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Bai M, Zhao W, Wang Y, Bi X, Su S, Qiu H, Gao Z. Towards low carbon demand and highly efficient nutrient removal: Establishing denitrifying phosphorus removal in anaerobic/anoxic/oxic + nitrification system. Bioresour Technol 2024; 395:130385. [PMID: 38281549 DOI: 10.1016/j.biortech.2024.130385] [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: 11/30/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 01/30/2024]
Abstract
A two-sludge anaerobic/anoxic/oxic + nitrification system with simultaneous nitrogen and phosphorus removal was studied for enhanced low-strength wastewater treatment. After 158 days of operation, excellent NH4+-N, chemical oxygen demand (COD) and PO43--P removal (99.0 %, 90.0 % and 92.0 %, respectively) were attained under a low carbon/nitrogen ratio of 5, resulting in effluent NH4+-N, COD and PO43--P concentrations of 0.3, 30.0 and 0.5 mg/L, respectively. The results demonstrate that the anaerobic/anoxic/oxic sequencing batch reactor (A2-SBR) and nitrification sequencing batch reactor (N-SBR) had favorable denitrifying phosphorus removal and nitrification performance, respectively. High-throughput sequencing results indicate that the phosphate-accumulating organisms Dechloromonas (1.1 %) and Tetrasphaera (1.2 %) were enriched in the A2-SBR, while the ammonia-oxidizing bacteria Nitrosomonas (7.8 %) and the nitrite-oxidizing bacteria Nitrospira (18.1 %) showed excellent accumulation in the N-SBR. Further analysis via functional prediction revealed that denitrification is the primary pathway of nitrogen metabolism throughout the system. Overall, the system achieved low carbon and high efficiency nutrient removal.
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Affiliation(s)
- Meng Bai
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao 266525, PR China
| | - Weihua Zhao
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao 266525, PR China.
| | - Yanyan Wang
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao 266525, PR China
| | - Xuejun Bi
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao 266525, PR China
| | - Shaoqing Su
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao 266525, PR China
| | - Haojie Qiu
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao 266525, PR China
| | - Zhongxiu Gao
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao 266525, PR China
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Li L, Wang H, Hu J, Fang Y, Zhou F, Yu J, Chi R, Xiao C. Comparison of microbial communities in unleached and leached ionic rare earth mines. Environ Sci Pollut Res Int 2024; 31:17511-17523. [PMID: 38342835 DOI: 10.1007/s11356-024-32221-4] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/23/2024] [Indexed: 02/13/2024]
Abstract
The leaching of ionic rare earth elements has caused serious environmental pollution and ecological damage. Microorganisms play a crucial role in soil ecosystems and are one of the most important components of these systems. However, there are fewer studies related to the changes that occur in microbial community structure and diversity before and after leaching in ionic rare earth mines. In this study, Illumina high-throughput sequencing was used to examine the diversity and composition of soil microorganisms on the summit, hillside, and foot valley surfaces of unleached and leached mines after in situ leaching. The results showed that microbial diversity and abundance in the surface soil of the unleached mine were higher than those in the leached mine, and leaching had a significant impact on the microbial community of mining soil. pH was the main factor affecting the microbial community. Proteobacteria, Actinobacteriota, and Chloroflexi were phyla that showed high abundance in the soil. Network analysis showed that microbial interactions can improve microbial adaptation and stability in harsh environments. PICRUSt2 predictions indicate functional changes and linkages in soil microbial communities.
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Affiliation(s)
- Lingyan Li
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Haitao Wang
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Jingang Hu
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Yun Fang
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Fang Zhou
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Junxia Yu
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Ruan Chi
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Chunqiao Xiao
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China.
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Gondard M, Lane M, Barratt J, Talundzic E, Qvarnstrom Y. Simultaneous targeted amplicon deep sequencing and library preparation for a time and cost-effective universal parasite diagnostic sequencing approach. Parasitol Res 2023; 122:3243-3256. [PMID: 37940706 PMCID: PMC10772880 DOI: 10.1007/s00436-023-07991-4] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/26/2023] [Indexed: 11/10/2023]
Abstract
We recently described a targeted amplicon deep sequencing (TADS) strategy that utilizes a nested PCR targeting the 18S rDNA gene of blood-borne parasites. The assay facilitates selective digestion of host DNA by targeting enzyme restriction sites present in vertebrates but absent in parasites. This enriching of parasite-derived amplicon drastically reduces the proportion of host-derived reads during sequencing and results in the sensitive detection of several clinically important blood parasites including Plasmodium spp., Babesia spp., kinetoplastids, and filarial nematodes. Despite these promising results, high costs and the laborious nature of metagenomics sequencing are prohibitive to the routine use of this assay in most laboratories. We describe and evaluate a new metagenomic approach that utilizes a set of primers modified from our original assay that incorporates Illumina barcodes and adapters during the PCR steps. This modification makes amplicons immediately compatible with sequencing on the Illumina MiSeq platform, removing the need for a separate library preparation, which is expensive and time-consuming. We compared this modified assay to our previous nested TADS assay in terms of preparation speed, limit of detection (LOD), and cost. Our modifications reduced assay turnaround times from 7 to 5 days. The cost decreased from approximately $40 per sample to $11 per sample. The modified assay displayed comparable performance in the detection and differentiation of human-infecting Plasmodium spp., Babesia spp., kinetoplastids, and filarial nematodes in clinical samples. The LOD of this modified approach was determined for malaria parasites and remained similar to that previously reported for our earlier assay (0.58 Plasmodium falciparum parasites/µL of blood). These modifications markedly reduced costs and turnaround times, making the assay more amenable to routine diagnostic applications.
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Affiliation(s)
- Mathilde Gondard
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Meredith Lane
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Synergy America Inc., Duluth, GA, USA
| | - Joel Barratt
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Eldin Talundzic
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Yvonne Qvarnstrom
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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Qiang W, Gunina A, Kuzyakov Y, Luo R, Zhang Y, Liu B, Pang X. Shifts of understory vegetation induced by thinning drive the expansion of soil rare fungi. J Environ Manage 2023; 342:118119. [PMID: 37207458 DOI: 10.1016/j.jenvman.2023.118119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/21/2023] [Accepted: 05/05/2023] [Indexed: 05/21/2023]
Abstract
The gap formation due to forest thinning regulates the understorey microclimate, ground vegetation, and soil biodiversity. However, little is known about abundant and rare taxa's various patterns and assemblage mechanisms under thinning gaps. Thinning gaps with increasing sizes (0, 74, 109, and 196 m2) were established 12 years ago in a 36-year-old spruce plantation in a temperate mountain climate. Soil fungal and bacterial communities were analyzed by MiSeq sequencing and related to soil physicochemical properties and aboveground vegetation. The functional microbial taxa were sorted by FAPROTAX and Fungi Functional Guild database. The bacterial community stabilized under varied thinning intensities and was not different from the control plots, whereas the richness of the rare fungal taxa was at least 1.5-fold higher in the large gaps than in the small ones. Total phosphorus and dissolved organic carbon were the main factors influencing microbial communities in soil under various thinning gaps. The diversity and richness of the entire fungal community and rare fungal taxa increased with the understorey vegetation coverage and shrub biomass after thinning. Gap formation by thinning stimulated the understorey vegetation, the rare saprotroph (Undefined Saprotroph), and mycorrhizal fungi (Ectomycorrhizal-Endophyte-Ericoid Mycorrhizal-Litter Saprotroph-Orchid Mycorrhizal and Bryophyte Parasite-Lichen Parasite-Ectomycorrhizal-Ericoid Mycorrhizal-Undefined Saprotroph), which may accelerate nutrient cycling in forest ecosystems. However, the abundance of Endophyte-Plant Pathogens increased by eight times, which showed the potential risk for the artificial spruce forests. Thus, fungi may be the driving force of forest restoration and nutrient cycling under the increasing intensity of thinning and may induce plant diseases. Therefore, vegetation coverage and microbial functional diversity should be considered to evaluate the sustainability of the artificial forest ecosystem and forest restoration.
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Affiliation(s)
- Wei Qiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Department of Environmental Chemistry, University of Kassel, Witzenhausen, Germany
| | - Anna Gunina
- Department of Environmental Chemistry, University of Kassel, Witzenhausen, Germany; Department of Soil Biology and Biochemistry, Dokuchaev Soil Science Institute, Russian Federation; Tyumen State University, 625003, Tyumen, Russia
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Goettingen, Göttingen, Germany; Peoples Friendship University of Russia (RUDN University), 117198, Moscow, Russia; Institute of Environmental Sciences, Kazan Federal University, 420049, Kazan, Russia
| | - Ruyi Luo
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China
| | - Yan Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China; Department of Environment and Geography, University of York, Heslington, York, North Yorkshire, UK
| | - Xueyong Pang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China.
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Abdeljalil S, Borgi I, Ben Hmad I, Frikha F, Verlaine O, Kerouaz B, Kchaou N, Ladjama A, Gargouri A. Large-scale analysis of the genome of the rare alkaline-halophilic Stachybotrys microspora reveals 46 cellulase genes. FEBS Open Bio 2023; 13:670-683. [PMID: 36748288 PMCID: PMC10068326 DOI: 10.1002/2211-5463.13573] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/08/2023] Open
Abstract
Fungi are of great importance in biotechnology, for example in the production of enzymes and metabolites. The main goal of this study was to obtain a high-coverage draft of the Stachybotrys microspora genome and to annotate and analyze the genome sequence data. The rare fungus S. microspora N1 strain is distinguished by its ability to grow in an alkaline halophilic environment and to efficiently secrete cellulolytic enzymes. Here we report the draft genome sequence composed of 3715 contigs, a genome size of 35 343 854 bp, with a GC content of 53.31% and a coverage around 20.5×. The identification of cellulolytic genes and of their corresponding functions was carried out through analysis and annotation of the whole genome sequence. Forty-six cellulases were identified using the fungicompanion bioinformatic tool. Interestingly, an S. microspora endoglucanase selected from those with a low isoelectric point was predicted to have a halophilic profile and share significant homology with a well-known bacterial halophilic cellulase. These results confirm previous biochemical studies revealing a halophilic character, which is a very rare feature among fungal cellulases. All these properties suggest that cellulases of S. microspora may have potential for use in the biofuel, textile, and detergent industries.
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Affiliation(s)
- Salma Abdeljalil
- Molecular Biotechnology of Eukaryotes Laboratory, Centre of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Ines Borgi
- Molecular Biotechnology of Eukaryotes Laboratory, Centre of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Ines Ben Hmad
- Molecular Biotechnology of Eukaryotes Laboratory, Centre of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Fakher Frikha
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Olivier Verlaine
- Bacterial Physiology and Genetic Institute, Centre for Protein Engineering, University of Liège, Belgium
| | - Bilal Kerouaz
- Laboratory of Applied Biochemistry and Microbiology, Department of Biochemistry, Faculty of Sciences, University Badji Mokhtar Annaba, Algeria
| | - Nesrine Kchaou
- Analytical Services Unit at the Center of Biotechnology of Sfax, Tunisia
| | - Ali Ladjama
- Laboratory of Applied Biochemistry and Microbiology, Department of Biochemistry, Faculty of Sciences, University Badji Mokhtar Annaba, Algeria
| | - Ali Gargouri
- Molecular Biotechnology of Eukaryotes Laboratory, Centre of Biotechnology of Sfax, University of Sfax, Tunisia
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Li B, Liu X, Zhu D, Su H, Guo K, Sun G, Li X, Sun L. Crop diversity promotes the recovery of fungal communities in saline-alkali areas of the Western Songnen Plain. Front Microbiol 2023; 14:1091117. [PMID: 36819047 PMCID: PMC9930164 DOI: 10.3389/fmicb.2023.1091117] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/05/2023] [Indexed: 02/04/2023] Open
Abstract
Introduction Phytoremediation is an effective strategy for saline land restoration. In the Western Songnen Plain, northeast China, soil fungal community recovery for saline phytoremediation has not been well documented among different cropping patterns. In this study, we tested how rotation, mixture, and monoculture cropping patterns impact fungal communities in saline-alkali soils to assess the variability between cropping patterns. Methods The fungal communities of the soils of the different cropping types were determined using Illumina Miseq sequencing. Results Mixture and rotation promoted an increase in operational taxonomic unit (OTU) richness, and OTU richness in the mixture system decreased with increasing soil depth. A principal coordinate analysis (PCoA) showed that cropping patterns and soil depths influenced the structure of fungal communities, which may be due to the impact of soil chemistry. This was reflected by soil total nitrogen (TN) and electrical conductivity (EC) being the key factors driving OTU richness, while soil available potassium (AK) and total phosphorus (TP) were significantly correlated with the relative abundance of fungal dominant genus. The relative abundance of Leptosphaerulina, Alternaria, Myrothecium, Gibberella, and Tetracladium varied significantly between cropping patterns, and Leptosphaerulina was significantly associated with soil chemistry. Soil depth caused significant differences in the relative abundance of Fusarium in rotation and mixture soils, with Fusarium more commonly active at 0-15 cm deep soil. Null-model analysis revealed that the fungal community assembly of the mixture soils in 0-15 cm deep soil was dominated by deterministic processes, unlike the other two cropping patterns. Furthermore, fungal symbiotic networks were more complex in rotation and mixture than in monoculture soils, reflected in more nodes, more module hubs, and connectors. The fungal networks in rotation and mixture soils were more stable than in monoculture soils, and mixture networks were obviously more connected than rotations. FUNGuild showed that the relative proportion of saprotroph in rotation and mixture was significantly higher than that in monocultures. The highest proportion of pathotroph and symbiotroph was exhibited in rotation and mixture soils, respectively. Discussion Overall, mixture is superior to crop rotation and monocultures in restoring fungal communities of the saline-alkali soils of the Western Songnen Plain, northeast China.
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Affiliation(s)
- Bin Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Xiaoqian Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Dan Zhu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Heng Su
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Kaiwen Guo
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Guangyu Sun
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Xin Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China,School of Forestry, Northeast Forestry University, Harbin, China,*Correspondence: Xin Li, ✉
| | - Lei Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, China,Lei Sun, ✉
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Liu K, Wang Q, Sun M, Gao S, Liu Q, Shan L, Guo J, Bian J. Soil bacterial communities of paddy are dependent on root compartment niches but independent of growth stages from Mollisols of Northeast China. Front Microbiol 2023; 14:1170611. [PMID: 37125155 PMCID: PMC10140518 DOI: 10.3389/fmicb.2023.1170611] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction Deep insights into adhering soil of root zones (rhizosphere and rhizoplane) microbial community could provide a better understanding of the plant-microbe relationship. To better understand the dynamics of these microbial assemblies over the plant life cycle in rhizodeposition along rice roots. Methods Here, we investigated bacterial distribution in bulk, rhizosphere, and rhizoplane soils at tillering, heading, and mature stage, from rice (Oryza sativa) fields of the Northeast China. Results and Discussion Our results revealed that soil bacterial α-diversity and community composition were significantly affected by root compartment niches but not by temporal change. Compared to rhizoplane soils in the same period, bulk in the heading and rhizosphere in the mature had the largest increase in Shannon's index, with 11.02 and 14.49% increases, respectively. Proteobacteria, Chloroflexi, Bacteroidetes, and Acidobacteria are predominant across all soil samples, bulk soil had more phyla increased across the growing season than that of root related-compartments. Deterministic mechanisms had a stronger impact on the bacterial community in the compartments connected to the roots, with the relative importance of the bulk soil, rhizoplane and rhizosphere at 83, 100, and 56%, respectively. Because of ecological niche drivers, the bacterial networks in bulk soils exhibit more complex networks than rhizosphere and rhizoplane soils, reflected by more nodes, edges, and connections. More module hub and connector were observed in bulk (6) and rhizoplane (5) networks than in rhizosphere (2). We also detected shifts from bulk to rhizoplane soils in some functional guilds of bacteria, which changed from sulfur and nitrogen utilization to more carbon and iron cycling processes. Taken together, our results suggest distinct bacterial network structure and distribution patterns among rhizosphere, rhizoplane, and bulk soils, which could possibly result in potential functional differentiation. And the potential functional differentiation may be influenced by plant root secretions, which still needs to be further explored.
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Affiliation(s)
- Kai Liu
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Qiuju Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
| | - Minglong Sun
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Shiwei Gao
- Suihua Branch of Heilongjiang Academy of Agricultural Sciences, Suihua, China
| | - Qing Liu
- Suihua Branch of Heilongjiang Academy of Agricultural Sciences, Suihua, China
| | - Lili Shan
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Junxiang Guo
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Jingyang Bian
- Daqing Branches of Heilongjiang Academy of Agricultural Sciences, Daqing, China
- *Correspondence: Jingyang Bian,
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Curry E, Prichard R, Lespine A. Genetic polymorphism, constitutive expression and tissue localization of Dirofilaria immitis P-glycoprotein 11: a putative marker of macrocyclic lactone resistance. Parasit Vectors 2022; 15:482. [PMID: 36544229 PMCID: PMC9773537 DOI: 10.1186/s13071-022-05571-6] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/02/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Dirofilaria immitis causes dirofilariosis, a potentially fatal condition in canids. Dirofilaria infections can be prevented with a macrocyclic lactone (ML) prophylactic regimen. However, some D. immitis isolates have become resistant to MLs. Genetic changes on the P-glycoprotein 11 gene, encoding an ABCB transporter, have been linked to the ML-resistant phenotypes and have been proposed as markers of drug resistance. However, nothing is known about the expression and the localization of this transporter in D. immitis, despite its strong link to ML-resistant phenotypes. METHODS We examined the clinically validated D. immitis P-glycoprotein 11 (DimPgp-11) single nucleotide polymorphism (SNP) via MiSeq analysis in three ML-susceptible isolates (Missouri, MP3 and Yazoo) and two ML-resistant isolates (JYD-34 and Metairie), and correlated the data with previously published MiSeq results of USA laboratory-maintained D. immitis isolates. The level of the expression of the DimPgp-11 messenger RNA transcript was analyzed by droplet digital PCR (ddPCR) and compared in the USA laboratory-maintained isolates, namely the ML-susceptible Missouri and Berkeley isolates, the putative ML-susceptible Georgia III and Big Head isolates and the ML-resistant isolate JYD-34. The immunolocalization of DimPgp-11 was visualized in the microfilaria (mf) life stage of the Missouri isolate using confocal microscopy. RESULTS The results confirmed that the SNP found on DimPgp-11 is differentially expressed in the USA laboratory-maintained isolates. The ML-susceptible isolates had an alternate allele frequency of between 0% and 15%, while it ranged between 17% and 56% in the ML-resistant isolates. The constitutive expression of DimPgp-11 was similar in the Berkeley, Georgia III and Big Head isolates, while it was significantly decreased in the ML-resistant JYD-34 isolate (P < 0.05), when compared to the ML-susceptible Missouri isolate. The DimPgp-11 protein was distinctly localized within the excretory-secretory (ES) duct, pore cells and the excretory cell and, more faintly, along the mf body wall. CONCLUSION Our data confirm that genetic polymorphism of DimPgp-11 is associated with ML resistance in USA laboratory-maintained D. imminits isolates. A link between DimPgp-11 and ML resistance in D. immitis is further supported by the lower protein expression in the ML-resistant JYD-34 isolate when compared with the ML-susceptible Missouri isolate. Interestingly, DimPgp-11 is strategically located surrounding the ES pore where it could play an active role in ML efflux.
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Affiliation(s)
- Emily Curry
- grid.14709.3b0000 0004 1936 8649Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, Montreal, QC Canada
| | - Roger Prichard
- grid.14709.3b0000 0004 1936 8649Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, Montreal, QC Canada
| | - Anne Lespine
- grid.508721.9INTHERES, INRAE, ENVT, Université de Toulouse, 31027 Toulouse Cedex 3, France
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He Q, Yan X, Fu Z, Zhang Y, Bi P, Mo X, Xu P, Ma J. Rapid start-up and stable operation of an aerobic/oxic/anoxic simultaneous nitrification, denitrification, and phosphorus removal reactor with no sludge discharge. Bioresour Technol 2022; 362:127777. [PMID: 35985464 DOI: 10.1016/j.biortech.2022.127777] [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: 07/02/2022] [Revised: 08/05/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
An anaerobic/aerobic/anoxic mode simultaneous nitrification, denitrification, and phosphorus removal system was visited for enhanced low-strength wastewater treatment and dramatic in situ sludge reduction. Results showed that rapid start-up was achieved with conventional activated sludge after 15 days, with effluent ammonia nitrogen, total nitrogen, total phosphorus, and chemical oxygen demand being 0.25, 7.89, 0.12, 24.37 mg/L, respectively. A two-stage biomass growth rate was observed with the sludge yield of 0.285 (day 1-50) and 0.017 g MLSS/g COD (day 51-110) without sludge discharge. Dynamics of bacterial community has been identified with outstanding accumulation of Candidatus_Competibacter up to 29.06 %, which contributed to both simultaneous nutrients removal and sludge reduction. Further analysis via PICRUSt2 revealed the main pathway of nitrogen metabolism, while proposed mechanism for phosphorus removal with no sludge discharge was analyzed from the intracellular and extracellular perspectives. Overall, this study provided guidance and reference for the development and application of A/O/A-SNDPR technology.
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Affiliation(s)
- Qiulai He
- Hunan Engineering Research Center of Water Security Technology and Application, Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, College of Civil Engineering, Hunan University, Changsha 410082, PR China.
| | - Xiaohui Yan
- Hunan Engineering Research Center of Water Security Technology and Application, Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, College of Civil Engineering, Hunan University, Changsha 410082, PR China
| | - Zhidong Fu
- Hunan Engineering Research Center of Water Security Technology and Application, Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, College of Civil Engineering, Hunan University, Changsha 410082, PR China
| | - Yihang Zhang
- Hunan Engineering Research Center of Water Security Technology and Application, Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, College of Civil Engineering, Hunan University, Changsha 410082, PR China
| | - Peng Bi
- Hunan Engineering Research Center of Water Security Technology and Application, Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, College of Civil Engineering, Hunan University, Changsha 410082, PR China
| | - Xingliang Mo
- Hunan Engineering Research Center of Water Security Technology and Application, Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, College of Civil Engineering, Hunan University, Changsha 410082, PR China
| | - Peng Xu
- Hunan Engineering Research Center of Water Security Technology and Application, Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, College of Civil Engineering, Hunan University, Changsha 410082, PR China
| | - Jingwei Ma
- Hunan Engineering Research Center of Water Security Technology and Application, Key Laboratory of Building Safety and Energy Efficiency, Ministry of Education, College of Civil Engineering, Hunan University, Changsha 410082, PR China
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10
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Sultan M, Wilson K, Abdulla OA, Busbee PB, Hall A, Carter T, Singh N, Chatterjee S, Nagarkatti P, Nagarkatti M. Endocannabinoid Anandamide Attenuates Acute Respiratory Distress Syndrome through Modulation of Microbiome in the Gut-Lung Axis. Cells 2021; 10:3305. [PMID: 34943813 PMCID: PMC8699344 DOI: 10.3390/cells10123305] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/08/2021] [Accepted: 11/17/2021] [Indexed: 02/07/2023] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a serious lung condition characterized by severe hypoxemia leading to limitations of oxygen needed for lung function. In this study, we investigated the effect of anandamide (AEA), an endogenous cannabinoid, on Staphylococcal enterotoxin B (SEB)-mediated ARDS in female mice. Single-cell RNA sequencing data showed that the lung epithelial cells from AEA-treated mice showed increased levels of antimicrobial peptides (AMPs) and tight junction proteins. MiSeq sequencing data on 16S RNA and LEfSe analysis demonstrated that SEB caused significant alterations in the microbiota, with increases in pathogenic bacteria in both the lungs and the gut, while treatment with AEA reversed this effect and induced beneficial bacteria. AEA treatment suppressed inflammation both in the lungs as well as gut-associated mesenteric lymph nodes (MLNs). AEA triggered several bacterial species that produced increased levels of short-chain fatty acids (SCFAs), including butyrate. Furthermore, administration of butyrate alone could attenuate SEB-mediated ARDS. Taken together, our data indicate that AEA treatment attenuates SEB-mediated ARDS by suppressing inflammation and preventing dysbiosis, both in the lungs and the gut, through the induction of AMPs, tight junction proteins, and SCFAs that stabilize the gut-lung microbial axis driving immune homeostasis.
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Affiliation(s)
- Muthanna Sultan
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina School of Medicine, Columbia, SC 29209, USA; (M.S.); (K.W.); (O.A.A.); (P.B.B.); (A.H.); (T.C.); (N.S.); (P.N.)
| | - Kiesha Wilson
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina School of Medicine, Columbia, SC 29209, USA; (M.S.); (K.W.); (O.A.A.); (P.B.B.); (A.H.); (T.C.); (N.S.); (P.N.)
| | - Osama A. Abdulla
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina School of Medicine, Columbia, SC 29209, USA; (M.S.); (K.W.); (O.A.A.); (P.B.B.); (A.H.); (T.C.); (N.S.); (P.N.)
| | - Philip Brandon Busbee
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina School of Medicine, Columbia, SC 29209, USA; (M.S.); (K.W.); (O.A.A.); (P.B.B.); (A.H.); (T.C.); (N.S.); (P.N.)
| | - Alina Hall
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina School of Medicine, Columbia, SC 29209, USA; (M.S.); (K.W.); (O.A.A.); (P.B.B.); (A.H.); (T.C.); (N.S.); (P.N.)
| | - Taylor Carter
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina School of Medicine, Columbia, SC 29209, USA; (M.S.); (K.W.); (O.A.A.); (P.B.B.); (A.H.); (T.C.); (N.S.); (P.N.)
| | - Narendra Singh
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina School of Medicine, Columbia, SC 29209, USA; (M.S.); (K.W.); (O.A.A.); (P.B.B.); (A.H.); (T.C.); (N.S.); (P.N.)
| | - Saurabh Chatterjee
- Environmental Health and Disease Laboratory, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA;
| | - Prakash Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina School of Medicine, Columbia, SC 29209, USA; (M.S.); (K.W.); (O.A.A.); (P.B.B.); (A.H.); (T.C.); (N.S.); (P.N.)
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina School of Medicine, Columbia, SC 29209, USA; (M.S.); (K.W.); (O.A.A.); (P.B.B.); (A.H.); (T.C.); (N.S.); (P.N.)
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11
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Wang H, Li X, Li X, Li F, Su Z, Zhang H. Community Composition and Co-Occurrence Patterns of Diazotrophs along a Soil Profile in Paddy Fields of Three Soil Types in China. Microb Ecol 2021; 82:961-970. [PMID: 33660069 DOI: 10.1007/s00248-021-01716-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 08/16/2020] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
Diazotrophs play a key role in biological nitrogen (N2) fixation. However, we know little about the distribution of the diazotrophic community along the soil profile in paddy fields. Here, we used Illumina MiSeq sequencing, targeting the nitrogenase reductase (nifH) gene, to investigate changes with depth (0-100 cm) in the diazotrophic community in paddy soils of three regions (Changshu, Hailun, and Yingtan) in China. The results indicated that most diazotrophs belonged to the phylum Proteobacteria, accounting for 78.05% of the total number of sequences. The diazotrophic diversity was generally highest in the 10-20 cm layer, and then significantly decreased with soil depth. Principal coordinate analysis and PERMANOVA indicated that the diazotrophic community structure was significantly affected by region and soil depth. There were obvious differences in the composition of the diazotrophic community between the topsoil (0-40 cm) and the subsoil (40-100 cm). Anaeromyxobacter, Sideroxydans, Methylomonas, Nostoc, Methanocella, and Methanosaeta were enriched in the topsoil, while Geobacter, Azoarcus, Bradyrhizobium, and Dechloromonas were concentrated in the subsoil. Furthermore, co-occurrence network analysis showed that the diazotrophic network in the topsoil was more complex than that in the subsoil. Distance-based redundancy analysis indicated that soil total C and N content and pH were the main factors influencing the vertical variation in the diazotrophic community. These results highlighted that depth has a great impact on the diazotrophic diversity, community composition, and co-occurrence patterns in paddy soil.
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Affiliation(s)
- Huanhuan Wang
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Xu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
| | - Xinyu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China.
| | - Fuli Li
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Zhencheng Su
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
| | - Huiwen Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
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12
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Ding J, Ma X, Han L, Zhao X, Li A, Xin Q, Lian W, Li Z, Ren H, Ren Z. Gut microbial alterations in neonatal jaundice pre- and post-treatment. Biosci Rep 2021; 41:BSR20210362. [PMID: 33860293 DOI: 10.1042/BSR20210362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 11/17/2022] Open
Abstract
Neonatal jaundice is a common disease that affects up to 60% of newborns. Herein, we performed a comparative analysis of the gut microbiome in neonatal jaundice and non-neonatal jaundice infants (NJIs) and identified gut microbial alterations in neonatal jaundice pre- and post-treatment. We prospectively collected 232 fecal samples from 51 infants at five time points (0, 1, 3, 6, and 12 months). Finally, 114 samples from 6 NJIs and 19 non-NJI completed MiSeq sequencing and analysis. We characterized the gut microbiome and identified microbial differences and gene functions. Meconium microbial diversity from NJI was decreased compared with that from non-NJI. The genus Gemella was decreased in NJI versus non-NJI. Eleven predicted microbial functions, including fructose 1,6-bisphosphatase III and pyruvate carboxylase subunit B, decreased, while three functions, including acetyl-CoA acyltransferase, increased in NJI. After treatments, the microbial community presented significant alteration-based β diversity. The phyla Firmicutes and Actinobacteria were increased, while Proteobacteria and Fusobacteria were decreased. Microbial alterations were also analyzed between 6 recovered NJI and 19 non-NJI. The gut microbiota was unique in the meconium microbiome from NJI, implying that early gut microbiome intervention could be promising for the management of neonatal jaundice. Alterations of gut microbiota from NJI can be of great value to bolster evidence-based prevention against 'bacterial dysbiosis'.
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13
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Chen H, Zheng C, Qiao Y, Du S, Li W, Zhang X, Zhao Z, Cao C, Zhang W. Long-term organic and inorganic fertilization alters the diazotrophic abundance, community structure, and co-occurrence patterns in a vertisol. Sci Total Environ 2021; 766:142441. [PMID: 33097271 DOI: 10.1016/j.scitotenv.2020.142441] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/10/2020] [Accepted: 09/12/2020] [Indexed: 06/11/2023]
Abstract
Diazotrophs play a critical role in converting air-inactive nitrogen to bio-available nitrogen. Assessing the influences of different fertilization regimes on diazotrophs is essential for a better understanding of their maintenance of soil fertility and agricultural sustainability. In this study, we targeted the nifH gene to investigate the effects of different long-term fertilization on the diazotrophic community in a vertisol, using real-time quantitative polymerase chain reaction (PCR) and MiSeq sequencing. Five fertilization regimes were tested: no fertilizer (CK), chemical nitrogen, phosphorus, and potassium fertilizer (NPK), organic fertilizer (O), chemical NPK plus organic fertilizer with an equivalent application rate of nitrogen (NPKO), and chemical NPK plus organic fertilizer with a high application rate of nitrogen (HNPKO). Our results showed that fertilization significantly affected the diazotrophic activity, abundance and composition. NPK tended to reduce the activity, abundance, operational taxonomic units (OTU)-richness and alpha-diversity of the diazotrophs, while O had the opposite effect. The effects of inorganic and organic fertilization on the diazotrophs depended on the N application rate, showing that the diazotrophic activity, abundance, and alpha-diversity in NPKO were higher than that of HNPKO. For the diazotrophic community structure, CK, O, and NPKO were grouped and separated from NPK and HNPKO. The diazotrophic community structure strongly correlated with the soil pH, electrical conductivity (EC), total carbon content (TC), and total nitrogen content (TN), among which pH was the major factor shaping the diazotrophic community structure. Different network patterns were observed between the long-term organic and non-organic fertilizers, suggesting that the organic amendment resulted in a more complicated diazotrophic community than the non-organic amendments. Rhizobium was the most important hub connecting members in the community. These results indicated that organic amendments are beneficial to diazotrophic activity, abundance, OTU richness, alpha-diversity, and the diazotrophic communities' potential interactions, which may enhance biological nitrogen fixation in vertisols.
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Affiliation(s)
- Huan Chen
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chengyan Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuqiang Qiao
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Shizhou Du
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Wei Li
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiangqian Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Zhu Zhao
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Chengfu Cao
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China.
| | - Weijian Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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14
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Liu L, Lu L, Li H, Meng Z, Dong T, Peng C, Xu X. Divergence of Phyllosphere Microbial Communities Between Females and Males of the Dioecious Populus cathayana. Mol Plant Microbe Interact 2021; 34:351-361. [PMID: 33290085 DOI: 10.1094/mpmi-07-20-0178-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, the differentiation of phyllosphere microbiota in dioecious plants remains largely unexplored. Here, the diversity and composition of female and male Populus cathayana phyllosphere bacterial and fungal communities were investigated using 16S rRNA/ITS1 gene-based MiSeq sequencing. The divergences of bacterial and fungal community compositions occurred between females and males. Both females and males had their unique phyllosphere bacterial and fungal microbiota, such as bacterial Gemmata spp. (5.41%) and fungal Pringsheimia spp. (0.03%) in females and bacterial Chitinophaga spp. (0.009%) and fungal Phaeococcomyces spp. (0.02%) in males. Significant differences in the relative abundance of phyla Proteobacteria and Planctomycetes bacteria and phyla Ascomycota and Basidiomycota fungi (P < 0.05) were also found between females and males. Some bacterial species of genera Spirosoma and Amnibacterium and fungal genera Venturia, Suillus, and Elmerina spp. were significantly enriched in males (P < 0.05). In contrast, levels of fungal genera Phoma and Aureobasidium spp. were significantly higher in females than in males (P < 0.05). The mineral, inorganic, and organic nutrients content contributed differently to the divergence of female and male phyllosphere microbial communities, with 87.08 and 45.17% of the variations being explained for bacterial and fungal communities, respectively. These results highlight the sexual discrimination of phyllosphere microbes on the dioecious plants and provide hints on the potential host-associated species in phyllosphere environments.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Liling Liu
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
- Institute of Ecology, China West Normal University, Nanchong 637009, China
| | - Lu Lu
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Huilin Li
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Zhensi Meng
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Tingfa Dong
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Chao Peng
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, China
| | - Xiao Xu
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
- Institute of Ecology, China West Normal University, Nanchong 637009, China
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15
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Liu J, Liu W, Zhang Y, Chen C, Wu W, Zhang TC. Microbial communities in rare earth mining soil after in-situ leaching mining. Sci Total Environ 2021; 755:142521. [PMID: 33035989 DOI: 10.1016/j.scitotenv.2020.142521] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 06/09/2020] [Revised: 09/19/2020] [Accepted: 09/20/2020] [Indexed: 06/11/2023]
Abstract
In-situ leaching technology is now widely used to exploit ion adsorption rare earth ore, which has caused serious environmental problems and deterioration of mining soil ecosystems. However, our knowledge about the influences of mining operation on the microbiota in these ecosystems is currently very limited. In this study, diversity and composition of prokaryote and ammonia-oxidizing microorganisms in rare earth mining soil after in-situ leaching practice were examined using quantitative Polymerase Chain Reaction (qPCR) and Illumina high-throughput sequencing. Results showed that in-situ leaching mining considerably impacted microbial communities of the mining soils. The abundances of bacterial, archaeal, and ammonia-oxidizing archaea (AOA) were significantly and negatively correlated with ionic rare earth elements (REEs), while their diversities were relatively stable. Total rare earth elements (TREEs) and ammonium were the strongest predictors of the bacterial community structure, and organic matter was the key factor predicting the variation in the archaeal community. Chloroflexi, Proteobacteria, Acidobacteria, and Actinobacteria were the most abundant bacterial phyla, and archaeal communities were dominated by Thaumarchaeota. Phylogenetic analysis indicated that unclassified Thaumarchaeota and Crenarchaeota were the predominant AOA groups. The non-detection of ammonia-oxidizing bacteria (AOB) and the abundance of AOA indicated that archaea rather than bacteria were predominantly responsible for ammonia oxidation in the mining soil. Network analysis demonstrated that positive interactions among microorganisms could increase their adaptability or resistance to this harsh environment. This study provides a comprehensive analysis of the prokaryotic communities and functional groups in rare earth mining soil after mining operation, as well as insight into the potential interactive mechanisms among soil microbes.
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Affiliation(s)
- Jingjing Liu
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, China.
| | - Wei Liu
- College of Chemistry and Environmental Science, Hebei University, Baoding, China
| | - Yingbin Zhang
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, China
| | - Chongjun Chen
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Weixiang Wu
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, China
| | - Tian C Zhang
- Department of Civil & Environmental Engineering, University of Nebraska-Lincoln, Omaha, USA
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16
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Zhu L, Zeng C, Yang S, Hou Z, Wang Y, Hu X, Senoo K, Wei W. Diversity and specificity of the bacterial community in Chinese horse milk cheese. Microbiologyopen 2020; 9:e1066. [PMID: 32741094 PMCID: PMC7424250 DOI: 10.1002/mbo3.1066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 03/23/2020] [Revised: 04/24/2020] [Accepted: 05/12/2020] [Indexed: 11/15/2022] Open
Abstract
The nutrition and flavor of cheese are generated by the microbial community. Thus, horse milk cheese with unique nutrition and flavor, an increasingly popular local cheese of the Xinjiang Uygur Autonomous Region of China, is considered to have diverse and specific bacterial community. To verify this hypothesis, horse, cow, and goat milk cheese samples produced under the same environmental conditions and manufacturing process were collected, and the 16S rRNA gene was targeted to determine the bacterial population size and community composition by real‐time quantitative PCR and high‐throughput sequencing. The bacterial community of horse milk cheese had a significantly larger bacterial population size, greater species richness, and a more diverse composition than those of cow and goat milk cheeses. Unlike the absolute dominance of Lactococcus and Streptococcus in cow and goat milk cheeses, Lactobacillus and Streptococcus dominated the bacterial community as the starter lactic acid bacteria in horse milk cheese. Additionally, horse milk cheese also contains a higher abundance of unclassified secondary bacteria and specific secondary bacteria (e.g., Psychrobacter, Sulfurisoma, Halomonas, and Brevibacterium) than cow and goat milk cheeses. These abundant, diverse, and specific starter lactic acid bacteria and secondary bacteria may generate unique nutrition and flavor of horse milk cheese.
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Affiliation(s)
- Lin Zhu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Chunlin Zeng
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Sai Yang
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, China
| | - Zhaozhi Hou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Yuan Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Xinyu Hu
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, China
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Wei Wei
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, China
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Chen F, Cheng G, Xu Y, Wang Y, Xia Q, Hu S. Rumen Microbiota Distribution Analyzed by High-Throughput Sequencing After Oral Doxycycline Administration in Beef Cattle. Front Vet Sci 2020; 7:251. [PMID: 32582771 PMCID: PMC7280444 DOI: 10.3389/fvets.2020.00251] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 10/16/2019] [Accepted: 04/16/2020] [Indexed: 12/12/2022] Open
Abstract
The beef cattle rumen is a heterogenous microbial ecosystem that is necessary for the host to digest food and support growth. The importance of the rumen microbiota (RM) is also widely recognized for its critical roles in metabolism and immunity. The level of health is indicated by a dynamic RM distribution. We performed high-throughput sequencing of the bacterial 16S rRNA gene to compare microbial populations between rumens in beef cattle with or without doxycycline treatment to assess dynamic microbiotic shifts following antibiotic administration. The results of the operational taxonomic unit analysis and alpha and beta diversity calculations showed that doxycycline-treated beef cattle had lower species richness and bacterial diversity than those without doxycycline. Bacteroidetes was the predominant phylum in rumen samples without doxycycline, while Proteobacteria was the governing phylum in the presence of doxycycline. On the family level, the top three predominant populations in group qlqlwy (not treated with doxycycline) were Prevotellaceae, Lachnospiraceae, and Ruminococcaceae, compared to Xanthomonadaceae, Prevotellaceae, and Rikenellaceae in group qlhlwy (treated with doxycycline). At the genus level, the top predominant population in group qlqlwy was unidentified_Prevotellaceae. However, in group qlhlwy, the top predominant population was Stenotrophomonas. The results revealed significant RM differences in beef cattle with or without doxycycline. Oral doxycycline may induce RM composition differences, and bacterial richness may also influence corresponding changes that could guide antibiotic use in adult ruminants. This study is the first to assess microbiota distribution in beef cattle rumen after doxycycline administration.
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Affiliation(s)
- Fengmei Chen
- Shandong Research Center for Technology of Reduction of Antibiotics Administered to Animal and Poultry, Shandong Vocational Animal Science and Veterinary College, Weifang, China
| | - Guangmin Cheng
- Shandong Research Center for Technology of Reduction of Antibiotics Administered to Animal and Poultry, Shandong Vocational Animal Science and Veterinary College, Weifang, China
| | - Yulin Xu
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, China.,College Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Yunzhou Wang
- Shandong Research Center for Technology of Reduction of Antibiotics Administered to Animal and Poultry, Shandong Vocational Animal Science and Veterinary College, Weifang, China
| | - Qingxiang Xia
- Shandong Research Center for Technology of Reduction of Antibiotics Administered to Animal and Poultry, Shandong Vocational Animal Science and Veterinary College, Weifang, China
| | - Shilin Hu
- Shandong Research Center for Technology of Reduction of Antibiotics Administered to Animal and Poultry, Shandong Vocational Animal Science and Veterinary College, Weifang, China
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18
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Fang J, Deng Y, Che R, Han C, Zhong W. Bacterial community composition in soils covered by different vegetation types in the Yancheng tidal marsh. Environ Sci Pollut Res Int 2020; 27:21517-21532. [PMID: 32279258 DOI: 10.1007/s11356-020-08629-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 09/29/2019] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Coastal wetland vegetation plays an important role in maintaining ecological function and is a key factor affecting the soil bacterial community. Spartina alterniflora was introduced to the Yancheng tidal marsh to stabilize the sediments and gradually replaced the native plants. However, the changes in the soil bacterial community profile caused by S. alterniflora invasion are poorly characterized. Here, we used MiSeq sequencing to compare the composition of the bacterial community in soil at different depths under exotic S. alterniflora (SA), native Phragmites australis (PA), and native Suaeda salsa (SS). The results showed that the pH value was lower, but the salinity, soil organic carbon, total nitrogen, and number of 16S rRNA genes were higher in SA soils than in PA and SS soils. Overall, Proteobacteria was the dominant bacterial phylum, followed by Chloroflexi, Acidobacteria, Planctomycetes, Gemmatimonadetes, and Nitrospirae. Anaerolineae in the Chloroflexi phylum showed the greatest difference based on vegetation, accounting for 14.4% of the overall bacterial community in SA soils but only about 3.8% of those in PA and SS soils. The composition, interaction, and predicted functional profiles of the bacterial community in SA soils were significantly different from those in PA and SS soils, especially for functions related to the sulfur and nitrogen cycles. Salinity was negatively correlated with the Shannon index and accounted for 37.7% of the total variation in the bacterial community, making it the most important environmental factor. Our results showed the differences in bacterial community composition among different vegetation types and soil depths in the Yancheng tidal marsh, which provides a microbial basis for a better understanding of the ecological functions in this ecosystem.
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Affiliation(s)
- Jie Fang
- School of Geography Science, Nanjing Normal University, Nanjing, China
| | - Yongcui Deng
- School of Geography Science, Nanjing Normal University, Nanjing, China.
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing, China.
| | - Rongxiao Che
- Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
| | - Cheng Han
- School of Geography Science, Nanjing Normal University, Nanjing, China
| | - Wenhui Zhong
- School of Geography Science, Nanjing Normal University, Nanjing, China
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing, China
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19
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Li X, Wang H, Li X, Li X, Zhang H. Distribution characteristics of fungal communities with depth in paddy fields of three soil types in China. J Microbiol 2020; 58:279-287. [PMID: 32103445 DOI: 10.1007/s12275-020-9409-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/17/2019] [Accepted: 01/13/2020] [Indexed: 11/29/2022]
Abstract
Little is known about the distribution of fungal communities with soil depth on relatively large scales. In this study, typical paddy soils in three regions (Hailun, Changshu, and Yingtan) from north to south China were selected to investigate the vertical distribution (0-100 cm) of the fungal community by Illumina MiSeq sequencing, and to identify the main factors influencing the fungal community distribution. The results indicated that the structure of the soil fungal community changed significantly with region and soil depth. Soil fungal taxa such as Zygomycota, Glomeromycota, Saccharomycete, Kazachstania, Mortierella, Massariosphaeria, Hypholoma, and Zopfiella were enriched at depths of 0-20 cm, whereas Dothideomycetes, Microbotryomycetes, Tremellomycetes, Sporobolomyces, Cryptococcus, Rhodotorula, Fusarium, and Pyrenochaetopsis had high relative abundances at 80-100 cm. Variance partitioning analysis indicated that the geographic distance contributed more to the fungal community variation than environmental variables on a large scale. In addition, soil total carbon and nitrogen contents were the main environmental factors driving the vertical distribution of the fungal community in paddy soils.
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Affiliation(s)
- Xu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, P. R. China
| | - Huanhuan Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, P. R. China.,Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xiang Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, P. R. China.,Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xinyu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, P. R. China.
| | - Huiwen Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, P. R. China
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20
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Gonzalez-Escalona N, Sharma SK. Closing Clostridium botulinum Group I Genomes Using a Combination of Short- and Long-Reads. Front Microbiol 2020; 11:239. [PMID: 32153532 PMCID: PMC7050642 DOI: 10.3389/fmicb.2020.00239] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 08/27/2019] [Accepted: 01/31/2020] [Indexed: 11/13/2022] Open
Abstract
Clostridium botulinum is a Gram-positive, spore-forming anaerobic bacterium that produces botulinum neurotoxin (BoNT). Closing their genomes provides information about their neurotoxin clusters' arrangement(s) and their location (e.g., chromosome or plasmid) which cannot be assessed using draft genomes. Therefore, we tested the use of long-read sequencing (nanopore sequencing) in combination with short-read sequencing to close two toxin-producing strains. These genomes could be used by the Public Health Emergency Preparedness and Response staff during botulism outbreaks. The genomes of two toxin-producing C. botulinum strains, one from an environmental sample (83F_CFSAN034202) and the other from a clinical sample (CDC51232_CFSAN034200) were sequenced using MinION and MiSeq devices. The genomes, including the chromosomes and the plasmids, were closed by a combination of long-read and short-read sequencing. They belonged to different C. botulinum sequence types (STs), with 83F belonging to ST4 and CDC51232 to ST7. A whole genome single nucleotide polymorphism (SNP) analysis clustered these two strains with strains in lineage 2 (e.g., 6CDC297) and 4 (e.g., NCTC2916) from Group I, respectively. These two strains were also bivalent strains with the BoNTB and BoNTA4 clusters located in the larger plasmid for CDC51232, and the BoNTB and BoNTA1 clusters located both in the chromosome for 83F. Overall, this study showed the advantage of combining these two sequencing methods to obtain high quality closed C. botulinum genomes that could be used for SNP phylogenies (source tracking) as well as for fast identification of BoNT clusters and their gene arrangements.
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Affiliation(s)
- Narjol Gonzalez-Escalona
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Shashi K Sharma
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
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21
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Chen Y, Tian W, Shao Y, Li YJ, Lin LA, Zhang YJ, Han H, Chen ZJ. Miscanthus cultivation shapes rhizosphere microbial community structure and function as assessed by Illumina MiSeq sequencing combined with PICRUSt and FUNGUIld analyses. Arch Microbiol 2020; 202:1157-71. [PMID: 32067064 DOI: 10.1007/s00203-020-01830-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 01/31/2020] [Accepted: 02/04/2020] [Indexed: 12/11/2022]
Abstract
Soil microbes play important roles in plant growth and in the biogeochemical cycling of earth's elements. However, the structure and functions of the microbial community associated with the growth of second-generation energy crops, such as Miscanthus, remain unclear. Thus, in this study, the composition and function of the bacterial and fungal communities associated with Miscanthus cultivation were analyzed by MiSeq sequencing combined with PICRUSt and FUNGUIld analyses. The results of community composition and diversity index analyses showed that Miscanthus cultivation significantly altered the bacterial and fungal community composition and reduced bacterial and fungal diversity. In addition, Miscanthus cultivation increased the soil organic matter (SOM) and total nitrogen (TN) contents. The correlation analysis between microbial community composition and environmental factors indicated that SOM and TN were the most important factors affecting bacterial and fungal communities. Miscanthus cultivation could enrich the abundances of Pseudomonas, Rhizobium, Luteibacter, Bradyrhizobium, Phenylobacterium and other common plant-promoting bacteria, while also increasing Cladophialophora, Hymenula, Magnaporthe, Mariannaea, etc., which predicted corresponded to the saprotrophic, plant pathogenic, and pathotrophic trophic modes. The PICRUSt predictive analysis indicated that Miscanthus cultivation altered the metabolic capabilities of bacterial communities, including the metabolism of carbon, nitrogen, and phosphorus cycle. In addition, FUNGUIld analysis indicated that Miscanthus cultivation altered the fungal trophic mode. The effects of Miscanthus on the communities and function of bacteria and fungi varied among Miscanthus species. Miscanthus specie Xiangdi NO 1 had the greatest impact on soil bacterial and fungal communities, whereas Miscanthus specie Wujiemang NO 1 had the greatest impact on soil bacteria and fungi functions. The results of this study provide a reference for the composition and function of microbial communities during the growth of Miscanthus.
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22
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Yu H, Xue D, Wang Y, Zheng W, Zhang G, Wang ZL. Molecular ecological network analysis of the response of soil microbial communities to depth gradients in farmland soils. Microbiologyopen 2020; 9:e983. [PMID: 31902141 PMCID: PMC7066466 DOI: 10.1002/mbo3.983] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 12/04/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022] Open
Abstract
Soil microorganisms are considered to be important indicators of soil fertility and soil quality. Most previous studies have focused solely on surface soil, but there were numerous active cells in deeper soil layers. However, studies regarding microbial communities in deeper soil layers were not comprehensive and sufficient. In this study, phylogenetic molecular ecological networks (pMENs) based on the 16S rRNA Miseq sequencing technique were applied to study the response of soil microbial communities to depth gradients and the changes of key genera along 3 meter depth gradients (0–0.2 m, 0.2–0.4 m 0.4–0.6 m, 0.6–0.8 m, 0.8–1.0 m, 1.0–1.3 m, 1.3–1.6 m, 1.6–2.0 m, 2.0–2.5 m, and 2.5–3.0 m). The results showed that the modularity of microbial communities was consistently high in all soil layers and each layer was similar, which indicated that microbial communities were more resistant to depth changes. The pMENs further demonstrated that microbial community interactions were stable as the depth increased and they cooperated well to adapt to changes in different soil gradients. This was evidenced by similar positive links, average degree, and average clustering coefficient. In addition, key genera were obtained by analyzing module hubs in the pMENs. There may be at least one dominant genus in each layer that adapted to and resisted changes in the soil environment. It seems microbial communities demonstrate a stable and strong adaptability to depth gradients in farmland soils.
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Affiliation(s)
- Hang Yu
- Tianjin Key Laboratory of Water Resources and Environment, Tianjin Normal University, Tianjin, China.,Tianjin Key Laboratory of Environmental Change and Ecological Restoration, School of Geographic and Environmental Sciences, Tianjin Normal University, Tianjin, China
| | - Dongmei Xue
- Tianjin Key Laboratory of Water Resources and Environment, Tianjin Normal University, Tianjin, China
| | - Yidong Wang
- Tianjin Key Laboratory of Water Resources and Environment, Tianjin Normal University, Tianjin, China
| | - Wei Zheng
- Tianjin Key Laboratory of Water Resources and Environment, Tianjin Normal University, Tianjin, China
| | - Guilong Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin, China
| | - Zhong-Liang Wang
- Tianjin Key Laboratory of Water Resources and Environment, Tianjin Normal University, Tianjin, China
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23
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Chen ZJ, Xu G, Ding CY, Zheng BH, Chen Y, Han H, Li YY, Shi JW, Hu LQ. Illumina MiSeq sequencing and network analysis the distribution and co-occurrence of bacterioplankton in Danjiangkou Reservoir, China. Arch Microbiol 2020; 202:859-73. [PMID: 31894394 DOI: 10.1007/s00203-019-01798-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 11/26/2019] [Accepted: 12/15/2019] [Indexed: 10/25/2022]
Abstract
Network analysis has contributed to studies of the interactions of microorganisms and the identification of key populations. However, such analysis has rarely been conducted in the study of reservoir bacterioplankton communities. This study investigated the bacterioplankton community composition in the surface water of the Danjiangkou Reservoir using the Illumina MiSeq sequencing platform. We observed that the bacterioplankton community primarily consisted of 27 phyla and 336 genera, including Actinobacteria, Proteobacteria, and Bacteroidetes, demonstrating the richness of the community composition. Redundancy analysis of the bacterioplankton communities and environmental variables showed that the total nitrogen (TN), pH, chemical oxygen demand (COD), and permanganate index (CODMn) were important factors affecting the bacterioplankton distribution. Network analysis was performed using the relative abundances of bacterioplankton based on the phylogenetic molecular ecological network (pMEN) method. The connectivity of node i within modules (Zi), the connectivity of node i among modules (Pi), and the number of key bacteria were high at the Taizishan and Heijizui sites, which were associated with higher TN contents than at the other sites. Among the physicochemical properties of water, TN, ammonia nitrogen (NH4-N), pH, COD, and dissolved oxygen (DO) might have great influences on the functional units of the bacterial communities in bacterioplankton molecular networks. This study improves the understanding of the structure and function of bacterioplankton communities in the Danjiangkou Reservoir.
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Liang Y, Zhang Y, Zhou C, Li H, Kang X, Wang L, Song J, Jiao N. Cumulative impact of long-term intensive mariculture on total and active bacterial communities in the core sediments of the Ailian Bay, North China. Sci Total Environ 2019; 691:1212-1224. [PMID: 31466202 DOI: 10.1016/j.scitotenv.2019.07.200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 04/04/2019] [Revised: 07/10/2019] [Accepted: 07/13/2019] [Indexed: 06/10/2023]
Abstract
The exponential growth of off-shore mariculture worldwide over the last 20 years has had significant impact on coastal sediment biogeochemistry. However, there are no long-term records of the cumulative impacts of mariculture on the benthic bacterial community. Here, total (DNA) and active (RNA) bacterial community compositions were characterized using MiSeq sequencing of 16S rRNA gene in four core sediments of the Ailian Bay, one of the typical intensive mariculture areas in China with more than fifty-year history of kelp and scallop cultivation. The γ-Proteobacteria, δ-Proteobacteria, Acidobacteria and Acitinobacteria were more abundant in the total bacterial communities, while β-Proteobacteria, Anaerolineae, Clostridia, Spirochaetes and Cyanobacteria were enriched in the active bacterial communities. Significant differences were observed between total and active benthic bacterial communities. The influences of different mariculture modes on the total bacterial communities were more significant than those on the active bacterial communities. Only limited groups of the total bacterial communities were significant influenced by the cumulative effects of the long-term mariculture. The bacterial genera with the function in the sulfide cycling and organic consumption were enriched in the total bacterial population of the integrated multi-trophic aquaculture (IMTA) areas. The variations of both total and active bacterial communities were significantly influenced by grain sizes, total organic carbon and nutrients. Both total and active bacterial communities exhibited a slightly stronger response to environmental factors than to spatial (distance) factors. The effects of mutualism might dominate the total and active bacterial networks in the Ailian Bay. The present study demonstrated that the cumulative influences of the long-term and intensive IMTA mariculture on total benthic bacterial communities in the sub-surface sediments of the Ailian Bay were stronger than those on the active benthic bacterial communities, which provided some insights into the potential ecological roles of specific taxa in the sediments of the IMTA ecosystems.
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Affiliation(s)
- Yantao Liang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Chao Zhou
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Hongmei Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Xuming Kang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Long Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Jinming Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nianzhi Jiao
- Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China
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25
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Zhao Y, Zhang F, Yang L, Wang D, Wang W. Response of soil bacterial community structure to different reclamation years of abandoned salinized farmland in arid China. Arch Microbiol 2019; 201:1219-32. [PMID: 31190086 DOI: 10.1007/s00203-019-01689-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/23/2019] [Accepted: 06/02/2019] [Indexed: 10/26/2022]
Abstract
In recent years, understanding the impact of reclamation of abandoned salinized field on microbial community structure is of great importance for ecosystem restoration in arid regions. The aim of this work was to investigate the effects of reclamation years on soil properties, bacterial community composition and diversity based on field sampling and llumina MiSeq sequencing. The five reclamation years are: unreclaimed salinized and reclaimed (1, 5, 10, and 15 years) fields. The results showed soil properties are significantly altered by abandoned salinized field. In particular, reclamation significantly decreased soil electrical conductivity, Cl-, SO42-, Na+, and Ca2+, during 5 years of reclamation. In addition, reclamation increased the richness and diversity of the bacterial community, except for the 1-year field soils. There was a large difference in the abundant bacterial phyla in 1-year field soils compared with other field soils. Proteobacteria were the most abundant in all of the field soils. Principal coordinates analysis showed that the abandoned and 1-year field soils exhibited specific differences in bacterial community structures compared with other field soils. Statistical analyses showed that available phosphorus, SO42-, Mg2+, and Ca2+ were the main physicochemical properties affecting the soil bacterial communities. Overall, reclamation improved soil physicochemical properties and altered the structure and composition of soil bacterial communities compared with unreclaimed salinized soil.
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26
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Pong LY, Parkkinen S, Dhanoa A, Gan HM, Wickremesinghe IAC, Syed Hassan S. MicroRNA profiling of mouse liver in response to DENV-1 infection by deep sequencing. PeerJ 2019; 7:e6697. [PMID: 31065454 PMCID: PMC6482938 DOI: 10.7717/peerj.6697] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 12/07/2018] [Accepted: 02/28/2019] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Dengue caused by dengue virus (DENV) serotypes -1 to -4 is the most important mosquito-borne viral disease in the tropical and sub-tropical countries worldwide. Yet many of the pathophysiological mechanisms of host responses during DENV infection remain largely unknown and incompletely understood. METHODS Using a mouse model, the miRNA expressions in liver during DENV-1 infection was investigated using high throughput miRNA sequencing. The differential expressions of miRNAs were then validated by qPCR, followed by target genes prediction. The identified miRNA targets were subjected to gene ontology (GO) annotation and pathway enrichment analysis to elucidate the potential biological pathways and molecular mechanisms associated with DENV-1 infection. RESULTS A total of 224 and 372 miRNAs out of 433 known mouse miRNAs were detected in the livers of DENV-1-infected and uninfected mice, respectively; of these, 207 miRNAs were present in both libraries. The miR-148a-3p and miR-122-5p were the two most abundant miRNAs in both groups. Thirty-one miRNAs were found to have at least 2-fold change in upregulation or downregulation, in which seven miRNAs were upregulated and 24 miRNAs were downregulated in the DENV-1-infected mouse livers. The miR-1a-3p was found to be the most downregulated miRNA in the DENV-1-infected mouse livers, with a significant fold change of 0.10. To validate the miRNA sequencing result, the expression pattern of 12 miRNAs, which were highly differentially expressed or most abundant, were assessed by qPCR and nine of them correlated positively with the one observed in deep sequencing. In silico functional analysis revealed that the adaptive immune responses involving TGF-beta, MAPK, PI3K-Akt, Rap1, Wnt and Ras signalling pathways were modulated collectively by 23 highly differentially expressed miRNAs during DENV-1 infection. CONCLUSION This study provides the first insight into the global miRNA expressions of mouse livers in response to DENV-1 infection in vivo and the possible roles of miRNAs in modulating the adaptive immune responses during DENV-1 infection.
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Affiliation(s)
- Lian Yih Pong
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
- Infectious Diseases and Health Cluster, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Sinikka Parkkinen
- Department of Biology, University of Eastern Finland, Joensuu, North Karelia, Finland
| | - Amreeta Dhanoa
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
- Infectious Diseases and Health Cluster, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Han Ming Gan
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | | | - Sharifah Syed Hassan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
- Infectious Diseases and Health Cluster, Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
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27
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He B, Li H, Hu Z, Zhang Y, Sun M, Qiu S, Zeng B. Difference in microbial community and taste compounds between Mucor-type and Aspergillus-type Douchi during koji-making. Food Res Int 2019; 121:136-143. [PMID: 31108734 DOI: 10.1016/j.foodres.2019.03.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 02/05/2023]
Abstract
Douchi has attracted people's attention because of its unique taste and rich health function. The microbes participated in the koji-making process contribute to taste compounds of Douchi. However, the majority of studies on Douchi focused on their functional components and the microbial community in single type of Douchi during koji-making so far. In the present study, the taste components of Mucor-type and Aspergillus-type Douchi were measured initially and the results showed that the amino acid and organic acid levels as well as the percentage of unsaturated fatty acids in Mucor-type Douchi were significantly higher than those in Aspergillus-type. The investigation of the microbial composition in two types of Douchi showed that Aspergillus, Candida, Meyerozyma and Lecanicillium were shared by >50% of samples during koji-making. Comparison of the microbial community between the two types of Douchi revealed that Meyerozyma and Lecanicillium were the main microbial community with significant difference during the initial stage of koji-making, while Candida was significantly different during the later stage of koji-making. When supplemented with Meyerozyma and Candida in Aspergillus-type Douchi, the level of all amino acid and organic acids as well as the percentage of unsaturated fatty acid was significant improved, which further validated the importance roles of the two microorganisms in enhancing the taste components of Douchi during koji-making. The results provide useful information on optimizing the microbial community structure of Douchi during the process of koji-making and improving the product quality.
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Affiliation(s)
- Bin He
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Haoran Li
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Zhihong Hu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Yihan Zhang
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Min Sun
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Shangkun Qiu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Bin Zeng
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science & Technology Normal University, Nanchang 330013, China.
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28
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Yang S, Zheng Q, Yuan M, Shi Z, Chiariello NR, Docherty KM, Dong S, Field CB, Gu Y, Gutknecht J, Hungate BA, Le Roux X, Ma X, Niboyet A, Yuan T, Zhou J, Yang Y. Long-term elevated CO 2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials. Sci Total Environ 2019; 652:1474-1481. [PMID: 30586832 DOI: 10.1016/j.scitotenv.2018.10.353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 08/07/2018] [Revised: 10/22/2018] [Accepted: 10/26/2018] [Indexed: 06/09/2023]
Abstract
The continuously increasing concentration of atmospheric CO2 has considerably altered ecosystem functioning. However, few studies have examined the long-term (i.e. over a decade) effect of elevated CO2 on soil microbial communities. Using 16S rRNA gene amplicons and a GeoChip microarray, we investigated soil microbial communities from a Californian annual grassland after 14 years of experimentally elevated CO2 (275 ppm higher than ambient). Both taxonomic and functional gene compositions of the soil microbial community were modified by elevated CO2. There was decrease in relative abundance for taxa with higher ribosomal RNA operon (rrn) copy number under elevated CO2, which is a functional trait that responds positively to resource availability in culture. In contrast, taxa with lower rrn copy number were increased by elevated CO2. As a consequence, the abundance-weighted average rrn copy number of significantly changed OTUs declined from 2.27 at ambient CO2 to 2.01 at elevated CO2. The nitrogen (N) fixation gene nifH and the ammonium-oxidizing gene amoA significantly decreased under elevated CO2 by 12.6% and 6.1%, respectively. Concomitantly, nitrifying enzyme activity decreased by 48.3% under elevated CO2, albeit this change was not significant. There was also a substantial but insignificant decrease in available soil N, with both nitrate (NO3-) (-27.4%) and ammonium (NH4+) (-15.4%) declining. Further, a large number of microbial genes related to carbon (C) degradation were also affected by elevated CO2, whereas those related to C fixation remained largely unchanged. The overall changes in microbial communities and soil N pools induced by long-term elevated CO2 suggest constrained microbial N decomposition, thereby slowing the potential maximum growth rate of the microbial community.
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Affiliation(s)
- Sihang Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Qiaoshu Zheng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Mengting Yuan
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Zhou Shi
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | | | - Kathryn M Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, USA
| | - Shikui Dong
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Beijing normal university, Beijing 100875, PR China
| | | | - Yunfu Gu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA; Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Jessica Gutknecht
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle 06120, Germany; Department of Soil, Water, and Climate, University of Minnesota, Twin Cities, Saint Paul, MN 55104, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Xavier Le Roux
- Microbial ecology Centre, INRA, CNRS, University of Lyon, University Lyon 1, UMR INRA 1418, UMR CNRS 5557, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne, France
| | - Xingyu Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Audrey Niboyet
- Institut d'Ecologie et des Sciences de l'Environnement de Paris (Sorbonne Université, CNRS, INRA, IRD, Université Paris Diderot, UPEC), 4 place Jussieu, 75005 Paris, France; AgroParisTech, 75005 Paris, France
| | - Tong Yuan
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China.
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He G, Huang J, Zhou R, Wu C, Jin Y. Effect of Fortified Daqu on the Microbial Community and Flavor in Chinese Strong-Flavor Liquor Brewing Process. Front Microbiol 2019; 10:56. [PMID: 30761106 PMCID: PMC6361764 DOI: 10.3389/fmicb.2019.00056] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [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: 08/13/2018] [Accepted: 01/14/2019] [Indexed: 02/01/2023] Open
Abstract
Daqu, an important fermentation starter for the production of Chinese liquor, as used in the current study included traditional Daqu and fortified Daqu inoculated with Bacillus velezensis and Bacillus subtilis. To evaluate the effect of fortified Daqu on strong-flavor liquor production, the differences of microbial communities among three inoculation patterns of fermented grains (FG) were analyzed by the Illumina MiSeq platform. A higher relative abundance of dominant genera including Bacillus, Lactococcus, Aspergillus, and Candida, and lower relative abundance of Lactobacillus, were observed in FG50, in which mixed Daqu (traditional: fortified Daqu = 1: 1, w/w, 50% fortified Daqu) was used as the starter. Then, volatile compounds of their distillations were also examined by HS-SPME-GC-MS. The results showed that the contents of skeleton flavor components, mainly including important esters and aromatic compounds, were higher in the corresponding liquor L50, which distillated from FG50. Moreover, most esters mainly positively correlated with Lactobacillus and Candida in the bottom layer of FG fermented with 50% fortified Daqu (FG50-B). Aromatic compounds were strongly positively correlated with Bacillus and Aspergillus in the middle layer of FG with 50% fortified Daqu used (FG50-M). In particular, hexyl hexanoate showed a positive correlation with higher abundances of Ruminococcus in the FG with addition of 100% fortified Daqu (FG100). This study observed microbial compositions in the FG with fortified Daqu addition, and it further revealed the correlations between pivotal microbes and main flavor compounds. These results may help to develop effective strategies to regulate microbes for the brewing process and further improve the flavors of Chinese liquor.
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Affiliation(s)
- Guiqiang He
- College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Jun Huang
- College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Rongqing Zhou
- College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China.,National Engineering Research Center of Solid-State Manufacturing, Luzhou, China
| | - Chongde Wu
- College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Yao Jin
- College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
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30
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Li X, Zhu Y, Ringø E, Wang X, Gong J, Yang D. Intestinal microbiome and its potential functions in bighead carp ( Aristichthys nobilis) under different feeding strategies. PeerJ 2018; 6:e6000. [PMID: 30533302 PMCID: PMC6283038 DOI: 10.7717/peerj.6000] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 06/07/2018] [Accepted: 10/25/2018] [Indexed: 01/06/2023] Open
Abstract
Bighead carps (Aristichthys nobilis) were divided into four groups with different feeding strategies: group A, nature live food only (fertiliser only, 200 g urea + 160 g ethylamine phosphate + 250 g Huangjintai bio-fertiliser); group B, nature live food + 1/2 formulated feed; group C, nature live food + formulated feed; and group D, formulated feed only. The intestinal microbiomes of the different groups were compared through the Illumina MiSeq sequencing of the bacterial 16S rRNA gene. The specific growth rate (SGR), survival and blood biochemical factors of the fish were also investigated. Results showed that feeding treatment influenced the intestinal communities in the fish. In specific, more bacterial phyla dominated in groups A and B (phyla Bacteroidetes, Fusobacteria, Firmicutes and Proteobacteria in group A, phyla Proteobacteria and Fusobacteria in group B) than in groups C and D (phylum Proteobacteria). The diversity was also lower in groups C and D than in groups A and B. Unweighted pair-group method analysis revealed a clear difference in intestinal microbiota among the different feeding treatments. No difference in survival rate was found among the treatment groups, but the SGR was significantly higher (P < 0.01) in groups B, C and D than in group A. Functional analysis showed that the intestinal bacteria correlated with fish glucose metabolism in group A but with lipid metabolic activity in groups B, C and D. In summary, the intestinal microbiomes and their potential functions vary in bighead carp under different feeding treatments. This study provides new insights into the gut microbiomes of filter-feeding and formulated diet-fed fish.
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Affiliation(s)
- Xuemei Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Areas of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Yongjiu Zhu
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Areas of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Einar Ringø
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Xuge Wang
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Areas of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Jinling Gong
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Areas of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Deguo Yang
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Areas of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
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31
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Che R, Deng Y, Wang F, Wang W, Xu Z, Hao Y, Xue K, Zhang B, Tang L, Zhou H, Cui X. Autotrophic and symbiotic diazotrophs dominate nitrogen-fixing communities in Tibetan grassland soils. Sci Total Environ 2018; 639:997-1006. [PMID: 29929338 DOI: 10.1016/j.scitotenv.2018.05.238] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [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: 03/14/2018] [Revised: 05/16/2018] [Accepted: 05/19/2018] [Indexed: 06/08/2023]
Abstract
Biological nitrogen fixation, conducted by soil diazotrophs, is the primary nitrogen source for natural grasslands. However, the diazotrophs in grassland soils are still far from fully investigated. Particularly, their regional-scale distribution patterns have never been systematically examined. Here, soils (0-5 cm) were sampled from 54 grasslands on the Tibetan Plateau to examine the diazotroph abundance, diversity, and community composition, as well as their distribution patterns and driving factors. The diazotroph abundance was expressed as nifH gene copies, measured using real-time PCR. The diversity and community composition of diazotrophs were analyzed through MiSeq sequencing of nifH genes. The results showed that Cyanobacteria (47.94%) and Proteobacteria (45.20%) dominated the soil diazotroph communities. Most Cyanobacteria were classified as Nostocales which are main components of biological crusts. Rhizobiales, most of which were identified as potential symbiotic diazotrophs, were also abundant in approximately half of the soil samples. The soil diazotroph abundance, diversity, and community composition followed the distribution patterns in line with mean annual precipitation. Moreover, they also showed significant correlations with prokaryotic abundance, plant biomass, vegetation cover, soil pH values, and soil nutrient contents. Among these environmental factors, the soil moisture, organic carbon, available phosphorus, and inorganic nitrogen contents could be the main drivers of diazotroph distribution due to their strong correlations with diazotroph indices. These findings suggest that autotrophic and symbiotic diazotrophs are the predominant nitrogen fixers in Tibetan grassland soils, and highlight the key roles of water and nutrient availability in determining the soil diazotroph distribution on the Tibetan Plateau.
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Affiliation(s)
- Rongxiao Che
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Yongcui Deng
- Nanjing Normal University, Nanjing 210097, China; Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing 210023, China
| | - Fang Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Weijin Wang
- Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Zhihong Xu
- Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Yanbin Hao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Xue
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Biao Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Tang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Huakun Zhou
- Key Laboratory of Restoration Ecology of Cold Area in Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Xiaoyong Cui
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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Xue D, Chen H, Luo X, Guan J, He Y, Zhao X. Microbial diversity in the rumen, reticulum, omasum, and abomasum of yak on a rapid fattening regime in an agro-pastoral transition zone. J Microbiol 2018; 56:734-743. [PMID: 30136259 DOI: 10.1007/s12275-018-8133-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 07/02/2018] [Accepted: 07/02/2018] [Indexed: 11/26/2022]
Abstract
The ruminant digestive system harbors a complex gut microbiome, which is poorly understood in the case of the four stomach compartments of yak. High-throughput sequencing and quantitative PCR were used to analyse microbial communities in the rumen, reticulum, omasum, and abomasum of six domesticated yak. The diversity of prokaryotes was higher in reticulum and omasum than in rumen and abomasum. Bacteroidetes predominated in the four stomach compartments, with abundance gradually decreasing in the trend rumen > reticulum > omasum > abomasum. Microorganism composition was different among the four compartments, all of which contained high levels of bacteria, methanogens, protozoa and anaerobic fungi. Some prokaryotic genera were associated with volatile fatty acids and pH. This study provides the first insights into the microorganism composition of four stomach compartments in yak, and may provide a foundation for future studies in this area.
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Affiliation(s)
- Dan Xue
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration, Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, P. R. China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, P. R. China
| | - Huai Chen
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration, Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, P. R. China.
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, P. R. China.
| | - Xiaolin Luo
- Sichuan Academy of Grassland Sciences, Chengdu, 611731, P. R. China.
| | - Jiuqiang Guan
- Sichuan Academy of Grassland Sciences, Chengdu, 611731, P. R. China
| | - Yixin He
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration, Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, P. R. China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, P. R. China
| | - Xinquan Zhao
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration, Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, P. R. China
- Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, 810008, P. R. China
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33
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Wei W, Yang M, Liu Y, Huang H, Ye C, Zheng J, Guo C, Hao M, He X, Zhu S. Fertilizer N application rate impacts plant-soil feedback in a sanqi production system. Sci Total Environ 2018; 633:796-807. [PMID: 29602118 DOI: 10.1016/j.scitotenv.2018.03.219] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [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: 11/10/2017] [Revised: 03/06/2018] [Accepted: 03/19/2018] [Indexed: 05/14/2023]
Abstract
Replant failure caused by negative plant-soil feedback (NPFS) in agricultural ecosystems is a critical factor restricting the development of sustainable agriculture. Soil nutrient availability has the capacity to affect plant-soil feedback. Here, we used sanqi (Panax notoginseng), which is severely threatened by NPSF, as a model plant to decipher the overall effects of nitrogen (N) rates on NPSF and the underlying mechanism. We found that a high rate of N at 450kgNha-1 (450N) aggravated the NPSF through the accumulation of pathogens in the soil compared with the optimal 250N. The increased N rates resulted in a significant increase in the soil electrical conductivity and available nitrogen but a decrease in the soil pH and C/N ratio. GeoChip 5.0 data demonstrated that these changed soil properties caused the soil to undergo stress (acidification, salinization and carbon starvation), as indicated by the enriched soil microbial gene abundances related to stress response and nutrition cycling (N, C and S). Accordingly, increased N rates reduced the richness and diversity of soil fungi and bacteria and eventually caused a shift in soil microbes from a bacterial-dominant community to a fungal-dominant community. In particular, the high 450N treatment significantly suppressed the abundance of copiotrophic bacteria, including beneficial genera Bacillus and Pseudomonas, thus weakening the antagonistic activity of these bacteria against fungal pathogens. Moreover, 450N application significantly enriched the abundance of pathogen pathogenicity-related genes. Once sanqi plants were grown in this N-stressed soil, their host-specific fungal pathogen Fusarium oxysporum significantly accumulated, which aggravated the process of NPSF. This study suggested that over-application of nitrogen is not beneficial for disease management or the reduction of fungicide application in agricultural production.
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Affiliation(s)
- Wei Wei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Min Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Yixiang Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Huichuan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Chen Ye
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Jianfen Zheng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Yunnan Tasly Notoginseng Planting Co., Ltd, Wenshan 663000, China
| | - Cunwu Guo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Minwen Hao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China.
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Wei Z, Feng K, Li S, Zhang Y, Chen H, Yin H, Xu M, Deng Y. Exploring abundance, diversity and variation of a widespread antibiotic resistance gene in wastewater treatment plants. Environ Int 2018; 117:186-195. [PMID: 29753149 DOI: 10.1016/j.envint.2018.05.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [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: 02/16/2018] [Revised: 04/24/2018] [Accepted: 05/03/2018] [Indexed: 06/08/2023]
Abstract
An updated sul1 gene sequence database was constructed and new degenerate primers were designed to better investigate the abundance, diversity, and variation of a ubiquitous antibiotic resistance gene, sul1, with PCR-based methods in activated sludge from wastewater treatment plants (WWTPs). The newly designed degenerate primers showed high specificity and higher coverage in both in-silico evaluations and activated sludge samples compared to previous sul1 primers. Using the new primers, the abundance and diversity of sul1 gene, together with 16S rRNA gene, in activated sludge from five WWTPs in summer and winter were determined by quantitative PCR and MiSeq sequencing. The sul1 gene was found to be prevalent and displayed a comparable abundance (0.081 copies per bacterial cell in average) to the total bacteria across all samples. However, compared to the significant seasonal and geographical divergences in the quantity and diversity of bacterial communities in WWTPs, there were no significant seasonal or geographical variations of representative clusters of sul1 gene in most cases. Additionally, the representative sul1 clusters showed fairly close phylogeny and there was no obvious correlation between sul1 gene and the dominant bacterial genera, as well as the int1 gene, suggesting that bacterial hosts of sul1 gene is not stable, the sul1 gene may be carried by mobile genetic elements, sometimes integrated with class 1 integrons and sometimes not. Thus mobile genetic elements likely play a greater role than specific microbial taxa in determining the composition of sul1 gene in WWTPs.
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Affiliation(s)
- Ziyan Wei
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Feng
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuzhen Li
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongrui Chen
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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Sun X, Zhou Y, Tan Y, Wu Z, Lu P, Zhang G, Yu F. Restoration with pioneer plants changes soil properties and remodels the diversity and structure of bacterial communities in rhizosphere and bulk soil of copper mine tailings in Jiangxi Province, China. Environ Sci Pollut Res Int 2018; 25:22106-22119. [PMID: 29802615 DOI: 10.1007/s11356-018-2244-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 01/12/2018] [Accepted: 05/06/2018] [Indexed: 06/08/2023]
Abstract
To unravel the ecological function played by pioneer plants in the practical restoration of mine tailings, it is vital to explore changes of soil characteristics and microbial communities in rhizosphere and bulk soil following the adaptation and survival of plants. In the present study, the diversity and structure of rhizospheric bacterial communities of three pioneer plants in copper mine tailings were investigated by Illumina MiSeq sequencing, and the effects of pioneer plants on soil properties were also evaluated. Significant soil improvement was detected in rhizospheric samples, and Alnus cremastogyne showed higher total organic matter, total nitrogen, and available phosphorus than two other herbaceous plants. Microbial diversity indices in rhizosphere and bulk soil of reclaimed tailings were significantly higher than bare tailings, even the soil properties of bulk soil in reclaimed tailings were not significantly different from those of bare tailings. A detailed taxonomic composition analysis demonstrated that Alphaproteobacteria and Deltaproteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes showed significantly higher relative abundance in rhizosphere and bulk soil. In contrast, Gammaproteobacteria and Firmicutes were abundant in bare tailings, in which Bacillus, Pseudomonas, and Lactococcus made up the majority of the bacterial community (63.04%). Many species within known heavy metal resistance and nutrient regulatory microorganism were identified in reclaimed tailings, and were more abundant among rhizospheric microbes. Hierarchical clustering and principal coordinate analysis (PCoA) analysis demonstrated that the bacterial profiles in the rhizosphere clustered strictly together according to plant types, and were distinguishable from bulk soil. However, we also identified a large shared OTUs that occurred repeatedly and was unaffected by highly diverse soil properties in rhizosphere and bulk samples. Redundancy analysis indicated that water content and Cu and As concentrations were the main environmental regulators of microbial composition. These results suggest that the interactive effect of pioneer plants and harsh soil environmental conditions remodel the specific bacterial communities in rhizosphere and bulk soil in mine tailings. And A. cremastogyne might be approximate candidate for phytoremediation of mine tailings for better soil amelioration effect and relative higher diversity of bacterial community in rhizosphere.
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Affiliation(s)
- Xiaoyan Sun
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China.
| | - Yanling Zhou
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Yinjing Tan
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Zhaoxiang Wu
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Ping Lu
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Guohua Zhang
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
| | - Faxin Yu
- Jiangxi Engineering and Technology Research Center for Ecological Remediation of Heavy Metal Pollution, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, 330096, People's Republic of China
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Oshiki M, Miura T, Kazama S, Segawa T, Ishii S, Hatamoto M, Yamaguchi T, Kubota K, Iguchi A, Tagawa T, Okubo T, Uemura S, Harada H, Kobayashi N, Araki N, Sano D. Microfluidic PCR Amplification and MiSeq Amplicon Sequencing Techniques for High-Throughput Detection and Genotyping of Human Pathogenic RNA Viruses in Human Feces, Sewage, and Oysters. Front Microbiol 2018; 9:830. [PMID: 29755444 PMCID: PMC5934477 DOI: 10.3389/fmicb.2018.00830] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 01/04/2018] [Accepted: 04/11/2018] [Indexed: 01/31/2023] Open
Abstract
Detection and genotyping of pathogenic RNA viruses in human and environmental samples are useful for monitoring the circulation and prevalence of these pathogens, whereas a conventional PCR assay followed by Sanger sequencing is time-consuming and laborious. The present study aimed to develop a high-throughput detection-and-genotyping tool for 11 human RNA viruses [Aichi virus; astrovirus; enterovirus; norovirus genogroup I (GI), GII, and GIV; hepatitis A virus; hepatitis E virus; rotavirus; sapovirus; and human parechovirus] using a microfluidic device and next-generation sequencer. Microfluidic nested PCR was carried out on a 48.48 Access Array chip, and the amplicons were recovered and used for MiSeq sequencing (Illumina, Tokyo, Japan); genotyping was conducted by homology searching and phylogenetic analysis of the obtained sequence reads. The detection limit of the 11 tested viruses ranged from 100 to 103 copies/μL in cDNA sample, corresponding to 101–104 copies/mL-sewage, 105–108 copies/g-human feces, and 102–105 copies/g-digestive tissues of oyster. The developed assay was successfully applied for simultaneous detection and genotyping of RNA viruses to samples of human feces, sewage, and artificially contaminated oysters. Microfluidic nested PCR followed by MiSeq sequencing enables efficient tracking of the fate of multiple RNA viruses in various environments, which is essential for a better understanding of the circulation of human pathogenic RNA viruses in the human population.
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Affiliation(s)
- Mamoru Oshiki
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Takayuki Miura
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
| | - Shinobu Kazama
- Center for Simulation Sciences and Informational Biology, Ochanomizu University, Bunkyô, Japan
| | - Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, Kofu, Japan
| | - Satoshi Ishii
- Department of Soil, Water and Climate, University of Minnesota, Minneapolis, MN, United States
| | - Masashi Hatamoto
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Japan
| | - Akinori Iguchi
- Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Tadashi Tagawa
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Tsutomu Okubo
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Shigeki Uemura
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Hideki Harada
- New Industry Creation Hatchery Center, Tohoku University, Sendai, Japan
| | - Naohiro Kobayashi
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Nobuo Araki
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Japan
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37
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Shen Z, Penton CR, Lv N, Xue C, Yuan X, Ruan Y, Li R, Shen Q. Banana Fusarium Wilt Disease Incidence Is Influenced by Shifts of Soil Microbial Communities Under Different Monoculture Spans. Microb Ecol 2018; 75:739-750. [PMID: 28791467 DOI: 10.1007/s00248-017-1052-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [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: 04/13/2017] [Accepted: 07/28/2017] [Indexed: 05/14/2023]
Abstract
The continuous cropping of banana in the same field may result in a serious soil-borne Fusarium wilt disease and a severe yield decline, a phenomenon known as soil sickness. Although soil microorganisms play key roles in maintaining soil health, the alternations of soil microbial community and relationship between these changes and soil sickness under banana monoculture are still unclear. Bacterial and fungal communities in the soil samples collected from banana fields with different monoculture spans were profiled by sequencing of the 16S rRNA genes and internal transcribed spacer using the MiSeq platform to explore the relationship between banana monoculture and Fusarium wilt disease in the present study. The results showed that successive cropping of banana was significantly correlated with the Fusarium wilt disease incidence. Fungal communities responded more obviously and quickly to banana consecutive monoculture than bacterial community. Moreover, a higher fungal richness significantly correlated to a higher banana Fusarium wilt disease incidence but a lower yield. Banana fungal pathogenic genus of Fusarium and Phyllosticta were closely associated with banana yield depletion and disease aggravation. Potential biocontrol agents, such as Funneliformis, Mortierella, Flavobacterium, and Acidobacteria subgroups, exhibited a significant correlation to lower disease occurrence. Further networks analysis revealed that the number of functionally interrelated modules decreased, the composition shifted from bacteria- to fungi-dominated among these modules, and more resources-competitive interactions within networks were observed after banana long-term monoculture. Our results also showed that bacterial and fungal communities were mainly driven by soil organic matter. Overall, the findings indicated that the bacterial and fungal community structures altered significantly after banana long-term monoculture, and the fungal richness, abundance of Fusarium, interactions between and within bacteria and fungi in ecological networks, and soil organic matter were associated with banana soil-borne Fusarium wilt disease.
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Affiliation(s)
- Zongzhuan Shen
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizer, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - C Ryan Penton
- College of Integrative Sciences and Arts, Julie Ann Wrigley Global Institute of Sustainability, Fundamental and Applied Microbiomics Institute, Arizona State University, Mesa, AZ, USA
| | - Nana Lv
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizer, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chao Xue
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizer, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xianfu Yuan
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizer, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunze Ruan
- Hainan key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Agriculture, Hainan University, Haikou, 570228, China
| | - Rong Li
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizer, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizer, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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38
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Zhang M, Wang N, Hu Y, Sun G. Changes in soil physicochemical properties and soil bacterial community in mulberry (Morus alba L.)/alfalfa (Medicago sativa L.) intercropping system. Microbiologyopen 2018. [PMID: 29536644 PMCID: PMC5912001 DOI: 10.1002/mbo3.555] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A better understanding of tree‐based intercropping effects on soil physicochemical properties and bacterial community has a potential contribution to improvement of agroforestry productivity and sustainability. In this study, we investigated the effects of mulberry/alfalfa intercropping on soil physicochemical properties and soil bacterial community by MiSeq sequencing of bacterial 16S rRNA gene. The results showed a significant increase in the contents of available nitrogen, available phosphate, available potassium, and total carbon in the rhizosphere soil of the intercropped alfalfa. Sequencing results showed that intercropping improved bacterial richness and diversity of mulberry and alfalfa based on richness estimates and diversity indices. The relative abundances of Proteobacteria, Actinobacteria, and Firmicutes were significantly higher in intercropping mulberry than in monoculture mulberry; and the abundances of Proteobacteria, Bacteroidetes, and Gemmatimonadetes in the intercropping alfalfa were markedly higher than that in monoculture alfalfa. Bacterial taxa with soil nutrients cycling were enriched in the intercropping system. There were higher relative abundances of Bacillus (0.32%), Pseudomonas (0.14%), and Microbacterium (0.07%) in intercropping mulberry soil, and Bradyrhizobium (1.0%), Sphingomonas (0.56%), Pseudomonas (0.18%), Microbacterium (0.15%), Rhizobium (0.09%), Neorhizobium (0.08%), Rhodococcus (0.06%), and Burkholderia (0.04%) in intercropping alfalfa soil. Variance partition analysis showed that planting pattern contributed 26.7% of the total variation of bacterial community, and soil environmental factors explained approximately 56.5% of the total variation. This result indicated that the soil environmental factors were more important than the planting pattern in shaping the bacterial community in the field soil. Overall, mulberry/alfalfa intercropping changed soil bacterial community, which was related to changes in soil total carbon, available phosphate, and available potassium.
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Affiliation(s)
- Meng‐Meng Zhang
- College of Life ScienceNortheast Forestry UniversityHarbinHeilongjiangChina
| | - Ning Wang
- College of Life ScienceNortheast Forestry UniversityHarbinHeilongjiangChina
| | - Yan‐Bo Hu
- College of Life ScienceNortheast Forestry UniversityHarbinHeilongjiangChina
| | - Guang‐Yu Sun
- College of Life ScienceNortheast Forestry UniversityHarbinHeilongjiangChina
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39
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Xing Z, Zhao T, Zhang L, Gao Y, Liu S, Yang X. Effects of copper on expression of methane monooxygenases, trichloroethylene degradation, and community structure in methanotrophic consortia. Eng Life Sci 2018; 18:236-243. [PMID: 32624902 DOI: 10.1002/elsc.201700153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/12/2017] [Accepted: 12/29/2017] [Indexed: 11/08/2022] Open
Abstract
Copper plays a key role in regulating the expression of enzymes that promote biodegradation of contaminants in methanotrophic consortia (MC). Here, we utilized MC isolated from landfill cover to investigate cometabolic degradation of trichloroethylene (TCE) at nine different copper (Cu2+) concentrations. The results demonstrated that an increase in Cu2+ concentration from 0 to 15 μM altered the specific first-order rate constant k 1,TCE, the expression levels of methane monooxygenase (pmoA and mmoX) genes, and the specific activity of soluble methane monooxygenase (sMMO). High efficiency TCE degradation (95%) and the expression levels of methane monooxygenase (MMO) were detected at a Cu2+ concentration of 0.03 μM. Notably, sMMO-specific activity ranged from 74.41 nmol/(mgcell h) in 15 μM Cu2+ to 654.99 nmol/(mgcell h) in 0.03 μM Cu2+, which contrasts with cultures of pure methanotrophs in which sMMO activity is depressed at high Cu2+ concentrations, indicating a special regulatory role for Cu2+ in MC. The results of MiSeq pyrosequencing indicated that higher Cu2+ concentrations stimulated the growth of methanotrophic microorganisms in MC. These findings have important implications for the elucidation of copper-mediated regulatory mechanisms in MC.
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Affiliation(s)
- Zhilin Xing
- Faculty of Urban Construction and Environment Engineering Chongqing University Chongqing P. R. China.,School of Chemistry and Chemical Engineering Chongqing University of Technology Chongqing P. R. China
| | - Tiantao Zhao
- Faculty of Urban Construction and Environment Engineering Chongqing University Chongqing P. R. China.,School of Chemistry and Chemical Engineering Chongqing University of Technology Chongqing P. R. China
| | - Lijie Zhang
- School of Chemistry and Chemical Engineering Chongqing University of Technology Chongqing P. R. China
| | - Yanhui Gao
- Faculty of Urban Construction and Environment Engineering Chongqing University Chongqing P. R. China.,School of Chemistry and Chemical Engineering Chongqing University of Technology Chongqing P. R. China
| | - Shuai Liu
- School of Chemistry and Chemical Engineering Chongqing University of Technology Chongqing P. R. China
| | - Xu Yang
- School of Chemistry and Chemical Engineering Chongqing University of Technology Chongqing P. R. China
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40
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Vogt JC, Abed RMM, Albach DC, Palinska KA. Bacterial and Archaeal Diversity in Hypersaline Cyanobacterial Mats Along a Transect in the Intertidal Flats of the Sultanate of Oman. Microb Ecol 2018; 75:331-347. [PMID: 28736793 DOI: 10.1007/s00248-017-1040-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 03/22/2017] [Accepted: 07/06/2017] [Indexed: 06/07/2023]
Abstract
Hypersaline intertidal zones are highly dynamic ecosystems that are exposed to multiple extreme environmental conditions including rapidly and frequently changing parameters (water, nutrients, temperature) as well as highly elevated salinity levels often caused by high temperatures and evaporation rates. Microbial mats in most extreme settings, as found at the coastline of the subtropical-arid Arabian Peninsula, have been relatively less studied compared to their counterparts around the world. We report, here, for the first time on the diversity of the bacterial and archaeal communities of marine microbial mats along an intertidal transect in a wide salt flat with strongly increased salinity employing Illumina MiSeq technology for amplicon sequencing of 16S rRNA gene fragments. Microbial communities were dominated by typical halotolerant to halophilic microorganisms, with clear shifts in community composition, richness, and diversity along the transect. Highly adapted specialists (e.g., Euhalothece, Salinibacter, Nanohaloarchaeota) were mainly found at the most extreme, upper tidal sites and less specialized organisms with wide tolerance ranges (e.g., Lyngbya, Rhodovibrio, Salisaeta, Halobacteria) in intermediate sites of the transect. The dominating taxa in the lower tidal sites were typical members of well-stabilized mats (e.g., Coleofasciculus, Anaerolineaceae, Thaumarchaeota). Up to 40% of the archaeal sequences per sample represented so far unknown phyla. In conclusion, the bacterial richness and diversity increased from upper towards lower tidal sites in line with increasing mat stabilization and functional diversity, opposed to that of cyanobacteria only and archaea, which showed their highest richness and diversity in upper tidal samples.
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Affiliation(s)
- Janina C Vogt
- Institute for Biology and Environmental Science (IBU), Plants Biodiversity and Evolution, Carl-von-Ossietzky University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany.
| | - Raeid M M Abed
- Biology Department, College of Science, Sultan Qaboos University, P.O. Box 36, 123, Al Khoud, Oman
| | - Dirk C Albach
- Institute for Biology and Environmental Science (IBU), Plants Biodiversity and Evolution, Carl-von-Ossietzky University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
| | - Katarzyna A Palinska
- Institute for Biology and Environmental Science (IBU), Plants Biodiversity and Evolution, Carl-von-Ossietzky University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
- Institute of Oceanography, Faculty of Oceanography and Geography, University of Gdansk, Al. J. Pilsudskiego 46, 80-378, Gdynia, Poland
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41
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Pei Y, Yu Z, Ji J, Khan A, Li X. Microbial Community Structure and Function Indicate the Severity of Chromium Contamination of the Yellow River. Front Microbiol 2018; 9:38. [PMID: 29472897 PMCID: PMC5810299 DOI: 10.3389/fmicb.2018.00038] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [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: 06/27/2017] [Accepted: 01/09/2018] [Indexed: 11/30/2022] Open
Abstract
The Yellow River is the most important water resource in northern China. In the recent past, heavy metal contamination has become severe due to industrial processes and other anthropogenic activities. In this study, riparian soil samples with varying levels of chromium (Cr) pollution severity were collected along the Gansu industrial reach of the Yellow River, including samples from uncontaminated sites (XC, XGU), slightly contaminated sites (LJX, XGD), and heavily contaminated sites (CG, XG). The Cr concentrations of these samples varied from 83.83 mg⋅kg-1 (XGU) to 506.58 mg⋅kg-1 (XG). The chromate [Cr (VI)] reducing ability in the soils collected in this study followed the sequence of the heavily contaminated > slightly contaminated > the un-contaminated. Common Cr remediation genes chrA and yieF were detected in the XG and CG samples. qRT-PCR results showed that the expression of chrA was up-regulated four and threefold in XG and CG samples, respectively, whereas the expression of yieF was up-regulated 66- and 7-fold in the same samples after 30 min treatment with Cr (VI). The copy numbers of chrA and yieF didn’t change after 35 days incubation with Cr (VI). The microbial communities in the Cr contaminated sampling sites were different from those in the uncontaminated samples. Especially, the relative abundances of Firmicutes and Bacteroidetes were higher while Actinobacteria was lower in the contaminated group than uncontaminated group. Further, potential indicator species, related to Cr such as Cr-remediation genera (Geobacter, PSB-M-3, Flavobacterium, and Methanosarcina); the Cr-sensitive genera (Skermanella, Iamia, Arthrobacter, and Candidatus Nitrososphaera) were also identified. These data revealed that Cr shifted microbial composition and function. Further, Cr (VI) reducing ability could be related with the expression of Cr remediation genes.
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Affiliation(s)
- Yaxin Pei
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhengsheng Yu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jing Ji
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Aman Khan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
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42
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Guo XP, Lu DP, Niu ZS, Feng JN, Chen YR, Tou FY, Liu M, Yang Y. Bacterial community structure in response to environmental impacts in the intertidal sediments along the Yangtze Estuary, China. Mar Pollut Bull 2018; 126:141-149. [PMID: 29421081 DOI: 10.1016/j.marpolbul.2017.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 08/22/2017] [Revised: 11/02/2017] [Accepted: 11/04/2017] [Indexed: 06/08/2023]
Abstract
This study was designed to investigate the characteristics of bacterial communities in intertidal sediments along the Yangtze Estuary and their responses to environmental factors. The results showed that bacterial abundance was significantly correlated with salinity, SO42- and total organic carbon, while bacterial diversity was significantly correlated with SO42- and total nitrogen. At different taxonomic levels, both the dominant taxa and their abundances varied among the eight samples, with Proteobacteria being the most dominant phylum in general. Cluster analysis revealed that the bacterial community structure was influenced by river runoff and sewerage discharge. Moreover, SO42-, salinity and total phosphorus were the vital environmental factors that influenced the bacterial community structure. Quantitative PCR and sequencing of sulphate-reducing bacteria indicated that the sulphate reduction process occurs frequently in intertidal sediments. These findings are important to understand the microbial ecology and biogeochemical cycles in estuarine environments.
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Affiliation(s)
- Xing-Pan Guo
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Da-Pei Lu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zuo-Shun Niu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jing-Nan Feng
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yu-Ru Chen
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Fei-Yun Tou
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yi Yang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
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43
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Xie X, He Z, Hu X, Yin H, Liu X, Yang Y. Large-scale seaweed cultivation diverges water and sediment microbial communities in the coast of Nan'ao Island, South China Sea. Sci Total Environ 2017; 598:97-108. [PMID: 28437776 DOI: 10.1016/j.scitotenv.2017.03.233] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [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: 10/05/2016] [Revised: 03/25/2017] [Accepted: 03/25/2017] [Indexed: 06/07/2023]
Abstract
Seaweed cultivation not only provides economy benefits, but also remediates the environment contaminated by mariculture of animals (e.g., fish, shrimps). However, the response of microbial communities to seaweed cultivation is poorly understood. In this study, we analyzed the diversity, composition, and structure of water and sediment microbial communities at a seaweed, Gracilaria lemaneiformis, cultivation zone and a control zone near Nan'ao Island, South China Sea by MiSeq sequencing of 16S rRNA gene amplicons. We found that large-scale cultivation of G. lemaneiformis increased dissolved oxygen (DO) and pH but decreased inorganic nutrients, possibly due to nutrient uptake, photosynthesis and other physiological processes of G. lemaneiformis. These environmental changes significantly (adonis, P<0.05) shifted the microbial community composition and structure of both water column and sediment samples in the G. lemaneiformis cultivation zone, compared to the control zone. Also, certain microbial taxa associated with seaweed, such as Arenibacter, Croceitalea, Glaciecola, Leucothrix and Maribacter were enriched at the cultivation zone. In addition, we have proposed a conceptual model to summarize the results in this study and guide future studies on relationships among seaweed processes, microbial communities and their environments. Thus, this study not only provides new insights into our understanding the effect of G. lemaneiformis cultivation on microbial communities, but also guides future studies on coastal ecosystems.
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Affiliation(s)
- Xinfei Xie
- Institute of Hydrobiology, Department of Ecology, Jinan University, Guangzhou, China; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Zhili He
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA; School of Environmental Science and Engineering, Environmental Microbiome Research Center, Sun Yat-Sen University, Guangzhou, China.
| | - Xiaojuan Hu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yufeng Yang
- Institute of Hydrobiology, Department of Ecology, Jinan University, Guangzhou, China.
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44
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Guo XP, Niu ZS, Lu DP, Feng JN, Chen YR, Tou FY, Liu M, Yang Y. Bacterial community structure in the intertidal biofilm along the Yangtze Estuary, China. Mar Pollut Bull 2017; 124:314-320. [PMID: 28755810 DOI: 10.1016/j.marpolbul.2017.07.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 06/01/2017] [Revised: 07/20/2017] [Accepted: 07/20/2017] [Indexed: 06/07/2023]
Abstract
In this study, the 16S rRNA-based Illumina MiSeq sequencing was used to investigate the bacterial community structure and composition of intertidal biofilm taken along the Yangtze Estuary. The results showed that 680,721 valid sequences of seven samples were assigned to 147,239 operational taxonomic units, which belonged to 49 phyla, 246 family and 314 genera. Compared to other studies on water and sediments in the study area, biofilms showed highest index of bacterial diversity and abundances. At different taxonomic levels, both dominant taxa and their abundances varied among the seven samples, with Proteobacteria as the dominant phylum in general. Principal component analysis and cluster analysis revealed that bacterial communities at WSK differed from those at other sampling sites. Salinity, dissolved oxygen, pH and nutrients were the vital environmental factors to influence the bacterial community structure of biofilms. These results may provide a new insight into the microbial ecology in estuarine environments.
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Affiliation(s)
- Xing-Pan Guo
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zuo-Shun Niu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Da-Pei Lu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jing-Nan Feng
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yu-Ru Chen
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Fei-Yun Tou
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yi Yang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
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45
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Chen Z, Zheng Y, Ding C, Ren X, Yuan J, Sun F, Li Y. Integrated metagenomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops. Ecotoxicol Environ Saf 2017; 145:111-118. [PMID: 28711820 DOI: 10.1016/j.ecoenv.2017.07.019] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [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: 03/31/2017] [Revised: 07/06/2017] [Accepted: 07/10/2017] [Indexed: 06/07/2023]
Abstract
Two energy crops (maize and soybean) were used in the remediation of cadmium-contaminated soils. These crops were used because they are fast growing, have a large biomass and are good sources for bioenergy production. The total accumulation of cadmium in maize and soybean plants was 393.01 and 263.24μg pot-1, respectively. The rhizosphere bacterial community composition was studied by MiSeq sequencing. Phylogenetic analysis was performed using 16S rRNA gene sequences. The rhizosphere bacteria were divided into 33 major phylogenetic groups according to phyla. The dominant phylogenetic groups included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes. Based on principal component analysis (PCA) and unweighted pair group with arithmetic mean (UPGMA) analysis, we found that the bacterial community was influenced by cadmium addition and bioenergy cropping. Three molecular ecological networks were constructed for the unplanted, soybean- and maize-planted bacterial communities grown in 50mgkg-1 cadmium-contaminated soils. The results indicated that bioenergy cropping increased the complexity of the bacterial community network as evidenced by a higher total number of nodes, the average geodesic distance (GD), the modularity and a shorter geodesic distance. Proteobacteria and Acidobacteria were the keystone bacteria connecting different co-expressed operational taxonomic units (OTUs). The results showed that bioenergy cropping altered the topological roles of individual OTUs and keystone populations. This is the first study to reveal the effects of bioenergy cropping on microbial interactions in the phytoremediation of cadmium-contaminated soils by network reconstruction. This method can greatly enhance our understanding of the mechanisms of plant-microbe-metal interactions in metal-polluted ecosystems.
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Affiliation(s)
- Zhaojin Chen
- Key Laboratory of Ecological Security for Water Source Region of Mid-line Project of South-to-North Diversion Project of Henan Province, College of Agricultural Engineering, Nanyang Normal University, Nanyang 473061, People's Republic of China; Henan Collaborative Innovation Center of Water Security for Water Source Region of Mid-line Project of South-to-North Diversion Project, Nanyang 473061, People's Republic of China.
| | - Yuan Zheng
- Key Laboratory of Ecological Security for Water Source Region of Mid-line Project of South-to-North Diversion Project of Henan Province, College of Agricultural Engineering, Nanyang Normal University, Nanyang 473061, People's Republic of China; Henan Collaborative Innovation Center of Water Security for Water Source Region of Mid-line Project of South-to-North Diversion Project, Nanyang 473061, People's Republic of China
| | - Chuanyu Ding
- Key Laboratory of Ecological Security for Water Source Region of Mid-line Project of South-to-North Diversion Project of Henan Province, College of Agricultural Engineering, Nanyang Normal University, Nanyang 473061, People's Republic of China; Henan Collaborative Innovation Center of Water Security for Water Source Region of Mid-line Project of South-to-North Diversion Project, Nanyang 473061, People's Republic of China
| | - Xuemin Ren
- Key Laboratory of Ecological Security for Water Source Region of Mid-line Project of South-to-North Diversion Project of Henan Province, College of Agricultural Engineering, Nanyang Normal University, Nanyang 473061, People's Republic of China; Henan Collaborative Innovation Center of Water Security for Water Source Region of Mid-line Project of South-to-North Diversion Project, Nanyang 473061, People's Republic of China
| | - Jian Yuan
- Key Laboratory of Ecological Security for Water Source Region of Mid-line Project of South-to-North Diversion Project of Henan Province, College of Agricultural Engineering, Nanyang Normal University, Nanyang 473061, People's Republic of China; Henan Collaborative Innovation Center of Water Security for Water Source Region of Mid-line Project of South-to-North Diversion Project, Nanyang 473061, People's Republic of China
| | - Feng Sun
- Key Laboratory of Ecological Security for Water Source Region of Mid-line Project of South-to-North Diversion Project of Henan Province, College of Agricultural Engineering, Nanyang Normal University, Nanyang 473061, People's Republic of China; Henan Collaborative Innovation Center of Water Security for Water Source Region of Mid-line Project of South-to-North Diversion Project, Nanyang 473061, People's Republic of China
| | - Yuying Li
- Key Laboratory of Ecological Security for Water Source Region of Mid-line Project of South-to-North Diversion Project of Henan Province, College of Agricultural Engineering, Nanyang Normal University, Nanyang 473061, People's Republic of China; Henan Collaborative Innovation Center of Water Security for Water Source Region of Mid-line Project of South-to-North Diversion Project, Nanyang 473061, People's Republic of China
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46
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Yu Z, Wang R, Li N, Zhang C, Liu J. Microbial diversity of the Tibetan tick Haemaphysalis tibetensis (Acari: Ixodidae). Exp Appl Acarol 2017; 73:237-244. [PMID: 28887650 DOI: 10.1007/s10493-017-0179-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 06/05/2017] [Accepted: 09/06/2017] [Indexed: 06/07/2023]
Abstract
The Tibetan tick Haemaphysalis tibetensis is widely distributed in the Tibetan Plateau, and is recognized as one of the primary parasites affecting domestic and wild animals. No information is available on its microbial diversity. In the current study, the microbiomes in H. tibetensis were explored using Illumina MiSeq sequencing. Results indicate that a total of 28 phyla and 38 genera were characterized from this tick, and most of the microbes were classified in the phylum Proteobacteria. Female and male H. tibetensis harbored similar composition of the microbes, with dominant bacteria from the genus Coxiella accounting for 87.5 and 66.5% in females and males, respectively. The abundance of bacteria belonging to the genus Rickettsia in females and males was 6.9 and 23.7%, respectively. These findings may help understand the relationship between this tick and its symbiontic microorganisms.
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Affiliation(s)
- Zhijun Yu
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Rongrong Wang
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Ningxin Li
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Chunmian Zhang
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Jingze Liu
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China.
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Min X, Wang Y, Chai L, Yang Z, Liao Q. High-resolution analyses reveal structural diversity patterns of microbial communities in Chromite Ore Processing Residue (COPR) contaminated soils. Chemosphere 2017; 183:266-276. [PMID: 28550784 DOI: 10.1016/j.chemosphere.2017.05.105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 01/30/2017] [Revised: 05/15/2017] [Accepted: 05/18/2017] [Indexed: 06/07/2023]
Abstract
To explore how heavy metal contamination in Chromite Ore Processing Residue (COPR) disposal sites determine the dissimilarities of indigenous microbial communities, 16S rRNA gene MiSeq sequencing and advanced statistical methods were applied. 13 soil samples were collected from three COPR disposal sites in Mouding of southwestern, Shangnan of northwestern and Yima of central China. The results of analyses of variance (ANOVA), similarities (ANOSIM), and non-metric multidimensional scaling (NMDS) showed that the structural diversity of the microbial communities in the samples with high total chromium (Cr) content (more than 300 mg kg-1; High group) were significantly lesser than in the Low group (less than 90 mg kg-1) regardless of their geographical distribution. But their diversity had virtually rehabilitated under the pressures of long-term metal contamination. Furthermore, the similarity percentage (SIMPER) analysis indicated that the major dissimilarity contributors Micrococcaceae, Delftia, and Streptophyta, possibly having Cr(VI)-resistant and/or Cr(VI)-reducing capability, were dominant in the High group, while Ramlibacter and Gemmatimonas with potential resistances to other heavy metals were prevalent in the Low group. In addition, the multivariate regression tree (MRT), aggregated boosted tree (ABT), and Mantel test revealed that total Cr content affiliated with Cr(VI) was the principal factor shaping the dissimilarities between the soil microbial communities in the COPR sites. Our findings provide a deep insight of the influence of these heavy metals on the microbial communities in the COPR disposal sites and will facilitate bioremediation on such site.
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Affiliation(s)
- Xiaobo Min
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083, Changsha, China; National Engineering Research Center for Heavy Metals Pollution Control and Treatment, 410083, Changsha, China
| | - Yangyang Wang
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083, Changsha, China; College of Environment and Planning, Henan University, 475004, Kaifeng, China
| | - Liyuan Chai
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083, Changsha, China; National Engineering Research Center for Heavy Metals Pollution Control and Treatment, 410083, Changsha, China
| | - Zhihui Yang
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083, Changsha, China; National Engineering Research Center for Heavy Metals Pollution Control and Treatment, 410083, Changsha, China
| | - Qi Liao
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083, Changsha, China; National Engineering Research Center for Heavy Metals Pollution Control and Treatment, 410083, Changsha, China.
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48
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Hill E, Linacre AMT, Toop S, Murphy NP, Strugnell JM. The complete mitochondrial genome of Axis porcinus (Mammalia: Cervidae) from Victoria, Australia, using MiSeq sequencing. Mitochondrial DNA B Resour 2017; 2:453-454. [PMID: 33473860 PMCID: PMC7800214 DOI: 10.1080/23802359.2017.1357451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The mitochondrial genome of the hog deer (Axis porcinus) was sequenced using an Illumina MiSeq. The assembled genome consists of 16,351 bp, and shared a 99.8% similarity to the published chital deer (Axis axis) genome, suggesting that they belong to the same species. Further research is ongoing to understand why these mitochondrial genomes are highly similar.
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Affiliation(s)
- Erin Hill
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Australia
| | | | - Simon Toop
- Game Management Authority, Melbourne, Australia
| | - Nicholas P Murphy
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Australia
| | - Jan M Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture, Marine Biology and Aquaculture, James Cook University, Townsville, Australia.,Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Australia
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Ren Z, Jiang J, Xie H, Li A, Lu H, Xu S, Zhou L, Zhang H, Cui G, Chen X, Liu Y, Wu L, Qin N, Sun R, Wang W, Li L, Zheng S. Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China. Oncotarget. 2017;8:95176-95191. [PMID: 29221120 PMCID: PMC5707014 DOI: 10.18632/oncotarget.18820] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 06/10/2017] [Indexed: 12/16/2022] Open
Abstract
Pancreatic carcinoma (PC) is a lethal cancer. Gut microbiota is associated with some risk factors of PC, e.g. obesity and types II diabetes. However, the specific gut microbial profile in clinical PC in China has never been reported. This prospective study collected 85 PC and 57 matched healthy controls (HC) to analyze microbial characteristics by MiSeq sequencing. The results showed that gut microbial diversity was decreased in PC with an unique microbial profile, which partly attributed to its decrease of alpha diversity. Microbial alterations in PC featured by the increase of certain pathogens and lipopolysaccharides-producing bacteria, and the decrease of probiotics and butyrate-producing bacteria. Microbial community in obstruction cases was separated from the un-obstructed cases. Streptococcus was associated with the bile. Furthermore, 23 microbial functions e.g. Leucine and LPS biosynthesis were enriched, while 13 functions were reduced in PC. Importantly, based on 40 genera associated with PC, microbial markers achieves a high classification power with AUC of 0.842. In conclusion, gut microbial profile was unique in PC, providing a microbial marker for non-invasive PC diagnosis.
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50
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Igarashi Y, Aihara H, Handa Y, Katsumata H, Fujii M, Nakano K, Hirao T. Development and evaluation of microsatellite markers for the critically endangered birch Betula chichibuensis (Betulaceae). Appl Plant Sci 2017; 5:apps1700016. [PMID: 28529833 PMCID: PMC5435406 DOI: 10.3732/apps.1700016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 03/30/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Microsatellite markers were developed and characterized for the critically endangered birch Betula chichibuensis (Betulaceae) to investigate the genetic structure of this species for conservation purposes. METHODS AND RESULTS Sixteen microsatellite markers with di-, tri-, and tetranucleotide repeat motifs were developed and optimized using MiSeq paired-end sequencing. Of these, 14 were polymorphic, with two to five alleles per locus, in 47 individuals from two newly discovered populations of B. chichibuensis in Japan. Observed and unbiased expected heterozygosities per locus ranged from 0.000 to 0.617 and from 0.000 to 0.629, respectively. These markers were tested for cross-species amplification in B. maximowicziana, B. platyphylla var. japonica, and B. schmidtii. CONCLUSIONS This set of microsatellite markers, the first developed for B. chichibuensis, will help elucidate spatial patterns of gene flow and levels of inbreeding in this species to aid its conservation.
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Affiliation(s)
- Yuji Igarashi
- The University of Tokyo Chichibu Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-49 Hinoda-machi, Chichibu, Saitama 368-0034, Japan
| | - Hiroki Aihara
- FASMAC Co. Ltd., 5-1-3 Midorigaoka, Atsugi, Kanagawa 243-0041, Japan
| | - Yoshihiro Handa
- FASMAC Co. Ltd., 5-1-3 Midorigaoka, Atsugi, Kanagawa 243-0041, Japan
| | - Hiroshi Katsumata
- FASMAC Co. Ltd., 5-1-3 Midorigaoka, Atsugi, Kanagawa 243-0041, Japan
| | - Masanori Fujii
- Institute for Environmental Sciences, 1-7 Ienomae, Obuchi, Rokkasho, Kamikita, Aomori 039-3212, Japan
| | - Koichiro Nakano
- FASMAC Co. Ltd., 5-1-3 Midorigaoka, Atsugi, Kanagawa 243-0041, Japan
| | - Toshihide Hirao
- The University of Tokyo Chichibu Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-49 Hinoda-machi, Chichibu, Saitama 368-0034, Japan
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