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Mu X, Shi S, Hu X, Gan X, Han Q, Yu Q, Qu J, Li H. Gut microbiome and antibiotic resistance genes in plateau model animal (Ochotona curzoniae) exhibit a relative stability under cold stress. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135472. [PMID: 39137548 DOI: 10.1016/j.jhazmat.2024.135472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/07/2024] [Accepted: 08/08/2024] [Indexed: 08/15/2024]
Abstract
Antibiotic resistance genes (ARGs) carried by gut pathogens may pose a threat to the host and ecological environment. However, few studies focus on the effects of cold stress on intestinal bacteria and ARGs in plateau animals. Here, we used 16S rRNA gene sequencing and gene chip technique to explore the difference of gut microbes and ARGs in plateau pika under 4 °C and 25 °C. The results showed that tetracycline and aminoglycoside resistance genes were the dominant ARGs in pika intestine. Seven kinds of high-risk ARGs (aadA-01, aadA-02, ermB, floR, mphA-01, mphA-02, tetM-02) existed in pika's intestine, and cold had no significant effect on the composition and structure of pika's intestinal ARGs. The dominant phyla in pika intestine were Bacteroidetes and Firmicutes. Cold influenced 0.47 % of pika intestinal bacteria in OTU level, while most other bacteria had no significant change. The diversity and community assembly of intestinal bacteria in pika remained relatively stable under cold conditions, while low temperature decreased gut microbial network complexity. In addition, low temperature led to the enrichment of glycine biosynthesis and metabolism-related pathways. Moreover, the correlation analysis showed that eight opportunistic pathogens (such as Clostridium, Staphylococcus, Streptococcus, etc.) detected in pika intestine might be potential hosts of ARGs.
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Affiliation(s)
- Xianxian Mu
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Shunqin Shi
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xueqian Hu
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xueying Gan
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qian Han
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qiaoling Yu
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China
| | - Jiapeng Qu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China.
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China; Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China.
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2
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Rao G, Song WL, Yan SZ, Chen SL. Unraveling the distribution pattern and driving forces of soil microorganisms under geographic barriers. Appl Environ Microbiol 2024:e0135924. [PMID: 39171904 DOI: 10.1128/aem.01359-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 07/31/2024] [Indexed: 08/23/2024] Open
Abstract
The Altai Mountains (ALE) and the Greater Khingan Mountains (GKM) in northern China are forest regions dominated by coniferous trees. These geographically isolated regions provide an ideal setting for studying microbial biogeographic patterns. In this study, we employed high-throughput techniques to obtain DNA sequences of soil myxomycetes, bacteria, and fungi and explored the mechanisms underlying the assembly of both local and cross-regional microbial communities in relation to environmental factors. Our investigation revealed that the environmental heterogeneity in ALE and GKM significantly affected the succession and assembly of soil bacterial communities at cross-regional scales. Specifically, the optimal environmental factors affecting bacterial Bray-Curtis similarity were elevation and temperature seasonality. The spatial factors and climate change impact on bacterial communities under the geographical barriers surpassed that of local soil microenvironments. The assembly pattern of bacterial communities transitions from local drift to cross-regional heterogeneous selection. Environmental factors had a relatively weak influence on myxomycetes and fungi. Both soil myxomycetes and fungi faced considerable dispersal limitation at local and cross-regional scales, ultimately leading to weak geographical distribution patterns.IMPORTANCEThe impact of environmental selection and dispersal on the soil microbial spatial distribution is a key concern in microbial biogeography, particularly in large-scale geographical patterns. However, our current understanding remains limited. Our study found that soil bacteria displayed a distinct cross-regional geographical distribution pattern, primarily influenced by environmental selection. Conversely, the cross-regional geographical distribution patterns of soil myxomycetes and fungi were relatively weak. Their composition exhibited a weak association with the environment at local and cross-regional scales, with assembly primarily driven by dispersal limitation.
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Affiliation(s)
- Gu Rao
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wen-Long Song
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shu-Zhen Yan
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuang-Lin Chen
- School of Life Sciences, Nanjing Normal University, Nanjing, China
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3
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Yao T, Ye L, Wang S, Lu J, Li H, Yu G. Effects of cadmium exposure on gut microbiota and antibiotic resistance genes in Haliotis diversicolor abalone. CHEMOSPHERE 2024; 352:141507. [PMID: 38387663 DOI: 10.1016/j.chemosphere.2024.141507] [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: 05/15/2023] [Revised: 12/03/2023] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Heavy metals in soil, water, and industrial production can affect the antibiotic resistance of bacteria. Antibiotic resistance in gut microbiota has been extensively researched. The effects of cadmium (Cd) was investigated on the gut microbiota and antibiotic resistance genes (ARGs) of Haliotis diversicolor, a commercially important abalone species. By exposing H. diversicolor to four concentrations of Cd (0 μg L-1 (control), 6.5 μg L-1 (low), 42.25 μg L-1 (medium), and 274.63 μg L-1 (high)) for 30 and 60 days, 16 types of ARG (aadA-01, aadA-02, cfr, dfrA1, ermB, floR, folA, mecA, sul2, tetB-01, tetC-01, tetD-01, tetG-01, tetM-02, tetQ, vanC-01), and 1213 genus and 27 phylum microbiomes were detected. ARGs can be resistant to aminoglycoside, beta-lactamase, macrolide-lincosamide-streptogramin B, multidrug, florfenicol, macrolide, sulfonamides, tetracyclines, and vancomycin. Cadmium exposure significantly alters the abundance of tetC-01, tetB-01, tetQ, sul2, and aadA-01. About 5% (61) of genus-level microorganisms were significantly affected by Cd exposure. Microbiota alpha and beta diversities in the 60-day 42.25 μg L-1 Cd treatment differed significantly from those in other treatments. In addition, 26 pathogens were detected, and two pathogens (Vibrio and Legionella) were significantly affected by Cd exposure. Significant correlations between pathogens and ARGs increased with increased Cd concentration after 60 days of Cd exposure. Cadmium exposure may cause gut microbiota disturbance in H. diversicolor and increase the likelihood of ARG transfer to pathogens, increasing potential ecological and economic risks.
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Affiliation(s)
- Tuo Yao
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Research Center of Hydrobiology, Jinan University, Guangzhou, China
| | - Lingtong Ye
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.
| | - Sijie Wang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Jie Lu
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Gang Yu
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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Tian J, Dungait JAJ, Hou R, Deng Y, Hartley IP, Yang Y, Kuzyakov Y, Zhang F, Cotrufo MF, Zhou J. Microbially mediated mechanisms underlie soil carbon accrual by conservation agriculture under decade-long warming. Nat Commun 2024; 15:377. [PMID: 38191568 PMCID: PMC10774409 DOI: 10.1038/s41467-023-44647-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/20/2023] [Indexed: 01/10/2024] Open
Abstract
Increasing soil organic carbon (SOC) in croplands by switching from conventional to conservation management may be hampered by stimulated microbial decomposition under warming. Here, we test the interactive effects of agricultural management and warming on SOC persistence and underlying microbial mechanisms in a decade-long controlled experiment on a wheat-maize cropping system. Warming increased SOC content and accelerated fungal community temporal turnover under conservation agriculture (no tillage, chopped crop residue), but not under conventional agriculture (annual tillage, crop residue removed). Microbial carbon use efficiency (CUE) and growth increased linearly over time, with stronger positive warming effects after 5 years under conservation agriculture. According to structural equation models, these increases arose from greater carbon inputs from the crops, which indirectly controlled microbial CUE via changes in fungal communities. As a result, fungal necromass increased from 28 to 53%, emerging as the strongest predictor of SOC content. Collectively, our results demonstrate how management and climatic factors can interact to alter microbial community composition, physiology and functions and, in turn, SOC formation and accrual in croplands.
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Affiliation(s)
- Jing Tian
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, 100193, Beijing, PR China.
| | - Jennifer A J Dungait
- Geography, Faculty of Environment, Science and Economy, University of Exeter, Rennes Drive, Exeter, EX4 4RJ, UK
- Carbon Management Centre, SRUC-Scotland's Rural College, Edinburgh, EH9 3JG, UK
| | - Ruixing Hou
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences (CAS), 100101, Beijing, PR China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, PR China
| | - Iain P Hartley
- Geography, Faculty of Environment, Science and Economy, University of Exeter, Rennes Drive, Exeter, EX4 4RJ, UK
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, PR China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, 37077, Göttingen, Germany
| | - Fusuo Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, 100193, Beijing, PR China.
| | - M Francesca Cotrufo
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA.
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA.
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.
- School of Computer Science, University of Oklahoma, Norman, OK, USA.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Yang X, Wang D, Tao Y, Shen M, Ma C, Cai C, Song L, Yin B, Zhu C. Does elevated CO 2 enhance the arsenic uptake by rice? Yes or maybe: Evidences from FACE experiments. CHEMOSPHERE 2023; 327:138543. [PMID: 36996921 DOI: 10.1016/j.chemosphere.2023.138543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/22/2023] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
Elevated CO2 (eCO2) strongly affects rice yield and quality in arsenic (As) paddy soils. However, understanding of the As accumulation in rice under coupled stress of eCO2 and soil As is still limited while data are scarce. It greatly limits the prediction for future rice safety. This study investigated the As uptake by rice grown in different As paddy soils under two CO2 conditions (ambient and ambient +200 μmol mol-1) in the free-air CO2 enrichment (FACE) system. Results showed that eCO2 lowered soil Eh at the tillering stage and caused higher concentrations of dissolved As and Fe2+ in soil pore water. Compared with the control, the increased As transfer abilities in rice straws under eCO2 contributed to the higher As accumulation in rice grains, and their total As concentrations were increased by 10.3-31.2%. Besides, the increased amounts of iron plaque (IP) under eCO2 failed to effectively inhibit the As uptake by rice due to the difference in critical stage between As immobilized by IP (mainly in maturing stage) and uptake by rice roots (about 50% contribution before filling stage). Risk assessments suggest that eCO2 enhanced the human health risks of As intake from rice grains produced in low-As paddy soils (<30 mg kg-1). In order to alleviate the As threats to rice under eCO2, we consider that proper soil drainage before filling stage to improve soil Eh can serve as an effective way to reduce As uptake by rice. Pursuing appropriate rice varieties to reduce the As transfer ability may be the other positive strategy.
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Affiliation(s)
- Xiong Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongming Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ye Tao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuanqi Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuang Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Lian Song
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Bin Yin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chunwu Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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Liu Z, Yu Z, Song B, Li Y, Fang J, Guo Y, Jin J, Adams JM. Elevated CO 2 and temperature increase arbuscular mycorrhizal fungal diversity, but decrease root colonization, in maize and wheat. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162321. [PMID: 36801413 DOI: 10.1016/j.scitotenv.2023.162321] [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: 12/19/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Anthropogenic climate change threatens ecosystem multifunctionality. Arbuscular mycorrhizal (AM) fungi are important symbionts that participate in mediating many ecosystem processes, and thus being potentially essential link in the chain of responses to climate change. Yet, how climate change affect the abundance and community structure of AM fungi associated with different crops remains elusive. Here, we investigated the changes in rhizosphere AM fungal communities and growth performance of maize and wheat grown in Mollisols under experimentally elevated CO2 (eCO2, +300 ppm), temperature (eT, +2 °C) and both in-combination (eCT) with open-top chambers, representing a scenario likely to occur by this century's end. The results showed that eCT significantly shifted AM fungal communities in both rhizospheres compared with control, but with no remarkable variation of the overall communities in maize rhizosphere, suggesting their greater resistance to climate change. Both eCO2 and eT increased rhizosphere AM fungal diversity, and conversely they reduced mycorrhizal colonization of both crops, probably since AM fungi had distinct adaptive strategies to climate change in rhizospheres (i.e., r-strategy) and roots (K-strategy), while the colonization intensity positively correlated with a decreased phosphorus (P)-uptake in two crops. Furthermore, co-occurrence network analysis showed that eCO2 strongly decreased the modularity and betweenness centrality of network structure than that of eT and eCT in both rhizospheres, along with the reduced network robustness, implied their destabilized communities under eCO2, while root stoichiometry (C:N and C:P ratio) was the most important factor associating with taxa in networks regardless of climate change. Overall, those findings suggest that rhizosphere AM fungal communities in wheat appear to be more sensitive to climate change than that in maize, further highlighting the importance of effective monitoring and managing AM fungi, which may allow crops to maintain critical levels of mineral nutrients (at least P) under future global change.
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Affiliation(s)
- Zihao Liu
- School of Geography and Oceanography, Nanjing University, Nanjing 210008, China
| | - Zhenhua Yu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, China.
| | - Bin Song
- School of Geography and Oceanography, Nanjing University, Nanjing 210008, China
| | - Yansheng Li
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, China
| | - Jie Fang
- School of Geography and Oceanography, Nanjing University, Nanjing 210008, China
| | - Yaping Guo
- School of Geography and Oceanography, Nanjing University, Nanjing 210008, China
| | - Jian Jin
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, China
| | - Jonathan M Adams
- School of Geography and Oceanography, Nanjing University, Nanjing 210008, 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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8
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Yang J, Yu Q, Su W, Wang S, Wang X, Han Q, Qu J, Li H. Metagenomics reveals elevated temperature causes nitrogen accumulation mainly by inhibiting nitrate reduction process in polluted water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 882:163631. [PMID: 37086993 DOI: 10.1016/j.scitotenv.2023.163631] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/17/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
Determining the response of functional genes and microbiota involved in the nitrogen (N) cycle to warming in the face of global climate change is a hotpot topic. However, whether and how elevated temperature affects the N-cycle genes in polluted water remains unclear. Based on metagenomics, we investigated the responses of the whole N-cycling genes and their microbial communities to the temperature gradients (23, 26, 29, 32, and 35 °C) using animal cadavers as an N-pollution model. We found that the abundance of gene families involved in glutamate metabolism, assimilatory nitrate reduction to nitrite (ANRN), and denitrification pathways decreased with temperature. Moreover, warming reduced the diversity of N-cycling microbial communities. Ecological network analysis indicated that elevated temperature intensified the mutual competition of N-cycle genes. The partial least squares path model (PLS-PM) showed that warming directly suppressed most N-cycle pathways, especially glutamate metabolism, denitrification, and ANRN pathways. Corpse decay also indirectly inhibited N-cycling via regulating N content and microbial communities. Our results highlight warming leads to N accumulation by inhibiting the ANRN and denitrification pathways, which may jeopardize ecological environment security. Our study is expected to provide valuable insights into the complex N-cycle process and N-pollution in warmer aquatic ecosystems.
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Affiliation(s)
- Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qiaoling Yu
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, College of pastoral agriculture science and technology, Lanzhou University, Lanzhou 730000, China
| | - Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Sijie Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xiaochen Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qian Han
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jiapeng Qu
- Key laboratory of adaptation and evolution of plateau biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai 810008, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, College of pastoral agriculture science and technology, Lanzhou University, Lanzhou 730000, China.
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9
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Yu Q, Han Q, Shi S, Sun X, Wang X, Wang S, Yang J, Su W, Nan Z, Li H. Metagenomics reveals the response of antibiotic resistance genes to elevated temperature in the Yellow River. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160324. [PMID: 36410491 DOI: 10.1016/j.scitotenv.2022.160324] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/08/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Climate warming may aggravate the threat of antibiotic resistance genes (ARGs) to environmental and human health. However, whether temperature can predict ARGs and influence their assembly processes remains unknown. Here, we used metagenomic sequencing to explore how gradually elevated water temperature (23 °C, 26 °C, 29 °C, 32 °C, 35 °C) influences ARG and mobile genetic element (MGE) profiles in the Yellow River. In total, 30 ARG types including 679 subtypes were detected in our water samples. Gradually increased temperature remarkably reduced ARG diversity but increased ARG abundance. Approximately 37 % of ARGs and 42 % of MGEs were predicted by temperature, while most others were not sensitive to temperature. For each 1 °C increase in temperature, the ARG abundance rose by 2133 TPM (Transcripts Per kilobase of exon model per Million mapped reads) abundance, and multidrug, tetracycline and peptide resistance genes had the fastest increases. Proteobacteria and Actinobacteria were the primary ARG hosts, with 558 and 226 ARG subtypes, respectively. Although ARG profiles were mainly governed by stochastic process, elevated temperature increased the deterministic process of ARGs in the Yellow River. The abundance of five high-risk ARGs (tetM, mecA, bacA, vatE and tetW) significantly increased with elevated water temperature, and these ARGs co-occurred with several opportunistic pathogens (Delftia, Legionella and Pseudomonas), implying that antibiotic resistance risk may increase under climate warming. Our study explored the possibility of predicting resistomes and their health risks through temperature, providing a novel approach to predict and control ARGs in water environments under climate warming.
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Affiliation(s)
- Qiaoling Yu
- College of Pastoral Agriculture Science and Technology, State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microiome, Lanzhou University, Lanzhou 730000, China
| | - Qian Han
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Shunqin Shi
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xiaofang Sun
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xiaochen Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Sijie Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Zhibiao Nan
- College of Pastoral Agriculture Science and Technology, State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microiome, Lanzhou University, Lanzhou 730000, China
| | - Huan Li
- College of Pastoral Agriculture Science and Technology, State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microiome, Lanzhou University, Lanzhou 730000, China; School of Public Health, Lanzhou University, Lanzhou 730000, China.
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10
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Plant Community Associates with Rare Rather than Abundant Fungal Taxa in Alpine Grassland Soils. Appl Environ Microbiol 2023; 89:e0186222. [PMID: 36602328 PMCID: PMC9888191 DOI: 10.1128/aem.01862-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The importance of the rare microbial biosphere in maintaining biodiversity and ecological functions has been highlighted recently. However, the current understanding of the spatial distribution of rare microbial taxa is still limited, with only a few investigations for rare prokaryotes and virtually none for rare fungi. Here, we investigated the spatial patterns of rare and abundant fungal taxa in alpine grassland soils across 2,000 km of the Qinghai-Tibetan plateau. We found that most locally rare fungal taxa remained rare (13.07%) or were absent (82.85%) in other sites, whereas only a small proportion (4.06%) shifted between rare and abundant among sites. Although they differed in terms of diversity levels and compositions, the distance decay relationships of both the rare and the abundant fungal taxa were valid and displayed similar turnover rates. Moreover, the community assemblies of both rare and abundant fungal taxa were predominantly controlled by deterministic rather than stochastic processes. Notably, the community composition of rare rather than abundant fungal taxa associated with the plant community composition. In summary, this study advances our understanding of the biogeographic features of rare fungal taxa in alpine grasslands and highlights the concordance between plant communities and rare fungal subcommunities in soil. IMPORTANCE Our current understanding of the ecology and functions of rare microbial taxa largely relies on research conducted on prokaryotes. Despite the key ecological roles of soil fungi, little is known about the biogeographic patterns and drivers of rare and abundant fungi in soils. In this study, we investigated the spatial patterns of rare and abundant fungal taxa in Qinghai-Tibetan plateau (QTP) alpine grassland soils across 2,000 km, with a special concentration on the importance of the plant communities in shaping rare fungal taxa. We showed that rare fungal taxa generally had a biogeographic pattern that was similar to that of abundant fungal taxa in alpine grassland soils on the QTP. Furthermore, the plant community composition was strongly related to the community composition of rare taxa but not abundant taxa. In summary, this study significantly increases our biogeographic and ecological knowledge of rare fungal taxa in alpine grassland soils.
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Yang X, Wang D, Tao Y, Shen M, Wei W, Cai C, Ding C, Li J, Song L, Yin B, Zhu C. Effects of elevated CO 2 on the Cd uptake by rice in Cd-contaminated paddy soils. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130140. [PMID: 36241499 DOI: 10.1016/j.jhazmat.2022.130140] [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: 07/25/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
The rising atmospheric CO2 is a major driver for climate change, directly affects rice production. Cadmium (Cd) in paddy soils also serves as a persistent concern. Currently, few studies consider the rice response to coupled stresses of elevated CO2 (eCO2) and soil Cd. Experimental evidence understanding the effects and mechanisms of eCO2 on Cd uptake by rice is lacking yet. In a free-air CO2 enrichment (FACE) system, a 3-year pot experiment was conducted to explore the Cd uptake by rice under two CO2 conditions (ambient and ambient + 200 µmol·mol-1) using combinations of in-situ Cd-contaminated soils and associated rice varieties. Results showed that more low-crystalline Fe oxides (Feh) in iron plaque (IP) were deposited on root surface with the increased dissolved Fe2+ due to lower soil redox status under eCO2. The Cd accumulation in rice was hindered due to more Cd associated with Feh (Feh-Cd) rather than uptake by roots. Taken together, the relative effects of eCO2 on Cd uptake by rice were consistent across years under different Cd-contaminated soils. Our findings will help to better understand the Cd uptake by rice under future climate conditions, and thus push the development of climate-crop-soil models and accurate prediction for food security.
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Affiliation(s)
- Xiong Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100010, China.
| | - Dongming Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100010, China
| | - Ye Tao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100010, China
| | - Min Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100010, China
| | - Wei Wei
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100010, China
| | - Chuang Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Changfeng Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jiuyu Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Lian Song
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Bin Yin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chunwu Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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Yang J, Yu Q, Su W, Wang S, Wang X, Han Q, Li H. Metagenomics reveals that temperature predicts a small proportion of antibiotic resistomes and mobile genetic elements in polluted water. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120793. [PMID: 36462677 DOI: 10.1016/j.envpol.2022.120793] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Climate warming multiplies the threat of antibiotic resistance genes (ARGs) to public health, but whether temperature may predict antibiotic resistomes in water environment remain unknown. Here, by metagenomic sequencing, we investigated the changes of resistome at five different temperature gradients (23, 26, 29, 32, and 35 °C) in polluted water by animal cadaver. Thirty ARG types including 668 subtypes were observed in our samples. Temperature significantly influenced ARG profiles and showed a negative correlation with ARG diversity. The ARG assembly process was dominated by a deterministic process (63.32%-95.08%) but showed a peak pattern with temperature. Notably, temperature may predict approximately 21% of ARGs and 36% of mobile genetic elements (MGEs), while most other ARGs or MGEs were insensitive to temperature. Three types (carbapenem, dicyclomycin, and diaminopyrimidine antibiotic) and 63 subtypes of ARGs that positively correlated with temperature were identified in the polluted water. Notably, we screened 21 subtypes of high-risk ARGs (bacA, mdtA, tetM, etc.) and 22 opportunistic pathogens (Aeromonas, Clostridium, Bacteroides, etc.) and found their positive co-occurrence with temperature, implying these potential biological or genetic pollutants may probably go up under global warming. Our study reveals the predictability of temperature on antibiotic resistance genes, providing a suitable approach to track the fate and spread of ARGs in water environment under climate warming.
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Affiliation(s)
- Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qiaoling Yu
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Sijie Wang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Xiaochen Wang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qian Han
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou, 730000, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China.
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Sun Y, Li X, Li X, Wang J. Deciphering the Fingerprint of Dissolved Organic Matter in the Soil Amended with Biodegradable and Conventional Microplastics Based on Optical and Molecular Signatures. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15746-15759. [PMID: 36301071 DOI: 10.1021/acs.est.2c06258] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Biodegradable polymers are promoted as promising alternatives for conventional non-degradable plastics, but they may also negatively impact soil ecosystems. Here, we estimated the effects of biodegradable (polylactide (PLA) and polybutylene succinate (PBS)) and non-biodegradable (polyethylene (PE) and polystyrene (PS)) microplastics at a concentration of 1% (w/w) on dissolved organic matter (DOM) in two soil types, a black soil (BS) and a yellow soil (YS), by using fluorescence excitation-emission matrix spectroscopy and ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). PBS significantly increased the contents of soil dissolved organic carbon (DOC) and the relative intensities of protein-like components. The turnover rates of soil DOM were statistically higher in PBS treatments (0.106 and 0.196, p < 0.001) than those in other microplastic groups. The FT-ICR-MS results indicated that more labile-active DOM molecules were preferentially obtained in biodegradable microplastic treatments, which may be attributed to the polymer degradation. The conventional microplastics showed no significant effects on the optical characteristics but changed the molecular compositions of the soil DOM. More labile DOM molecules were observed in BS samples treated with PE compared to the control, while the conventional microplastics decreased the DOM lability in YS soil. The distinct priming effects of plastic-leached DOM may trigger the DOM changes in different soils. This study provided important information for further understanding the impact of microplastics on soil carbon processes.
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Affiliation(s)
- Yuanze Sun
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xinfei Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaomin Li
- Institute of Quality Standard and Testing Technology for Agro-Products, The Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
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Ji L, Zhang L, Wang Z, Zhu X, Ning K. High biodiversity and distinct assembly patterns of microbial communities in groundwater compared with surface water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155345. [PMID: 35460778 DOI: 10.1016/j.scitotenv.2022.155345] [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: 11/30/2021] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
The differences in bacterial community assembly mechanism between surface water and groundwater, as well as the driving factors of environmental factors, are still unknown. Here we aimed to answer these questions by analyzing microbial community samples from surface water and groundwater. We observed a strong connection between microbial communities in surface water and groundwater and several human pathogens are shared between surface water and groundwater; however, the richness and diversity of groundwater microbial communities were greater than those of surface water, regardless of the season. Additionally, bacterial community compositions of surface water and groundwater differed significantly between seasons. Most importantly, the groundwater community exhibited a highly deterministic assembly process (56% contributed by deterministic process, with neutral community model R2 = 0.277) compared with surface water (51% contributed by deterministic process, with R2 = 0.526). This study provides a deep understanding of the effects of environmental factors on surface water and groundwater microbial communities, to better protect water resources.
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Affiliation(s)
- Lei Ji
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Lu Zhang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi Wang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China.
| | - Xue Zhu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
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Deterministic Factors Determine the Comammox Community Composition in the Pearl River Estuary Ecosystem. Microbiol Spectr 2022; 10:e0101622. [PMID: 35913204 PMCID: PMC9431512 DOI: 10.1128/spectrum.01016-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Complete ammonia oxidizers (comammox) have been widely detected in riverine and estuarine ecosystems. However, knowledge about the process of comammox community assembly from freshwater to marine environments is still limited. Here, based on deep sequencing, we investigated the community composition of comammox along a salinity gradient in the Pearl River Estuary (PRE), South China. Our results showed that comammox microorganisms in the PRE sediments were extremely diverse and displayed distinct distributional patterns between upstream and downstream habitats. Quantitative PCR demonstrated that comammox was the dominant ammonia-oxidizing microorganism (AOM) in the PRE upstream sediments, and ammonia-oxidizing archaea (AOA) dominated the PRE downstream sediments, while ammonia-oxidizing bacteria (AOB) were not dominant in any section of the PRE. Neutral modeling revealed that stochastic processes explained a limited part of the variation in the comammox community. The majority of beta nearest-taxon index values were higher than 2, indicating that comammox community assembly in the PRE sediments was better explained through a deterministic process than through a stochastic process. Salinity and total nitrogen were the most important contributing factors that shaped the comammox community. This study expanded the current knowledge of the diversity and niche preference of comammox in the estuarine ecosystem, and further enhances our understanding of the assembly of comammox community from freshwater to marine environments. IMPORTANCE Microbial communities are shaped by stochastic (emigration, immigration, birth, death, and genetic drift of species) and deterministic (e.g., environmental factors) processes. However, it remains unknown as to which type of process is more important in influencing the comammox community assembly from freshwater to marine environments. In this study, we compared the relative importance of stochastic and deterministic processes in shaping the assembly of the comammox community, which demonstrated that the deterministic process was more important in determining the community assembly patterns in the PRE ecosystem.
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Su W, Wang S, Yang J, Yu Q, Wirth S, Huang X, Qi W, Zhang X, Li H. Corpse decay of wild animals leads to the divergent succession of nrfA-type microbial communities. Appl Microbiol Biotechnol 2022; 106:5287-5300. [PMID: 35802158 DOI: 10.1007/s00253-022-12065-z] [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: 05/23/2022] [Revised: 06/27/2022] [Accepted: 07/02/2022] [Indexed: 11/29/2022]
Abstract
Animal carcasses introduce large amounts of nitrates and ammonium into the soil ecosystem. Some of this ammonium is transformed from nitrite through the nrfA-type microbial community. However, it is unclear how nrfA-type microorganisms respond to the decomposition of corpses. This study applied high-throughput sequencing to characterize the ecological succession of nrfA-type microbial communities in grassland soil. Our results showed that Cyclobacterium and Trueperella were the predominant genera for nrfA-type communities in soil with a decomposing corpse (experimental group), while Cyclobacterium and Archangium were dominant in soil without a corpse (control group). The alpha diversity indexes and the resistance and resilience indexes of the microbial communities initially increased and then decreased during decomposition. Compared with the control group, nrfA-encoding community structure in the experimental group gradually became divergent with succession and temporal turnover accelerated. Network analysis revealed that the microbial communities of the experimental group had more complex interactions than those of the control groups. Moreover, the bacterial community assembly in the experimental group was governed by stochastic processes, and the communities of the experimental group had a weaker dispersal capacity than those of the control group. Our results reveal the succession patterns of the nrfA-type microbial communities during degradation of wild animal corpses, which can offer references for demonstrating the ecological mechanism underlying the changes in the nrfA-type microbial community during carcass decay. KEY POINTS: • Corpse decay accelerates the temporal turnover of the nrfA-type community in soil. • Corpse decay changes the ecological succession of the nrfA-type community in soil. • Corpse decay leads to a complex co-occurrence pattern of the nrfA-type community in soil.
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Affiliation(s)
- Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Sijie Wang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qiaoling Yu
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Stephan Wirth
- Leibniz-Centre for Agricultural Landscape Research (ZALF), Institute of Landscape Biogeochemistry, Eberswalder Str. 84, 15374, Muncheberg, Germany
| | - Xiaodan Huang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Wanpeng Qi
- Genesky Biotechnologies Inc., Shanghai, 201315, China
| | - Xiao Zhang
- Key Laboratory of National Forestry and Grassland Administration On Silviculture in Loess Plateau, College of Forestry, Northwest A&F University, Yangling, 712100, China.
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou, 730000, China. .,State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, College of pastoral agriculture science and technology, Lanzhou University, Gansu, 730000, China.
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Biofilm Structural and Functional Features on Microplastic Surfaces in Greenhouse Agricultural Soil. SUSTAINABILITY 2022. [DOI: 10.3390/su14127024] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Microplastics (MPs) enter the soil through a variety of pathways, including plastic mulching, sludge, and organic manure application. In recent years, domestic and foreign experts and scholars have been concerned about the residues and contamination of MPs in the soil of greenhouse agriculture. In this investigation, five types of MPs including low-density polyethylene (LDPE), high-density polyethylene (HDPE), polystyrene (PS), polypropylene (PP), and polyethylene terephthalate (PET), and two concentrations (1% and 5%, w/w) were used in a 30-day external exposure test. Evidence of microbial enrichment was found on the surface of the MPs. The total amount of biofilm on the surface of MPs increased dramatically with increasing exposure time and MP concentrations. The polysaccharide content of extracellular polymers (EPS) in biofilms was significantly different, and the maximum PS1 (1% (w/w) PS) concentration was 50.17 mg/L. However, EPS protein content did not change significantly. The dominant bacteria on the surface of MPs with different types and concentrations were specific, and the relative abundance of Patescibacteria was significantly changed at the phylum level. At the genus level, Methylophaga, Saccharimonadales, and Sphingomonas dominated the flora of LDPE1 (1% (w/w) LDPE), PS1, and PET5 (5% (w/w) PET). The dominant bacteria decompose organic materials and biodegrade organic contaminants. According to the FAPROTAX functional prediction study, chemoheterotrophy and aerobic chemoheterotrophyplay a role in ecosystem processes such as carbon cycle and climate regulation. The application of LDPE1 has a greater impact on the carbon cycle. Plant development and soil nutrients in greenhouse agriculture may be influenced by the interaction between MPs and microorganisms in the growing area, while MP biofilms have an impact on the surrounding environment and pose an ecological hazard.
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Zhang B, Yang T, Sun C, Wen X. Drivers of microbial beta-diversity in wastewater treatment plants in China. J Environ Sci (China) 2022; 115:341-349. [PMID: 34969461 DOI: 10.1016/j.jes.2021.07.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 06/14/2023]
Abstract
As one of the most well-documented biogeographic patterns, the distance-decay relationship provides insights into the underlying mechanisms driving biodiversity distribution. Although wastewater treatment plants (WWTPs) are well-controlled engineered ecosystems, this pattern has been seen among microbial communities in activated sludge (AS). However, little is known about the relative importance of environmental heterogeneity and dispersal limitation in shaping AS microbial community across China; especially they are related to spatial scale and organism types. Here, we assessed the distance-decay relationship based on different spatial scales and microbial phylogenetic groups by analyzing 132 activated sludge (AS) samples across China comprising 3,379,200 16S rRNA sequences. Our results indicated that the drivers of distance-decay pattern in China were scale-dependent. Microbial biogeographic patterns in WWTPs were mainly driven by dispersal limitation at both local and national scales. In contrast, conductivity, SRT, and pH played dominant roles in shaping AS microbial community compositions at the regional scale. Turnover rates and the drivers of beta-diversity also varied with microorganism populations. Moreover, a quantitative relationship between dispersal limitation ratio and AS microbial turnover rate was generated. Collectively, these results highlighted the importance of considering multiple spatial scales and micro-organism types for understanding microbial biogeography in WWTPs and provided new insights into predicting variations in AS community structure in response to environmental disturbance.
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Affiliation(s)
- Bing Zhang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China
| | - Ting Yang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Chenxiang Sun
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xianghua Wen
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China.
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Guo Z, Bao Y, Liu J. Environmental Difference and Spatial Distance Affect the Fidelity of Variation Source of Microbial Community Structure in Air-Dried Soils. Microorganisms 2022; 10:microorganisms10040672. [PMID: 35456724 PMCID: PMC9031423 DOI: 10.3390/microorganisms10040672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 12/04/2022] Open
Abstract
Air-dried soil archives are important for microbial ecology research, although the process of air-drying preservation inevitably destroys the original microbial information in soils. Only upon fully understanding the limitations of air-dried soil can it play a greater role. The value of air-dried soil depends on the fidelity of microbial community structure information in the air-dried soil relative to that in fresh soil. To evaluate this, high-throughput sequencing was applied to investigate the microbial community of fresh soils and 227 days air-dried archives from typical farmland under a large spatial scale, and PERMANOVA was used to analyze the explanation proportion (EP) of the spatial factor on the microbial community structure in any paired-fresh or air-dried soils. The results show that for any paired soils, the value of EP ranged from 42.4% to 97.9% (p < 0.001). Importantly, taking fresh soil as a reference, the value of EP declined in air-dried soils (effect size r = 0.79, p < 0.001). Furthermore, the standardized difference in EP between fresh and air-dried soil (NDEP) was used to characterize the fidelity of variance source of microbial community structure in air-dried soils, and correlation tests showed that NDEP was negatively correlated with spatial distance (r = −0.21, p < 0.01) and with environmental difference (r = −0.37, p < 0.001). Further analyses show that larger NDEP was observed at a spatial distance <25 km or an environmental difference <0.58. Variance partitioning analysis showed that 28.0% of the variation in NDEP could be explained, with environmental difference constituting 14.0% and the interaction between the environmental difference and spatial distance constituting the remaining 14.0%. Soil texture was the most important factor for predicting NDEP, followed by soil pH and annual average temperature. This study not only emphasizes the possible decline in EP when using air-dried soils to reveal microbial community patterns, but also implies that air-dried soil is more suitable for addressing scientific questions under a large spatial scale or environmental differences.
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Affiliation(s)
- Zhiying Guo
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (Y.B.); (J.L.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
| | - Yuanyuan Bao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (Y.B.); (J.L.)
| | - Jie Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (Y.B.); (J.L.)
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Yu Q, Yang J, Su W, Li T, Feng T, Li H. Heavy metals and microbiome are negligible drivers than mobile genetic elements in determining particle-attached and free-living resistomes in the Yellow River. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127564. [PMID: 34736202 DOI: 10.1016/j.jhazmat.2021.127564] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/27/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Suspended particles in water can shelter both microorganisms and contaminants. However, the emerging pollutants antibiotic resistance genes (ARGs) in free-living (FL) or particle-attached (PA) bacteria in aquatic environments are less explored. In this study, we compared the free-living and particle-attached ARGs during four seasons in the Yellow River using high-throughput quantitative PCR techniques and 16S rRNA gene sequencing. Our results demonstrated that both the free-living water and particles were dominated by tetracycline and beta-lactamase resistance genes. The PA-ARGs had a higher absolute abundance than FL-ARGs in the Yellow River, regardless of the season. Both PA-ARGs and FL-ARGs had the highest absolute abundance and diversity during winter. Mobile genetic elements (MGEs) were the dominant driver for both size-fractionated ARGs. However, the microbiome had less influence on PA-ARG profiles than the FL-ARG profiles, while the effects of the heavy metals on ARGs were negligible. The community assembly of both FL-ARG and PA-ARG can be explained by neutral processes. Several opportunistic pathogens (e.g., Escherichia coli) associated with human health exhibited a higher relative abundance in the particles than during a free-living lifestyle. Parts of these pathogens were potential ARG hosts. As such, it is important to monitor the ARGs and opportunistic pathogens from size-fractionated bacteria and develop targeted strategies to manage ARG dissemination and opportunistic pathogens to ensure public health.
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Affiliation(s)
- Qiaoling Yu
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Tongtong Li
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Tianshu Feng
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China; Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China.
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Sun Y, Duan C, Cao N, Li X, Li X, Chen Y, Huang Y, Wang J. Effects of microplastics on soil microbiome: The impacts of polymer type, shape, and concentration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150516. [PMID: 34592287 DOI: 10.1016/j.scitotenv.2021.150516] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 06/13/2023]
Abstract
Increasing research has recognized that the ubiquitous presence of microplastics in terrestrial environments is undeniable, which potentially alters the soil ecosystem properties and processes. The fact that microplastics with diverse characteristics enter into the soil may induce distinct effects on soil ecosystems. Our knowledge of the impacts of microplastics with different polymers, shapes, and concentrations on soil bacterial communities is still limited. To address this, we examined the effects of spherical microplastics (150 μm) with different polymers (i.e., polyethylene (PE), polystyrene (PS), and polypropylene (PP)) and four shapes of PP microplastics (i.e., fiber, film, foam, and particle) at a constant concentration (1%, w/w) on the soil bacterial community in an agricultural soil over 60 days. Treatments with different concentrations (0.01-20%, w/w) of PP microplastic particles (150 μm) were also included. The bacterial communities in PE and PP treatments showed a similar pattern but separated from those in PS-treated soils, indicating the polymer backbone structure is an important factor modulating the soil bacterial responses. Fiber, foam, and film microplastics significantly affected the soil bacterial composition as compared to the particle. The community dissimilarity of soil bacteria was significantly (R2 = 0.592, p < 0.001) correlated with the changes of microplastic concentration. The random forest model identified that certain bacteria belonging to Patescibacteria were closely linked to microplastic contamination. Additionally, analysis of the predicted function further showed that microplastics with different characteristics caused distinct effects on microbial community function. Our findings suggested that the idiosyncrasies of microplastics should not be neglected when studying their effects on terrestrial ecosystems.
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Affiliation(s)
- Yuanze Sun
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Chongxue Duan
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Na Cao
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xinfei Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaomin Li
- Institute of Quality Standard and Testing Technology for Agro-Products, The Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Yumei Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yi Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
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22
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Yu Q, Feng T, Yang J, Su W, Zhou R, Wang Y, Zhang H, Li H. Seasonal distribution of antibiotic resistance genes in the Yellow River water and tap water, and their potential transmission from water to human. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118304. [PMID: 34627965 DOI: 10.1016/j.envpol.2021.118304] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/05/2021] [Accepted: 10/05/2021] [Indexed: 05/25/2023]
Abstract
The prevalence and transmission of antibiotic resistance genes (ARGs) and opportunistic pathogens in water environments can pose great threat to public health. However, the dissemination of ARGs and opportunistic pathogens from water environments to humans has been poorly explored. Here, we employed 16S rRNA gene sequencing and high-throughput quantitative PCR techniques to explore the seasonal distribution of ARGs and opportunistic pathogens in the Yellow River water (source water) and tap water, as well as their relationships with healthy humans at Lanzhou, China. Physiochemical analysis was applied to detect water quality parameters and heavy metal contents. The absolute abundance and diversity of ARGs in the Yellow River and tap water demonstrated distinct seasonal patterns. In winter, the Yellow river water had the highest ARG abundance and diversity, while tap water owned the lowest. Mobile genetic elements (MGEs) were the predominant driver of ARG profiles in both the Yellow river and tap water. Null model analysis showed that ARG assembly in the Yellow River was more influenced by stochastic processes than tap water and this was independent of seasons. Total organic carbon and arsenic contents exhibited positive correlations with many ARGs. Opportunistic pathogens Aeromonas and Pseudomonas may be potential hosts for ARGs. Approximately 80% of detected ARGs were shared between water samples and the human gut. These persistent ARGs could not be entirely eliminated through drinking water treatment processes. Thus, it is crucial to protect sources of tap water from anthropogenic pollution and improve water treatment technologies to reduce the dissemination of ARGs and ensure drinking-water biosafety for human health.
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Affiliation(s)
- Qiaoling Yu
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Tianshu Feng
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Rui Zhou
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Yijie Wang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Hong Zhang
- Anhui Microanaly Gene Co., Ltd., Hefei, 230601, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou, 730000, China; Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China.
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23
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Wang Y, Lu G, Yu H, Du X, He Q, Yao S, Zhao L, Huang C, Wen X, Deng Y. Meadow degradation increases spatial turnover rates of the fungal community through both niche selection and dispersal limitation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149362. [PMID: 34375268 DOI: 10.1016/j.scitotenv.2021.149362] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/08/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
The alpine meadow ecosystem, as the main ecosystem of the Qinghai-Tibet Plateau, has been heavily degraded over the past several decades due to overgrazing and climate change. Although soil microorganisms play key roles in the stability and succession of grassland ecosystems, their response to grassland degradation has not been investigated at spatial scale. Here, we systematically analyzed the spatial turnover rates of soil prokaryotic and fungal communities in degraded and undegraded meadows through distance-decay relationship (DDR) and species area relationship (SAR), as well as the community assembly mechanisms behind them. Although the composition and structure of both fungal and prokaryotic communities showed significant changes between undegraded and degraded meadows, steeper spatial turnover rates were only observed in fungi (Degraded Alpine Meadow β = 0.0142, Undegraded Alpine Meadow β = 0.0077, P < 0.05). Mantel tests indicated that edaphic variables and vegetation factors showed significant correlations to the β diversity of fungal community only in degraded meadow, suggesting soil and vegetation heterogeneity both contributed to the variation of fungal community in that system. Correspondingly, a novel phylogenetic null model analysis demonstrated that environmental selection was enhanced in the fungal community assembly process during meadow degradation. Interestingly, dispersal limitation was also enhanced for the fungal community in the degraded meadow, and its relative contribution to other assembly process (i.e. selection and drift) showed a significant linear increase with spatial distance, suggesting that dispersal limitation played a greater role as distance increased. Our findings indicated the spatial scaling of the fungal community is altered during meadow degradation by both niche selection and dispersal limitation. This study provides a new perspective for the assessment of soil microbial responses to vegetation changes in alpine areas.
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Affiliation(s)
- Yingcheng Wang
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China; CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China
| | - Guangxin Lu
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Hao Yu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Environmental Science and Engineering, Liaoning Technical University, Fuxin 123000, China
| | - Xiongfeng Du
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Qing He
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Shiting Yao
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Lirong Zhao
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Caixia Huang
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Xiaocheng Wen
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China.
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24
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Yu Q, Zhou R, Wang Y, Su W, Yang J, Feng T, Dou Y, Li H. Carcass decay deteriorates water quality and modifies the nirS denitrifying communities in different degradation stages. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 785:147185. [PMID: 33933763 DOI: 10.1016/j.scitotenv.2021.147185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/19/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Corpse degradation may release amounts of hazardous materials (e.g., cadaverine, putrescine and ammonia) into surrounding areas, which deteriorate environments and result in nitrogen contamination. Nitrate or nitrite can be reduced to nitrogen gas by denitrifying bacteria, thus alleviating nitrogen contamination and purifying aquatic environments. However, the reaction of nirS-encoding denitrifiers to carcass degradation is less studied. Therefore, water physiochemical analysis and high-throughput sequencing were applied to explore the successional pattern of nirS denitrifying communities in the Yellow River water and tap water during three stages of animal cadaver decay (submerged fresh, advanced floating decay as well as sunken remains) and relevant control group. Nitrate nitrogen (NO3-N) and ammonia nitrogen (NH4+-N) concentration in corpse groups were highly elevated compared with control groups. The dominant phylum for nirS denitrifying communities was Proteobacteria. Abundant denitrifying genera Paracoccus, Alicycliphilus and Diaphorobacter were detected, and these genera have been reported to participate in the degradation of organic pollutants. Particularly, nirS-type community structures were remarkably influenced by corpse decay and became similar with succession. Water total dissolved solids (TDS), salinity, conductivity (CON) and phosphate were primary impacting factors driving the community structures, but the effect of water type was almost negligible. Notably, denitrifying community assembly was dominated by deterministic processes rather than stochastic processes, and the relative importance of deterministic processes among most corpse groups was higher than that in control groups, indicating that environmental filtering regulates the denitrifying communities. Our results provide new insight into environmental purification for hazardous materials produced by corpse degradation, thereby providing valuable advice to environmental administration.
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Affiliation(s)
- Qiaoling Yu
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Rui Zhou
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Yijie Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Tianshu Feng
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Yaqi Dou
- Hubei Aquaculture Technology Extension Center (Hubei Aquatic Breeds Introduction and Breeding Center), Wuhan 430070, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China; Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China..
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25
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Huang M, Chai L, Jiang D, Zhang M, Jia W, Huang Y, Zhou J. Dissolved organic matter (DOM) quality drives biogeographic patterns of soil bacterial communities and their association networks in semi-arid regions. FEMS Microbiol Ecol 2021; 97:6307509. [PMID: 34156067 DOI: 10.1093/femsec/fiab083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/18/2021] [Indexed: 11/13/2022] Open
Abstract
It is of great interest to elucidate the biogeographic patterns of soil microorganisms and their driving forces, which is fundamental to predicting alterations in microbial-mediated functions arising from environment changes. Although dissolved organic matter (DOM) represents an important resource for soil microorganisms, knowledge of how its quality affects microbial biogeography is limited. Here, we characterized soil bacterial communities and DOM quality in 45 soil samples collected from a 1500-km sampling transect through semi-arid regions in northern China which are currently suffering great pressure from climate change, using Illumina Miseq sequencing and fluorescence spectroscopy, respectively. We found that DOM quality (i.e. the source of DOM and the humification degree of DOM) had profound shaping influence on the biogeographic patterns exhibited by bacterial diversity, community composition and association networks. Specifically, the composition of bacteria community closely associated with DOM quality. Plant-derived DOM sustained higher bacterial diversity relative to microbial-derived DOM. Meanwhile, bacterial diversity linearly increased with increasing humification degree of DOM. Additionally, plant-derived DOM was observed to foster more complex bacterial association networks with less competition. Together, our work contributes to the factors underlying biogeographic patterns not only of bacterial diversity, community composition but also of their association networks and reports previously undocumented important role of DOM quality in shaping these patterns.
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Affiliation(s)
- Muke Huang
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Liwei Chai
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Dalin Jiang
- Gradute School of Life and Environmental Science, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Mengjun Zhang
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Weiqian Jia
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yi Huang
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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26
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Du X, Deng Y, Li S, Escalas A, Feng K, He Q, Wang Z, Wu Y, Wang D, Peng X, Wang S. Steeper spatial scaling patterns of subsoil microbiota are shaped by deterministic assembly process. Mol Ecol 2020; 30:1072-1085. [PMID: 33320382 DOI: 10.1111/mec.15777] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 11/04/2020] [Accepted: 12/03/2020] [Indexed: 12/26/2022]
Abstract
Although many studies have investigated the spatial scaling of microbial communities living in surface soils, very little is known about the patterns within deeper strata, nor is the mechanism behind them. Here, we systematically assessed spatial scaling of prokaryotic biodiversity within three different strata (Upper: 0-20 cm, Middle: 20-40 cm, and Substratum: 40-100 cm) in a typical grassland by examining both distance-decay (DDRs) and species-area relationships (SARs), taxonomically and phylogenetically, as well as community assembly processes. Each layer exhibited significant biogeographic patterns in both DDR and SAR (p < .05), with taxonomic turnover rates higher than phylogenetic ones. Specifically, the spatial turnover rates, β and z values, respectively, ranged from 0.016 ± 0.005 to 0.023 ± 0.005 and 0.065 ± 0.002 to 0.077 ± 0.004 across soil strata, and both increased with depth. Moreover, the prokaryotic community in grassland soils assembled mainly according to deterministic rather than stochastic mechanisms. By using normalized stochasticity ratio (NST) based on null model, the relative importance of deterministic ratios increased from 48.0 to 63.3% from Upper to Substratum, meanwhile a phylogenetic based method revealed average βNTI also increased with depth, from -5.29 to 19.5. Using variation partitioning and distance approaches, both geographic distance and soil properties were found to strongly affect biodiversity structure, the proportions increasing with depth, but spatial distance was always the main underlying factor. These indicated increasingly deterministic proportions in accelerating turnover rates for spatial assembly of prokaryotic biodiversity. Our study provided new insights on biogeography in different strata, revealing importance of assembly patterns and mechanisms of prokaryote communities in below-surface soils.
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Affiliation(s)
- Xiongfeng Du
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Institute for Marine Science and Technology, Shandong University, Qingdao, China
| | - Shuzhen Li
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.,State Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Arthur Escalas
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Montpellier Cedex 5, France
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Qing He
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhujun Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yueni Wu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Danrui Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xi Peng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shang Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
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27
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Yu Q, Zhou R, Wang Y, Feng T, Li H. Corpse decomposition increases nitrogen pollution and alters the succession of nirK-type denitrifying communities in different water types. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 747:141472. [PMID: 32795804 DOI: 10.1016/j.scitotenv.2020.141472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/02/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
Cadaver decomposition as high-quality nutrient inputs may exert strong perturbation on the aquatic environments, such as high nitrogen or nitrate pollution. Denitrifying bacteria may reduce nitrate to nitrogen gas, thereby decreasing the nitrogen pollution and improving self-purification ability of aquatic ecosystem. However, how nirK denitrifying communities in water respond to cadaver decomposition remains unknown. Thus, we employed high-throughput sequencing and chemical analysis to investigate the succession of nirK-type denitrifying communities in tap water and Yellow river water (experimental groups) as well as their corresponding control groups during two important stages of fish corpse decomposition called advanced floating decay and sunken remains. Our data showed that the concentration of NH4+-N in the experimental groups increased approximately 3-4 times compared with the control groups. Proteobacteria was the predominant phylum for nirK denitrifying communities. Several potential pathogenic genera, such as Brucella and Achromobacter, were enriched in the corpse groups. Notably, nirK-type community structures were significantly impacted by cadaver decomposition. Community structures in the corpse groups become more similar with succession, indicating community convergence at the final stage. Water pH, oxidation-reduction potential (ORP) and treatment were three important factors affecting the community structures. However, water type was not a main driving factor determining carcass-associated nirK-type bacterial communities. Four phylogenetic clusters were detected in the denitrifying communities, but showed significantly different distribution between the corpse and control groups. These results provide an in-depth understanding for nirK denitrifying functional bacteria and potential pathogenic bacteria during carrion decomposition process, which offer valuable reference to environmental evaluation and management.
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Affiliation(s)
- Qiaoling Yu
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Rui Zhou
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Yijie Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Tianshu Feng
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China; Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China.
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28
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He Z, Deng Y, Xu M, Li J, Liang J, Xiong J, Yu H, Wu B, Wu L, Xue K, Shi S, Carrillo Y, Van Nostrand JD, Hobbie SE, Reich PB, Schadt CW, Kent AD, Pendall E, Wallenstein M, Luo Y, Yan Q, Zhou J. Microbial functional genes commonly respond to elevated carbon dioxide. ENVIRONMENT INTERNATIONAL 2020; 144:106068. [PMID: 32871382 DOI: 10.1016/j.envint.2020.106068] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Atmospheric CO2 concentration is increasing, largely due to anthropogenic activities. Previous studies of individual free-air CO2 enrichment (FACE) experimental sites have shown significant impacts of elevated CO2 (eCO2) on soil microbial communities; however, no common microbial response patterns have yet emerged, challenging our ability to predict ecosystem functioning and sustainability in the future eCO2 environment. Here we analyzed 66 soil microbial communities from five FACE sites, and showed common microbial response patterns to eCO2, especially for key functional genes involved in carbon and nitrogen fixation (e.g., pcc/acc for carbon fixation, nifH for nitrogen fixation), carbon decomposition (e.g., amyA and pulA for labile carbon decomposition, mnp and lcc for recalcitrant carbon decomposition), and greenhouse gas emissions (e.g., mcrA for methane production, norB for nitrous oxide production) across five FACE sites. Also, the relative abundance of those key genes was generally increased and directionally associated with increased biomass, soil carbon decomposition, and soil moisture. In addition, a further literature survey of more disparate FACE experimental sites indicated increased biomass, soil carbon decay, nitrogen fixation, methane and nitrous oxide emissions, plant and soil carbon and nitrogen under eCO2. A conceptual framework was developed to link commonly responsive functional genes with ecosystem processes, such as pcc/acc vs. soil carbon storage, amyA/pulA/mnp/lcc vs. soil carbon decomposition, and nifH vs. nitrogen availability, suggesting that such common responses of microbial functional genes may have the potential to predict ecosystem functioning and sustainability in the future eCO2 environment.
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Affiliation(s)
- Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States; College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
| | - Ye Deng
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Meiying Xu
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Juan Li
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Junyi Liang
- Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States
| | - Jinbo Xiong
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Hao Yu
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Harbin Institute of Technology, Harbin 150001, China; School of Environmental Science and Engineering, Liaoning Technical University, Fuxin 123000, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States
| | - Liyou Wu
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States
| | - Kai Xue
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States
| | - Shengjing Shi
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, United States
| | - Yolima Carrillo
- Hawkesbury Institute for the Environment, University of Western Sydney, Sydney 2751, Australia; University of Wyoming, Laramie, WY 82071, United States
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States
| | - Sarah E Hobbie
- The University of Minnesota, St. Paul, MN 55108, United States
| | - Peter B Reich
- Hawkesbury Institute for the Environment, University of Western Sydney, Sydney 2751, Australia; The University of Minnesota, St. Paul, MN 55108, United States
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Angela D Kent
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Elise Pendall
- Hawkesbury Institute for the Environment, University of Western Sydney, Sydney 2751, Australia; University of Wyoming, Laramie, WY 82071, United States
| | - Matthew Wallenstein
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO 80523, United States
| | - Yiqi Luo
- Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States.
| | - Jizhong Zhou
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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Zhu R, Liu J, Wang J, Han W, Shen Z, Muraina TO, Chen J, Sun D. Comparison of soil microbial community between reseeding grassland and natural grassland in Songnen Meadow. Sci Rep 2020; 10:16884. [PMID: 33037306 PMCID: PMC7547709 DOI: 10.1038/s41598-020-74023-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/18/2020] [Indexed: 11/23/2022] Open
Abstract
Microorganisms have important ecological functions in ecosystems. Reseeding is considered as one of the main strategies for preventing grassland degradation in China. However, the response of soil microbial community and diversity to reseeding grassland (RG) and natural grassland (NG) remains unclear, especially in the Songnen Meadow. In this study, the soil microbial community compositions of two vegetation restoration types (RG vs NG) were analyzed using a high-throughput sequencing technique. A total of 23,142 microbial OTUs were detected, phylogenetically derived from 11 known bacterial phyla. Soil advantage categories included Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes, which together accounted for > 78% of the all phyla in vegetation restoration. The soil microbial diversity was higher in RG than in NG. Two types of vegetation restoration had significantly different characteristics of soil microbial community (P < 0.001). Based on a molecular ecological network analysis, we found that the network in RG had a longer average path distance and modularity than in NG network, making it more resilient to environment changes. Meanwhile, the results of the canonical correspondence analysis and molecular ecological network analysis showed that soil pH (6.34 ± 0.35 in RG and 7.26 ± 0.28 in NG) was the main factor affecting soil microbial community structure, followed by soil moisture (SM) in the Songnen meadow, China. Besides, soil microbial community characteristics can vary significantly in different vegetation restoration. Thus, we suggested that it was necessary and reasonable for this area to popularize reseeding grassland in the future.
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Affiliation(s)
- Ruifen Zhu
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China
| | - Jielin Liu
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China
| | - Jianli Wang
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China
| | - Weibo Han
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China
| | - Zhongbao Shen
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China
| | - Taofeek O Muraina
- National Hulunber Grassland Ecosystem Observation and Research Station, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 10008, China
- Department of Animal Health and Production, Oyo State College of Agriculture and Technology, P.M.B. 10, Igbo-Ora, Oyo State, Nigeria
| | - Jishan Chen
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China.
| | - Dequan Sun
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China.
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30
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Wang J, Huang M, Wang Q, Sun Y, Zhao Y, Huang Y. LDPE microplastics significantly alter the temporal turnover of soil microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 726:138682. [PMID: 32481223 DOI: 10.1016/j.scitotenv.2020.138682] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/08/2020] [Accepted: 04/11/2020] [Indexed: 06/11/2023]
Abstract
Although the ubiquitous presence of microplastics in various environments is increasingly well studied, knowledge of the effects of microplastics on ambient microbial communities is still insufficient. To estimate the response of soil bacterial community succession and temporal turnover to microplastic amendment, a soil microcosm experiment was carried out with polyethylene microplastics. The soil samples under control and microplastic amendment conditions were collected for sequencing analysis using Illumina MiSeq technology. Microplastic amendment was found to significantly alter soil bacterial community structure, and the community differences were increased linearly with the incubation time. Compared with the turnover rate of bacterial community in the control samples (0.0103, p < .05, based on Bray-Curtis similarity), the succession rate was significantly (p < .001) higher in the soil with microplastic amendment (0.0309, p < .001). In addition, the effects of microplastic amendment on the time-decay relationships (TDRs) on taxonomic divisions revealed considerable variations of TDRs values, indicating the effects were lineage dependent. Our results propose that the presence of microbial in soil ecosystem may lead to a faster succession rate of soil bacterial community, which provides new insights into the evolutionary consequences of microplastics in terrestrial environment.
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Affiliation(s)
- Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
| | - Muke Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Qian Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Yuanze Sun
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Yanran Zhao
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Yi Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
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31
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Liu W, Graham EB, Zhong L, Zhang J, Li S, Lin X, Feng Y. Long-Term Stochasticity Combines With Short-Term Variability in Assembly Processes to Underlie Rice Paddy Sustainability. Front Microbiol 2020; 11:873. [PMID: 32499764 PMCID: PMC7243440 DOI: 10.3389/fmicb.2020.00873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 04/14/2020] [Indexed: 12/04/2022] Open
Abstract
Revealing temporal patterns of community assembly processes is important for understanding how microorganisms underlie the sustainability of agroecosystem. The ancient terraced rice paddies at Longji provide an ideal platform to study temporal dynamics of agroecosystem sustainability due to their chronosequential records of soil physicochemistry and well-archived microbial information along 630-year rice cultivation. We used statistical null models to evaluate microbial assembly processes along the soil chronosequences of Longji rice paddies through time. Stochastic and deterministic assembly processes jointly governed microbial community composition within successional eras (less than 250 years), and within-era determinism was mainly driven by soil fertility and redox conditions alone or in combination. Conversely, across successional eras (i.e., over 300 years), stochasticity linearly increased with increasing duration between eras and was eventually predominant for the whole 630 years. We suggest that the impact of stochasticity vs. determinism on assembly is timescale-dependent, and we propose that the importance of stochastic assembly of microbial community at longer timescales is due to the gradual changes in soil properties under long-term rice cultivation, which in turn contribute to the sustainability of paddy ecosystem by maintaining a diverse community of microorganisms with multi-functional traits. In total, our results indicate that knowledge on the timescales at which assembly processes govern microbial community composition is key to understanding the ecological mechanisms generating agroecosystem sustainability.
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Affiliation(s)
- Wenjing Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- The College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Emily B. Graham
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Linghao Zhong
- Department of Chemistry, Pennsylvania State University, Mont Alto, PA, United States
| | - Jianwei Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Shijie Li
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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32
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Zhang CJ, Pan J, Duan CH, Wang YM, Liu Y, Sun J, Zhou HC, Song X, Li M. Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes. mSystems 2019; 4:e00442-19. [PMID: 31506265 PMCID: PMC6739103 DOI: 10.1128/msystems.00442-19] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 08/14/2019] [Indexed: 11/21/2022] Open
Abstract
Mangroves, as a blue carbon reservoir, provide an environment for a variety of microorganisms. Mangroves lie in special locations connecting coastal and estuarine areas and experience fluctuating conditions, which are expected to intensify with climate change, creating a need to better understand the relative roles of stochastic and deterministic processes in shaping microbial community assembly. Here, a study of microbial communities inhabiting mangrove sediments across southeastern China, spanning mangroves in six nature reserves, was conducted. We performed high-throughput DNA sequencing of these samples and compared them with data of 1,370 sediment samples collected from the Earth Microbiome Project (EMP) to compare the microbial diversity of mangroves with that of other biomes. Our results showed that prokaryotic alpha diversity in mangroves was significantly higher than that in other biomes and that microbial beta diversity generally clustered according to biome types. The core operational taxonomic units (OTUs) in mangroves were mostly assigned to Gammaproteobacteria, Deltaproteobacteria, Chloroflexi, and Euryarchaeota The majority of beta nearest-taxon index values were higher than 2, indicating that community assembly in mangroves was better explained through a deterministic process than through a stochastic process. Mean annual precipitation (MAP) and total organic carbon (TOC) were main deterministic factors explaining variation in the microbial community. This study fills a gap in addressing the unique microbial diversity of mangrove ecosystems and their microbial community assembly mechanisms.IMPORTANCE Understanding the underlying mechanisms of microbial community assembly patterns is a vital issue in microbial ecology. Mangroves, as an important and special ecosystem, provide a unique environment for examining the relative importance of stochastic and deterministic processes. We made the first global-scale comparison and found that microbial diversity was significantly different in mangrove sediments compared to that of other biomes. Furthermore, our results suggest that a deterministic process is more important in shaping microbial community assembly in mangroves.
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Affiliation(s)
- Cui-Jing Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Chang-Hai Duan
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yong-Ming Wang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Jian Sun
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Hai-Chao Zhou
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Xin Song
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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33
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Guo X, Zhou X, Hale L, Yuan M, Ning D, Feng J, Shi Z, Li Z, Feng B, Gao Q, Wu L, Shi W, Zhou A, Fu Y, Wu L, He Z, Van Nostrand JD, Qiu G, Liu X, Luo Y, Tiedje JM, Yang Y, Zhou J. Climate warming accelerates temporal scaling of grassland soil microbial biodiversity. Nat Ecol Evol 2019; 3:612-619. [PMID: 30911147 DOI: 10.1038/s41559-019-0848-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 02/05/2019] [Indexed: 12/24/2022]
Abstract
Determining the temporal scaling of biodiversity, typically described as species-time relationships (STRs), in the face of global climate change is a central issue in ecology because it is fundamental to biodiversity preservation and ecosystem management. However, whether and how climate change affects microbial STRs remains unclear, mainly due to the scarcity of long-term experimental data. Here, we examine the STRs and phylogenetic-time relationships (PTRs) of soil bacteria and fungi in a long-term multifactorial global change experiment with warming (+3 °C), half precipitation (-50%), double precipitation (+100%) and clipping (annual plant biomass removal). Soil bacteria and fungi all exhibited strong STRs and PTRs across the 12 experimental conditions. Strikingly, warming accelerated the bacterial and fungal STR and PTR exponents (that is, the w values), yielding significantly (P < 0.001) higher temporal scaling rates. While the STRs and PTRs were significantly shifted by altered precipitation, clipping and their combinations, warming played the predominant role. In addition, comparison with the previous literature revealed that soil bacteria and fungi had considerably higher overall temporal scaling rates (w = 0.39-0.64) than those of plants and animals (w = 0.21-0.38). Our results on warming-enhanced temporal scaling of microbial biodiversity suggest that the strategies of soil biodiversity preservation and ecosystem management may need to be adjusted in a warmer world.
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Affiliation(s)
- Xue Guo
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Xishu Zhou
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Lauren Hale
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Water Management Research Unit, SJVASC, USDA-ARS, Parlier, CA, USA
| | - Mengting Yuan
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Daliang Ning
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Jiajie Feng
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Zhou Shi
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Zhenxin Li
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Bin Feng
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Qun Gao
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Linwei Wu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Weiling Shi
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Aifen Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Ying Fu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Liyou Wu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Zhili He
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Guanzhou Qiu
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Xueduan Liu
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yiqi Luo
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.,Department of Earth System Science, Tsinghua University, Beijing, China
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA. .,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA. .,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China. .,School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA. .,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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34
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Yu Y, Wu M, Petropoulos E, Zhang J, Nie J, Liao Y, Li Z, Lin X, Feng Y. Responses of paddy soil bacterial community assembly to different long-term fertilizations in southeast China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 656:625-633. [PMID: 30529966 DOI: 10.1016/j.scitotenv.2018.11.359] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/23/2018] [Accepted: 11/24/2018] [Indexed: 06/09/2023]
Abstract
Recent works have shown that long-term fertilization has a critical influence on soil microbial communities; however, the underlying ecological assemblage of microbial community as well as its linkage with soil fertility and crop yield are still poorly understood. In this study, using analysis of high-throughput sequencing of 16S rRNA gene amplicons, we investigate mean pairwise phylogenetic distance (MPD), nearest relative index (NRI), taxonomic compositions and network topological properties to evaluate the assembly of the soil microbial community developed in 30-year fertilized soils. The phylogenetic signal indicates that environmental filtering was a more important assembly process that structure the microbial community than the stochastic process. Increase of soil fertility indexes, such as cation exchange capacity (CEC), soil organic matter (SOM) and available P (AP), driven by balanced fertilizations and straw returning amendment, result in the decrease of environmental filtering on the bacterial community assembly. Network parameters show that the amendment of straw returning provides with more niches, which lead to more complex phylotype co-occurrence. Increase of crop yield under balanced fertilizations might due to the increase of soil microbial function traits, which is associated with decreasing influence of environmental filtering. The significantly increased bacterial genera, Candidatus Koribacter, Candidatus Solibacter, and Fimbriimonas, in straw returning treatments, might be the key species in the competition caused by long-term environmental filtering. These results are helpful for a unified understanding of the ecological processes for microbial communities in different fertilized agroecosystem and the development of sustainable agriculture.
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Affiliation(s)
- Yongjie Yu
- College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, PR China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Meng Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Evangelos Petropoulos
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jianwei Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Jun Nie
- Soil and Fertilizer Institute of Hunan Province, Changsha 410125, PR China; Key Field Monitoring Experimental Station for Reddish Paddy Soil Eco-Environment in Wangcheng, Ministry of Agriculture of China, Changsha 410125, PR China
| | - Yulin Liao
- Soil and Fertilizer Institute of Hunan Province, Changsha 410125, PR China; Key Field Monitoring Experimental Station for Reddish Paddy Soil Eco-Environment in Wangcheng, Ministry of Agriculture of China, Changsha 410125, PR China
| | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China.
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China.
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35
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Wang XB, Yao J, Zhang HY, Wang XG, Li KH, Lü XT, Wang ZW, Zhou JZ, Han XG. Environmental and spatial variables determine the taxonomic but not functional structure patterns of microbial communities in alpine grasslands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:960-968. [PMID: 30453265 DOI: 10.1016/j.scitotenv.2018.11.138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/07/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
There is considerable debate regarding how the taxonomic diversity of microbial communities relates to the functional diversity across space while similar questions have been explored in macro-organism communities. Here, we investigated the taxonomic and functional diversity patterns of soil microbial communities by coupling the data obtained from marker genes sequencing and functional gene surveys. Meanwhile, we evaluated the relative effects of environment and geographic distance on shaping these patterns in alpine grasslands of northern China. Although the taxonomic diversity and composition of microbial communities varied across sites, we found no consistent changes in the functional structure. Both the environmental factors and geographic distance concurrently affected the taxonomic diversity patterns but they had no effects on the spatial variations in functional genes. The functional alpha diversity was weakly correlated to the taxonomic alpha diversity across sites. Moreover, we found no significant relationship between the taxonomic and functional composition similarity among microbial communities. Together, our results provide evidence that spatial variation in microbial functions could be independent of their variations in taxonomic diversity. Even the drivers of spatial variations in the functional structure could be totally different from those of taxonomic variations such as environmental differences and dispersal limitation. Our findings suggest that spatial variations of microbial function structure within a community would not follow the variations of taxonomic structures due to different drivers between both of them over space.
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Affiliation(s)
- Xiao-Bo Wang
- Erguna Forest-Steppe Ecotone Research Station, Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, China; Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA.
| | - Jing Yao
- Erguna Forest-Steppe Ecotone Research Station, Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Hai-Yang Zhang
- Erguna Forest-Steppe Ecotone Research Station, Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Xiao-Guang Wang
- College of Environment and Resources, Dalian Minzu University, Dalian 116600, China
| | - Kai-Hui Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China.
| | - Xiao-Tao Lü
- Erguna Forest-Steppe Ecotone Research Station, Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Zheng-Wen Wang
- Erguna Forest-Steppe Ecotone Research Station, Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Ji-Zhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA.
| | - Xing-Guo Han
- Erguna Forest-Steppe Ecotone Research Station, Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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36
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Zhang J, Tang H, Zhu J, Lin X, Feng Y. Effects of elevated ground-level ozone on paddy soil bacterial community and assembly mechanisms across four years. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:505-513. [PMID: 30447589 DOI: 10.1016/j.scitotenv.2018.11.130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
It is well known that elevated ground-level ozone (eO3) poses a threat to the ecosystem. Little knowledge about the underground variables, especially on soil microorganisms, however, has been revealed. Such knowledge will tremendously help to advance our understanding of the correlation between ecosystems and climate change, as well as our ability to predict future trajectory. For this purpose, we have collected soil DNA samples (eO3 vs. Ambient, each having 36 samples) over four years. Our results have verified the temporal responses and the underlying assembly mechanisms of the paddy bacterial community to eO3. Contrary to the widespread consensus, it was found that eO3 stimulated bacterial alpha diversities. The higher complexity and the centralization of the co-occurrence network of the bacterial community suggested that this stimulation was due to a microbial survival strategy in response to the limited resources, which led to the instability of the community. Furthermore, the observed slower temporal turnover of the bacterial community composition in response to eO3 was due to the decreased deterministic processes derived from plants, which implied that eO3 disrupted the coordination between soil microorganisms and rice crop. All above phenomena provided novel insights into the adverse influences of eO3 on the soil microbial community. If O3 concentration increases continuously, the adverse effects will be aggravated and harm the related ecological functions.
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Affiliation(s)
- Jianwei Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Haoye Tang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Jianguo Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China.
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37
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Raut S, Polley HW, Fay PA, Kang S. Bacterial community response to a preindustrial-to-future CO 2 gradient is limited and soil specific in Texas Prairie grassland. GLOBAL CHANGE BIOLOGY 2018; 24:5815-5827. [PMID: 30230661 DOI: 10.1111/gcb.14453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 09/07/2018] [Indexed: 06/08/2023]
Abstract
Rising atmospheric CO2 concentration directly stimulates plant productivity and affects nutrient dynamics in the soil. However, the influence of CO2 enrichment on soil bacterial communities remains elusive, likely due to their complex interactions with a wide range of plant and soil properties. Here, we investigated the bacterial community response to a decade long preindustrial-to-future CO2 gradient (250-500 ppm) among three contrasting soil types using 16S rRNA gene amplicon sequencing. In addition, we examined the effect of seasonal variation and plant species composition on bacterial communities. We found that Shannon index (H') and Faith's phylogenetic diversity (PD) did not change in response to the CO2 gradient (R2 = 0.01, p > 0.05). CO2 gradient and season also had a negligible effect on overall community structure, although silty clay soil communities were better structured on a CO2 gradient (p < 0.001) among three soils. Similarly, CO2 gradient had no significant effect on the relative abundance of different phyla. However, we observed soil-specific variation of CO2 effects in a few individual families. For example, the abundance of Pirellulaceae family decreased linearly with CO2 gradient, but only in sandy loam soils. Conversely, the abundance of Micromonosporaceae and Gaillaceae families increased with CO2 gradient in clay soils. Soil water content (SWC) and nutrient properties were the key environmental constraints shaping bacterial community structure, one manifestation of which was a decline in bacterial diversity with increasing SWC. Furthermore, the impact of plant species composition on community structure was secondary to the strong influence of soil properties. Taken together, our findings indicate that bacterial communities may be largely unresponsive to indirect effects of CO2 enrichment through plants. Instead, bacterial communities are strongly regulated by edaphic conditions, presumably because soil differences create distinct environmental niches for bacteria.
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Affiliation(s)
- Swastika Raut
- Department of Biology, Baylor University, Waco, Texas
| | - Herbert W Polley
- Grassland, Soil and Water Research Laboratory, Department of Agriculture, Agricultural Research Service, Temple, Texas
| | - Philip A Fay
- Grassland, Soil and Water Research Laboratory, Department of Agriculture, Agricultural Research Service, Temple, Texas
| | - Sanghoon Kang
- Department of Biology, Baylor University, Waco, Texas
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Feng Y, Chen R, Stegen JC, Guo Z, Zhang J, Li Z, Lin X. Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions. Mol Ecol 2018; 27:5238-5251. [DOI: 10.1111/mec.14914] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 10/03/2018] [Accepted: 10/09/2018] [Indexed: 01/26/2023]
Affiliation(s)
- Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - Ruirui Chen
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - James C. Stegen
- Earth and Biological Sciences Directorate Ecosystem Sciences Team Pacific Northwest National Laboratory Richland Washington
| | - Zhiying Guo
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - Jianwei Zhang
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing China
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Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes. mSystems 2018; 3:mSystems00167-18. [PMID: 30374458 PMCID: PMC6199470 DOI: 10.1128/msystems.00167-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 09/14/2018] [Indexed: 01/27/2023] Open
Abstract
Soil bacteria are key to ecosystem function and maintenance of soil fertility. Leveraging associations of current geographic distributions of bacteria with historic climate, we predict that soil bacterial diversity will increase across the majority (∼75%) of the Tibetan Plateau and northern North America if bacterial communities equilibrate with existing climatic conditions. This prediction is possible because the current distributions of soil bacteria have stronger correlations with climate from ∼50 years ago than with current climate. This lag is likely associated with the time it takes for soil properties to adjust to changes in climate. The predicted changes are location specific and differ across bacterial taxa, including some bacteria that are predicted to have reductions in their distributions. These findings illuminate the widespread potential of climate change to influence belowground diversity and the importance of considering bacterial communities when assessing climate impacts on terrestrial ecosystems. IMPORTANCE There have been many studies highlighting how plant and animal communities lag behind climate change, causing extinction and diversity debts that will slowly be paid as communities equilibrate. By virtue of their short generation times and dispersal abilities, soil bacteria might be expected to respond to climate change quickly and to be effectively in equilibrium with current climatic conditions. We found strong evidence to the contrary in Tibet and North America. These findings could significantly improve understanding of climate impacts on soil microbial communities.
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40
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Deng Y, Ning D, Qin Y, Xue K, Wu L, He Z, Yin H, Liang Y, Buzzard V, Michaletz ST, Zhou J. Spatial scaling of forest soil microbial communities across a temperature gradient. Environ Microbiol 2018; 20:3504-3513. [PMID: 30051570 DOI: 10.1111/1462-2920.14303] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 04/03/2018] [Accepted: 05/31/2018] [Indexed: 11/29/2022]
Abstract
Temperature is an important correlate of global patterns of biodiversity, yet the mechanisms driving these relationships are not well understood. Taxa-area relationships (TARs) have been intensively examined, but the effects of temperature on TARs, particularly for microbial communities, are largely undocumented. Here we present a continental-scale description of temperature-dependent nested TARs of microbial communities (bacteria and archaea) from soils of six forest sites spanning a temperature gradient from subalpine Colorado to tropical Panama. Our results revealed that spatial scaling rates (z-values) of microbial communities varied with both taxonomic resolutions and phylogenetic groups. Additionally, microbial TAR z-values increased with temperature (r = 0.739, P < 0.05), but were not correlated with other environmental variables tested (P > 0.05), indicating that microbial spatial scaling rate is temperature-dependent. Understanding how temperature affects the spatial scaling of microbial biodiversity is of fundamental importance for preservation of soil biodiversity and management of ecosystems.
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Affiliation(s)
- Ye Deng
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China.,CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Daliang Ning
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Yujia Qin
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Kai Xue
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liyou Wu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Zhili He
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA.,School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Huaqun Yin
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA.,School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Yuting Liang
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Vanessa Buzzard
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Sean T Michaletz
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA.,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94270, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
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Zheng B, Zhu Y, Sardans J, Peñuelas J, Su J. QMEC: a tool for high-throughput quantitative assessment of microbial functional potential in C, N, P, and S biogeochemical cycling. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1451-1462. [DOI: 10.1007/s11427-018-9364-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 07/26/2018] [Indexed: 02/07/2023]
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42
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Yu H, He Z, Wang A, Xie J, Wu L, Van Nostrand JD, Jin D, Shao Z, Schadt CW, Zhou J, Deng Y. Divergent Responses of Forest Soil Microbial Communities under Elevated CO 2 in Different Depths of Upper Soil Layers. Appl Environ Microbiol 2018; 84:e01694-17. [PMID: 29079614 PMCID: PMC5734029 DOI: 10.1128/aem.01694-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/15/2017] [Indexed: 02/07/2023] Open
Abstract
Numerous studies have shown that the continuous increase of atmosphere CO2 concentrations may have profound effects on the forest ecosystem and its functions. However, little is known about the response of belowground soil microbial communities under elevated atmospheric CO2 (eCO2) at different soil depth profiles in forest ecosystems. Here, we examined soil microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) after a 10-year eCO2 exposure using a high-throughput functional gene microarray (GeoChip). The results showed that eCO2 significantly shifted the compositions, including phylogenetic and functional gene structures, of soil microbial communities at both soil depths. Key functional genes, including those involved in carbon degradation and fixation, methane metabolism, denitrification, ammonification, and nitrogen fixation, were stimulated under eCO2 at both soil depths, although the stimulation effect of eCO2 on these functional markers was greater at the soil depth of 0 to 5 cm than of 5 to 15 cm. Moreover, a canonical correspondence analysis suggested that NO3-N, total nitrogen (TN), total carbon (TC), and leaf litter were significantly correlated with the composition of the whole microbial community. This study revealed a positive feedback of eCO2 in forest soil microbial communities, which may provide new insight for a further understanding of forest ecosystem responses to global CO2 increases.IMPORTANCE The concentration of atmospheric carbon dioxide (CO2) has continuously been increasing since the industrial revolution. Understanding the response of soil microbial communities to elevated atmospheric CO2 (eCO2) is important for predicting the contribution of the forest ecosystem to global atmospheric change. This study analyzed the effect of eCO2 on microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) in a forest ecosystem. Our findings suggest that the compositional and functional structures of microbial communities shifted under eCO2 at both soil depths. More functional genes involved in carbon, nitrogen, and phosphorus cycling were stimulated under eCO2 at the soil depth of 0 to 5 cm than at the depth of 5 to 15 cm.
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Affiliation(s)
- Hao Yu
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
- College of Environmental Science and Engineering, Liaoning Technical University, Fuxin, China
| | - Zhili He
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, the University of Oklahoma, Norman, Oklahoma, USA
| | - Aijie Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Jianping Xie
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Changsha, China
| | - Liyou Wu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, the University of Oklahoma, Norman, Oklahoma, USA
| | - Joy D Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, the University of Oklahoma, Norman, Oklahoma, USA
| | - Decai Jin
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Zhimin Shao
- College of Environmental Science and Engineering, Liaoning Technical University, Fuxin, China
| | | | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, the University of Oklahoma, Norman, Oklahoma, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, the University of Oklahoma, Norman, Oklahoma, USA
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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43
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Feng Y, Guo Z, Zhong L, Zhao F, Zhang J, Lin X. Balanced Fertilization Decreases Environmental Filtering on Soil Bacterial Community Assemblage in North China. Front Microbiol 2017; 8:2376. [PMID: 29250052 PMCID: PMC5716987 DOI: 10.3389/fmicb.2017.02376] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/16/2017] [Indexed: 01/11/2023] Open
Abstract
Although increasing evidences have emerged for responses of soil microorganisms to fertilizations, the knowledge regarding community assemblages that cause variations in composition is still lacking, as well as the possible feedback to soil fertility. Phylogenetic conservatism of species indicates their similar environmental preferences and/or function traits and phylogenetic signals further can infer community assemblages and influenced ecological processes. Here, we calculated the mean pairwise phylogenetic distance and nearest relative index, characterizing phylogenetic signal and the undergone ecological process to evaluate the community assembly of soil bacterial phylotypes in 20-year fertilized soils. The bacterial community assembly is structured by environmental filtering, regardless of fertilization regime. Soil phosphorous (P) availability imposes selection on community assemblage and influences their community turnover among fertilizations. When P nutrient lacks, the effect of environmental filtering becomes stronger, hence bacterial functional traits become more coherent; this process results into increased intraspecific interactions characterized by co-occurrence network analysis. In contrast, when P nutrient becomes abundant, the environmental selection is mitigated; function traits are evened. This process reduces intraspecific interactions and increases carbon sequestration efficiency, which is finally of great favor to the increases in soil fertility. This study has made the first attempt, at the bacterial level, to understand how fertilization affects agroecosystems. When more phylogenetic information on how nutrient cycling-related microbes respond to fertilization becomes available, the systematic knowledge will eventually provide guidance to optimal fertilization strategies.
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Affiliation(s)
- Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Zhiying Guo
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Linghao Zhong
- Department of Chemistry, Pennsylvania State University at Mont Alto, Mont Alto, PA,United States
| | - Fei Zhao
- Nanjing Institute for Comprehensive Utilization of Wild Plants, Nanjing, China
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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Abstract
Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research.
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Affiliation(s)
- Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, Oklahoma, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Daliang Ning
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, Oklahoma, USA
- Consolidated Core Laboratory, University of Oklahoma, Norman, Oklahoma, USA
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45
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Zhou J, Ning D. Stochastic Community Assembly: Does It Matter in Microbial Ecology? Microbiol Mol Biol Rev 2017. [PMID: 29021219 DOI: 10.1128/mmbr] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research.
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Affiliation(s)
- Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, Oklahoma, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Daliang Ning
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, Oklahoma, USA
- Consolidated Core Laboratory, University of Oklahoma, Norman, Oklahoma, USA
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46
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A novel method to determine the minimum number of sequences required for reliable microbial community analysis. J Microbiol Methods 2017; 139:196-201. [PMID: 28602755 DOI: 10.1016/j.mimet.2017.06.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 06/06/2017] [Accepted: 06/06/2017] [Indexed: 12/31/2022]
Abstract
Although high-throughput sequencing is an efficient approach to study the structure of microbial communities in detail, it is still impossible to enumerate all individuals using this method. Therefore, it is a common strategy to generate sampling datasets that are representative of the assemblages. However, the representativeness of these sampling datasets has never been assessed. In this study, we developed a method to determine the minimum number sequences that are required to be analyzed to obtain a reliable description of microbial community structure. First, a set of datasets from microbial communities were constructed by in silico sampling at different depths. Second, the correlation equation between dissimilarity of the sampling datasets and sampling depths was fitted, and thereby the minimum number of 16S rRNA gene sequences was predicted. Finally, we verified the method using empirical data of microbiota from a laboratory mesocosm. Our method showed that at least 5,528,079 sequences were required to reliably characterize microbial communities inhabiting the mesocosms. However, if only dominant OTUs (>1%) were considered, thousands of sequences were enough. This promising method provides a criterion to ensure sequencing sufficiency when analyzing the structure of natural microbial communities.
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