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Zhai K, Hua Y, Liang J, Li J, Wang Z, Liu L, Gao M, Sa R, Zhao M. Soil microbial diversity under different types of interference in birch secondary forest in the Greater Khingan Mountains in China. Front Microbiol 2023; 14:1267746. [PMID: 37954244 PMCID: PMC10635414 DOI: 10.3389/fmicb.2023.1267746] [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: 08/03/2023] [Accepted: 10/05/2023] [Indexed: 11/14/2023] Open
Abstract
Introduction Soil microorganisms are an important component of soil ecosystems with an indispensable role in forest ecosystems. We analyzed the soil microbial diversity in birch secondary forest formed by natural restoration or artificial reconstruction after interference by burning, clear cutting, and gradient cutting, and the Betula platyphylla Suk undisturbed forest in the Greater Khingan Mountains in China. Methods Illumina high-throughput sequencing technology was used to analyze the characteristics of the soil microbial community during the restoration process of birch secondary forest caused by the different types of interference. The relationships between bacteria and fungi were analyzed. The gene functions of the soil bacterial community and the ecological functions of soil fungi were predicted using PICRUSt and FunGuild, respectively. Results At the phylum level, the species and quantity of bacteria were more abundant than that of fungi. At the genus level, no obvious differences in the abundance of bacteria were observed; there were obvious differences in the abundance of fungi. Among the eight sample plots, the artificial larch forest belt had the highest bacterial and fungal alpha diversity, which was slightly higher than undisturbed forest, while the other sample plots were significantly lower. Gradual cutting pure birch forest bacteria and fungi had the highest beta diversity, and artificial larch forest belt bacteria and heavy burn sample plot fungi had the lowest beta diversity. Samples from the cutting and burning sample plots were significantly different from the undisturbed forest at the phylum level of Acidobacteriae, Acidimicrobiia, Mortierellomycetes and Sordariomycetes. We found statistical differences in biomarkers between bacterial and fungal communities in undisturbed forest and artificial larch forest belt and burn sample plots. PICRUSt prediction and FunGuild prediction showed that soil bacterial and fungal communities were rich in gene and ecological functions, respectively. In the microbial network, the stability or anti-interference performance of the fungal community was higher than that of bacteria. Conclusion Our data reveal the characteristics of the soil microbial community during the restoration process of Betula platyphylla Suk secondary forest under different types of disturbance, which is of great significance for understanding the role of soil microorganisms in the forest ecological cycle.
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Affiliation(s)
- Kaitao Zhai
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Yongchun Hua
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Jingwen Liang
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Jing Li
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Zirui Wang
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Lei Liu
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Minglong Gao
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Rula Sa
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Mingmin Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
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Kim N, Jo J, Lee J, Lee GH, Yu BY, Pyo H, Lee J, Choi J. Environmental forensics using stable and radioactive isotopes in naturally attenuated soil after phenol-leakage accidents. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132007. [PMID: 37527592 DOI: 10.1016/j.jhazmat.2023.132007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/02/2023] [Accepted: 07/04/2023] [Indexed: 08/03/2023]
Abstract
Phenol is a carcinogenic and hazardous chemical used in multiple industries and poses a high risk of chemical spills into the environment. To date, environmental forensic research has not focused on chemically remediated soils. In this study, an advanced environmental forensic analysis was performed on microbial communities and breakdown products of phenol, carbon stable isotopes, and radioactive isotopes in phenol-contaminated soil. As indicators of phenol-spill accidents after natural attenuation, higher δ13C levels and lower 14C/12C ratios were observed in phenol-contaminated soil compared with uncontaminated soil. In addition, 16s rRNA gene analysis revealed that phenol-breakdown products identified by gas chromatography-mass spectrometry and the presence of soil bacteria, such as Nocardioides, Faecalibacterium, and Bacteroides, were indicators of phenol-leakage accidents. Therefore, the proposed environmental forensic strategy is a valuable tool for identifying the location of previously occurring chemical accidents and estimating the ecological impact after the natural attenuation of contaminated soils.
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Affiliation(s)
- Naeun Kim
- Center for Sustainable Environment Research, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Graduate School of Energy and Environment, Korea University, Seoul 02841, Republic of Korea
| | - Jungman Jo
- Center for Sustainable Environment Research, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Civil & Environmental Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jinkyung Lee
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Gwan-Ho Lee
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Byung-Yong Yu
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Heesoo Pyo
- International Advanced Analysis Institute, B-339, 140 Tongil-ro, Deogyang-gu, Goyang-si, Gyeonggi-do 10594, Republic of Korea
| | - Jeongae Lee
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.
| | - Jaeyoung Choi
- Center for Sustainable Environment Research, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Graduate School of Energy and Environment, Korea University, Seoul 02841, Republic of Korea.
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Kumari S, Leon Magdaleno JS, Grewal RK, Narsing Rao MP, Rajjak Shaikh A, Cavallo L, Chawla M, Kumar M. High potential for biomass-degrading CAZymes revealed by pine forest soil metagenomics. J Biomol Struct Dyn 2023:1-12. [PMID: 37768075 DOI: 10.1080/07391102.2023.2262600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
The undisturbed environment in Netarhat, with its high levels of accumulated lignocellulosic biomass, presents an opportunity to identify microbes for biomass digestion. This study focuses on the bioprospecting of native soil microbes from the Netarhat forest in Jharkhand, India, with the potential for lignocellulosic substrate digestion. These biocatalysts could help overcome the bottleneck of biomass saccharification and reduce the overall cost of biofuel production, replacing harmful fossil fuels. The study used metagenomic analysis of pine forest soil via whole genome shotgun sequencing, revealing that most of the reads matched with the bacterial species, very low percentage of reads (0.1%) belongs to fungal species, with 13% of unclassified reads. Actinobacteria were found to be predominant among the bacterial species. MetaErg annotation identified 11,830 protein family genes and 2 metabolic marker genes in the soil samples. Based on the Carbohydrate Active EnZyme (CAZy) database, 3,996 carbohydrate enzyme families were identified, with family Glycosyl hydrolase (GH) dominating with 1,704 genes. Most observed GH families in the study were GH0, 3, 5, 6. 9, 12. 13, 15, 16, 39, 43, 57, and 97. Modelling analysis of a representative GH 43 gene suggested a strong affinity for cellulose than xylan. This study highlights the lignocellulosic digestion potential of the native microfauna of the lesser-known pine forest of Netarhat.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sonam Kumari
- Department of Life Sciences, School of Natural Sciences, Central University of Jharkhand, Ranchi, Jharkhand, India
| | - Jorge S Leon Magdaleno
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ravneet Kaur Grewal
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, Talca, Chile
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Luigi Cavallo
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohit Chawla
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Manoj Kumar
- Department of Life Sciences, School of Natural Sciences, Central University of Jharkhand, Ranchi, Jharkhand, India
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Li S, Lian WH, Han JR, Ali M, Lin ZL, Liu YH, Li L, Zhang DY, Jiang XZ, Li WJ, Dong L. Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis. NPJ Biofilms Microbiomes 2023; 9:67. [PMID: 37736746 PMCID: PMC10516943 DOI: 10.1038/s41522-023-00439-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023] Open
Abstract
Deserts occupy one-third of the Earth's terrestrial surface and represent a potentially significant reservoir of microbial biodiversity, yet the majority of desert microorganisms remain uncharacterized and are seen as "microbial dark matter". Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts.
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Affiliation(s)
- Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
- School of Life Science, Jiaying University, Meizhou, 514015, China
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Jia-Rui Han
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Mukhtiar Ali
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Zhi-Liang Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Dong-Ya Zhang
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd., Guangzhou, 510700, China
| | - Xian-Zhi Jiang
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd., Guangzhou, 510700, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China.
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Rodríguez R, Barra PJ, Larama G, Carrion VJ, de la Luz Mora M, Hale L, Durán P. Microbiome engineering optimized by Antarctic microbiota to support a plant host under water deficit. FRONTIERS IN PLANT SCIENCE 2023; 14:1241612. [PMID: 37780522 PMCID: PMC10541027 DOI: 10.3389/fpls.2023.1241612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023]
Abstract
Climate change challenges modern agriculture to develop alternative and eco-friendly solutions to alleviate abiotic and/or biotic stresses. The use of soil microbiomes from extreme environments opens new avenues to discover novel microorganisms and microbial functions to protect plants. In this study we confirm the ability of a bioinoculant, generated by natural engineering, to promote host development under water stress. Microbiome engineering was mediated through three factors i) Antarctic soil donation, ii) water deficit and iii) multigenerational tomato host selection. We revealed that tomato plants growing in soils supplemented with Antarctic microbiota were tolerant to water deficit stress after 10 generations. A clear increase in tomato seedling tolerance against water deficit stress was observed in all soils over generations of Host Mediated Microbiome Engineering, being Fildes mixture the most representatives, which was evidenced by an increased survival time, plant stress index, biomass accumulation, and decreased leaf proline content. Microbial community analysis using 16s rRNA gene amplicon sequencing data suggested a microbiome restructuring that could be associated with increased tolerance of water deficit. Additionally, the results showed a significant increase in the relative abundance of Candidatus Nitrosocosmicus and Bacillus spp. which could be key taxa associated with the observed tolerance improvement. We proposed that in situ microbiota engineering through the evolution of three factors (long-standing extreme climate adaption and host and stress selection) could represent a promising strategy for novel generation of microbial inoculants.
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Affiliation(s)
- Rodrigo Rodríguez
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
- Agroscientific SpA, Temuco, Chile
| | - Patricio J. Barra
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Giovanni Larama
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
| | | | - María de la Luz Mora
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Lauren Hale
- USDA, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Paola Durán
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
- Facultad de Ciencias Agropecuarias y Medioambiente, Departamento de Producción Agropecuaria, Universidad de La Frontera, Temuco, Chile
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Khan MH, Liu H, Zhu A, Khan MH, Hussain S, Cao H. Conservation tillage practices affect soil microbial diversity and composition in experimental fields. Front Microbiol 2023; 14:1227297. [PMID: 37601340 PMCID: PMC10433396 DOI: 10.3389/fmicb.2023.1227297] [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: 05/23/2023] [Accepted: 07/06/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Conservation tillage is a widely used technique worldwide, but the effects of conservation tillage on bacterial community structure are poorly understood. We explored proportional alterations in the bacterial community under different tillage treatments. Methodology Hence, this study utilized high-throughput sequencing technique to investigate the structure and assembly processes of microbial communities in different tillage treatments. Results and discussion Tillage treatments included tillage no-straw retention (CntWt), no-tillage with straw retention (CntWntS), tillage with straw retention (CntWtS), no-tillage and no-straw retention (CntWnt). The influence of tillage practices on soil bacterial communities was investigated using Illumina MiSeq sequencing. Different tillage methods and straw retention systems significantly influenced soil parameters such as total potassium and pH were not affected by tillage practices, while straw retention significantly affected soil parameters including nitrogen content, available phosphorus and available potassium. Straw retention decreased bacterial diversity while increased bacterial richness. The effect of straw retention and tillage on bacterial communities was greater than with no tillage. Phylogenetic β-diversity analysis showed that deterministic homogeneous selection processes were dominated, while stochastic processes were more pronounced in tillage without straw retention. Ecological network analysis showed that microbial community correlation was increased in CntWntS and CntWnt. Straw retention treatment significantly increased the relative abundance of bacterial taxa Proteobacteria, Bacteroidetes, and OD1, while Nitrospirae, Actinobacteria, and Verrucomicrobia significantly decreased. Conclusion The conservation tillage practices significantly affect soil properties, bacterial composition, and assembly processes; however, further studies are required to investigate the impact of different crops, tillage practices and physiological characteristics on bacterial community structure and functions.
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Affiliation(s)
- Muzammil Hassan Khan
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Hao Liu
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Anning Zhu
- Fengqiu Agro-Ecological Experimental Station, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Mudassir Hassan Khan
- Department of Biological Sciences, Karakoram International University, Gilgit, Pakistan
| | - Sarfraz Hussain
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Hui Cao
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
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Guo Y, Cheng S, Fang H, Yang Y, Li Y, Shi F, Zhou Y. Copper and cadmium co-contamination affects soil bacterial taxonomic and functional attributes in paddy soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 329:121724. [PMID: 37105465 DOI: 10.1016/j.envpol.2023.121724] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/21/2023]
Abstract
Microorganisms inhabiting heavy metal-contaminated soils have evolved specific metabolic capabilities to survive, which has the potential for effective bioremediation. However, the ecological consequence of copper (Cu) and cadmium (Cd) on bacterial taxonomic and functional attributes of rice field remains unclear. Here, we selected paddy soils along a polluted river in southern China to evaluate the role of Cu and Cd contaminant fractions in regulating bacterial co-occurrence patterns. We also assessed the effects of these heavy metal fractions on the relative abundance of functional genes using shotgun metagenomic analysis. Soil Cu and Cd concentrations in paddy soils gradually decreased from upstream to downstream of the river, and had a greater impact on bacterial communities and metabolic potentials than soil general properties. Soil Cu and Cd contamination led to drastic changes in the cumulative relative abundance of ecological modules in bacterial co-occurrence networks. Bacteria associated with AD3, HSB_OF53-F07 (both belonging to Chloroflexi), Rokubacteriales, and Nitrospira were identified as tolerant to Cu and Cd contamination. The Cu and Cd contaminant fractions were positively correlated with the genes involved in metal resistance, carbon (C) fixation, nitrification, and denitrification, but negatively correlated with the genes related to nitrogen (N) fixation. These results indicated that soil Cu and Cd pollution not only enriched metal resistant genes, but also affected genes related to microbial C and N cycling. This is critical for facilitating microbiome bioremediation of metal-contaminated paddy soils.
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Affiliation(s)
- Yifan Guo
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shulan Cheng
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Huajun Fang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; The Zhongke-Ji'an Institute for Eco-Environmental Sciences, Ji'an, 343000, China; Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, 810001, China.
| | - Yan Yang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuna Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangying Shi
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Zhou
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Zhang J, Feng Y, Maestre FT, Berdugo M, Wang J, Coleine C, Sáez-Sandino T, García-Velázquez L, Singh BK, Delgado-Baquerizo M. Water availability creates global thresholds in multidimensional soil biodiversity and functions. Nat Ecol Evol 2023; 7:1002-1011. [PMID: 37169879 DOI: 10.1038/s41559-023-02071-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/17/2023] [Indexed: 05/13/2023]
Abstract
Soils support an immense portion of Earth's biodiversity and maintain multiple ecosystem functions which are essential for human well-being. Environmental thresholds are known to govern global vegetation patterns, but it is still unknown whether they can be used to predict the distribution of soil organisms and functions across global biomes. Using a global field survey of 383 sites across contrasting climatic and vegetation conditions, here we showed that soil biodiversity and functions exhibited pervasive nonlinear patterns worldwide and are mainly governed by water availability (precipitation and potential evapotranspiration). Changes in water availability resulted in drastic shifts in soil biodiversity (bacteria, fungi, protists and invertebrates) and soil functions including plant-microbe interactions, plant productivity, soil biogeochemical cycles and soil carbon sequestration. Our findings highlight that crossing specific water availability thresholds can have critical consequences for the provision of essential ecosystem services needed to sustain our planet.
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Affiliation(s)
- Jianwei Zhang
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Youzhi Feng
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, China.
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, China.
| | - Fernando T Maestre
- Instituto Multidisciplinar para el Estudio del Medio 'Ramón Margalef', Universidad de Alicante, Alicante, Spain
- Departamento de Ecología, Universidad de Alicante, Alicante, Spain
| | - Miguel Berdugo
- Department of Environment Systems Science, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Depatamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain
| | - Juntao Wang
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Tadeo Sáez-Sandino
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Sevilla, Spain
| | - Laura García-Velázquez
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Sevilla, Spain
| | - Brajesh K Singh
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain.
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Masrahi AS. Effect of long-term influx of tertiary treated wastewater on native bacterial communities in a dry valley topsoil: 16S rRNA gene-based metagenomic analysis of composition and functional profile. PeerJ 2023; 11:e15583. [PMID: 37397028 PMCID: PMC10309050 DOI: 10.7717/peerj.15583] [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: 01/30/2023] [Accepted: 05/26/2023] [Indexed: 07/04/2023] Open
Abstract
Although dumping treated wastewater into soil might provide nutrients and organic matter, it can also expose the ecosystem to biological and chemical risks. A vital indication of soil health and quality is the soil microbial community. The current work used next-generation 16S rRNA gene amplicon sequencing to evaluate the effects of the long-term influx of tertiary treated wastewater (TWW) into Wadi Uranah, a dry valley in Makkah city, Saudi Arabia, on native topsoil bacterial community composition and predicted functions. The findings demonstrated that neither the compositions of microbial communities nor their predicted functions using PICRUSt2 differed significantly (p > 0.05) between polluted valley soil (PolVS) and unpolluted valley soil (UPVS). Alpha and beta diversity, however, showed that the PolVS samples had a considerably higher level of diversity and variability. Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were the most prevalent phyla in both groups. Noticeable relative variations existed in some metabolic pathways such as cofactor, prosthetic group, electron carrier degradation, aldehyde degradation, and Entner-Doudoroff (ED) pathways. Overall, our findings suggest that because both groups have very similar core microbiomes and functions, the long-term disposal of tertiary TWW into Wadi Uranah may have little to no influence on the composition and function of soil bacterial communities. In addition, the long-term discharge of tertiary TWW after partially treated wastewater's initial disposal may have helped the native soil microbial community recover.
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Wang Z, Dalton KR, Lee M, Parks CG, Beane Freeman LE, Zhu Q, González A, Knight R, Zhao S, Motsinger-Reif AA, London SJ. Metagenomics reveals novel microbial signatures of farm exposures in house dust. Front Microbiol 2023; 14:1202194. [PMID: 37415812 PMCID: PMC10321240 DOI: 10.3389/fmicb.2023.1202194] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/26/2023] [Indexed: 07/08/2023] Open
Abstract
Indoor home dust microbial communities, important contributors to human health, are shaped by environmental factors, including farm-related exposures. Advanced metagenomic whole genome shotgun sequencing (WGS) improves detection and characterization of microbiota in the indoor built-environment dust microbiome, compared to conventional 16S rRNA amplicon sequencing (16S). We hypothesized that the improved characterization of indoor dust microbial communities by WGS will enhance detection of exposure-outcome associations. The objective of this study was to identify novel associations of environmental exposures with the dust microbiome from the homes of 781 farmers and farm spouses enrolled in the Agricultural Lung Health Study. We examined various farm-related exposures, including living on a farm, crop versus animal production, and type of animal production, as well as non-farm exposures, including home cleanliness and indoor pets. We assessed the association of the exposures on within-sample alpha diversity and between-sample beta diversity, and the differential abundance of specific microbes by exposure. Results were compared to previous findings using 16S. We found most farm exposures were significantly positively associated with both alpha and beta diversity. Many microbes exhibited differential abundance related to farm exposures, mainly in the phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. The identification of novel differential taxa associated with farming at the genera level, including Rhodococcus, Bifidobacterium, Corynebacterium, and Pseudomonas, was a benefit of WGS compared to 16S. Our findings indicate that characterization of dust microbiota, an important component of the indoor environment relevant to human health, is heavily influenced by sequencing techniques. WGS is a powerful tool to survey the microbial community that provides novel insights on the impact of environmental exposures on indoor dust microbiota. These findings can inform the design of future studies in environmental health.
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Affiliation(s)
- Ziyue Wang
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, United States
| | - Kathryn R. Dalton
- Genomics and the Environment in Respiratory and Allergic Health Group, Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, United States
| | - Mikyeong Lee
- Genomics and the Environment in Respiratory and Allergic Health Group, Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, United States
| | - Christine G. Parks
- Genomics and the Environment in Respiratory and Allergic Health Group, Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, United States
| | - Laura E. Beane Freeman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Qiyun Zhu
- School of Life Sciences, Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
| | - Antonio González
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, United States
| | - Shanshan Zhao
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, United States
| | - Alison A. Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, United States
| | - Stephanie J. London
- Genomics and the Environment in Respiratory and Allergic Health Group, Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, United States
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Li B, Yan T. Metagenomic next generation sequencing for studying antibiotic resistance genes in the environment. ADVANCES IN APPLIED MICROBIOLOGY 2023; 123:41-89. [PMID: 37400174 DOI: 10.1016/bs.aambs.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Bacterial antimicrobial resistance (AMR) is a persisting and growing threat to human health. Characterization of antibiotic resistance genes (ARGs) in the environment is important to understand and control ARG-associated microbial risks. Numerous challenges exist in monitoring ARGs in the environment, due to the extraordinary diversity of ARGs, low abundance of ARGs with respect to the complex environmental microbiomes, difficulties in linking ARGs with bacterial hosts by molecular methods, difficulties in achieving quantification and high throughput simultaneously, difficulties in assessing mobility potential of ARGs, and difficulties in determining the specific AMR determinant genes. Advances in the next generation sequencing (NGS) technologies and related computational and bioinformatic tools are facilitating rapid identification and characterization ARGs in genomes and metagenomes from environmental samples. This chapter discusses NGS-based strategies, including amplicon-based sequencing, whole genome sequencing, bacterial population-targeted metagenome sequencing, metagenomic NGS, quantitative metagenomic sequencing, and functional/phenotypic metagenomic sequencing. Current bioinformatic tools for analyzing sequencing data for studying environmental ARGs are also discussed.
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Affiliation(s)
- Bo Li
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Tao Yan
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI, United States.
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Nam NN, Do HDK, Loan Trinh KT, Lee NY. Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions. Foods 2023; 12:foods12112140. [PMID: 37297385 DOI: 10.3390/foods12112140] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.
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Affiliation(s)
- Nguyen Nhat Nam
- Biotechnology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 72820, Vietnam
| | - Kieu The Loan Trinh
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
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Tang Q, Li Q, Tong L, Wu R, Xu J. Rhizospheric soil organic carbon accumulated but its molecular groups redistributed via rhizospheric soil microorganisms along multi-root Cerasus humilis plantation chronosequence at the karst rocky desertification control area. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27588-9. [PMID: 37184792 DOI: 10.1007/s11356-023-27588-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 05/08/2023] [Indexed: 05/16/2023]
Abstract
Though the relationships between the microorganism communities and the edaphic factors in rhizosphere soil along the plantation chronosequence have been widely reported, few researches have appeared on the interrelationship about rhizospheric soil microorganism community and soil organic carbon (SOC) under multi-root Cerasus humilis plantations of different age. In our study, the rhizospheric soil microbial communities, soil physicochemistry, and SOC molecular groups in plantations of 1-, 3-, and 5-year-old Cerasus humilis were investigated in karst rocky desertification control area of southwest China. It was found that karst rhizospheric soil moisture, total nitrogen, available potassium, and 46-60 ppm N-alkyl/methoxyl C decreased; however, SOC and fungal:bacterial ratio decreased along multi-root Cerasus humilis plantation chronosequence. Proteobacteria, Actinobacteriota, Acidobacteriota, and Ascomycota were recognized as the top 4 phyla in the karst rhizospheric soil microbial co-occurrence network. Moreover, Cerasus humilis plantations exerted significantly direct effect on rhizospheric soil microbial communities and soil physicochemical properties exerted significantly direct effects on SOC molecular groups. Our results suggested that the increased Cerasus humilis plantation years will promote C sequestration (e.g., SOC) with the continued input of root litter, root exudates, and plant litter. The inputted and activated C can be preferentially consumed by rhizospheric soil microorganisms and converted into microbial-derived compounds, which are finally incorporated into recalcitrant SOC pools. Hence, Cerasus humilis redistributed SOC molecular groups via rhizospheric soil microorganisms, and increased ratio of fungi:bacteria in rhizosphere was associated with C sequestration which could not be regarded as a widespread rule. Though our study is the first attempt to recognize the interaction between rhizospheric soil microbial community and SOC molecular groups at the karst rocky desertification control area, it provides a baseline for further research that ecological restoration can promote soil C sequestration via soil microorganisms in the early period of eco-restoration at karst area.
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Affiliation(s)
- Qin Tang
- Key Laboratory of Karst Ecosystem and Treatment of Rocky Desertification, Ministry of Natural Resources, Key Laboratory of Karst Dynamics, Ministry of Natural Resources & Guangxi, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, 541004, Guangxi, China
- School of Environmental Studies, China University of Geosciences, Wuhan, 430078, China
- International Research Center On Karst Under the Auspices of United Nations Educational, Scientific and Cultural Organization, Guilin, 541004, Guangxi, China
| | - Qiang Li
- Key Laboratory of Karst Ecosystem and Treatment of Rocky Desertification, Ministry of Natural Resources, Key Laboratory of Karst Dynamics, Ministry of Natural Resources & Guangxi, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, 541004, Guangxi, China.
- International Research Center On Karst Under the Auspices of United Nations Educational, Scientific and Cultural Organization, Guilin, 541004, Guangxi, China.
| | - Lingchen Tong
- Key Laboratory of Karst Ecosystem and Treatment of Rocky Desertification, Ministry of Natural Resources, Key Laboratory of Karst Dynamics, Ministry of Natural Resources & Guangxi, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, 541004, Guangxi, China
- International Research Center On Karst Under the Auspices of United Nations Educational, Scientific and Cultural Organization, Guilin, 541004, Guangxi, China
| | - Rui Wu
- Key Laboratory of Karst Ecosystem and Treatment of Rocky Desertification, Ministry of Natural Resources, Key Laboratory of Karst Dynamics, Ministry of Natural Resources & Guangxi, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, 541004, Guangxi, China
- International Research Center On Karst Under the Auspices of United Nations Educational, Scientific and Cultural Organization, Guilin, 541004, Guangxi, China
| | - Jiao Xu
- Key Laboratory of Karst Ecosystem and Treatment of Rocky Desertification, Ministry of Natural Resources, Key Laboratory of Karst Dynamics, Ministry of Natural Resources & Guangxi, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, 541004, Guangxi, China
- International Research Center On Karst Under the Auspices of United Nations Educational, Scientific and Cultural Organization, Guilin, 541004, Guangxi, China
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Wang X, Han Q, Yu Q, Wang S, Yang J, Su W, Wan-Yan R, Sun X, Li H. Mammalian carcass decay increases carbon storage and temporal turnover of carbon-fixing microbes in alpine meadow soil. ENVIRONMENTAL RESEARCH 2023; 225:115653. [PMID: 36898422 DOI: 10.1016/j.envres.2023.115653] [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: 01/03/2023] [Revised: 02/20/2023] [Accepted: 03/06/2023] [Indexed: 06/18/2023]
Abstract
Corpse decomposition is of great significance to the carbon cycle of natural ecosystem. Carbon fixation is a carbon conversion process that converts carbon dioxide into organic carbon, which greatly contributes to carbon emission reduction. However, the effects of wild animal carcass decay on carbon-fixing microbes in grassland soil environment are still unknown. In this research, thirty wild mammal (Ochotona curzoniae) corpses were placed on alpine meadow soil to study the carbon storage and carbon-fixing microbiota succession for a 94-day decomposition using next-generation sequencing. Our results revealed that 1) the concentration of total carbon increased approximately 2.24-11.22% in the corpse group. 2) Several carbon-fixing bacterial species (Calothrix parietina, Ancylobacter rudongensis, Rhodopseudomonas palustris) may predict the concentration of total carbon. 3) Animal cadaver degradation caused the differentiation of carbon-fixing microbiota structures during succession and made the medium-stage networks of carbon-fixing microbes more complicated. 4) The temporal turnover rate in the experimental groups was higher than that in the control groups, indicating a quick change of gravesoil carbon-fixing microbiota. 5) The deterministic process dominates the assembly mechanism of experimental groups (ranging from 53.42% to 94.94%), which reflects that the carbon-fixing microbial community in gravesoil can be regulated. Under global climate change, this study provides a new perspective for understanding the effects of wild animal carcass decay on soil carbon storage and carbon-fixing microbes.
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Affiliation(s)
- Xiaochen Wang
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qian Han
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qiaoling Yu
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Sijie Wang
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Jiawei Yang
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Wanghong Su
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Ruijun Wan-Yan
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Xiaofang Sun
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Huan Li
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China.
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65
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Dick JM, Tan J. Chemical Links Between Redox Conditions and Estimated Community Proteomes from 16S rRNA and Reference Protein Sequences. MICROBIAL ECOLOGY 2023; 85:1338-1355. [PMID: 35503575 DOI: 10.1007/s00248-022-01988-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/28/2022] [Indexed: 05/10/2023]
Abstract
Environmental influences on community structure are often assessed through multivariate analyses in order to relate microbial abundances to separately measured physicochemical variables. However, genes and proteins are themselves chemical entities; in combination with genome databases, differences in microbial abundances directly encode for chemical variability. We predicted that the carbon oxidation state of estimated community proteomes, obtained by combining taxonomic abundances from published 16S rRNA gene sequencing datasets with reference microbial proteomes from the NCBI Reference Sequence (RefSeq) database, would reflect environmental oxidation-reduction conditions. Analysis of multiple datasets confirms the geobiochemical predictions for environmental redox gradients in hydrothermal systems, stratified lakes and marine environments, and shale gas wells. The geobiochemical signal is largest for the steep redox gradients associated with hydrothermal systems and between injected water and produced fluids from shale gas wells, demonstrating that microbial community composition can be a chemical proxy for environmental redox gradients. Although estimates of oxidation state from 16S amplicon and metagenomic sequences are correlated, the 16S-based estimates show stronger associations with redox gradients in some environments.
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Affiliation(s)
- Jeffrey M Dick
- Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China.
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
| | - Jingqiang Tan
- Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China
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66
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He L, Sun X, Li S, Zhou W, Chen Z, Bai X. The vertical distribution and control factor of microbial biomass and bacterial community at macroecological scales. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161754. [PMID: 36709888 DOI: 10.1016/j.scitotenv.2023.161754] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/04/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Microorganisms exist throughout the soil profile and those microorganisms living in deeper soil horizons likely play key roles in regulating biogeochemical processes. However, the vertical differentiations of microbes along soil depth and their global biogeographical patterns remain poorly understood. Herein, we conducted a global meta-analysis to clarify the vertical changes of microbial biomass, diversity, and microbial relative abundance across the soil profiles. Data was collected from 43 peer-reviewed articles of 110 soil profiles (467 observations in total) from around the world. We found soil microbial biomass and bacterial diversity decreased with depth in soils. Among examined edaphic factors, the depth variation in soil pH exhibited significant negative associations with the depth change in microbial biomass and bacterial Shannon index, while soil total organic carbon (TOC) and total nitrogen (TN) exhibited significant positive associations. For the major bacteria phyla, the relative abundances of Proteobacteria and Bacteroidetes decreased with soil depth, while Chloroflexi, Gemmatimonadetes, and Nitrospirae increased. We found both parallels and differences in the biogeographical patterns of microbial attribute of topsoil vs. subsoil. Microbial biomass was significantly controlled by the soil nutrient concentrations in both topsoil and subsoil compared with climatic factors, while bacterial Shannon index was significantly controlled by the edaphic factors and across latitudes or climatic factors. Moreover, mean annual precipitation can also be used as a predictor of microbial biomass in subsoil which is different from topsoil. Collectively, our results provide a novel integrative view of how microbial biomass and bacterial community response to soil depth change and clarify the controlling factors of the global distribution patterns of microbial biomass and diversity, which are critical to enhance ecosystem simulation models and for formulating sustainable ecosystem management and conservation policies.
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Affiliation(s)
- Libing He
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xiangyang Sun
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Suyan Li
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Wenzhi Zhou
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Zhe Chen
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xueting Bai
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
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67
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Liang Q, Mod HK, Luo S, Ma B, Yang K, Chen B, Qi W, Zhao Z, Du G, Guisan A, Ma X, Le Roux X. Taxonomic and functional biogeographies of soil bacterial communities across the Tibet plateau are better explained by abiotic conditions than distance and plant community composition. Mol Ecol 2023. [PMID: 37060060 DOI: 10.1111/mec.16952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/26/2023] [Accepted: 03/29/2023] [Indexed: 04/16/2023]
Abstract
The processes governing soil bacteria biogeography are still not fully understood. It remains unknown how the importance of environmental filtering and dispersal differs between bacterial taxonomic and functional biogeography, and whether their importance is scale-dependent. We sampled soils across the Tibet plateau, with distances among plots ranging from 20 m to 1550 km. Taxonomic composition of bacterial community was characterized by 16S amplicon sequencing and functional community composition by qPCR targeting 9 functional groups involved in N dynamics. Factors representing climate, soil and plant community were measured to assess different facets of environmental dissimilarity. Both bacterial taxonomic and functional dissimilarities were more related to abiotic dissimilarity than biotic (vegetation) dissimilarity or distance. Taxonomic dissimilarity was mostly explained by differences in soil pH and mean annual temperature (MAT), while functional dissimilarity was linked to differences in soil N and P availabilities and N:P ratio. Soil pH and MAT remained the main determinants of taxonomic dissimilarity across spatial scales. In contrast, the explanatory variables of N-related functional dissimilarity varied across the scales, with soil moisture and organic matter having the highest role across short distances (<~330 km), and available P, N:P ratio and distance being important over long distances (>~660 km). Our results demonstrate how biodiversity dimension (taxonomic versus functional aspects) and spatial scale influence the factors driving soil bacterial biogeography.
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Affiliation(s)
- Qingqing Liang
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Heidi K Mod
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Shuaiwei Luo
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Beibei Ma
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Kena Yang
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Beibei Chen
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Wei Qi
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Zhigang Zhao
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Guozhen Du
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Xiaojun Ma
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xavier Le Roux
- INRAE, Université de Lyon, Université Lyon 1, CNRS, vetAgroSup, UMR 1418 INRAE, UMR 5557 CNRS, Ecologie Microbienne LEM, Villeurbanne, France
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68
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Wang Z, Dalton KR, Lee M, Parks CG, Beane Freeman LE, Zhu Q, Gonz Lez A, Knight R, Zhao S, Motsinger-Reif AA, London SJ. Metagenomics reveals novel microbial signatures of farm exposures in house dust. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.07.23288301. [PMID: 37090637 PMCID: PMC10120797 DOI: 10.1101/2023.04.07.23288301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Indoor home dust microbial communities, important contributors to human health outcomes, are shaped by environmental factors, including farm-related exposures. Detection and characterization of microbiota are influenced by sequencing methodology; however, it is unknown if advanced metagenomic whole genome shotgun sequencing (WGS) can detect novel associations between environmental exposures and the indoor built-environment dust microbiome, compared to conventional 16S rRNA amplicon sequencing (16S). This study aimed to better depict indoor dust microbial communities using WGS to investigate novel associations with environmental risk factors from the homes of 781 farmers and farm spouses enrolled in the Agricultural Lung Health Study. We examined various farm-related exposures, including living on a farm, crop versus animal production, and type of animal production, as well as non-farm exposures, including home cleanliness and indoor pets. We assessed the association of the exposures on within-sample alpha diversity and between-sample beta diversity, and the differential abundance of specific microbes by exposure. Results were compared to previous findings using 16S. We found most farm exposures were significantly positively associated with both alpha and beta diversity. Many microbes exhibited differential abundance related to farm exposures, mainly in the phyla Actinobacteria, Bacteroidetes, Firmicutes , and Proteobacteria . The identification of novel differential taxa associated with farming at the genera level, including Rhodococcus, Bifidobacterium, Corynebacterium , and Pseudomonas , was a benefit of WGS compared to 16S. Our findings indicate that characterization of dust microbiota, an important component of the indoor environment relevant to human health, is heavily influenced by sequencing techniques. WGS is a powerful tool to survey the microbial community that provides novel insights on the impact of environmental exposures on indoor dust microbiota, and should be an important consideration in designing future studies in environmental health.
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69
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Ren Z, Ma K, Jia X, Wang Q, Zhang C, Li X. Metagenomics Unveils Microbial Diversity and Their Biogeochemical Roles in Water and Sediment of Thermokarst Lakes in the Yellow River Source Area. MICROBIAL ECOLOGY 2023; 85:904-915. [PMID: 35650293 DOI: 10.1007/s00248-022-02053-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/25/2022] [Indexed: 05/04/2023]
Abstract
Thermokarst lakes have long been recognized as biogeochemical hotspots, especially as sources of greenhouse gases. On the Qinghai-Tibet Plateau, thermokarst lakes are experiencing extensive changes due to faster warming. For a deep understanding of internal lake biogeochemical processes, we applied metagenomic analyses to investigate the microbial diversity and their biogeochemical roles in sediment and water of thermokarst lakes in the Yellow River Source Area (YRSA). Sediment microbial communities (SMCs) had lower species and gene richness than water microbial communities (WMCs). Bacteria were the most abundant component in both SMCs and WMCs with significantly different abundant genera. The functional analyses showed that both SMCs and WMCs had low potential in methanogenesis but strong in aerobic respiration, nitrogen assimilation, exopolyphosphatase, glycerophosphodiester phosphodiesterases, and polyphosphate kinase. Moreover, SMCs were enriched in genes involved in anaerobic carbon fixation, aerobic carbon fixation, fermentation, most nitrogen metabolism pathways, dissimilatory sulfate reduction, sulfide oxidation, polysulfide reduction, 2-phosphonopropionate transporter, and phosphate regulation. WMCs were enriched in genes involved in assimilatory sulfate reduction, sulfur mineralization, phosphonoacetate hydrolase, and phosphonate transport. Functional potentials suggest the differences of greenhouse gas emission, nutrient cycling, and living strategies between SMCs and WMCs. This study provides insight into the main biogeochemical processes and their properties in thermokarst lakes in YRSA, improving our understanding of the roles and fates of these lakes in a warming world.
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Affiliation(s)
- Ze Ren
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China.
- School of Environment, Beijing Normal University, Beijing, 100875, China.
| | - Kang Ma
- School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Xuan Jia
- College of Education for the Future, Beijing Normal University, Zhuhai, 519087, China
| | - Qing Wang
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China
- School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Cheng Zhang
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China
- School of Engineering Technology, Beijing Normal University, Zhuhai, 519087, China
| | - Xia Li
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China
- School of Environment, Beijing Normal University, Beijing, 100875, China
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Chen W, Yu T, Zhao C, Li B, Qin Y, Li H, Tang H, Liu J, Zhang X. Development and Determinants of Topsoil Bacterial and Fungal Communities of Afforestation by Aerial Sowing in Tengger Desert, China. J Fungi (Basel) 2023; 9:jof9040399. [PMID: 37108854 PMCID: PMC10144444 DOI: 10.3390/jof9040399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/20/2023] [Accepted: 03/23/2023] [Indexed: 04/29/2023] Open
Abstract
It was previously reported that afforestation in the desert can help improve soil texture, carbon accumulation, and nutrient status. However, the effects of afforestation on soil microbial composition, diversity, and microbial interactions with soil physicochemical properties have been rarely evaluated quantitatively. Using the method of space-for-time substitutions, we assessed the development and determinants of topsoil bacterial and fungal communities over nearly 40 years of successive afforestation by aerial sowing in Tengger Desert, China. The results showed that afforestation by aerial sowing comprised a considerable proportion of Chloroflexi and Acidobacteria in the bacterial community in addition to the ubiquitous phyla found in desert but had fewer effects on the dominant phyla of the fungal community. At the phylum level, the bacterial community was clearly clustered into two groups. However, it was difficult to differentiate the constituents of the fungal community based on principal coordinate analysis. The richness of the bacterial and fungal communities was significantly higher after five years than at zero years and three years. Additionally, the bacterial community varied parabolically and reached its largest size at twenty years, while the fungal community increased exponentially. Soil physicochemical properties were found to have divergent effects on the abundance and diversity of bacterial and fungal communities, among which salt- and carbon-associated properties (e.g., electrical conductivity, calcium, magnesium, total carbon, and organic carbon) were closely related with the abundance of bacterial-dominant phyla and the diversity of bacteria and fungi, but nutrient-associated properties (e.g., total phosphorus and available phosphorus) were not. The results indicate that afforestation through the salt secretions of plants leaves and carbon inputs from litter promote the development of topsoil bacterial and fungal communities in the desert.
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Affiliation(s)
- Weiyu Chen
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Alxa Desert Eco-Hydrology Experimental Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tengfei Yu
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Alxa Desert Eco-Hydrology Experimental Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Chenguang Zhao
- Alxa Institute of Forestry and Grassland, Alxa 750306, China
| | - Baofeng Li
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Alxa Desert Eco-Hydrology Experimental Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yanyan Qin
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Huiying Li
- Alxa Institute of Forestry and Grassland, Alxa 750306, China
| | - Haojie Tang
- Alxa Forestry and Grassland Projection Station, Alxa 750306, China
| | - Junliang Liu
- Alxa Forestry and Grassland Projection Station, Alxa 750306, China
| | - Xiaoyou Zhang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
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Wan Q, Li L, Liu B, Zhang Z, Liu Y, Xie M. Different and unified responses of soil bacterial and fungal community composition and predicted functional potential to 3 years’ drought stress in a semiarid alpine grassland. Front Microbiol 2023; 14:1104944. [PMID: 37082184 PMCID: PMC10112540 DOI: 10.3389/fmicb.2023.1104944] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/23/2023] [Indexed: 03/17/2023] Open
Abstract
IntroductionSoil microbial communities are key to functional processes in terrestrial ecosystems, and they serve as an important indicator of grasslands status. However, the responses of soil microbial communities and functional potential to drought stress in semiarid alpine grasslands remain unclear.MethodsHere, a field experiment was conducted under ambient precipitation as a control, −20% and −40% of precipitation to explore the responses of soil microbial diversity, community composition, and predicted functional potential to drought stress in a semiarid alpine grassland located in the northwest of China. Moreover, 16S rRNA gene and ITS sequencing were used to detect bacterial and fungal communities, and the PICRUST and FUNGuild databases were used to predict bacterial and fungal functional groups.ResultsResults showed drought stress substantially changes the community diversity of bacteria and fungi, among which the bacteria community is more sensitive to drought stress than fungi, indicating that the diversity or structure of soil bacteria community could serve as an indicator of alpine grasslands status. However, the fungal community still has difficulty maintaining resistance under excessive drought stress. Our paper also highlighted that soil moisture content, plant diversity (Shannon Wiener, Pieiou, and Simpson), and soil organic matter are the main drivers affecting soil bacterial and fungal community composition and predicted functional potential. Notably, the soil microbial functional potential could be predictable through taxonomic community profiles.ConclusionOur research provides insight for exploring the mechanisms of microbial community composition and functional response to climate change (longer drought) in a semiarid alpine grassland.
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Affiliation(s)
- Qian Wan
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Lei Li,
| | - Bo Liu
- Shandong Provincial Key Laboratory of Soil Conservation and Environmental Protection, College of Resources and Environment, Linyi University, Linyi, China
| | - Zhihao Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yalan Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingyu Xie
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
- University of Chinese Academy of Sciences, Beijing, China
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Villegas LEM, Radl J, Dimopoulos G, Short SM. Bacterial communities of Aedes aegypti mosquitoes differ between crop and midgut tissues. PLoS Negl Trop Dis 2023; 17:e0011218. [PMID: 36989328 PMCID: PMC10085046 DOI: 10.1371/journal.pntd.0011218] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 04/10/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Microbiota studies of Aedes aegypti and other mosquitoes generally focus on the bacterial communities found in adult female midguts. However, other compartments of the digestive tract maintain communities of bacteria which remain almost entirely unstudied. For example, the Dipteran crop is a food storage organ, but few studies have looked at the microbiome of crops in mosquitoes, and only a single previous study has investigated the crop in Ae. aegypti. In this study, we used both culture-dependent and culture-independent methods to compare the bacterial communities in midguts and crops of laboratory reared Ae. aegypti. Both methods revealed a trend towards higher abundance, but also higher variability, of bacteria in the midgut than the crop. When present, bacteria from the genus Elizabethkingia (family Weeksellaceae) dominated midgut bacterial communities. In crops, we found a higher diversity of bacteria, and these communities were generally dominated by acetic acid bacteria (family Acetobacteriaceae) from the genera Tanticharoenia and Asaia. These three taxa drove significant community structure differences between the tissues. We used FAPROTAX to predict the metabolic functions of these communities and found that crop bacterial communities were significantly more likely to contain bacteria capable of methanol oxidation and methylotrophy. Both the presence of acetic acid bacteria (which commonly catabolize sugar to produce acetic acid) and the functional profile that includes methanol oxidation (which is correlated with bacteria found with natural sources like nectar) may relate to the presence of sugar, which is stored in the mosquito crop. A better understanding of what bacteria are present in the digestive tract of mosquitoes and how these communities assemble will inform how the microbiota impacts mosquito physiology and the full spectrum of functions provided by the microbiota. It may also facilitate better methods of engineering the mosquito microbiome for vector control or prevention of disease transmission.
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Affiliation(s)
| | - James Radl
- Department of Entomology, The Ohio State University, Columbus, Ohio, United States of America
| | - George Dimopoulos
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Sarah M. Short
- Department of Entomology, The Ohio State University, Columbus, Ohio, United States of America
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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PhyloPlus: a Universal Tool for Phylogenetic Interrogation of Metagenomic Communities. mBio 2023; 14:e0345522. [PMID: 36645293 PMCID: PMC9973285 DOI: 10.1128/mbio.03455-22] [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] [Indexed: 01/17/2023] Open
Abstract
Phylogeny is a powerful tool that can be incorporated into quantitative descriptions of community diversity, yet its use has been limited largely due to the difficulty in constructing phylogenies which incorporate the wide genomic diversity of microbial communities. Here, we describe the development of a web portal, PhyloPlus, which enables users to generate customized phylogenies that may be applied to any bacterial or archaeal communities. We demonstrate the power of phylogeny by comparing metrics that employ phylogeny with those that do not when applied to data sets from two metagenomic studies (fermented food, n = 58; human microbiome, n = 60). This example shows how inclusion of all bacterial species identified by taxonomic classifiers (Kraken2 and Kaiju) made the phylogeny perfectly congruent to the corresponding classification outputs. Our phylogeny-based approach also enabled the construction of more constrained null models which (i) shed light into community structure and (ii) minimize potential inflation of type I errors. Construction of such null models allowed for the observation of under-dispersion in 44 (75.86%) food samples, with the metacommunity defined as bacteria that were found in different food matrices. We also observed that closely related species with high abundance and uneven distribution across different sites could potentially exaggerate the dissimilarity between phylogenetically similar communities if they were measured using traditional species-based metrics (Padj. = 0.003), whereas this effect was mitigated by incorporating phylogeny (Padj. = 1). In summary, our tool can provide additional insights into microbial communities of interest and facilitate the use of phylogeny-based approaches in metagenomic analyses. IMPORTANCE There has been an explosion of interest in how microbial diversity affects human health, food safety, and environmental functions among many other processes. Accurately measuring the diversity and structure of those communities is central to understanding their effects. Here, we describe the development of a freely available online tool, PhyloPlus, which allows users to generate custom phylogenies that may be applied to any data set, thereby removing a major obstacle to the application of phylogeny to metagenomic data analysis. We demonstrate that the genetic relatedness of the organisms within those communities is a critical feature of their overall diversity, and that using a phylogeny which captures and quantifies this diversity allows for much more accurate descriptions while preventing misleading conclusions based on estimates that ignore evolutionary relationships.
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Liu X, Wang H, Wang W, Cheng X, Wang Y, Li Q, Li L, Ma L, Lu X, Tuovinen OH. Nitrate determines the bacterial habitat specialization and impacts microbial functions in a subsurface karst cave. Front Microbiol 2023; 14:1115449. [PMID: 36846803 PMCID: PMC9947541 DOI: 10.3389/fmicb.2023.1115449] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Karst caves are usually considered as natural laboratories to study pristine microbiomes in subsurface biosphere. However, effects of the increasingly detected nitrate in underground karst ecosystem due to the acid rain impact on microbiota and their functions in subsurface karst caves have remained largely unknown. In this study, samples of weathered rocks and sediments were collected from the Chang Cave, Hubei province and subjected to high-throughput sequencing of 16S rRNA genes. The results showed that nitrate significantly impacted bacterial compositions, interactions, and functions in different habitats. Bacterial communities clustered according to their habitats with distinguished indicator groups identified for each individual habitat. Nitrate shaped the overall bacterial communities across two habitats with a contribution of 27.2%, whereas the pH and TOC, respectively, structured bacterial communities in weathered rocks and sediments. Alpha and beta diversities of bacterial communities increased with nitrate concentration in both habitats, with nitrate directly affecting alpha diversity in sediments, but indirectly on weathered rocks by lowering pH. Nitrate impacted more on bacterial communities in weathered rocks at the genus level than in sediments because more genera significantly correlated with nitrate concentration in weathered rocks. Diverse keystone taxa involved in nitrogen cycling were identified in the co-occurrence networks such as nitrate reducers, ammonium-oxidizers, and N2-fixers. Tax4Fun2 analysis further confirmed the dominance of genes involved in nitrogen cycling. Genes of methane metabolism and carbon fixation were also dominant. The dominance of dissimilatory and assimilatory nitrate reduction in nitrogen cycling substantiated nitrate impact on bacterial functions. Our results for the first time revealed the impact of nitrate on subsurface karst ecosystem in terms of bacterial compositions, interactions, and functions, providing an important reference for further deciphering the disturbance of human activities on the subsurface biosphere.
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Affiliation(s)
- Xiaoyan Liu
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China,*Correspondence: Hongmei Wang, ;
| | - Weiqi Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaoyu Cheng
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yiheng Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Qing Li
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Lu Li
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Liyuan Ma
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaolu Lu
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Olli H. Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH, United States
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Satoh S, Tanaka R, Yokono M, Endoh D, Yabuki T, Tanaka A. Phylogeny analysis of whole protein-coding genes in metagenomic data detected an environmental gradient for the microbiota. PLoS One 2023; 18:e0281288. [PMID: 36730456 PMCID: PMC9894459 DOI: 10.1371/journal.pone.0281288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023] Open
Abstract
Environmental factors affect the growth of microorganisms and therefore alter the composition of microbiota. Correlative analysis of the relationship between metagenomic composition and the environmental gradient can help elucidate key environmental factors and establishment principles for microbial communities. However, a reasonable method to quantitatively compare whole metagenomic data and identify the primary environmental factors for the establishment of microbiota has not been reported so far. In this study, we developed a method to compare whole proteomes deduced from metagenomic shotgun sequencing data, and quantitatively display their phylogenetic relationships as metagenomic trees. We called this method Metagenomic Phylogeny by Average Sequence Similarity (MPASS). We also compared one of the metagenomic trees with dendrograms of environmental factors using a comparison tool for phylogenetic trees. The MPASS method correctly constructed metagenomic trees of simulated metagenomes and soil and water samples. The topology of the metagenomic tree of samples from the Kirishima hot springs area in Japan was highly similarity to that of the dendrograms based on previously reported environmental factors for this area. The topology of the metagenomic tree also reflected the dynamics of microbiota at the taxonomic and functional levels. Our results strongly suggest that MPASS can successfully classify metagenomic shotgun sequencing data based on the similarity of whole protein-coding sequences, and will be useful for the identification of principal environmental factors for the establishment of microbial communities. Custom Perl script for the MPASS pipeline is available at https://github.com/s0sat/MPASS.
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Affiliation(s)
- Soichirou Satoh
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
- * E-mail:
| | - Rei Tanaka
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Makio Yokono
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Japan
| | - Daiji Endoh
- Department of Radiation Biology, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Tetsuo Yabuki
- General Education Department, Hokusei Gakuen University, Sapporo, Japan
| | - Ayumi Tanaka
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
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Du L, Zhong S, Luo K, Yang S, Xia J, Chen Q. Effect of metal pollution on the distribution and co-occurrence pattern of bacterial, archaeal and fungal communities throughout the soil profiles. CHEMOSPHERE 2023; 315:137692. [PMID: 36596328 DOI: 10.1016/j.chemosphere.2022.137692] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
Metal pollution has raised negative impact on microbes, but little is known about the distribution and co-occurrence pattern of bacterial, fungal and archaeal communities along the soil profiles at multiple metal contamination sites. Here, we characterized the variations of metal concentrations and microbial communities with soil depth along five deep bores at the Tanghe Sewage Reservoir, a typical metal contamination area on the North China Plain. Co, Cd, Mg, Se, and Li were identified as the major contaminants in this area, and the pollution load index was 1.88, 1.54 and 1.62 in the shallow layer (0-0.6 m), deep layer (>2.0 m) and middle layer (0.6-2.0 m), respectively. The diversities and compositions of bacterial, archaeal and fungal communities varied significantly along the soil profiles. Deterministic process played a crucial role in shaping the difference of microbial community compositions among different soil layers, in which metal levels contributed more than soil physiochemical parameters. Furthermore, the interspecific co-occurrence network was most complex in the middle layer, indicating that metal pollution could decrease microbial network complexity. Bacterial keystone species in the co-occurrence networks showed both positive and negative correlations with polluted metals, whereas most archaeal and fungal keystone species were negatively related to multiple metals. These findings increased our understanding of distribution patterns, co-occurrence networks and environmental drivers of microbial communities in metal pollution soils.
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Affiliation(s)
- Lei Du
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, PR China; College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, PR China
| | - Sining Zhong
- Fujian Agriculture and Forestry University, College of Resources and Environment, Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, Fuzhou, 350002, PR China
| | - Kongyan Luo
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, PR China
| | - Shanqing Yang
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, PR China
| | - Jianxin Xia
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, PR China.
| | - Qian Chen
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, PR China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, PR China.
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Panda A, Tuller T. Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis. NPJ Biofilms Microbiomes 2023; 9:5. [PMID: 36693851 PMCID: PMC9873608 DOI: 10.1038/s41522-023-00372-w] [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: 01/15/2022] [Accepted: 01/11/2023] [Indexed: 01/25/2023] Open
Abstract
Codon and amino acid usage were associated with almost every aspect of microbial life. However, how the environment may impact the codon and amino acid choice of microbial communities at the habitat level is not clearly understood. Therefore, in this study, we analyzed codon and amino acid usage patterns of a large number of environmental samples collected from diverse ecological niches. Our results suggested that samples derived from similar environmental niches, in general, show overall similar codon and amino acid distribution as compared to samples from other habitats. To substantiate the relative impact of the environment, we considered several factors, such as their similarity in GC content, or in functional or taxonomic abundance. Our analysis demonstrated that none of these factors can fully explain the trends that we observed at the codon or amino acid level implying a direct environmental influence on them. Further, our analysis demonstrated different levels of selection on codon bias in different microbial communities with the highest bias in host-associated environments such as the digestive system or oral samples and the lowest level of selection in soil and water samples. Considering a large number of metagenomic samples here we showed that microorganisms collected from similar environmental backgrounds exhibit similar patterns of codon and amino acid usage irrespective of the location or time from where the samples were collected. Thus our study suggested a direct impact of the environment on codon and amino usage of microorganisms that cannot be explained considering the influence of other factors.
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Affiliation(s)
- Arup Panda
- grid.12136.370000 0004 1937 0546Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, 69978 Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, 69978, Israel.
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Abulaizi M, Chen M, Yang Z, Hu Y, Zhu X, Jia H. Response of soil bacterial community to alpine wetland degradation in arid Central Asia. FRONTIERS IN PLANT SCIENCE 2023; 13:990597. [PMID: 36684714 PMCID: PMC9848402 DOI: 10.3389/fpls.2022.990597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
A large number of studies have reported the importance of bacterial communities in ecosystems and their responses to soil degradation, but the response mechanism in arid alpine wetlands is still unclear. Here, the non-degraded (ND), slightly degraded (SD), and heavily degraded (HD) regions of Bayinbuluk alpine wetland were used to analyzed the diversity, structure and function of bacterial communities in three degraded wetlands using 16S rRNA. The results showed that with the increase of degradation degree, the content of soil moisture (SM) and available nitrogen (AN) decreased significantly, plant species richness and total vegetation coverage decreased significantly, Cyperaceae (Cy) coverage decreased significantly, and Gramineae (Gr) coverage increased significantly. Degradation did not significantly affect the diversity of the bacterial community, but changed the relative abundance of the community structure. Degradation significantly increased the relative abundance of Actinobacteria (ND: 3.95%; SD: 7.27%; HD: 23.97%) and Gemmatimonadetes (ND: 0.39%; SD: 2.17%; HD: 10.78%), while significantly reducing the relative abundance of Chloroflexi (ND: 13.92%; SD: 8.68%; HD: 3.55%) and Nitrospirae (ND: 6.18%; SD: 0.45%; HD: 2.32%). Degradation significantly reduced some of the potential functions in the bacterial community associated with the carbon (C), nitrogen (N) and sulfur (S) cycles, such as hydrocarbon degradation (ND: 25.00%; SD: 1.74%; HD: 6.59%), such as aerobic ammonia oxidation (ND: 5.96%; SD: 22.82%; HD: 4.55%), and dark sulfide oxidation (ND: 32.68%; SD: 0.37%; HD: 0.28%). Distance-based redundancy analysis (db-RDA) results showed that the bacteria community was significantly related to the TC (total carbon) and Gr (P < 0.05). The results of linear discriminant analysis effect size (LEfSe) analysis indicate significant enrichments of Alphaproteobacteria and Sphingomonas in the HD area. The vegetation communities and soil nutrients changed significantly with increasing soil degradation levels, and Sphingomonas could be used as potential biomarker of degraded alpine wetlands.
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Affiliation(s)
- Maidinuer Abulaizi
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
| | - Mo Chen
- College of Grassland Science, Xinjiang Agricultural University, Urumqi, China
| | - Zailei Yang
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
| | - Yang Hu
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
| | - Xinping Zhu
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
| | - Hongtao Jia
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
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Li S, Fan W, Xu G, Cao Y, Zhao X, Hao S, Deng B, Ren S, Hu S. Bio-organic fertilizers improve Dendrocalamus farinosus growth by remolding the soil microbiome and metabolome. Front Microbiol 2023; 14:1117355. [PMID: 36876063 PMCID: PMC9975161 DOI: 10.3389/fmicb.2023.1117355] [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: 12/06/2022] [Accepted: 01/24/2023] [Indexed: 02/17/2023] Open
Abstract
Organic and microbial fertilizers have potential advantages over inorganic fertilizers in improving soil fertility and crop yield without harmful side-effects. However, the effects of these bio-organic fertilizers on the soil microbiome and metabolome remain largely unknown, especially in the context of bamboo cultivation. In this study, we cultivated Dendrocalamus farinosus (D. farinosus) plants under five different fertilization conditions: organic fertilizer (OF), Bacillus amyloliquefaciens bio-fertilizer (Ba), Bacillus mucilaginosus Krassilnikov bio-fertilizer (BmK), organic fertilizer plus Bacillus amyloliquefaciens bio-fertilizer (OFBa), and organic fertilizer plus Bacillus mucilaginosus Krassilnikov bio-fertilizer (OFBmK). We conducted 16S rRNA sequencing and liquid chromatography/mass spectrometry (LC-MS) to evaluate the soil bacterial composition and soil metabolic activity in the different treatment groups. The results demonstrate that all the fertilization conditions altered the soil bacterial community composition. Moreover, the combination of organic and microbial fertilizers (i.e., in the OFBa and OFBmK groups) significantly affected the relative abundance of soil bacterial species; the largest number of dominant microbial communities were found in the OFBa group, which were strongly correlated with each other. Additionally, non-targeted metabolomics revealed that the levels of soil lipids and lipid-like molecules, and organic acids and their derivatives, were greatly altered under all treatment conditions. The levels of galactitol, guanine, and deoxycytidine were also markedly decreased in the OFBa and OFBmK groups. Moreover, we constructed a regulatory network to delineated the relationships between bamboo phenotype, soil enzymatic activity, soil differential metabolites, and dominant microbial. The network revealed that bio-organic fertilizers promoted bamboo growth by modifying the soil microbiome and metabolome. Accordingly, we concluded that the use of organic fertilizers, microbial fertilizers, or their combination regulated bacterial composition and soil metabolic processes. These findings provide new insights into how D. farinosus-bacterial interactions are affected by different fertilization regiments, which are directly applicable to the agricultural cultivation of bamboo.
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Affiliation(s)
- Shangmeng Li
- Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang, China.,Engineering Research Center for Biomass Resource Utilizaiton and Modification of Sichuan Province, Mianyang, China
| | - Wei Fan
- Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang, China.,Engineering Research Center for Biomass Resource Utilizaiton and Modification of Sichuan Province, Mianyang, China
| | - Gang Xu
- Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang, China.,Engineering Research Center for Biomass Resource Utilizaiton and Modification of Sichuan Province, Mianyang, China
| | - Ying Cao
- Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang, China.,Engineering Research Center for Biomass Resource Utilizaiton and Modification of Sichuan Province, Mianyang, China
| | - Xin Zhao
- Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang, China.,Engineering Research Center for Biomass Resource Utilizaiton and Modification of Sichuan Province, Mianyang, China
| | - Suwei Hao
- Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang, China.,Engineering Research Center for Biomass Resource Utilizaiton and Modification of Sichuan Province, Mianyang, China
| | - Bin Deng
- Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang, China.,Engineering Research Center for Biomass Resource Utilizaiton and Modification of Sichuan Province, Mianyang, China
| | - Siyuan Ren
- Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang, China.,Engineering Research Center for Biomass Resource Utilizaiton and Modification of Sichuan Province, Mianyang, China
| | - Shanglian Hu
- Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang, China.,Engineering Research Center for Biomass Resource Utilizaiton and Modification of Sichuan Province, Mianyang, China
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80
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Selmani Z, Attard E, Lauga B, Barakat M, Ortet P, Tulumello J, Achouak W, Kaci Y, Heulin T. Culturing the desert microbiota. Front Microbiol 2023; 14:1098150. [PMID: 37113232 PMCID: PMC10126307 DOI: 10.3389/fmicb.2023.1098150] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Over the last 30 years, the description of microbial diversity has been mainly based on culture-independent approaches (metabarcoding and metagenomics) allowing an in-depth analysis of microbial diversity that no other approach allows. Bearing in mind that culture-dependent approaches cannot replace culture-independent approaches, we have improved an original method for isolating strains consisting of "culturing" grains of sand directly on Petri dishes (grain-by-grain method). This method allowed to cultivate up to 10% of the bacteria counted on the surface of grains of the three sites studied in the Great Western Erg in Algeria (Timoudi, Béni Abbès, and Taghit), knowing that on average about 10 bacterial cells colonize each grain. The diversity of culturable bacteria (collection of 290 strains) predicted by 16S rRNA gene sequencing revealed that Arthrobacter subterraneus, Arthrobacter tecti, Pseudarthrobacter phenanthrenivorans, Pseudarthrobacter psychrotolerans, and Massilia agri are the dominant species. The comparison of the culture-dependent and -independent (16S rRNA gene metabarcoding) approaches at the Timoudi site revealed 18 bacterial genera common to both approaches with a relative overestimation of the genera Arthrobacter/Pseudarthrobacter and Kocuria, and a relative underestimation of the genera Blastococcus and Domibacillus by the bacterial culturing approach. The bacterial isolates will allow further study on the mechanisms of tolerance to desiccation, especially in Pseudomonadota (Proteobacteria).
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Affiliation(s)
- Zakia Selmani
- Laboratoire de Biologie et Physiologie des Organismes, Faculté des Sciences Biologiques, University of Science and Technology Houari Boumediene (USTHB), Algiers, Algeria
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Eleonore Attard
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l’Adour, Pau, France
| | - Béatrice Lauga
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l’Adour, Pau, France
| | - Mohamed Barakat
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Philippe Ortet
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Joris Tulumello
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Wafa Achouak
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Yahia Kaci
- Laboratoire de Biologie et Physiologie des Organismes, Faculté des Sciences Biologiques, University of Science and Technology Houari Boumediene (USTHB), Algiers, Algeria
| | - Thierry Heulin
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
- *Correspondence: Thierry Heulin,
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81
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Carrascosa A, Pascual JA, López-García Á, Romo-Vaquero M, De Santiago A, Ros M, Petropoulos SA, Alguacil MDM. Effects of inorganic and compost tea fertilizers application on the taxonomic and functional microbial diversity of the purslane rhizosphere. FRONTIERS IN PLANT SCIENCE 2023; 14:1159823. [PMID: 37152179 PMCID: PMC10159062 DOI: 10.3389/fpls.2023.1159823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/27/2023] [Indexed: 05/09/2023]
Abstract
Introduction Soil fertility is a major determinant of plant-microbial interactions, thus, directly and indirectly affecting crop productivity and ecosystem functions. In this study, we analysed for the first time the effects of fertilizer addition on the cropping of purslane (Portulaca oleracea) with particular attention to the taxonomic and functional characteristics of their associated soil microbiota. Methods We tested the effects of different doses of inorganic fertilization differing in the amount of N:P:K namely IT1 (300:100:100); IT2 (300:200:100); IT3 (300:200:200); and IT4 (600:100:100) (ppm N:P:K ratio) and organic fertilization (compost tea) which reached at the end of the assay the dose of 300 ppm N. Results and discussion Purslane growth and soil quality parameters and their microbial community structure, abundance of fungal functional groups and prevailing bacterial metabolic functions were monitored. The application of compost tea and inorganic fertilizers significantly increased the purslane shoot biomass, and some soil chemical properties such as pH and soil enzymatic activities related to C, N and P biogeochemical cycles. The bacterial and fungal community compositions were significantly affected by the organic and chemical fertilizers input. The majority of inorganic fertilization treatments decreased the fungal and bacterial diversity as well as some predictive bacterial functional pathways. Conclusions These findings suggest that the inorganic fertilization might lead to a change of microbial functioning. However, in order to get stronger evidence that supports the found pattern, longer time-frame experiments that ideally include sampling across different seasons are needed. Thus, further research is still needed to investigate the effects of fertilizations on purslane productivity under commercial field conditions.
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Affiliation(s)
- Angel Carrascosa
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, Murcia, Spain
| | - Jose Antonio Pascual
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, Murcia, Spain
| | - Álvaro López-García
- Instituto Interuniversitario de investigación del Sistema Tierra en Andalucía, Universidad de Jaén, Jaén, Spain
| | - María Romo-Vaquero
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Food Science and Technology, Campus de Espinardo, Murcia, Spain
| | - Ana De Santiago
- Centro de Investigaciones Científicas y Tecnológicas de Extremadura (CICYTEX), Área de Protección Vegetal, Subárea de gestión y usos de suelos agrícolas y forestales, Instituto de Investigación Finca la Orden, Badajoz, Spain
| | - Margarita Ros
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, Murcia, Spain
| | - Spyridon A. Petropoulos
- Department of Agriculture, Crop Production and Rural Environment, University of Thessaly, Volos, Greece
| | - Maria Del Mar Alguacil
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, Murcia, Spain
- *Correspondence: Maria Del Mar Alguacil,
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82
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Fan K, Chu H, Eldridge DJ, Gaitan JJ, Liu YR, Sokoya B, Wang JT, Hu HW, He JZ, Sun W, Cui H, Alfaro FD, Abades S, Bastida F, Díaz-López M, Bamigboye AR, Berdugo M, Blanco-Pastor JL, Grebenc T, Duran J, Illán JG, Makhalanyane TP, Mukherjee A, Nahberger TU, Peñaloza-Bojacá GF, Plaza C, Verma JP, Rey A, Rodríguez A, Siebe C, Teixido AL, Trivedi P, Wang L, Wang J, Yang T, Zhou XQ, Zhou X, Zaady E, Tedersoo L, Delgado-Baquerizo M. Soil biodiversity supports the delivery of multiple ecosystem functions in urban greenspaces. Nat Ecol Evol 2023; 7:113-126. [PMID: 36631668 DOI: 10.1038/s41559-022-01935-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 10/03/2022] [Indexed: 01/13/2023]
Abstract
While the contribution of biodiversity to supporting multiple ecosystem functions is well established in natural ecosystems, the relationship of the above- and below-ground diversity with ecosystem multifunctionality remains virtually unknown in urban greenspaces. Here we conducted a standardized survey of urban greenspaces from 56 municipalities across six continents, aiming to investigate the relationships of plant and soil biodiversity (diversity of bacteria, fungi, protists and invertebrates, and metagenomics-based functional diversity) with 18 surrogates of ecosystem functions from nine ecosystem services. We found that soil biodiversity across biomes was significantly and positively correlated with multiple dimensions of ecosystem functions, and contributed to key ecosystem services such as microbially driven carbon pools, organic matter decomposition, plant productivity, nutrient cycling, water regulation, plant-soil mutualism, plant pathogen control and antibiotic resistance regulation. Plant diversity only indirectly influenced multifunctionality in urban greenspaces via changes in soil conditions that were associated with soil biodiversity. These findings were maintained after controlling for climate, spatial context, soil properties, vegetation and management practices. This study provides solid evidence that conserving soil biodiversity in urban greenspaces is key to supporting multiple dimensions of ecosystem functioning, which is critical for the sustainability of urban ecosystems and human wellbeing.
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Affiliation(s)
- Kunkun Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Juan J Gaitan
- National Institute of Agricultural Technology (INTA), Institute of Soil Science, Hurlingham, Argentina.,National University of Luján, Department of Technology, Luján, Argentina.,National Research Council of Argentina (CONICET), Buenos Aires, Argentina
| | - Yu-Rong Liu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Blessing Sokoya
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
| | - Jun-Tao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Ji-Zheng He
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Wei Sun
- Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Haiying Cui
- Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Fernando D Alfaro
- GEMA Center for Genomics, Ecology and Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, Santiago, Chile
| | - Sebastian Abades
- GEMA Center for Genomics, Ecology and Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, Santiago, Chile
| | | | | | - Adebola R Bamigboye
- Natural History Museum (Botany Unit), Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Miguel Berdugo
- Institut de Biologia Evolutiva (UPF-CSIC), Barcelona, Spain.,Institute of Integrative Biology, Department of Environment Systems Science, ETH Zurich, Univeritätstrasse, Zurich, Switzerland
| | | | - Tine Grebenc
- Department of Forest Physiology and Genetics, Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Jorge Duran
- Misión Biolóxica de Galicia, Consejo Superior de Investigaciones Científicas, Pontevedra, Spain.,Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra, Portugal
| | - Javier G Illán
- Department of Entomology, Washington State University, Pullman, WA, USA
| | - Thulani P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Arpan Mukherjee
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Tina U Nahberger
- Department of Forest Physiology and Genetics, Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Gabriel F Peñaloza-Bojacá
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Brazil
| | - César Plaza
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Jay Prakash Verma
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh, India.,Soil Microbiology Lab, Department of Soil Science, Federal University of Ceara, Fortaleza, Brazil
| | - Ana Rey
- Department of Biogeography and Global Change, National Museum of Natural History (MNCN), Spanish National Research Council (CSIC) C/ Serrano 115bis, Madrid, Spain
| | - Alexandra Rodríguez
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra, Portugal
| | - Christina Siebe
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, México D.F., México
| | - Alberto L Teixido
- Departamento de Botância e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Boa Esperança, Cuiabá, Brazil
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Ling Wang
- Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Jianyong Wang
- Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Tianxue Yang
- Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Xin-Quan Zhou
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Xiaobing Zhou
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Eli Zaady
- Department of Natural Resources, Agricultural Research Organization, Institute of Plant Sciences, Gilat Research Center, Negev, Israel
| | - Leho Tedersoo
- Department of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain. .,Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain.
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Effects of Mustard Invasions on Soil Microbial Abundances and Fungal Assemblages in Southern California. DIVERSITY 2023. [DOI: 10.3390/d15010050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Although mustards (family, Brassicaceae) are common across southern California, research has not focused on the effects of type-conversion of native California sage scrub (CSS) to areas dominated by invasive mustards. To better understand how mustard invasions, primarily the short-pod mustard, Hirschfeldia incana, impact soil microbial assemblages, we examined microbial abundance and assemblages from intact CSS and adjacent mustard-dominated soils at three sites. We also explored if germination rates for various plant species differed between CSS and mustard soils. We found that mustard invasions reduce soil microbial abundances by more than 50% and alter soil fungal assemblages. Fungal richness, diversity, and evenness did not differ between habitats, highlighting that these habitats harbor unique microbial assemblages. While mustard allelopathy is predicted to be the primary driver of these changes, mustard invasions also increased soil pH. Although functional consequences of these shifts are unknown, low mustard germination in CSS soils supports biological resistance to mustard invasion in CSS. Overall, our results demonstrate that mustard invasions, H. incana in particular, exert a strong selecting force on soil microbial assemblages, which can influence effective CSS restoration and preservation of ecosystem services.
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84
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Kalntremtziou M, Papaioannou IA, Vangalis V, Polemis E, Pappas KM, Zervakis GI, Typas MA. Evaluation of the lignocellulose degradation potential of Mediterranean forests soil microbial communities through diversity and targeted functional metagenomics. Front Microbiol 2023; 14:1121993. [PMID: 36922966 PMCID: PMC10008878 DOI: 10.3389/fmicb.2023.1121993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/31/2023] [Indexed: 02/28/2023] Open
Abstract
The enzymatic arsenal of several soil microorganisms renders them particularly suitable for the degradation of lignocellulose, a process of distinct ecological significance with promising biotechnological implications. In this study, we investigated the spatiotemporal diversity and distribution of bacteria and fungi with 16S and Internally Trascribed Spacer (ITS) ribosomal RNA next-generation-sequencing (NGS), focusing on forest mainland Abies cephalonica and insular Quercus ilex habitats of Greece. We analyzed samples during winter and summer periods, from different soil depths, and we applied optimized and combined targeted meta-omics approaches aiming at the peroxidase-catalase family enzymes to gain insights into the lignocellulose degradation process at the soil microbial community level. The microbial communities recorded showed distinct patterns of response to season, soil depth and vegetation type. Overall, in both forests Proteobacteria, Actinobacteria, Acidobacteria were the most abundant bacteria phyla, while the other phyla and the super-kingdom of Archaea were detected in very low numbers. Members of the orders Agaricales, Russulales, Sebacinales, Gomphales, Geastrales, Hysterangiales, Thelephorales, and Trechisporales (Basidiomycota), and Pezizales, Sordariales, Eurotiales, Pleosporales, Helotiales, and Diaporthales (Ascomycota) were the most abundant for Fungi. By using optimized "universal" PCR primers that targeted the peroxidase-catalase enzyme family, we identified several known and novel sequences from various Basidiomycota, even from taxa appearing at low abundance. The majority of the sequences recovered were manganese peroxidases from several genera of Agaricales, Hysterangiales, Gomphales, Geastrales, Russulales, Hymenochaetales, and Trechisporales, while lignin -and versatile-peroxidases were limited to two to eight species, respectively. Comparisons of the obtained sequences with publicly available data allowed a detailed structural analysis of polymorphisms and functionally relevant amino-acid residues at phylogenetic level. The targeted metagenomics applied here revealed an important role in lignocellulose degradation of hitherto understudied orders of Basidiomycota, such as the Hysterangiales and Gomphales, while it also suggested the auxiliary activity of particular members of Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes. The application of NGS-based metagenomics approaches allows a better understanding of the complex process of lignocellulolysis at the microbial community level as well as the identification of candidate taxa and genes for targeted functional investigations and genetic modifications.
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Affiliation(s)
- Maria Kalntremtziou
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis A Papaioannou
- Zentrum für Molekulare Biologie der Universität Heidelberg, ZMBH, University of Heidelberg, Heidelberg, Germany
| | - Vasileios Vangalis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Elias Polemis
- Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece
| | - Katherine M Pappas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios I Zervakis
- Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece
| | - Milton A Typas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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85
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Defining Composition and Function of the Rhizosphere Microbiota of Barley Genotypes Exposed to Growth-Limiting Nitrogen Supplies. mSystems 2022; 7:e0093422. [PMID: 36342125 PMCID: PMC9765016 DOI: 10.1128/msystems.00934-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The microbiota populating the rhizosphere, the interface between roots and soil, can modulate plant growth, development, and health. These microbial communities are not stochastically assembled from the surrounding soil, but their composition and putative function are controlled, at least partially, by the host plant. Here, we use the staple cereal barley as a model to gain novel insights into the impact of differential applications of nitrogen, a rate-limiting step for global crop production, on the host genetic control of the rhizosphere microbiota. Using a high-throughput amplicon sequencing survey, we determined that nitrogen availability for plant uptake is a factor promoting the selective enrichment of individual taxa in the rhizosphere of wild and domesticated barley genotypes. Shotgun sequencing and metagenome-assembled genomes revealed that this taxonomic diversification is mirrored by a functional specialization, manifested by the differential enrichment of multiple Gene Ontology terms, of the microbiota of plants exposed to nitrogen conditions limiting barley growth. Finally, a plant soil feedback experiment revealed that host control of the barley microbiota underpins the assembly of a phylogenetically diverse group of bacteria putatively required to sustain plant performance under nitrogen-limiting supplies. Taken together, our observations indicate that under nitrogen conditions limiting plant growth, host-microbe and microbe-microbe interactions fine-tune the host genetic selection of the barley microbiota at both taxonomic and functional levels. The disruption of these recruitment cues negatively impacts plant growth. IMPORTANCE The microbiota inhabiting the rhizosphere, the thin layer of soil surrounding plant roots, can promote the growth, development, and health of their host plants. Previous research indicated that differences in the genetic composition of the host plant coincide with variations in the composition of the rhizosphere microbiota. This is particularly evident when looking at the microbiota associated with input-demanding modern cultivated varieties and their wild relatives, which have evolved under marginal conditions. However, the functional significance of these differences remains to be fully elucidated. We investigated the rhizosphere microbiota of wild and cultivated genotypes of the global crop barley and determined that nutrient conditions limiting plant growth amplify the host control on microbes at the root-soil interface. This is reflected in a plant- and genotype-dependent functional specialization of the rhizosphere microbiota, which appears to be required for optimal plant growth. These findings provide novel insights into the significance of the rhizosphere microbiota for plant growth and sustainable agriculture.
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86
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Ren Z, Cao S, Chen T, Zhang C, Yu J. Bacterial functional redundancy and carbon metabolism potentials in soil, sediment, and water of thermokarst landscapes across the Qinghai-Tibet Plateau: Implications for the fate of permafrost carbon. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158340. [PMID: 36041614 DOI: 10.1016/j.scitotenv.2022.158340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/23/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Permafrost thaw create widespread thermokarst landscapes. As a result, distinct habitats are provided to harbor different bacterial communities in degraded permafrost soil (PBCs), thermokarst lake sediment (SBCs), and lake water (WBCs), driving carbon metabolism differentially. In this study, we investigated functional diversity and redundancy, and carbon metabolism potentials of PBCs, SBCs, and WBCs in thermokarst landscapes across the Qinghai-Tibet Plateau. The results showed that PBCs and SBCs had higher taxonomic and functional alpha diversity than WBCs, while WBCs had lower functional redundancy. WBCs had the highest beta diversity followed by SBCs and PBCs, suggesting strong determination of taxonomic variations on functional differences. Community assembly processes also had significant influences on beta diversity, especially for SBCs. Metabolism pathways of carbohydrate metabolism, methane metabolism, and carbon fixation were enriched differentially in PBCs, SBCs, and WBCs, suggesting different C fate in distinct habitats. Carbohydrate metabolism data suggested that PBCs might have stronger potentials to mineralize a greater diversity of organic carbon substrate than SBCs and WBCs, promoting degradation of organic carbon stocks in degraded permafrost soils. Methane metabolism data showed that SBCs had a stronger methanogenesis potential followed by PBCs and WBCs, while PBCs had a stronger methane oxidation potential. High abundance of genes involving in formaldehyde assimilation might suggested that a large proportion of produced methane might be assimilated by methanotrophs in the thermokarst landscapes. Both aerobic and anaerobic carbon fixation pathways were enriched in PBCs. The results added our understanding of functional properties and biogeochemical carbon cycles in thermokarst landscapes, improving our abilities in accurate modeling of carbon dynamics and the ultimate fate of permafrost carbon in a warming world.
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Affiliation(s)
- Ze Ren
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China; School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Shengkui Cao
- School of Geographical Science, Qinghai Normal University, Xining 810008, China.
| | - Tao Chen
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Lanzhou 730020, China
| | - Cheng Zhang
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China; School of Engineering Technology, Beijing Normal University, Zhuhai 519087, China
| | - Jinlei Yu
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai 200241, China
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87
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Singh N, Singh V, Rai SN, Vamanu E, Singh MP. Metagenomic Analysis of Garden Soil-Derived Microbial Consortia and Unveiling Their Metabolic Potential in Mitigating Toxic Hexavalent Chromium. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122094. [PMID: 36556458 PMCID: PMC9781466 DOI: 10.3390/life12122094] [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: 11/03/2022] [Revised: 12/07/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022]
Abstract
Soil microbial communities connect to the functional environment and play an important role in the biogeochemical cycle and waste degradation. The current study evaluated the distribution of the core microbial population of garden soil in the Varanasi region of Uttar Pradesh, India and their metabolic potential for mitigating toxic hexavalent chromium from wastewater. Metagenomes contain 0.2 million reads and 56.5% GC content. The metagenomic analysis provided insight into the relative abundance of soil microbial communities and revealed the domination of around 200 bacterial species belonging to different phyla and four archaeal phyla. The top 10 abundant genera in garden soil were Gemmata, Planctomyces, Steroidobacter, Pirellula, Pedomicrobium, Rhodoplanes, Nitrospira Mycobacterium, Pseudonocardia, and Acinetobacter. In this study, Gemmata was dominating bacterial genera. Euryarchaeota, Parvarchaeota, and Crenarchaeota archaeal species were present with low abundance in soil samples. X-ray photoelectric spectroscopy (XPS) analysis indicates the presence of carbon, nitrogen-oxygen, calcium, phosphorous, and silica in the soil. Soil-derived bacterial consortia showed high hexavalent chromium [Cr (VI)] removal efficiency (99.37%). The bacterial consortia isolated from garden soil had an important role in the hexavalent chromium bioremediation, and thus, this study could be beneficial for the design of a heavy-metal treatment system.
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Affiliation(s)
- Nidhi Singh
- Centre of Bioinformatics, University of Allahabad, Prayagraj 211002, India
| | - Veer Singh
- School of Biochemical Engineering, Indian Institute of Technology, Banaras Hindu University, Varanasi 221005, India
| | - Sachchida Nand Rai
- Centre of Biotechnology, University of Allahabad, Prayagraj 211002, India
| | - Emanuel Vamanu
- Faculty of Biotechnology, University of Agricultural Sciences and Veterinary Medicine of Bucharest, 011464 Bucharest, Romania
- Correspondence: (E.V.); (M.P.S.)
| | - Mohan P. Singh
- Centre of Biotechnology, University of Allahabad, Prayagraj 211002, India
- Correspondence: (E.V.); (M.P.S.)
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88
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Fernández-Guisuraga JM, Calvo L, Ansola G, Pinto R, Sáenz de Miera LE. The effect of sheep grazing abandonment on soil bacterial communities in productive mountain grasslands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158398. [PMID: 36049688 DOI: 10.1016/j.scitotenv.2022.158398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/25/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Livestock grazing abandonment entails important shifts on the overall ecosystem function, but the effects of this land-use change on specific bacterial taxa remain poorly understood in mountain grasslands. Moreover, we currently lack knowledge about the feedbacks between changes in ecosystem functions affected by livestock abandonment in mountain grasslands and the soil bacterial communities. Here, we evaluated the behavior of bacterial communities' structure and composition at taxa level as a function of short (1-year) and long-term (15-years) grazing abandonment in a mountain grassland. We also linked the observed responses in the bacterial communities to changes in several ecosystem functions (i.e. primary production, plant species biodiversity, carbon stocks and soil fertility). The alpha diversity of the bacterial communities did not show a significant response as a consequence of grazing abandonment. However, we identified significant changes on the overall composition of soil bacterial communities between the long-term abandoned grassland areas and grazed or abandoned areas in the short term. We also evidenced a balance between the number of operational taxonomic units (OTUs) whose relative abundance is favored by livestock grazing (19.51 %) and those with higher relative abundances in long-term grazing exclusion areas (20.23 %) that could behave as indicators of grazing abandonment. Structural Equation Modeling analyses proved that several bacterial taxa associated with relevant ecosystem functions, such as Rhodospirillales order within Alphaproteobacteria phylum, featured significant changes in their relative abundance between grazing treatments. The direct and indirect effects of grazing exclusion on woody species encroachment and soil organic carbon were strongly linked to the changes in the abundance of bacterial taxa indicators. The assessment of the bacterial community response to livestock abandonment in mountain grasslands may thus provide early warning signs before subtle changes in ecosystem functions occur.
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Affiliation(s)
- José Manuel Fernández-Guisuraga
- Department of Biodiversity and Environmental Management, Faculty of Biological and Environmental Sciences, University of León, 24071 León, Spain.
| | - Leonor Calvo
- Department of Biodiversity and Environmental Management, Faculty of Biological and Environmental Sciences, University of León, 24071 León, Spain
| | - Gemma Ansola
- Department of Biodiversity and Environmental Management, Faculty of Biological and Environmental Sciences, University of León, 24071 León, Spain
| | - Rayo Pinto
- Department of Biodiversity and Environmental Management, Faculty of Biological and Environmental Sciences, University of León, 24071 León, Spain
| | - Luis E Sáenz de Miera
- Department of Molecular Biology, Faculty of Biological and Environmental Sciences, University of León, 24071 León, Spain
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89
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Shaffer JP, Nothias LF, Thompson LR, Sanders JG, Salido RA, Couvillion SP, Brejnrod AD, Lejzerowicz F, Haiminen N, Huang S, Lutz HL, Zhu Q, Martino C, Morton JT, Karthikeyan S, Nothias-Esposito M, Dührkop K, Böcker S, Kim HW, Aksenov AA, Bittremieux W, Minich JJ, Marotz C, Bryant MM, Sanders K, Schwartz T, Humphrey G, Vásquez-Baeza Y, Tripathi A, Parida L, Carrieri AP, Beck KL, Das P, González A, McDonald D, Ladau J, Karst SM, Albertsen M, Ackermann G, DeReus J, Thomas T, Petras D, Shade A, Stegen J, Song SJ, Metz TO, Swafford AD, Dorrestein PC, Jansson JK, Gilbert JA, Knight R. Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity. Nat Microbiol 2022; 7:2128-2150. [PMID: 36443458 PMCID: PMC9712116 DOI: 10.1038/s41564-022-01266-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 10/10/2022] [Indexed: 11/30/2022]
Abstract
Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth's environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.
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Affiliation(s)
- Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Louis-Félix Nothias
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Luke R Thompson
- Northern Gulf Institute, Mississippi State University, Starkville, MS, USA
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA
| | - Jon G Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Rodolfo A Salido
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Sneha P Couvillion
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Asker D Brejnrod
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Franck Lejzerowicz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Niina Haiminen
- IBM Research, T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Holly L Lutz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Cameron Martino
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - James T Morton
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Smruthi Karthikeyan
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mélissa Nothias-Esposito
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kai Dührkop
- Chair for Bioinformatics, Friedrich Schiller University, Jena, Germany
| | - Sebastian Böcker
- Chair for Bioinformatics, Friedrich Schiller University, Jena, Germany
| | - Hyun Woo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, Gyeonggi-do, Korea
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Chemistry, University of Connecticut, Storrs, CT, USA
| | - Wout Bittremieux
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Jeremiah J Minich
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - MacKenzie M Bryant
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Karenina Sanders
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tara Schwartz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yoshiki Vásquez-Baeza
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Anupriya Tripathi
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Laxmi Parida
- IBM Research, T.J. Watson Research Center, Yorktown Heights, NY, USA
| | | | - Kristen L Beck
- IBM Research, Almaden Research Center, San Jose, CA, USA
| | - Promi Das
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Antonio González
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Joshua Ladau
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Søren M Karst
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institute, Copenhagen, Denmark
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jeff DeReus
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Science, The University of New South Wales, Sydney, New South Wales, Australia
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Baden-Württemberg, Germany
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - James Stegen
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Se Jin Song
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Thomas O Metz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jack A Gilbert
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
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90
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Sridhar B, Lawrence GB, Debenport SJ, Fahey TJ, Buckley DH, Wilhelm RC, Goodale CL. Watershed-scale liming reveals the short- and long-term effects of pH on the forest soil microbiome and carbon cycling. Environ Microbiol 2022; 24:6184-6199. [PMID: 35799501 DOI: 10.1111/1462-2920.16119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/28/2022] [Indexed: 01/12/2023]
Abstract
Soil microbial community composition routinely correlates with pH, reflecting both direct pH effects on microbial physiology and long-term biogeochemical feedbacks. We used two watershed-scale liming experiments to identify short- (2 years) and long-term (25 years) changes in the structure and function of bacterial and fungal communities in organic horizons (Oe and Oa ) of acid forest soils. Liming increased soil pH, extractable calcium, and soil carbon stocks, reduced biomass-specific respiration, and caused major changes in the soil microbiome in the short and long term. More taxa responded to liming in the short term (70%) than in the long term (30%), with most showing consistent directional responses at both sites. The ratio of change in relative abundance between limed and reference sites was twofold higher at the long than the short-term site, indicating that the effects of liming grew over time. Liming impacts were most pronounced in fungi, as steep declines of dominant ectomycorrhizal fungi (Cenococcum and Russula) occurred at both sites. Liming favoured neutrophilic bacteria over acidophilic populations according to estimated environmental pH optima. Collectively, these results demonstrate that a liming-induced change of one pH unit has an immediate and persistent effect on the structure and function of microbial communities in acid forest soils. The corresponding suppression of respiration indicates that anthropogenic alterations of soil pH, as driven by acid deposition or liming, can affect forest floor C stocks due to pH-driven shifts in community structure.
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Affiliation(s)
- Bhavya Sridhar
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | | | - Spencer J Debenport
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Timothy J Fahey
- Department of Natural Resources, Cornell University, Ithaca, New York, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Roland C Wilhelm
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Christine L Goodale
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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91
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Li P, Zhang J, Ding S, Yan P, Zhang P, Ding S. Environmental Effects on Taxonomic Turnover in Soil Fauna across Multiple Forest Ecosystems in East Asia. INSECTS 2022; 13:1103. [PMID: 36555013 PMCID: PMC9786105 DOI: 10.3390/insects13121103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
The large-scale spatial variation in and causes of biotic turnover of soil fauna remain poorly understood. Analyses were conducted based on published data from 14 independent sampling sites across five forest ecosystems in East Asia. Jaccard and Sørensen's indices were used to measure turnover rates in soil fauna orders. A redundancy analysis was used to investigate multiple environmental controls of the composition of soil fauna communities. The results showed that both Jaccard's and Sørensen's index increased significantly with increasing latitude difference. The environment explained 54.1%, 50.6%, 57.3% and 50.9% of the total variance, and spatial factors explained 13.8%, 15.9%, 21.0% and 12.6% of the total variance in the orders' composition regarding overall, phytophagous, predatory and saprophagous fauna, respectively. In addition, climate factors in environmental processes were observed to have a stronger effect than soil factors on the orders' turnover rates. Our results support the hypothesis that the effect of environment factors on soil animal taxa turnover is more important than the effect of spatial factors. Climatic factors explained more variation in the turnover of phytophagic fauna, but soil and environment factors equally explained the variation in the turnover of predatory fauna. This study provides evidence to support both environmental filtering and dispersal limitation hypotheses at the regional and population scales.
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Affiliation(s)
- Peikun Li
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions, Ministry of Education, College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
- College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
| | - Jian Zhang
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions, Ministry of Education, College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
- College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
| | - Shunping Ding
- Plant Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Peisen Yan
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions, Ministry of Education, College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
- College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
| | - Panpan Zhang
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions, Ministry of Education, College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
- College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
| | - Shengyan Ding
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions, Ministry of Education, College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
- College of Geography and Environmental Science, Henan University, Kaifeng 475004, China
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92
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García-Carmona M, Lepinay C, García-Orenes F, Baldrian P, Arcenegui V, Cajthaml T, Mataix-Solera J. Moss biocrust accelerates the recovery and resilience of soil microbial communities in fire-affected semi-arid Mediterranean soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157467. [PMID: 35868386 DOI: 10.1016/j.scitotenv.2022.157467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
After wildfires in Mediterranean ecosystems, ruderal mosses are pioneer species, stabilizing the soil surface previous to the establishment of vascular vegetation. However, little is known about the implication of pioneer moss biocrusts for the recovery and resilience of soils in early post-fire stages in semi-arid areas. Therefore, we studied the effects of the burgeoning biocrust on soil physicochemical and biochemical properties and the diversity and composition of microbial communities after a moderate-to-high wildfire severity. Seven months after the wildfire, the biocrust softened the strong impact of the fire in soils, affecting the diversity and composition of bacteria and fungi community compared to the uncrusted soils exposed to unfavourable environmental stress. Soil moisture, phosphorous, and enzyme activities representing the altered biogeochemical cycles after the fire, were the main explanatory variables for biocrust microbial community composition under the semi-arid conditions. High bacterial diversity was found in soils under mosses, while long-lasting legacies are expected in the fungal community, which showed greater sensitivity to the fire. The composition of bacterial and fungal communities at several taxonomical levels was profoundly altered by the presence of the moss biocrust, showing a rapid successional transition toward the unburned soil community. Pioneer moss biocrust play an important role improving the resilience of soil microbial communities. In the context of increasing fire intensity, studying the moss biocrust effects on the recovery of soils microbiome is essential to understanding the resistance and resilience of Mediterranean forests to wildfires.
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Affiliation(s)
- Minerva García-Carmona
- GEA-Environmental Soil Science Group, Department of Agrochemistry and Environment, Universidad Miguel Hernández, Avenida de la Universidad s/n, 03202 Elche, Spain.
| | - Clémentine Lepinay
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220 Praha 4, Czech Republic
| | - Fuensanta García-Orenes
- GEA-Environmental Soil Science Group, Department of Agrochemistry and Environment, Universidad Miguel Hernández, Avenida de la Universidad s/n, 03202 Elche, Spain
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220 Praha 4, Czech Republic
| | - Victoria Arcenegui
- GEA-Environmental Soil Science Group, Department of Agrochemistry and Environment, Universidad Miguel Hernández, Avenida de la Universidad s/n, 03202 Elche, Spain
| | - Tomáš Cajthaml
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220 Praha 4, Czech Republic
| | - Jorge Mataix-Solera
- GEA-Environmental Soil Science Group, Department of Agrochemistry and Environment, Universidad Miguel Hernández, Avenida de la Universidad s/n, 03202 Elche, Spain
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93
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Xu M, Su S, Zhang Z, Jiang S, Zhang J, Xu Y, Hu X. Two sides of the same coin: Meta-analysis uncovered the potential benefits and risks of traditional fermented foods at a large geographical scale. Front Microbiol 2022; 13:1045096. [PMID: 36406420 PMCID: PMC9668881 DOI: 10.3389/fmicb.2022.1045096] [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: 09/15/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Traditional fermented foods, which are well-known microbial resources, are also bright national cultural inheritances. Recently, traditional fermented foods have received great attention due to their potential probiotic properties. Based on shotgun metagenomic sequencing data, we analyzed the microbial diversity, taxonomic composition, metabolic pathways, and the potential benefits and risks of fermented foods through a meta-analysis including 179 selected samples, as well as our own sequencing data collected from Hainan Province, China. As expected, raw materials, regions (differentiated by climatic zones), and substrates were the main driving forces for the microbial diversity and taxonomic composition of traditional fermented foods. Interestingly, a higher content of beneficial bacteria but a low biomass of opportunistic pathogens and antibiotic resistance genes were observed in the fermented dairy products, indicating that fermented dairy products are the most beneficial and reliable fermented foods. In contrast, despite the high microbial diversity found in the fermented soy products, their consumption risk was still high due to the enrichment of opportunistic pathogens and transferable antibiotic resistance genes. Overall, we provided the most comprehensive assessment of the microbiome of fermented food to date and generated a new view of its potential benefits and risks related to human health.
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Affiliation(s)
- Meng Xu
- School of Food Science and Engineering, Hainan University, Haikou, China
- School of Public Administration, Hainan University, Haikou, China
| | - Shunyong Su
- School of Food Science and Engineering, Hainan University, Haikou, China
- School of Public Administration, Hainan University, Haikou, China
| | - Zeng Zhang
- School of Food Science and Engineering, Hainan University, Haikou, China
- School of Public Administration, Hainan University, Haikou, China
| | - Shuaiming Jiang
- School of Food Science and Engineering, Hainan University, Haikou, China
- School of Public Administration, Hainan University, Haikou, China
| | - Jiachao Zhang
- School of Food Science and Engineering, Hainan University, Haikou, China
- School of Public Administration, Hainan University, Haikou, China
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou, China
| | - Yanqing Xu
- School of Food Science and Engineering, Hainan University, Haikou, China
- School of Public Administration, Hainan University, Haikou, China
- *Correspondence: Yanqing Xu,
| | - Xiaosong Hu
- School of Food Science and Engineering, Hainan University, Haikou, China
- School of Public Administration, Hainan University, Haikou, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Xiaosong Hu,
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94
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Xi D, Jin S, Wu J. Soil bacterial community is more sensitive than fungal community to canopy nitrogen deposition and understory removal in a Chinese fir plantation. Front Microbiol 2022; 13:1015936. [PMID: 36312973 PMCID: PMC9597510 DOI: 10.3389/fmicb.2022.1015936] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/20/2022] [Indexed: 11/29/2022] Open
Abstract
Soil microorganisms are key regulators for plant growth and ecosystem health of forest ecosystem. Although previous research has demonstrated that soil microorganisms are greatly affected by understory nitrogen (N) addition, little is known about the effects of canopy N addition (CNA) and understory management on soil microorganisms in forests. In this study, we conducted a full designed field experiment with four treatments: CNA (25 kg N ha-1 year-1), understory removal (UR), canopy N addition, and understory removal (CNAUR) (25 kg N ha-1 year-1), and control in a Chinese fir plantation. High-throughput sequencing and qPCR techniques were used to determine the abundance, diversity, and composition of bacterial and fungal communities in three soil layers. Our results showed that CNA increased bacterial diversity in the 10-20 cm soil layer but decreased bacterial abundance in the 20-40 cm soil layer and fungal diversity in the 0-10 cm soil layer. UR increased bacterial abundance only in the 20-40 cm soil layer. CNA, not UR significantly altered the compositions of soil bacterial and fungal community compositions, especially in the 0-20 cm soil layer. CNA sharply reduced the relative abundance of copiotrophic taxa (i.e., taxa in the bacterial phylum Proteobacteria and the orders Eurotiales and Helotiales in the fungal phylum Ascomycota) but increased the relative abundance of oligotrophic taxa (i.e., in the bacterial phylum Verrucomicrobia). RDA analysis revealed that soil pH, DON, and DOC were the main factors associated with the variation in bacterial and fungal communities. Our findings suggest that short-term CNA changes both soil bacterial and fungal communities, with stronger responses in the surface and middle soil than in the deep soil layer, and that UR may enhance this effect on the soil bacterial abundance. This study improves our understanding of soil microorganisms in plantations managed with understory removal and that experience increases in N deposition.
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Affiliation(s)
- Dan Xi
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shaofei Jin
- Department of Geography, Minjiang University, Fuzhou, China
| | - Jianping Wu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, Yunnan University, Kunming, China
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Sciences, Yunnan University, Kunming, China
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95
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Pascoal F, Areosa I, Torgo L, Branco P, Baptista MS, Lee CK, Cary SC, Magalhães C. The spatial distribution and biogeochemical drivers of nitrogen cycle genes in an Antarctic desert. Front Microbiol 2022; 13:927129. [PMID: 36274733 PMCID: PMC9583160 DOI: 10.3389/fmicb.2022.927129] [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: 04/23/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
Antarctic deserts, such as the McMurdo Dry Valleys (MDV), represent extremely cold and dry environments. Consequently, MDV are suitable for studying the environment limits on the cycling of key elements that are necessary for life, like nitrogen. The spatial distribution and biogeochemical drivers of nitrogen-cycling pathways remain elusive in the Antarctic deserts because most studies focus on specific nitrogen-cycling genes and/or organisms. In this study, we analyzed metagenome and relevant environmental data of 32 MDV soils to generate a complete picture of the nitrogen-cycling potential in MDV microbial communities and advance our knowledge of the complexity and distribution of nitrogen biogeochemistry in these harsh environments. We found evidence of nitrogen-cycling genes potentially capable of fully oxidizing and reducing molecular nitrogen, despite the inhospitable conditions of MDV. Strong positive correlations were identified between genes involved in nitrogen cycling. Clear relationships between nitrogen-cycling pathways and environmental parameters also indicate abiotic and biotic variables, like pH, water availability, and biological complexity that collectively impose limits on the distribution of nitrogen-cycling genes. Accordingly, the spatial distribution of nitrogen-cycling genes was more concentrated near the lakes and glaciers. Association rules revealed non-linear correlations between complex combinations of environmental variables and nitrogen-cycling genes. Association rules for the presence of denitrification genes presented a distinct combination of environmental variables from the remaining nitrogen-cycling genes. This study contributes to an integrative picture of the nitrogen-cycling potential in MDV.
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Affiliation(s)
- Francisco Pascoal
- Interdisciplinary Center of Marine and Environmental Research, University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Inês Areosa
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
| | - Luís Torgo
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
| | - Paula Branco
- School of Electrical Engineering and Computer Science, University of Ottawa, Ottawa, ON, Canada
| | - Mafalda S. Baptista
- Interdisciplinary Center of Marine and Environmental Research, University of Porto, Porto, Portugal
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Charles K. Lee
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- School of Science, University of Waikato, Hamilton, New Zealand
| | - S. Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- School of Science, University of Waikato, Hamilton, New Zealand
- S. Craig Cary,
| | - Catarina Magalhães
- Interdisciplinary Center of Marine and Environmental Research, University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
- *Correspondence: Catarina Magalhães,
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96
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Wei X, Yu L, Han B, Liu K, Shao X, Jia S. Spatial variations of root-associated bacterial communities of alpine plants in the Qinghai-Tibet Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156086. [PMID: 35605870 DOI: 10.1016/j.scitotenv.2022.156086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Exploring the geospatial variation of root-associated microbiomes is critical for understanding plant-microbe-environment interactions and plant environmental adaptability. Root-associated bacterial communities from the three compartments [rhizosphere surrounding soil (RSS), rhizosphere soil (rhizosphere), and root endosphere (endophytic)] are influenced by multiple factors, including plant species and geographical locations. Nonetheless, these communities remain poorly understood under harsh conditions. In this study, we selected four dominant alpine plants on the Qinghai-Tibet Plateau (i.e., Elymus nutans, Festuca sinensis, Kobresia pygmaea, and Kobresia humilis) to investigate their root-associated bacterial communities across 11 geographical locations and determine the factors driving spatial variation. The results showed that the microbiota of the three compartments had significantly different community compositions, with more Pseudomonadaceae and Enterobacteriaceae present in the endosphere. Spatial variations in root endophytic microbiota were mainly governed by stochastic processes, which were different from the deterministic processes in the other two compartments. Meanwhile, the geographical location had greater effects on bacterial communities than plant species, and the spatial variation of α-diversity in the endosphere was much higher than that in the RSS and rhizosphere. We further found that the differentiation of bacterial diversity in the endosphere among sympatric plant species was enhanced by higher annual precipitation, lower soil nutrients (carbon and nitrogen), and pH. For example, the coefficient of variation of endosphere Pseudomonadaceae abundance was positively correlated with annual mean precipitation, whereas that of Enterobacteriaceae abundance was negatively correlated with soil pH. The co-occurrence network analysis identified a higher proportion of bacterial coexistence in the endosphere (70.9%) than in the RSS (49.5%) and rhizosphere soil (50.9%). Finally, we revealed the relative convergence of endophytic communities among sympatric plant species in the alpine grasslands.
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Affiliation(s)
- Xiaoting Wei
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lu Yu
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Bing Han
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Kesi Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xinqing Shao
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China.
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97
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Du G, Sun Z, Bao S, Zhong Q, Yang S. Diversity of bacterial community in Jerusalem artichoke (Helianthus tuberosus L.) during storage is associated with the genotype and carbohydrates. Front Microbiol 2022; 13:986659. [PMID: 36187957 PMCID: PMC9520535 DOI: 10.3389/fmicb.2022.986659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Jerusalem artichoke (JA) is a fructan-accumulating crop that has gained popularity in recent years. The objective of the present study was to determine the dynamics of the JA-microbiome during storage. The microbial population on the surface of the JA tuber was determined by next-generation sequencing of 16S rRNA amplicons. Subsequently, the changes in carbohydrate and degree of polymerization of fructan in tubers during storage were measured. Among different genotypes of JA varieties, intergeneric differences were observed in the diversity and abundance of bacterial communities distributed on the surface of tubers. Additionally, bacterial diversity was significantly higher in storage-tolerant varieties relative to the storage-intolerant varieties. Redundancy analysis (RDA) and the correlation matrix indicated a relationship between changes in the carbohydrates and microbial community succession during tuber storage. The tuber decay rate correlated positively with the degree of polymerization of fructan. Moreover, Dysgonomonas and Acinetobacter in perishable varieties correlated significantly with the decay rate. Therefore, the bacteria associated with the decay rate may be involved in the degradation of the degree of polymerization of fructan. Furthermore, Serratia showed a significant positive correlation with inulin during storage but a negative correlation with the decay rate, suggesting its antagonistic role against pathogenic bacteria on the surface of JA tubers. However, the above correlation was not observed in the storage-tolerant varieties. Functional annotation analysis revealed that storage-tolerant JA varieties maintain tuber quality through enrichment of biocontrol bacteria, including Flavobacterium, Sphingobacterium, and Staphylococcus to resist pathogens. These results suggested that crop genotype and the structural composition of carbohydrates may result in differential selective enrichment effects of microbial communities on the surface of JA varieties. In this study, the relationship between microbial community succession and changes in tuber carbohydrates during JA storage was revealed for the first time through the combination of high-throughput sequencing, high-performance liquid chromatography (HPLC), and high-performance ion-exchange chromatography (HPIC). Overall, the findings of this study are expected to provide new insights into the dynamics of microbial-crop interactions during storage.
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Affiliation(s)
- Guolian Du
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Qinghai University, Xining, China
| | - Zhu Sun
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Qinghai University, Xining, China
| | - Shanhua Bao
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Qinghai University, Xining, China
| | - Qiwen Zhong
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Qinghai University, Xining, China
- *Correspondence: Qiwen Zhong,
| | - Shipeng Yang
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Qinghai University, Xining, China
- Shipeng Yang,
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98
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Li B, Shen C, Wu HY, Zhang LM, Wang J, Liu S, Jing Z, Ge Y. Environmental selection dominates over dispersal limitation in shaping bacterial biogeographical patterns across different soil horizons of the Qinghai-Tibet Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156177. [PMID: 35613642 DOI: 10.1016/j.scitotenv.2022.156177] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/13/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Soil microbial biogeographical patterns have been widely explored from horizontal to vertical scales. However, studies of microbial vertical distributions were still limited (e.g., how soil genetic horizons influence microbial distributions). To shed light on this question, we investigated soil bacterial communities across three soil horizons (topsoil: horizon A; midsoil: horizon B; subsoil: horizon C) of 60 soil profiles along a 3500 km transect in the Qinghai-Tibet Plateau. We found that bacterial diversity was highest in the topsoil and lowest in the subsoil, and community composition significantly differed across soil horizons. The network complexity decreased from topsoil to subsoil. There were significant geographical/environmental distance-decay relationships (DDR) in three soil horizons, with a lower slope from topsoil to subsoil due to the decreased environmental heterogeneity. Variation partitioning analysis (VPA) showed that bacterial community variations were explained more by environmental than spatial factors. Although environmental selection processes played a dominant role, null model analysis revealed that deterministic processes (mainly variable selection) decreased with deeper soil horizons, while stochastic processes (mainly dispersal limitation) increased from topsoil to subsoil. These results suggested that microbial biogeographical patterns and community assembly processes were soil horizon dependent. Our study provides new insights into the microbial vertical distributions in large-scale alpine regions and highlights the vital role of soil genetic horizons in affecting microbial community assembly, which has implications for understanding the pedogenetic process and microbial responses to extreme environment under climate change.
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Affiliation(s)
- Bojian Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Congcong Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua-Yong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jichen Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siyi Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongwang Jing
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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99
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A curated data resource of 214K metagenomes for characterization of the global antimicrobial resistome. PLoS Biol 2022; 20:e3001792. [PMID: 36067158 PMCID: PMC9447899 DOI: 10.1371/journal.pbio.3001792] [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: 05/12/2022] [Accepted: 08/09/2022] [Indexed: 11/19/2022] Open
Abstract
The growing threat of antimicrobial resistance (AMR) calls for new epidemiological surveillance methods, as well as a deeper understanding of how antimicrobial resistance genes (ARGs) have been transmitted around the world. The large pool of sequencing data available in public repositories provides an excellent resource for monitoring the temporal and spatial dissemination of AMR in different ecological settings. However, only a limited number of research groups globally have the computational resources to analyze such data. We retrieved 442 Tbp of sequencing reads from 214,095 metagenomic samples from the European Nucleotide Archive (ENA) and aligned them using a uniform approach against ARGs and 16S/18S rRNA genes. Here, we present the results of this extensive computational analysis and share the counts of reads aligned. Over 6.76∙108 read fragments were assigned to ARGs and 3.21∙109 to rRNA genes, where we observed distinct differences in both the abundance of ARGs and the link between microbiome and resistome compositions across various sampling types. This collection is another step towards establishing global surveillance of AMR and can serve as a resource for further research into the environmental spread and dynamic changes of ARGs. The growing threat of antimicrobial resistance (AMR) calls for new epidemiological surveillance methods and a deeper understanding of how resistance genes are transmitted around the world. This study presents a large-scale remapping of sequencing reads of publicly available metagenomic datasets that can be used to monitor the global prevalence of AMR genes.
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100
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Sridhar B, Wilhelm RC, Debenport SJ, Fahey TJ, Buckley DH, Goodale CL. Microbial community shifts correspond with suppression of decomposition 25 years after liming of acidic forest soils. GLOBAL CHANGE BIOLOGY 2022; 28:5399-5415. [PMID: 35770362 DOI: 10.1111/gcb.16321] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
Microbial community structure and function regularly covary with soil pH, yet effects of these interactions on soil carbon are rarely tested experimentally within natural ecosystems. We investigated the enduring (25 year) impacts of liming on microbial community structure and decomposition at an acidic northern hardwood forest, where experimental liming increased pH one unit and surprisingly doubled the organic carbon stocks of the forest floor. We show that this increase in carbon storage corresponded with restructuring of the bacterial and fungal communities that drive decomposition. In the Oe horizon, liming reduced the activities of five extracellular enzymes that mediate decomposition, while the Oa horizon showed an especially large (64%) reduction in the activity of a sixth, peroxidase, which is an oxidative enzyme central to lignocellulose degradation. Decreased enzyme activities corresponded with loss of microbial taxa important for lignocellulose decay, including large reductions in the dominant ectomycorrhizal genera Russula and Cenococcum, saprotrophic and wood decaying fungi, and Actinobacteria (Thermomonosporaceae). These results demonstrate the importance of pH as a dominant regulator of microbial community structure and illustrate how changes to this structure can produce large, otherwise unexpected increases in carbon storage in forest soils.
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Affiliation(s)
- Bhavya Sridhar
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Roland C Wilhelm
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Spencer J Debenport
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Timothy J Fahey
- Department of Natural Resources, Cornell University, Ithaca, New York, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Christine L Goodale
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, New York, USA
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