration stages. The influences of aboveground vegetation and belowground soil properties on soil bacterial communities were also unclear during this process. Here we sequenced the soil bacterial communities in different stages of sand fixation. Sand fixation increased the diversity of the bacterial communities, among which the populations of Actinobacteria, Acidobacteria and Gemmatimonadetes changed significantly. The function prediction showed sand fixation increased Gram-positive and aerobic bacteria. Bacterial structure is significantly correlated with plant richness, coverage and biomass. In particular, we found species identity was an important determinant in structuring bacterial composition. Soil properties were all significantly correlated with soil bacterial community richness and diversity. Fusobacteria was strongly positively correlated with sand, Chloroflexi with total N and Gemmatimonadetes with SOM and total C. It suggested that soil nutrients (TC, TN and SOM) have large consequences for soil bacterial community dissimilarities. These results indicated that vegetation richness, especially species identity, together with improvement in soil nutrients, play key roles in driving the shifts in soil microbial community structure and function during restoration process.
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Affiliation(s)
- Meiling Liu
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
| | - Xinrong Li
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
| | - Ruiqing Zhu
- Institute of Biology, Gansu Academy of Sciences, Lanzhou, Gansu, 730000, China
| | - Ning Chen
- School of Life Science, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Ling Ding
- Foreign Language School, Linyi University, Linyi, Shandong, 267000, China
| | - Cuiyun Chen
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
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Huang M, Chai L, Jiang D, Zhang M, Jia W, Huang Y, Zhou J. Dissolved organic matter (DOM) quality drives biogeographic patterns of soil bacterial communities and their association networks in semi-arid regions. FEMS Microbiol Ecol 2021; 97:6307509. [PMID: 34156067 DOI: 10.1093/femsec/fiab083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/18/2021] [Indexed: 11/13/2022] Open
Abstract
It is of great interest to elucidate the biogeographic patterns of soil microorganisms and their driving forces, which is fundamental to predicting alterations in microbial-mediated functions arising from environment changes. Although dissolved organic matter (DOM) represents an important resource for soil microorganisms, knowledge of how its quality affects microbial biogeography is limited. Here, we characterized soil bacterial communities and DOM quality in 45 soil samples collected from a 1500-km sampling transect through semi-arid regions in northern China which are currently suffering great pressure from climate change, using Illumina Miseq sequencing and fluorescence spectroscopy, respectively. We found that DOM quality (i.e. the source of DOM and the humification degree of DOM) had profound shaping influence on the biogeographic patterns exhibited by bacterial diversity, community composition and association networks. Specifically, the composition of bacteria community closely associated with DOM quality. Plant-derived DOM sustained higher bacterial diversity relative to microbial-derived DOM. Meanwhile, bacterial diversity linearly increased with increasing humification degree of DOM. Additionally, plant-derived DOM was observed to foster more complex bacterial association networks with less competition. Together, our work contributes to the factors underlying biogeographic patterns not only of bacterial diversity, community composition but also of their association networks and reports previously undocumented important role of DOM quality in shaping these patterns.
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Affiliation(s)
- Muke Huang
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Liwei Chai
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Dalin Jiang
- Gradute School of Life and Environmental Science, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Mengjun Zhang
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Weiqian Jia
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yi Huang
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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Cheng J, Han Z, Cong J, Yu J, Zhou J, Zhao M, Zhang Y. Edaphic variables are better indicators of soil microbial functional structure than plant-related ones in subtropical broad-leaved forests. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 773:145630. [PMID: 33582323 DOI: 10.1016/j.scitotenv.2021.145630] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/25/2021] [Accepted: 01/31/2021] [Indexed: 06/12/2023]
Abstract
Soil microorganisms play important roles in the ecosystem functioning of subtropical broad-leaved forests (SBFs). However, the patterns and environmental indicators of soil microbial functional structure remain unclear in SBFs. In the present work, we used a functional microarray (GeoChip 4.0) to examine the soil microbial functional structure of three types of SBFs, including a deciduous broad-leaved forest (DBF), a mixed evergreen-deciduous broad-leaved forest (MBF), and an evergreen broad-leaved forest (EBF). We found that microbial functional structure was significantly different among SBFs (P < 0.05). Compared to the DBF and the EBF, the MBF had higher functional α-diversity (P = 0.001, F = 12.55) but lower β-diversity (P < 0.001, F = 61.09), and showed more complex functional gene networks. Besides, the MBF had higher relative abundances of functional genes for carbon (C) decomposition, C fixation, nitrogen (N) cycling, sulfur (S) cycling, and phosphorus (P) cycling (P < 0.05), indicating stronger microbial functional capabilities of nutrient cycling processes. Edaphic variables (i.e., soil pH and soil nutrient content) were revealed as better indicators of soil microbial functional structure than plant-related ones (i.e., vegetation type and plant diversity) in SBFs. For example, functional gene structure of the DBF was significantly related to soil total S (P = 0.041), that of the MBF was significantly related to soil organic C (P = 0.027) and plant available P (P = 0.034), and that of the EBF was significantly related to soil pH (P = 0.006) and total potassium (K) (P = 0.038). Overall, through the analysis of microbial functional gene profiles, this study yields unique insights into the environmental indicators of patterns and mechanisms of soil microbial functional structure in SBFs.
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Affiliation(s)
- Jingmin Cheng
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Zhongjie Han
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China.
| | - Jing Cong
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Jingjing Yu
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China.
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Mengxin Zhao
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Yuguang Zhang
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China.
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Zhang M, Wang L, Wu G, Wang X, Lv H, Chen J, Liu Y, Pang H, Tan Z. Effects of Lactobacillus plantarum on the Fermentation Profile and Microbiological Composition of Wheat Fermented Silage Under the Freezing and Thawing Low Temperatures. Front Microbiol 2021; 12:671287. [PMID: 34177851 PMCID: PMC8221580 DOI: 10.3389/fmicb.2021.671287] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/06/2021] [Indexed: 11/13/2022] Open
Abstract
The corruption and/or poor quality of silages caused by low temperature and freeze-thaw conditions makes it imperative to identify effective starters and low temperature silage fermentation technology that can assist the animal feed industry and improve livestock productivity. The effect of L. plantarum QZ227 on the wheat silage quality was evaluated under conditions at constant low temperatures followed by repeated freezing and thawing at low temperatures. QZ227 became the predominant strain in 10 days and underwent a more intensive lactic acid bacteria fermentation than CK. QZ227 accumulated more lactic acid, but lower pH and ammonia nitrogen in the fermentation. During the repeated freezing and thawing process, the accumulated lactic acid in the silage fermented by QZ227 remained relatively stable. Relative to CK, QZ227 reduced the abundance of fungal pathogens in silage at a constant 5°C, including Aspergillus, Sporidiobolaceae, Hypocreaceae, Pleosporales, Cutaneotrichosporon, Alternaria, and Cystobasidiomycetes. Under varying low temperature conditions from days 40 to days 60, QZ227 reduced the pathogenic abundance of fungi such as Pichia, Aspergillus, Agaricales, and Plectosphaerella. QZ227 also reduced the pathogenic abundance of Mucoromycota after the silage had been exposed to oxygen. In conclusion, QZ227 can be used as a silage additive in the fermentation process at both constant and variable low temperatures to ensure fast and vigorous fermentation because it promotes the rapid accumulation of lactic acid, and reduces pH values and aerobic corruption compared to the CK.
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Affiliation(s)
- Miao Zhang
- Henan Key Laboratory of Ion-Beam Bioengineering, College of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Lei Wang
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Guofang Wu
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Xing Wang
- Henan Key Laboratory of Ion-Beam Bioengineering, College of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Haoxin Lv
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, China
| | - Jun Chen
- Henan Key Laboratory of Ion-Beam Bioengineering, College of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Yuan Liu
- Henan Key Laboratory of Ion-Beam Bioengineering, College of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Huili Pang
- Henan Key Laboratory of Ion-Beam Bioengineering, College of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhongfang Tan
- Henan Key Laboratory of Ion-Beam Bioengineering, College of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
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Li H, Yang S, Semenov MV, Yao F, Ye J, Bu R, Ma R, Lin J, Kurganova I, Wang X, Deng Y, Kravchenko I, Jiang Y, Kuzyakov Y. Temperature sensitivity of SOM decomposition is linked with a K-selected microbial community. GLOBAL CHANGE BIOLOGY 2021; 27:2763-2779. [PMID: 33709545 DOI: 10.1111/gcb.15593] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Temperature sensitivity (Q10 ) of soil organic matter (SOM) decomposition is a crucial parameter to predict the fate of soil carbon (C) under global warming. Nonetheless, the response pattern of Q10 to continuous warming and the underlying mechanisms are still under debate, especially considering the complex interactions between Q10 , SOM quality, and soil microorganisms. We examined the Q10 of SOM decomposition across a mean annual temperature (MAT) gradient from -1.9 to 5.1°C in temperate mixed forest ecosystems in parallel with SOM quality and bioavailability, microbial taxonomic composition, and functional genes responsible for organic carbon decomposition. Within this temperature gradient of 7.0°C, the Q10 values increased with MAT, but decreased with SOM bioavailability. The Q10 values increased with the prevalence of K-strategy of soil microbial community, which was characterized by: (i) high ratios of oligotrophic to copiotrophic taxa, (ii) ectomycorrhizal to saprotrophic fungi, (iii) functional genes responsible for degradation of recalcitrant to that of labile C, and (iv) low average 16S rRNA operon copy number. Because the recalcitrant organic matter was mainly utilized by the K-strategists, these findings independently support the carbon quality-temperature theory from the perspective of microbial taxonomic composition and functions. A year-long incubation experiment was performed to determine the response of labile and recalcitrant C pools to warming based on the two-pool model. The decomposition of recalcitrant SOM was more sensitive to increased temperature in southern warm regions, which might attribute to the dominance of K-selected microbial communities. It implies that climate warming would mobilize the larger recalcitrant pools in warm regions, exacerbating the positive feedback between increased MAT and CO2 efflux. This is the first attempt to link temperature sensitivity of SOM decomposition with microbial eco-strategies by incorporating the genetic information and disentangling the complex relationship between Q10 and soil microorganisms.
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Affiliation(s)
- Hui Li
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Shan Yang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Mikhail V Semenov
- Department of Soil Biology and Biochemistry, Dokuchaev Soil Science Institute, Russian Academy of Sciences, Moscow, Russia
| | - Fei Yao
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Ji Ye
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Rencang Bu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Ruiao Ma
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Junjie Lin
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- Key Laboratory of Water Environment Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Wanzhou, China
| | - Irina Kurganova
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Russia
| | - Xugao Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Irina Kravchenko
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Yong Jiang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Yakov Kuzyakov
- Department of Agricultural Soil Science, Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen, Germany
- Agro-Technological Institute, RUDN University, Moscow, Russia
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You Y, Aho K, Lohse KA, Schwabedissen SG, Ledbetter RN, Magnuson TS. Biological Soil Crust Bacterial Communities Vary Along Climatic and Shrub Cover Gradients Within a Sagebrush Steppe Ecosystem. Front Microbiol 2021; 12:569791. [PMID: 34025590 PMCID: PMC8134670 DOI: 10.3389/fmicb.2021.569791] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 04/13/2021] [Indexed: 11/19/2022] Open
Abstract
Numerous studies have examined bacterial communities in biological soil crusts (BSCs) associated with warm arid to semiarid ecosystems. Few, however, have examined bacterial communities in BSCs associated with cold steppe ecosystems, which often span a wide range of climate conditions and are sensitive to trends predicted by relevant climate models. Here, we utilized Illumina sequencing to examine BSC bacterial communities with respect to climatic gradients (elevation), land management practices (grazing vs. non-grazing), and shrub/intershrub patches in a cold sagebrush steppe ecosystem in southwestern Idaho, United States. Particular attention was paid to shifts in bacterial community structure and composition. BSC bacterial communities, including keystone N-fixing taxa, shifted dramatically with both elevation and shrub-canopy microclimates within elevational zones. BSC cover and BSC cyanobacteria abundance were much higher at lower elevation (warmer and drier) sites and in intershrub areas. Shrub-understory BSCs were significantly associated with several non-cyanobacteria diazotrophic genera, including Mesorhizobium and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. High elevation (wetter and colder) sites had distinct, highly diverse, but low-cover BSC communities that were significantly indicated by non-cyanobacterial diazotrophic taxa including families in the order Rhizobiales and the family Frankiaceae. Abiotic soil characteristics, especially pH and ammonium, varied with both elevation and shrub/intershrub level, and were strongly associated with BSC community composition. Functional inference using the PICRUSt pipeline identified shifts in putative N-fixing taxa with respect to both the elevational gradient and the presence/absence of shrub canopy cover. These results add to current understanding of biocrust microbial ecology in cold steppe, serving as a baseline for future mechanistic research.
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Chen Q, Yuan Y, Hu Y, Wang J, Si G, Xu R, Zhou J, Xi C, Hu A, Zhang G. Excessive nitrogen addition accelerates N assimilation and P utilization by enhancing organic carbon decomposition in a Tibetan alpine steppe. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:142848. [PMID: 33268263 DOI: 10.1016/j.scitotenv.2020.142848] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 09/23/2020] [Accepted: 10/03/2020] [Indexed: 05/23/2023]
Abstract
High amounts of deposited nitrogen (N) dramatically influence the stability and functions of alpine ecosystems by changing soil microbial community functions, but the mechanism is still unclear. To investigate the impacts of increased N deposition on microbial community functions, a 2-year multilevel N addition (0, 10, 20, 40, 80 and 160 kg N ha-1 year-1) field experiment was set up in an alpine steppe on the Tibetan Plateau. Soil microbial functional genes (GeoChip 4.6), together with soil enzyme activity, soil organic compounds and environmental variables, were used to explore the response of microbial community functions to N additions. The results showed that the N addition rate of 40 kg N ha-1 year-1 was the critical value for soil microbial functional genes in this alpine steppe. A small amount of added N (≤40 kg N ha-1 year-1) had no significant effects on the abundance of microbial functional genes, while high amounts of added N (>40 kg N ha-1 year-1) significantly increased the abundance of soil organic carbon degradation genes. Additionally, the abundance of microbial functional genes associated with NH4+, including ammonification, N fixation and assimilatory nitrate reduction pathways, was significantly increased under high N additions. Further, high N additions also increased soil organic phosphorus utilization, which was indicated by the increase in the abundance of phytase genes and alkaline phosphatase activity. Plant richness, soil NO2-/NH4+ and WSOC/WSON were significantly correlated with the abundance of microbial functional genes, which drove the changes in microbial community functions under N additions. These findings help us to predict that increased N deposition in the future may alter soil microbial functional structure, which will lead to changes in microbially-mediated biogeochemical dynamics in alpine steppes on the Tibetan Plateau and will have extraordinary impacts on microbial C, N and P cycles.
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Affiliation(s)
- Qiuyu Chen
- CAS Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Yanli Yuan
- CAS Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Yilun Hu
- CAS Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Wang
- Land and Resources College, China West Normal University, Nanchong 637009, Sichuan, China
| | - Guicai Si
- Lanzhou Center for Oil and Gas Resources, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Ri Xu
- CAS Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University Oklahoma, Norman, OK 73019, USA; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Chuanwu Xi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ang Hu
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Gengxin Zhang
- CAS Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, China.
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Yuan C, Li F, Yuan Z, Li G, Liang X. Response of bacterial communities to mining activity in the alpine area of the Tianshan Mountain region, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:15806-15818. [PMID: 33241503 DOI: 10.1007/s11356-020-11744-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/18/2020] [Indexed: 06/11/2023]
Abstract
Anthropogenic activities, such as mining, influence soil bacterial community composition and microbial distributions. In the current study, the patterns in microbial distribution and the environmental drivers shaping the soil bacterial community composition in the alpine mining area of the Tianshan Mountain region, China, were investigated, and the bacterial communities were analyzed using 16S rDNA pyrosequencing. The environmental factors and their relationships with the microbial community composition, structure, and diversity were also assessed. The soil organic carbon (SOC) concentration increased along the elevation gradient, with the highest concentration in the mining area, which increased microbial abundance and species richness. Some metals, like Ca, Cu, Pb, and Zn, accumulated significantly in the tailing area and were negatively correlated with the microbial community structure. Proteobacteria, Acidobacteria, Actinobacteria, and Verrucomicrobia were the dominant phyla; these dominant phyla were more abundant in the areas without mining than in the areas with mining at the same altitude. The relative abundance of Proteobacteria and Verrucomicrobia significantly increased along the elevation gradient, while that of Actinobacteria in the mining camp area was more than twice those in the other areas due to higher soil pH. Soil biomass was the highest in the valley. Collectively, these results elucidate the influence of anthropogenic mining activities on soil microbial communities in alpine mining soils and provide a basis for the future management of heavy metal-contaminated areas using the indigenous dominant bacterial phyla.
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Affiliation(s)
- Chengyu Yuan
- College of Water Resources and Architectural Engineering, Tarim University, Xinjiang, 843300, China
| | - Fayong Li
- College of Water Resources and Architectural Engineering, Tarim University, Xinjiang, 843300, China.
| | - Ziqiang Yuan
- Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Guoyu Li
- Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Xinqiang Liang
- College of Environmental and Resources Sciences, Zhejiang University, Hangzhou, 310058, China
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Donhauser J, Qi W, Bergk-Pinto B, Frey B. High temperatures enhance the microbial genetic potential to recycle C and N from necromass in high-mountain soils. GLOBAL CHANGE BIOLOGY 2021; 27:1365-1386. [PMID: 33336444 DOI: 10.1111/gcb.15492] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/28/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Climate change is strongly affecting high-mountain soils and warming in particular is associated with pronounced changes in microbe-mediated C and N cycling, affecting plant-soil interactions and greenhouse gas balances and therefore feedbacks to global warming. We used shotgun metagenomics to assess changes in microbial community structures, as well as changes in microbial C- and N-cycling potential and stress response genes and we linked these data with changes in soil C and N pools and temperature-dependent measurements of bacterial growth rates. We did so by incubating high-elevation soil from the Swiss Alps at 4°C, 15°C, 25°C, or 35°C for 1 month. We found no shift with increasing temperature in the C-substrate-degrader community towards taxa more capable of degrading recalcitrant organic matter. Conversely, at 35°C, we found an increase in genes associated with the degradation and modification of microbial cell walls, together with high bacterial growth rates. Together, these findings suggest that the rapidly growing high-temperature community is fueled by necromass from heat-sensitive taxa. This interpretation was further supported by a shift in the microbial N-cycling potential towards N mineralization and assimilation under higher temperatures, along with reduced potential for conversions among inorganic N forms. Microbial stress-response genes reacted inconsistently to increasing temperature, suggesting that the high-temperature community was not severely stressed by these conditions. Rather, soil microbes were able to acclimate by changing the thermal properties of membranes and cell walls as indicated by an increase in genes involved in membrane and cell wall modifications as well as a shift in the optimum temperature for bacterial growth towards the treatment temperature. Overall, our results suggest that high temperatures, as they may occur with heat waves under global warming, promote a highly active microbial community capable of rapid mineralization of microbial necromass, which may transiently amplify warming effects.
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Affiliation(s)
- Jonathan Donhauser
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Benoît Bergk-Pinto
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, France
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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Perez-Mon C, Qi W, Vikram S, Frossard A, Makhalanyane T, Cowan D, Frey B. Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps). Microb Genom 2021; 7:000558. [PMID: 33848236 PMCID: PMC8208683 DOI: 10.1099/mgen.0.000558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The warming-induced thawing of permafrost promotes microbial activity, often resulting in enhanced greenhouse gas emissions. The ability of permafrost microorganisms to survive the in situ sub-zero temperatures, their energetic strategies and their metabolic versatility in using soil organic materials determine their growth and functionality upon thawing. Hence, functional characterization of the permafrost microbiome, particularly in the underexplored mid-latitudinal alpine regions, is a crucial first step in predicting its responses to the changing climate, and the consequences for soil-climate feedbacks. In this study, for the first time, the functional potential and metabolic capabilities of a temperate mountain permafrost microbiome from central Europe has been analysed using shotgun metagenomics. Permafrost and active layers from the summit of Muot da Barba Peider (MBP) [Swiss Alps, 2979 m above sea level (a.s.l.)] revealed a strikingly high functional diversity in the permafrost (north-facing soils at a depth of 160 cm). Permafrost metagenomes were enriched in stress-response genes (e.g. cold-shock genes, chaperones), as well as in genes involved in cell defence and competition (e.g. antiviral proteins, antibiotics, motility, nutrient-uptake ABC transporters), compared with active-layer metagenomes. Permafrost also showed a higher potential for the synthesis of carbohydrate-active enzymes, and an overrepresentation of genes involved in fermentation, carbon fixation, denitrification and nitrogen reduction reactions. Collectively, these findings demonstrate the potential capabilities of permafrost microorganisms to thrive in cold and oligotrophic conditions, and highlight their metabolic versatility in carbon and nitrogen cycling. Our study provides a first insight into the high functional gene diversity of the central European mountain permafrost microbiome. Our findings extend our understanding of the microbial ecology of permafrost and represent a baseline for future investigations comparing the functional profiles of permafrost microbial communities at different latitudes.
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Affiliation(s)
- Carla Perez-Mon
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- *Correspondence: Carla Perez-Mon,
| | - Weihong Qi
- Functional Genomics Center of the University of Zurich and the ETH Zurich, Zurich, Switzerland
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Aline Frossard
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Thulani Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Don Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- *Correspondence: Beat Frey,
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Guo H, Han S, Lee DJ. Genomic studies on natural and engineered aquatic denitrifying eco-systems: A research update. BIORESOURCE TECHNOLOGY 2021; 326:124740. [PMID: 33497924 DOI: 10.1016/j.biortech.2021.124740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 06/12/2023]
Abstract
Excess nitrogenous compounds in municipal or industrial wastewaters can stimulate growth of denitrifying bacteria, in return, to convert potentially hazardous nitrate to inorganic nitrogen gas. To explore the community structure, distributions and succession of functional strains, and their interactions with other microbial communities, contemporary studies were performed based on detailed genomic analysis. This mini-review updated contemporary genomic studies on denitrifying genes in natural and engineered aquatic systems, with the constructed wetlands being the demonstrative system for the latter. Prospects for the employment of genomic studies on denitrifying systems for process design, optimization and development of novel denitrifying processes were discussed.
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Affiliation(s)
- Hongliang Guo
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Song Han
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; College of Technology and Engineering, National Taiwan Normal University, Taipei 10610, Taiwan; College of Engineering, Tunghai University, Taichung 40070, Taiwan.
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