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Su Q, Wu Y, Wang S, Li Y, Zhao J, Huang F, Wu J. The reverse function of lignin-degrading enzymes: The polymerization ability to promote the formation of humic substances in domesticated composting. Bioresour Technol 2023; 380:129059. [PMID: 37075849 DOI: 10.1016/j.biortech.2023.129059] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
This study aimed to confirm the ability of lignin peroxidase (LiP) and manganese peroxidase (MnP) in promoting the formation of humic substances (HS) during domesticated composting. Three raw materials with different lignin types were used for composting, including rice straw, tree branches, and pine needles. Results suggested that LiP and MnP activity increased during domesticated composting. But HS formation was only promoted by LiP. The effect of MnP was insignificant, which might be caused by the lack of enzyme cofactors like Mn2+. Meanwhile, bacteria highly associated with LiP and MnP production were identified as core bacteria. Function prediction of 16S-PICRUSt2 showed that the function of core bacteria was consistent with total bacterial functions which mainly promoted compost humification. Therefore, it speculated that LiP and MnP had the ability to promote HS formation during composting. Accordingly, it is a new understanding of the role of biological enzymes in composting.
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Affiliation(s)
- Qunyang Su
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - You Wu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Siyi Wang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yirui Li
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Jinghan Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Fuli Huang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Junqiu Wu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
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Luo ZH, Li Q, Chen N, Tang LY, Liao B, Yang TT, Huang LN. Genome-resolved metagenomics reveals depth-related patterns of microbial community structure and functions in a highly stratified, AMD overlaying mine tailings. J Hazard Mater 2023; 447:130774. [PMID: 36641850 DOI: 10.1016/j.jhazmat.2023.130774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Acid mine drainage (AMD) is a worldwide environmental problem, yet bioremediation is hampered by a limited knowledge of the reductive microbial processes in the AMD ecosystem. Here, we generate extensive metagenome and geochemical datasets to investigate how microbial populations and metabolic capacities driving major element cycles are structured in a highly stratified, AMD overlaying tailings environment. The results demonstrated an explicit depth-dependent differentiation of microbial community composition and function profiles between the surface and deeper tailings layers, paralleling the dramatic shifts in major physical and geochemical properties. Specifically, key genes involved in sulfur and iron oxidation were significantly enriched in the surface tailings, whereas those associated with reductive nitrogen, sulfur, and iron processes were enriched in the deeper layers. Genome-resolved metagenomics retrieved 406 intermediate or high-quality genomes spanning 26 phyla, including major new groups (e.g., Patescibacteria and DPANN). Metabolic models involving nitrogen, sulfur, iron, and carbon cycles were proposed based on the functional potentials of the abundant microbial genomes, emphasizing syntrophy and the importance of lesser-known taxa in the degradation of complex carbon compounds. These results have implications for in situ AMD bioremediation.
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Affiliation(s)
- Zhen-Hao Luo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qi Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Nan Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ling-Yun Tang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bin Liao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tao-Tao Yang
- Guangdong Heavy Metal Mine Ecological Restoration Engineering Technology Research Center, Shaoguan, China
| | - Li-Nan Huang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
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3
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Ding C, Xu X, Liu Y, Huang X, Xi M, Liu H, Deyett E, Dumont MG, Di H, Hernández M, Xu J, Li Y. Diversity and assembly of active bacteria and their potential function along soil aggregates in a paddy field. Sci Total Environ 2023; 866:161360. [PMID: 36610629 DOI: 10.1016/j.scitotenv.2022.161360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 12/23/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Numerous studies have found that soil microbiomes differ at the aggregate level indicating they provide spatially heterogeneous habitats for microbial communities to develop. However, an understanding of the assembly processes and the functional profile of microbes at the aggregate level remain largely rudimentary, particularly for those active members in soil aggregates. In this study, we investigated the diversity, co-occurrence network, assembly process and predictive functional profile of active bacteria in aggregates of different sizes using H218O-based DNA stable isotope probing (SIP) and 16S rRNA gene sequencing. Most of the bacterial reads were active with 91 % of total reads incorporating labelled water during the incubation. The active microbial community belonged mostly of Proteobacteria and Actinobacteria, with a relative abundance of 55.32 % and 28.12 %, respectively. Assembly processes of the active bacteria were more stochastic than total bacteria, while the assembly processes of total bacteria were more influenced by deterministic processes. Furthermore, many functional profiles such as environmental information processing increased in active bacteria (19.39 %) compared to total bacteria (11.22 %). After incubation, the diversity and relative abundance of active bacteria of certain phyla increased, such as Proteobacteria (50.70 % to 59.95 %), Gemmatimonadetes (2.63 % to 4.11 %), and Bacteroidetes (1.50 % to 2.84 %). In small macroaggregates (SMA: 0.25-2 mm), the active bacterial community and its assembly processes differed from that of other soil aggregates (MA: microaggregates, <0.25 mm; LMA: large macroaggregates, 2-4 mm). For functional profiles, the relative abundance of important functions, such as amino acid metabolism, signal transduction and cell motility, increased with incubation days and/or in SMA compared to other aggregates. This study provides robust evidence that the community of active bacteria and its assembly processes in soil aggregates differed from total bacteria, and suggests the importance of dominant active bacteria (such as Proteobacteria) for the predicted functional profiles in the soil ecosystem.
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Affiliation(s)
- Chenxiao Ding
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xinji Xu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yaowei Liu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xing Huang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - MengYuan Xi
- Department of Botany and Plant Sciences, University of California, Riverside 92521, USA
| | - Haiyang Liu
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China
| | - Elizabeth Deyett
- Department of Botany and Plant Sciences, University of California, Riverside 92521, USA
| | - Marc G Dumont
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Hongjie Di
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Marcela Hernández
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Jianming Xu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yong Li
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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Park T, Ma L, Gao S, Bu D, Yu Z. Heat stress impacts the multi-domain ruminal microbiota and some of the functional features independent of its effect on feed intake in lactating dairy cows. J Anim Sci Biotechnol 2022; 13:71. [PMID: 35701804 PMCID: PMC9199214 DOI: 10.1186/s40104-022-00717-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 04/10/2022] [Indexed: 11/23/2022] Open
Abstract
Background Heat stress (HS) affects the ruminal microbiota and decreases the lactation performance of dairy cows. Because HS decreases feed intake, the results of previous studies were confounded by the effect of HS on feed intake. This study examined the direct effect of HS on the ruminal microbiota using lactating Holstein cows that were pair-fed and housed in environmental chambers in a 2 × 2 crossover design. The cows were pair-fed the same amount of identical total mixed ration to eliminate the effect of feed or feed intake. The composition and structure of the microbiota of prokaryotes, fungi, and protozoa were analyzed using metataxonomics and compared between two thermal conditions: pair-fed thermoneutrality (PFTN, thermal humidity index: 65.5) and HS (87.2 for daytime and 81.8 for nighttime). Results The HS conditions altered the structure of the prokaryotic microbiota and the protozoal microbiota, but not the fungal microbiota. Heat stress significantly increased the relative abundance of Bacteroidetes (primarily Gram-negative bacteria) while decreasing that of Firmicutes (primarily Gram-positive bacteria) and the Firmicutes-to-Bacteroidetes ratio. Some genera were exclusively found in the heat-stressed cows and thermal control cows. Some co-occurrence and mutual exclusion between some genera were also found exclusively for each thermal condition. Heat stress did not significantly affect the overall functional features predicted using the 16S rRNA gene sequences and ITS1 sequences, but some enzyme-coding genes altered their relative abundance in response to HS. Conclusions Overall, HS affected the prokaryotes, fungi, and protozoa of the ruminal microbiota in lactating Holstein cows to a different extent, but the effect on the structure of ruminal microbiota and functional profiles was limited when not confounded by the effect on feed intake. However, some genera and co-occurrence were exclusively found in the rumen of heat-stressed cows. These effects should be attributed to the direct effect of heat stress on the host metabolism, physiology, and behavior. Some of the “heat-stress resistant” microbes may be useful as potential probiotics for cows under heat stress. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-022-00717-z.
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Affiliation(s)
- Tansol Park
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA.,Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, Republic of Korea
| | - Lu Ma
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Shengtao Gao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Dengpan Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China. .,CAAS-ICRAF Joint Lab on Agroforestry and Sustainable Animal Husbandry, Beijing, 100193, People's Republic of China.
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA.
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Zhang Y, Huo Y, Zhang Z, Zhu S, Fan W, Wang X, Huo M. Deciphering the influence of multiple anthropogenic inputs on taxonomic and functional profiles of the microbial communities in Yitong River, Northeast China. Environ Sci Pollut Res Int 2022; 29:39973-39984. [PMID: 35112248 DOI: 10.1007/s11356-021-18386-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
We conducted the analysis of physicochemical parameters, 16S rRNA amplicon sequencing and real-time quantitative polymerase chain reaction to explore the impact of human inputs on the bacterioplankton communities within a tributary of the largest river flowing through a megacity in northeast China. Agriculture largely accounted for the alteration of diversity and functions of the microbial communities. Furthermore, nitrate and total phosphorus declined at the reservoir outlet. The WWTP effluent discharge caused a decrease of the relative abundance of Actinobacteria and Cyanobacteria, while the impact on the variation of alpha diversity of river microbial community was slight. Carbon fixation and nitrogen cycle varied with the change of land use type. The rare taxa contributed with a predominant role in the response to environmental variables and NH3-N as well as NO3--N were the main environmental factors that drove the shift in the bacterial community. The occurrence of the human-specific fecal indicator was mostly derived from agriculture, and its increase in relative abundance was observed in the WWTP effluent. Thus, our study provides guidance for ecological assessment and management of rivers by revealing the response pattern of river bacterioplankton to multiple types of anthropogenic stressors.
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Affiliation(s)
- Ying Zhang
- School of Environment, Northeast Normal University, Changchun, 130117, China
| | - Yang Huo
- Science and Technology Innovation Center for Municipal Wastewater Treatment and Water Quality Protection, Northeast Normal University, Changchun, 130117, China.
- School of Physics, Northeast Normal University, Changchun, 130024, China.
| | - Zhiruo Zhang
- Key Laboratory of Songliao Aquatic Environment, Ministry of Education, Jilin Jianzhu University, Changchun, 130118, China
| | - Suiyi Zhu
- School of Environment, Northeast Normal University, Changchun, 130117, China
- Science and Technology Innovation Center for Municipal Wastewater Treatment and Water Quality Protection, Northeast Normal University, Changchun, 130117, China
| | - Wei Fan
- School of Environment, Northeast Normal University, Changchun, 130117, China
| | - Xianze Wang
- School of Environment, Northeast Normal University, Changchun, 130117, China
- Science and Technology Innovation Center for Municipal Wastewater Treatment and Water Quality Protection, Northeast Normal University, Changchun, 130117, China
| | - Mingxin Huo
- School of Environment, Northeast Normal University, Changchun, 130117, China.
- Science and Technology Innovation Center for Municipal Wastewater Treatment and Water Quality Protection, Northeast Normal University, Changchun, 130117, China.
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Shao K, Yao X, Wu Z, Jiang X, Hu Y, Tang X, Xu Q, Gao G. The bacterial community composition and its environmental drivers in the rivers around eutrophic Chaohu Lake, China. BMC Microbiol 2021; 21:179. [PMID: 34126927 PMCID: PMC8201733 DOI: 10.1186/s12866-021-02252-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 05/17/2021] [Indexed: 11/19/2022] Open
Abstract
Background Bacterial community play a key role in environmental and ecological processes in river ecosystems. Rivers are used as receiving body for treated and untreated urban wastewaters that brings high loads of sewage and excrement bacteria. However, little is known about the bacterial community structure and functional files in the rivers around the eutrophic Chaohu Lake, the fifth largest freshwater lake in China, has been subjected to severe eutrophication and cyanobacterial blooms over the past few decades. Therefore, understanding the taxonomic and functional compositions of bacterial communities in the river will contribute to understanding aquatic microbial ecology. The main aims were to (1) examine the structure of bacterial communities and functional profiles in this system; (2) find the environmental factors of bacterial community variations. Results We studied 88 sites at rivers in the Chaohu Lake basin, and determined bacterial communities using Illumina Miseq sequencing of the 16 S rRNA gene, and predicted functional profiles using PICRUSt2. A total of 3,390,497 bacterial 16 S rRNA gene sequences were obtained, representing 17 phyla, and 424 genera; The dominant phyla present in all samples were Bacteroidetes (1.4-82.50 %), followed by Proteobacteria (12.6–97.30 %), Actinobacteria (0.1–17.20 %). Flavobacterium was the most numerous genera, and accounted for 0.12–80.34 % of assigned 16 S reads, followed by Acinetobacter (0.33–49.28 %). Other dominant bacterial genera including Massilia (0.06–25.40 %), Psychrobacter (0-36.23 %), Chryseobacterium (0.01–22.86 %), Brevundimonas (0.01–12.82 %), Pseudomonas (0-59.73 %), Duganella (0.08–23.37 %), Unidentified Micrococcaceae (0-8.49 %). The functional profiles of the bacterial populations indicated an relation with many human diseases, including infectious diseases. Overall results, using the β diversity measures, coupled with heatmap and RDA showed that there were spatial variations in the bacterial community composition at river sites, and Chemical oxygen demand (CODMn) and (NH4+ )were the dominant environmental drivers affecting the bacterial community variance. Conclusions The high proportion of the opportunistic pathogens (Acinetobacter, Massilia, Brevundimonas) indicated that the discharge of sewage without adequate treatment into the rivers around Chaohu Lake. We propose that these bacteria could be more effective bioindicators for long-term sewage monitoring in eutrophic lakes. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02252-9.
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Affiliation(s)
- Keqiang Shao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Xin Yao
- School of Environment and Planning, Liaocheng University, 252000, Liaocheng, China
| | - Zhaoshi Wu
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Xingyu Jiang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Yang Hu
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Qiujin Xu
- Chinese Research Academy of Environmental Sciences, 100012, Beijing, China
| | - Guang Gao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 210008, Nanjing, China.
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Chen L, Zhang J, Dai H, Hu BX, Tong J, Gui D, Zhang X, Xia C. Comparison of the groundwater microbial community in a salt-freshwater mixing zone during the dry and wet seasons. J Environ Manage 2020; 271:110969. [PMID: 32583802 DOI: 10.1016/j.jenvman.2020.110969] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/22/2020] [Accepted: 06/14/2020] [Indexed: 06/11/2023]
Abstract
To gain a better understanding of the microbial community in salt-freshwater mixing zones, in this study, the influence of seasonal variation on the groundwater microbial community was evaluated by high throughput 16S rDNA gene sequencing. The results showed that notable changes in microbial community occurred in a salt-freshwater mixing zone and the groundwater samples in the dry season were more saline than those in the wet season. The increase in precipitation during the wet season relieved local seawater intrusion. Microbial diversity varied greatly with seasons, while no obvious change pattern was found. Proteobacteria was identified as the dominant phylum in all samples. The genus Hydrogenophaga dominated in the dry season, while the genus Acidovorax dominated in the wet season. Dissolved oxygen affected the diversity of the microbial communities during the dry and wet season, while groundwater level had a strong influence on the structure of microbial communities. Phylogenetic molecular network analysis of the microbial communities indicated that increased seawater intrusion led to a more compact microbial network and strengthening the groundwater microbial interactions.
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Affiliation(s)
- Lin Chen
- School of Water Resources and Environment, China University of Geosciences (Beijing), 100083, Beijing, China; Shenyang Geological Survey, China Geological Survey, 110034, Shenyang, China
| | - Jin Zhang
- Institute of Groundwater and Earth Science, Jinan University, 510632, Guangzhou, China; Green Development Institute of Zhaoqing, 526000, Zhaoqing, China; Guangdong-Hongkong-Macau Joint Laboratory of Collaborative Innovation for Environmental Quality, 510632, Guangzhou, China
| | - Heng Dai
- Institute of Groundwater and Earth Science, Jinan University, 510632, Guangzhou, China.
| | - Bill X Hu
- School of Water Resources and Environment, China University of Geosciences (Beijing), 100083, Beijing, China; Institute of Groundwater and Earth Science, Jinan University, 510632, Guangzhou, China.
| | - Juxiu Tong
- School of Water Resources and Environment, China University of Geosciences (Beijing), 100083, Beijing, China
| | - Dongwei Gui
- Cele National Station of Observation and Research for Desert-Grassland Ecosystem, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Xiaoying Zhang
- College of Construct Engineering, Jilin University, 130012, Changchun, China
| | - Chuanan Xia
- Institute of Groundwater and Earth Science, Jinan University, 510632, Guangzhou, China
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Park T, Ma L, Ma Y, Zhou X, Bu D, Yu Z. Dietary energy sources and levels shift the multi-kingdom microbiota and functions in the rumen of lactating dairy cows. J Anim Sci Biotechnol 2020; 11:66. [PMID: 32582444 PMCID: PMC7310258 DOI: 10.1186/s40104-020-00461-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/13/2020] [Indexed: 11/23/2022] Open
Abstract
Background Dietary energy source and level in lactation diets can profoundly affect milk yield and composition. Such dietary effects on lactation performance are underpinned by alteration of the rumen microbiota, of which bacteria, archaea, fungi, and protozoa may vary differently. However, few studies have examined all the four groups of rumen microbes. This study investigated the effect of both the level and source of dietary energy on rumen bacteria, archaea, fungi, and protozoa in the rumen of lactating dairy cows. A 2 × 2 factorial design resulted in four dietary treatments: low and high dietary energy levels (LE: 1.52–1.53; and HE: 1.71–1.72 Mcal/kg dry matter) and two dietary energy sources (GC: finely ground corn; and SFC: steam-flaked corn). We used a replicated 4 × 4 Latin square design using eight primiparous Chinese Holstein cows with each period lasting for 21 d. The rumen microbiota was analyzed using metataxonomics based on kingdom-specific phylogenetic markers [16S rRNA gene for bacteria and archaea, 18S rRNA gene for protozoa, and internally transcribed spacer 1 (ITS1) for fungi] followed with subsequent functional prediction using PICRUSt2. Results The GC resulted in a higher prokaryotic (bacterial and archaeal) species richness and Faith’s phylogenetic diversity than SFC. For the eukaryotic (fungi and protozoa) microbiota, the LE diets led to significantly higher values of the above measurements than the HE diets. Among the major classified taxa, 23 genera across all the kingdoms differed in relative abundance between the two dietary energy levels, while only six genera (none being protozoal) were differentially abundant between the two energy sources. Based on prokaryotic amplicon sequence variants (ASVs) from all the samples, overall functional profiles predicted using PICRUSt2 differed significantly between LE and HE but not between the two energy sources. FishTaco analysis identified Ruminococcus and Coprococcus as the taxa potentially contributing to the enriched KEGG pathways for biosynthesis of amino acids and to the metabolisms of pyruvate, glycerophospholipid, and nicotinate and nicotinamide in the rumen of HE-fed cows. The co-occurrence networks were also affected by the dietary treatments, especially the LE and GC diets, resulting in distinct co-occurrence networks. Several microbial genera appeared to be strongly correlated with one or more lactation traits. Conclusions Dietary energy level affected the overall rumen multi-kingdom microbiota while little difference was noted between ground corn and steam-flaked corn. Some genera were also affected differently by the four dietary treatments, including genera that had been shown to be correlated with lactation performance or feed efficiency. The co-occurrence patterns among the genera exclusively found for each dietary treatment may suggest possible metabolic interactions specifically affected by the dietary treatment. Some of the major taxa were positively correlated to milk properties and may potentially serve as biomarkers of one or more lactation traits.
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Affiliation(s)
- Tansol Park
- Department of Animal Sciences, The Ohio State University, Columbus, OH USA
| | - Lu Ma
- The State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Ying Ma
- The State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Xiaoqiao Zhou
- The State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Dengpan Bu
- The State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.,CAAS-ICRAF Joint Lab on Agroforestry and Sustainable Animal Husbandry, Beijing, P. R. China
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH USA
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Shobo CO, Alisoltani A, Abia ALK, Mtshali PS, Ismail A, Zishiri O, Horn JD, Brysiewicz P, Essack SY, Bester LA. Bacterial diversity and functional profile of microbial populations on surfaces in public hospital environments in South Africa: A high throughput metagenomic analysis. Sci Total Environ 2020; 719:137360. [PMID: 32114226 DOI: 10.1016/j.scitotenv.2020.137360] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
With the introduction of the One Health approach to global health advocated by the World Health Organization, the role of the environment as a reservoir and transmission route for diverse microorganisms is increasingly being recognised globally. This study investigated the diversity and functional profiles of bacterial communities using high-throughput metagenomics of the 16S rRNA gene in samples collected from environmental surfaces in different levels of healthcare in South Africa. A total of 150 samples were collected in three public hospitals [District (A), Regional (C) and Central (B)] from intensive care and paediatric wards. Military hospitals were excluded. Swabs were taken from mattresses, drip stands, ward telephones, patient files and sinks. A total of 7,996,346 reads were found, of which 7,319,569 were quality-filtered reads. Unique (and shared) microbial community structures were identified within the different hospital levels, locations and sample source. A total of 11 phyla, 29 classes, 50 orders, 105 families, 190 genera and 288 known species were identified. The primary phyla identified were Proteobacteria, Firmicutes and Actinobacteria. The dominant class identified was Gamma-proteobacteria, followed by Bacilli and Actinobacteria. Acinetobacter (16.08%), Citrobacter (13.64%), Staphylococcus (9.65%) and Corynebacterium (6.15%) were predominant genera. Although the functional profile analysis identified citrate cycle (TCA), signal transduction mechanisms, bisphenol degradation, tyrosine metabolism and transcription-factors as the dominant pathways, human disease functional classes, including involvement in antibiotic resistance, were significantly identified. The drip stands, patient files and ward telephones in all the wards of Hospitals A and C contained a higher number of human diseases functional classes. These findings highlight the potential of different hospital environments to serve as reservoirs and possible sources of bacterial pathogens; thus, the need for better monitoring and hygienic practices within the hospital environment.
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Affiliation(s)
- Christiana Omowunmi Shobo
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Medical Microbiology, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Arghavan Alisoltani
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Philip Senzo Mtshali
- Sequencing Core Facility, National Institute for Communicable Diseases, Division of National Health Laboratory Service, Sandringham, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, Division of National Health Laboratory Service, Sandringham, Johannesburg, South Africa
| | - Oliver Zishiri
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
| | - Juliana Deidre Horn
- South Africa Military Health Service, Area Military Health Care, KwaZulu-Natal, Durban, South Africa
| | - Petra Brysiewicz
- Discipline of Nursing, School of Nursing & Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Sabiha Yusuf Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Linda Antoinette Bester
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
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Liu K, Cai M, Hu C, Sun X, Cheng Q, Jia W, Yang T, Nie M, Zhao X. Selenium (Se) reduces Sclerotinia stem rot disease incidence of oilseed rape by increasing plant Se concentration and shifting soil microbial community and functional profiles. Environ Pollut 2019; 254:113051. [PMID: 31450117 DOI: 10.1016/j.envpol.2019.113051] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 07/27/2019] [Accepted: 08/11/2019] [Indexed: 05/21/2023]
Abstract
Sclerotinia stem rot (SSR), a soil-borne plant disease, cause the yield loss of oilseed rape. Selenium (Se), a beneficial element of plant, improves plant resistance to pathogens, and regulates microbial communities in soil. Soil microbial communities has been identified to play an important role in plant health. We studied whether the changes in soil microbiome under influence of Se associated with oilseed rape health. SSR disease incidence of oilseed rape and soil biochemical properties were investigated in Enshi district, "The World Capital of Selenium", and soil bacterial and fungal communities were analyzed by 16S rRNA and ITS sequencing, respectively. Results showed that Se had a strong effect on SSR incidence, and disease incidence inversely related with plant Se concentration. Besides, soil Se enhanced the microbiome diversities and the relative abundance of PGPR (plant growth promoting rhizobacteria), such as Bryobacter, Nitrospirae, Rhizobiales, Xanthobacteraceae, Nitrosomonadaceae and Basidiomycota. Furthermore, Soil Se decreased the relative abundance of pathogenic fungi, such as Olpidium, Armillaria, Coniosporium, Microbotryomycetes and Chytridiomycetes. Additionally, Se increased nitrogen metabolism, carbohydrate metabolism and cell processes related functional profiles in soil. The enrichment of Se in plants and improvement of soil microbial community were related to increased plant resistance to pathogen infection. These findings suggested that Se has potential to be developed as an ecological fungicide for biological control of SSR.
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Affiliation(s)
- Kang Liu
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Miaomiao Cai
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Chengxiao Hu
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuecheng Sun
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Qin Cheng
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Jia
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Tao Yang
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Min Nie
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaohu Zhao
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
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11
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Abstract
BACKGROUND Although a few comparison methods based on the biological meaning of gene lists have been developed, the goProfiles approach is one of the few that are being used for that purpose. It consists of projecting lists of genes into predefined levels of the Gene Ontology, in such a way that a multinomial model can be used for estimation and testing. Of particular interest is the fact that it may be used for proving equivalence (in the sense of "enough similarity") between two lists, instead of proving differences between them, which seems conceptually better suited to the end goal of establishing similarity among gene lists. An equivalence method has been derived that uses a distance-based approach and the confidence interval inclusion principle. Equivalence is declared if the upper limit of a one-sided confidence interval for the distance between two profiles is below a pre-established equivalence limit. RESULTS In this work, this method is extended to establish the equivalence of any number of gene lists. Additionally, an algorithm to obtain the smallest equivalence limit that would allow equivalence between two or more lists to be declared is presented. This algorithm is at the base of an iterative method of graphic visualization to represent the most to least equivalent gene lists. These methods deal adequately with the problem of adjusting for multiple testing. The applicability of these techniques is illustrated in two typical situations: (i) a collection of cancer-related gene lists, suggesting which of them are more reasonable to combine -as claimed by the authors- and (ii) a collection of pathogenesis-based transcript sets, showing which of these are more closely related. The methods developed are available in the goProfiles Bioconductor package. CONCLUSIONS The method provides a simple yet powerful and statistically well-grounded way to classify a set of genes or other feature lists by establishing their equivalence at a given equivalence threshold. The classification results can be viewed using standard visualization methods. This may be applied to a variety of problems, from deciding whether a series of datasets generating the lists can be combined to the simplification of groups of lists.
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Affiliation(s)
- Alex Sánchez-Pla
- Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Avinguda Diagonal, 648, Barcelona, 08028 Spain
| | - Miquel Salicrú
- Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Avinguda Diagonal, 648, Barcelona, 08028 Spain
| | - Jordi Ocaña
- Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Avinguda Diagonal, 648, Barcelona, 08028 Spain
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Almasri NA, Saleh M, Abu-Dahab S, Malkawi SH, Nordmark E. Functional profiles of children with cerebral palsy in Jordan based on the association between gross motor function and manual ability. BMC Pediatr 2018; 18:276. [PMID: 30131063 PMCID: PMC6103966 DOI: 10.1186/s12887-018-1257-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 08/17/2018] [Indexed: 11/18/2022] Open
Abstract
Background Cerebral palsy (CP) is the most common cause of physical disability in childhood. A major challenge for delivering effective services for children with CP is the heterogeneity of the medical condition. Categorizing children into homogeneous groups based on functional profiles is expected to improve service planning. The aims of this study were to (1) to describe functional profiles of children with CP based on the Gross Motor Function Classification System-Expanded & Revised (GMFCS-E & R) and the Manual Ability Classification System (MACS); and (2) to examine associations and agreements between the GMFCS-E & R and the MACS for all participants then for subgroups based on subtypes of CP and chronological age of children. Methods A convenience sample of 124 children with CP (mean age 4.5, SD 2.9 years, 56% male) participated in the study. Children were classified into the GMFCS-E & R and the MACS levels by research assistants based on parents input. Research assistants determined the subtypes of CP. Results Thirty six percent of the participants were able to ambulate independently (GMFCS-E & R levels I-II) and 64% were able to handle objects independently (MACS levels I-II). The most common functional profile of children with CP in our study is the “manual abilities better than gross motor function”. An overall strong correlation was found between the GMFCS-E & R and the MACS (rs = .73, p < .001), the correlations vary significantly based on subtypes of CP and chronological age of children. A very strong correlation was found in children with spastic quadriplegia (rs = .81, p < .001), moderate with spastic diplegia (rs = .64, p < .001), and weak with spastic hemiplegia (rs = .37, p < .001). Conclusions The GMFCS- E & R and the MACS provide complementary but distinctive information related to mobility and manual abilities of children with CP. Subtypes of CP and chronological age differentiated functional profiles. Functional abilities of children with CP in Jordan have similar patterns to children with CP in other countries. Functional profiles can inform clinicians, researchers, and policy makers.
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Affiliation(s)
- Nihad A Almasri
- Department of Physiotherapy, School of Rehabilitation Sciences, The University of Jordan, Queen Rania Al Abdallah St, Amman, 11942, Jordan.
| | - Maysoun Saleh
- Department of Physiotherapy, School of Rehabilitation Sciences, The University of Jordan, Queen Rania Al Abdallah St, Amman, 11942, Jordan
| | - Sana Abu-Dahab
- Department of occupational therapy, School of Rehabilitation Sciences, The University of Jordan, Queen Rania Al Abdallah St, Amman, 11942, Jordan
| | - Somaya H Malkawi
- Department of occupational therapy, School of Rehabilitation Sciences, The University of Jordan, Queen Rania Al Abdallah St, Amman, 11942, Jordan
| | - Eva Nordmark
- Faculty of Medicine, Lund university, P.0. 157, SE-221 00, Lund, Sweden
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