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Bushra R, Ahmed I, Li JL, Lian Z, Li S, Ali A, Uzair B, Amin A, Ehsan M, Liu YH, Li WJ. Untapped rich microbiota of mangroves of Pakistan: diversity and community compositions. Folia Microbiol (Praha) 2024; 69:595-612. [PMID: 37843797 DOI: 10.1007/s12223-023-01095-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023]
Abstract
The mangrove ecosystem is the world's fourth most productive ecosystem in terms of service value and offering rich biological resources. Microorganisms play vital roles in these ecological processes, thus researching the mangroves-microbiota is crucial for a deeper comprehension of mangroves dynamics. Amplicon sequencing that targeted V4 region of 16S rRNA gene was employed to profile the microbial diversities and community compositions of 19 soil samples, which were collected from the rhizosphere of 3 plant species (i.e., Avicennia marina, Ceriops tagal, and Rhizophora mucronata) in the mangrove forests of Lasbela coast, Pakistan. A total of 67 bacterial phyla were observed from three mangroves species, and these taxa were classified into 188 classes, 453 orders, 759 families, and 1327 genera. We found that Proteobacteria (34.9-38.4%) and Desulfobacteria (7.6-10.0%) were the dominant phyla followed by Chloroflexi (6.6-7.3%), Gemmatimonadota (5.4-6.8%), Bacteroidota (4.3-5.5%), Planctomycetota (4.4-4.9%) and Acidobacteriota (2.7-3.4%), Actinobacteriota (2.5-3.3%), and Crenarchaeota (2.5-3.3%). After considering the distribution of taxonomic groups, we prescribe that the distinctions in bacterial community composition and diversity are ascribed to the changes in physicochemical attributes of the soil samples (i.e., electrical conductivity (ECe), pH, total organic matter (OM), total organic carbon (OC), available phosphorus (P), and extractable potassium (CaCO3). The findings of this study indicated a high-level species diversity in Pakistani mangroves. The outcomes may also aid in the development of effective conservation policies for mangrove ecosystems, which have been hotspots for anthropogenic impacts in Pakistan. To our knowledge, this is the first microbial research from a Pakistani mangrove forest.
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Affiliation(s)
- Rabia Bushra
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad 45500, Pakistan
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad 45500, Pakistan.
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zhenghan Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ahmad Ali
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad 45500, Pakistan
| | - Bushra Uzair
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Arshia Amin
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad 45500, Pakistan
| | | | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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He R, Hu S, Li Q, Zhao D, Wu QL, Zeng J. Greater transmission capacities and small-world characteristics of bacterial communities in the above- than those in the below- ground niches of a typical submerged macrophyte, Vallisneria natans. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166229. [PMID: 37586539 DOI: 10.1016/j.scitotenv.2023.166229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/06/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
Leaves and roots of submerged macrophytes provide extended surfaces and stable internal tissues for distinct microorganisms to rest, but how these microorganisms interact with each other across different niches and ultimately drive the distribution through horizontal and vertical transmissions remains largely undetermined. Knowledge of the mechanisms of assemblage and transmission in aquatic macrophytes-associated microbial communities will help to better understanding their important roles in plant fitness and benefit ecological functions. Here, we conducted a microcosmic experiment based on in situ lake samples to investigate the bacterial community assemblage, transmission, and co-occurrence patterns in different niches of a typical submerged macrophyte, Vallisneria natans (V. natans), including seed endosphere, as well as environmental (water and bulk sediment), epiphytic (phyllosphere and rhizosphere), and endophytic (leaf and root endosphere) microhabitats of both leaves and roots representatives of the above- and below- ground niches (AGNs and BGNs), respectively. We found the bacterial communities colonized in epiphytic niches not only exhibited the highest diversity compared to adjacent environmental and endophytic niches, but also dominated the interactions between those bacterial members of neighboring niches in both AGNs and BGNs. The host plants promoted niche specificity at bacterial community-level, as confirmed by the proportion of bacterial specialists increased with plant proximity, especially in the BGNs. Furthermore, the bacterial taxa colonized in the AGNs exhibited higher horizontal and vertical transmission capacities than those in the BGNs, especially in the vertical transmission from seeds to leaves (41.38 %) than roots (0.42 %). Meanwhile, the bacterial co-occurrence network in AGNs was shown to have stronger small-world characteristics but weaker stability than those in the BGNs. Overall, this study cast new light on the plant microbiome in the aquatic environment, thus better promoting the potential development of strategies for breeding aquatic macrophyte holobiont with enhanced water purification and pollutant removal capabilities in the future.
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Affiliation(s)
- Rujia He
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Nanjing 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Siwen Hu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Nanjing 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qisheng Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Dayong Zhao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Nanjing 210098, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Center for Evolution and Conservation Biology, Southern Marine Sciences and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100039, China.
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Yuan Z, Zeng Z, Liu F. Community structures of mangrove endophytic and rhizosphere bacteria in Zhangjiangkou National Mangrove Nature Reserve. Sci Rep 2023; 13:17127. [PMID: 37816825 PMCID: PMC10564911 DOI: 10.1038/s41598-023-44447-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/08/2023] [Indexed: 10/12/2023] Open
Abstract
Bacterial communities play an important role in mangrove ecosystems. In order to gain information on the bacterial communities in mangrove species and rhizospheres grown in Zhangjiangkou National Mangrove Nature Reserve, this study collected root, branch, and leaf samples from five mangrove species as well as rhizosphere and non-rhizosphere samples and analyzed the community structure of endophytic bacteria and bacteria in rhizosphere and non-rhizosphere using Illumina high-throughput sequencing technique. Bacteria in 52 phyla, 64 classes, 152 orders, 295 families, and 794 genera were identified, which mainly belonged to Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Nitrospirota. At each taxonomic level, the community structure of the rhizosphere bacteria varied slightly with mangrove species, but endophytic bacteria differed greatly with plant species. The diversity indices of endophytic bacteria in branch and leaf samples of Acanthus ilicifolius were significantly lower, and endophytic bacteria in the plant tissues had higher abundance in the replication/repair and translation Clusters of Orthologous Genes functional categories but lower abundance in the carbohydrate metabolism category. This study helps to understand the community structure and diversity characteristics of endophytic and rhizosphere bacteria in different mangrove plants. Provide a theoretical basis for in-depth research on the functions of mangrove ecosystems.
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Affiliation(s)
- Zongsheng Yuan
- College of Geography and Oceanography, Minjiang University, Fuzhou, Fujian, China
| | - Zhihao Zeng
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Fang Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
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Sui J, He X, Yi G, Zhou L, Liu S, Chen Q, Xiao X, Wu J. Diversity and structure of the root-associated bacterial microbiomes of four mangrove tree species, revealed by high-throughput sequencing. PeerJ 2023; 11:e16156. [PMID: 37810771 PMCID: PMC10559887 DOI: 10.7717/peerj.16156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/31/2023] [Indexed: 10/10/2023] Open
Abstract
Background Root-associated microbes of the mangrove trees play important roles in protecting and maintaining mangrove ecosystems. At present, most of our understanding of mangrove root-related microbial diversity is obtained from specific mangrove species in selected geographic regions. Relatively little is known about the composition of the bacterial microbiota existing in disparate mangrove species microenvironments, particularly the relationship among different mangrove species in tropical environments. Methods We collected the root, rhizosphere soil, and non-rhizosphere soil of four mangrove trees (Acanthus ilicifolius, Bruguiera gymnorrhiza, Clerodendrum inerme, and Lumnitzera racemosa) and detected the 16S rRNA gene by a conventional PCR. We performed high throughput sequencing using Illumina Novaseq 6000 platform (2 × 250 paired ends) to investigate the bacterial communities related with the different mangrove species. Results We analyzed the bacterial diversity and composition related to the diverse ecological niches of mangrove species. Our data confirmed distinct distribution patterns of bacterial communities in the three rhizocompartments of the four mangrove species. Microbiome composition varied with compartments and host mangrove species. The bacterial communities between the endosphere and the other two compartments were distinctly diverse independent of mangrove species. The large degree of overlap in critical community members of the same rhizocompartment across distinct mangrove species was found at the phylum level. Furthermore, this is the first report of Acidothermus found in mangrove environments. In conclusion, understanding the complicated host-microbe associations in different mangrove species could lay the foundation for the exploitation of the microbial resource and the production of secondary metabolites.
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Affiliation(s)
- Jinlei Sui
- Public Research Center, Hainan Medical College, Haikou, China
| | - Xiaowen He
- Public Research Center, Hainan Medical College, Haikou, China
| | - Guohui Yi
- Public Research Center, Hainan Medical College, Haikou, China
| | - Limin Zhou
- Public Research Center, Hainan Medical College, Haikou, China
| | - Shunqing Liu
- Public Research Center, Hainan Medical College, Haikou, China
| | - Qianqian Chen
- Public Research Center, Hainan Medical College, Haikou, China
| | - Xiaohu Xiao
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jinyan Wu
- Public Research Center, Hainan Medical College, Haikou, China
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Yan Z, Meng H, Zhang Q, Bi Y, Gao X, Lei Y. Effects of cadmium and flooding on the formation of iron plaques, the rhizosphere bacterial community structure, and root exudates in Kandelia obovata seedlings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158190. [PMID: 35995174 DOI: 10.1016/j.scitotenv.2022.158190] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
In the rhizosphere, plant root exudates (REs) serve as a bridge between plant and soil functional microorganisms, which play a key role in the redox cycle of iron (Fe). This study examined the effects of periodic flooding and cadmium (Cd) on plant REs, the rhizosphere bacterial community structure, and the formation of root Fe plaques in the typical mangrove plant Kandelia obovata, as well as the relationship between REs and Fe redox cycling bacteria. Based on two-way analysis of variance, flooding and Cd had a considerable effect on the REs of K. obovata. DOC, NH4+-N, NO3--N, dissolved inorganic phosphorus, acetic acid, and malonic acid concentrations in REs of K. obovata increased considerably with the increase of Cd concentration under 5 and 10 h flooding conditions. Fe plaque development in the plant root was stimulated by flooding and Cd, although flooding was more effective. After Cd treatment, the ways in which Fe-oxidizing bacteria (FeOB) and Fe-reducing bacteria (FeRB) were enriched in the rhizosphere and rhizoplane of plants were different. Thiobacillus and Sideroxydans (dominant FeOB) were more abundant in the plant rhizosphere, whereas Acinetobacter (dominant FeRB) was more abundant in the rhizoplane. Cd considerably decreased the relative abundance of unclassified_f_Gallionellaceae in the rhizosphere and rhizoplane but dramatically enhanced the relative abundance of Thiobacillus, Shewanella, and unclassified_f_Geobacteraceae. Unclassified_f_Geobacteraceae and Thiobacillus exhibited substantial positive correlations with citric acid and DOC in REs in the rhizosphere and rhizoplane but strong negative correlations with Sideroxydans. The findings indicate that Cd and flooding treatments may play a role in the production and breakdown of Fe plaque in K. obovata roots by affecting the relative abundance of Fe redox cycling bacteria in the rhizosphere and rhizoplane.
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Affiliation(s)
- Zhongzheng Yan
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China.
| | - Huijie Meng
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Qiqiong Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Yuxin Bi
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Xiaoqing Gao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Ying Lei
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
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Wang S, Jiao C, Zhao D, Zeng J, Xing P, Liu Y, Wu QL. Disentangling the assembly mechanisms of bacterial communities in a transition zone between the alpine steppe and alpine meadow ecosystems on the Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157446. [PMID: 35863578 DOI: 10.1016/j.scitotenv.2022.157446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Alpine meadows and alpine steppes are two major grassland types distributed on the Tibetan Plateau. Due in large part to the differences in hydrothermal and nutrient conditions following the thawing of lakeshore permafrost, alpine meadows and alpine steppes which are characterized by disparate above- and below-ground biomass, could emerge together in the grassland transition zone between meadows and steppes of the Tibetan Plateau. Bacterial communities are essential components of alpine grassland ecosystems and respond rapidly to environmental changes. Despite their ecological significance, it remains poorly elucidated whether and how the assembly patterns of bacterial communities differed between alpine meadows and alpine steppes. Here, to disentangle the assembly mechanisms of bacterial communities from alpine meadows and alpine steppes, we collected samples from three diverse habitats (i.e., sediments, rhizosphere soils and bulk soils) in both alpine meadow and steppe ecosystems on the Tibetan Plateau. Our results indicated that in both meadows and steppes, rhizosphere bacterial communities exhibited higher alpha-diversity but lower beta-diversity compared to the bacterial communities in sediments and bulk soils. However, the close relationships of bacterial communities between different habitats weakened from meadows to steppes. Null model analysis indicated that the importance of environmental selection shaping bacterial community assemblages in all habitats decreased from meadows to steppes, whereas the role of dispersal limitation showed an opposite pattern. Moreover, pH was the primary driver of phylogenetic turnover of bacterial communities in the steppes across all habitats, whereas the dominant drivers of phylogenetic turnover of bacterial communities in meadows varied with habitat types. Overall, our findings provide novel insights into understanding the differences in microbial communities between meadows and steppes in the grassland transition zone on the Tibetan Plateau.
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Affiliation(s)
- Shuren Wang
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Congcong Jiao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China.
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Yongqin Liu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou, China.; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China
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Jia W, Wang S, He X, Zhao X. Different factors drive the assembly of pine and Panax notoginseng-associated microbiomes in Panax notoginseng-pine agroforestry systems. Front Microbiol 2022; 13:1018989. [DOI: 10.3389/fmicb.2022.1018989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/24/2022] [Indexed: 11/15/2022] Open
Abstract
Land-use conversion affects the composition and assembly of plant-associated microbiomes, which in turn affects plant growth, development, and ecosystem functioning. However, agroforestry systems, as sustainable land types, have received little attention regarding the dynamics of different plant-associated microbes. In this study, we used high-throughput sequencing technology to analyze the assembly mechanisms and the driving factors of pine- and Panax notoginseng (P.n.)-associated microbiomes during the conversion of different pine forests (Pinus kesiya var. langbianensis and Pinus armandii) into P.n.-pine agroforestry systems. The results showed that the conversion of pure pine forest into P.n.-pine agroforestry systems significantly altered the diversity of pine-associated fungi rather than the community structure, and the community structure of P.n.-associated fungi rather than the diversity. Additionally, plant-associated fungi were more responsive to land-use change than bacteria. Main effect analysis revealed that compartment rather than genotype was the driving factor of pine- and P.n.-associated microbiomes, but P.n. cultivation also significantly affected the assembly of pine-associated microbiomes. In addition, there was a transfer of P.n. endophytes to pine trees in agroforestry systems and the beneficial microbiomes (Massilia, Marmoricola, Herbaspirillum, etc.) were enlarged in pine roots. Therefore, the diversity of the assembly mechanisms of P.n.- and pine-associated microbiomes played an important role in the P.n.--pine agroforestry systems and were the basis for the sustainable development of the P.n.--pine agroforestry systems.
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Swanson E, Sbissi I, Ktari A, Cherif-Silini H, Ghodhbane-Gtari F, Tisa LS, Gtari M. Decrypting phytomicrobiome of the neurotoxic actinorhizal species, Coriaria myrtifolia, and dispersal boundary of Frankia cluster 2 in soil outward compatible host rhizosphere. Front Microbiol 2022; 13:1027317. [PMID: 36439809 PMCID: PMC9684332 DOI: 10.3389/fmicb.2022.1027317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/21/2022] [Indexed: 11/12/2022] Open
Abstract
The actinorhizal plant, Coriaria myrtifolia, is a neurotoxic plant species endemic to the western Mediterranean area, which forms a nitrogen-fixing symbiosis with members of Frankia cluster 2. Contrarily to other Frankia clusters, the occurrence and mode of dispersal for infective cluster 2 units outside of the host plant rhizosphere remains controversial. The present study was designed to investigate the structure of the microbiomes of C. myrtifolia phytosphere, rhizosphere, and soil samples extending outward linearly up to 1 km. Results showed that the epiphyte and endophyte communities were not significantly different from each other for most of the plant tissues. The communities associated with the below-ground tissues (nodule and root) were significantly different from those found on the above-ground tissues (fruit, leaves, and stems) and had a higher community richness. Coriaria myrtifolia phytomicrobiomes were dominated by Cyanobacteria for leaf, stem, and fruit while Actinobacteria and Proteobacteria were dominant in the root and nodule organelles. The nodule, a special niche for nitrogen fixation, was mainly inhabited by Frankia but contained several non-Frankia bacteria. Beside Frankia cluster 2, the presence of clusters 1, 4, and large numbers of cluster 3 strains have been detected in nodules, roots, and rhizospheres of C. myrtifolia. Despite Frankia being found in all plots using plant trapping bioassays with C. myrtifolia seedlings, Frankia cluster 2 was not detected in soil metagenomes showing the limits of detection by this approach. This result also suggests that in the absence of appropriate host plant species, Frankia cluster 2 has a reduced number of infective units present in the soil outward from the rhizosphere.
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Affiliation(s)
- Erik Swanson
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Imed Sbissi
- LR Ecologie Pastorale, Institut des Régions Arides, Médenine, Tunisia
| | - Amir Ktari
- USCR Bactériologie Moléculaire and Génomique, Institut National des Sciences Appliquées and de Technologie, Université de Carthage, Tunis Cedex, Tunisia
| | - Hafsa Cherif-Silini
- LR Microbiologie Appliquée, Département de Microbiologie, Faculté des Sciences Naturelles et de la Vie, Université Ferhat Abbas, Sétif, Algeria
| | - Faten Ghodhbane-Gtari
- USCR Bactériologie Moléculaire and Génomique, Institut National des Sciences Appliquées and de Technologie, Université de Carthage, Tunis Cedex, Tunisia
- Institut Supérieur de Biotechnologie de Sidi Thabet, Université de La Manouba, Biotechnopôle, Sidi Thabet, Sidi Thabet, Tunisia
| | - Louis S. Tisa
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
- *Correspondence: Louis S. Tisa,
| | - Maher Gtari
- USCR Bactériologie Moléculaire and Génomique, Institut National des Sciences Appliquées and de Technologie, Université de Carthage, Tunis Cedex, Tunisia
- Maher Gtari,
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Rolando JL, Kolton M, Song T, Kostka JE. The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA. MICROBIOME 2022; 10:37. [PMID: 35227326 PMCID: PMC8886783 DOI: 10.1186/s40168-021-01187-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/25/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Salt marshes are dominated by the smooth cordgrass Spartina alterniflora on the US Atlantic and Gulf of Mexico coastlines. Although soil microorganisms are well known to mediate important biogeochemical cycles in salt marshes, little is known about the role of root microbiomes in supporting the health and productivity of marsh plant hosts. Leveraging in situ gradients in aboveground plant biomass as a natural laboratory, we investigated the relationships between S. alterniflora primary productivity, sediment redox potential, and the physiological ecology of bulk sediment, rhizosphere, and root microbial communities at two Georgia barrier islands over two growing seasons. RESULTS A marked decrease in prokaryotic alpha diversity with high abundance and increased phylogenetic dispersion was found in the S. alterniflora root microbiome. Significantly higher rates of enzymatic organic matter decomposition, as well as the relative abundances of putative sulfur (S)-oxidizing, sulfate-reducing, and nitrifying prokaryotes correlated with plant productivity. Moreover, these functional guilds were overrepresented in the S. alterniflora rhizosphere and root core microbiomes. Core microbiome bacteria from the Candidatus Thiodiazotropha genus, with the metabolic potential to couple S oxidation with C and N fixation, were shown to be highly abundant in the root and rhizosphere of S. alterniflora. CONCLUSIONS The S. alterniflora root microbiome is dominated by highly active and competitive species taking advantage of available carbon substrates in the oxidized root zone. Two microbially mediated mechanisms are proposed to stimulate S. alterniflora primary productivity: (i) enhanced microbial activity replenishes nutrients and terminal electron acceptors in higher biomass stands, and (ii) coupling of chemolithotrophic S oxidation with carbon (C) and nitrogen (N) fixation by root- and rhizosphere-associated prokaryotes detoxifies sulfide in the root zone while potentially transferring fixed C and N to the host plant. Video Abstract.
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Affiliation(s)
- Jose L Rolando
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - Max Kolton
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion, University of the Negev, Beer Sheva, Israel
| | - Tianze Song
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - Joel E Kostka
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA.
- Georgia Institute of Technology, School of Earth and Atmospheric Sciences, Atlanta, GA, 30332, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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Fang H, Zheng K, Zhang J, Gu X, Zhao Y, Zheng Y, Wang Q. Differences in gene expression and endophytic bacterial diversity in Atractylodes macrocephala Koidz. rhizomes from different growth years. Can J Microbiol 2022; 68:353-366. [PMID: 35080442 DOI: 10.1139/cjm-2021-0262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Atractylodes macrocephala Koidz. (AMK) is widely used owing to its pharmacological activity in traditional Chinese medicine (TCM). Here, we aimed to characterize the differentially expressed genes (DEGs) of one- and three-year growth (OYG and TYG) rhizomes of AMK combined with the endophytic bacterial diversity analysis using high-throughput RNA-sequencing. 114,572 unigenes were annotated in six public databases. 3570 DEGs revealed a clear difference, of which 936 and 2634 genes were up- and down-regulated, respectively. The results of KEGG pathway analysis indicated that DEGs corresponding to the terpenoid synthesis gene were downregulated in TYG rhizomes. 414,424 sequences corresponding to the 16S rRNA gene were divided into 1267 operational taxonomic units (OTUs). Moreover, the diversity of endophytic bacteria changed with species in OYG (773) and TYG (1201) rhizomes at OTU level, and Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla. Comparison of species differences among different growth years revealed that some species were significantly different, such as Actinomycetes, Variovorax, Cloacibacterium, etc. Interestingly, the decrease in the function-related metabolism of terpenoids and polyketides was found to be correlated the low expression of terpene synthesis genes in TYG rhizomes assessed using PICRUSt2. These data provide a scientific basis for elucidating the mechanism underlying metabolite accumulation and endophytic bacterial diversity in relation to the growth years in AMK.
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Affiliation(s)
- Huiyong Fang
- Hebei University of Chinese Medicine, 441322, Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Shijiazhuang, China.,Hebei University of Chinese Medicine, 441322, College of Pharmacy, Shijiazhuang, College of Pharmacy, China;
| | - Kaiyan Zheng
- Hebei University of Chinese Medicine, 441322, Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Shijiazhuang, China.,Hebei University of Chinese Medicine, 441322, College of Pharmacy, Shijiazhuang, China;
| | - Jianyun Zhang
- Hebei University of Chinese Medicine, 441322, Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Shijiazhuang, China, 050200.,Hebei University of Chinese Medicine, 441322, College of Pharmacy, Shijiazhuang, China, 050200;
| | - Xian Gu
- Hebei University of Chinese Medicine, 441322, Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Shijiazhuang, China.,Hebei University of Chinese Medicine, 441322, College of Pharmacy, Shijiazhuang, China;
| | - Yanyun Zhao
- Hebei University of Chinese Medicine, 441322, Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Shijiazhuang, China.,Hebei University of Chinese Medicine, 441322, College of Pharmacy, Shijiazhuang, China;
| | - Yuguang Zheng
- Hebei Chemical and Pharmaceutical College, 118457, Shijiazhuang, Hebei, China.,Hebei University of Chinese Medicine, 441322, Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Shijiazhuang, China;
| | - Qian Wang
- Hebei University of Chinese Medicine, 441322, Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Shijiazhuang, China.,Hebei University of Chinese Medicine, 441322, College of Pharmacy, Shijiazhuang, China;
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11
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He R, Zeng J, Zhao D, Wang S, Wu QL. Decreased spatial variation and deterministic processes of bacterial community assembly in the rhizosphere of Phragmites australis across the Middle-Lower Yangtze plain. Mol Ecol 2021; 31:1180-1195. [PMID: 34846091 DOI: 10.1111/mec.16298] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/31/2021] [Accepted: 11/22/2021] [Indexed: 12/13/2022]
Abstract
Comparison of the spatial distribution and assembly processes between bulk and rhizosphere bacterial communities at multiple spatial scales is vital for understanding the generation and maintenance of microbial diversity under the influence of plants. However, biogeographical patterns and the underlying mechanisms of microbial communities in bulk and rhizosphere sediments of aquatic ecosystems remain unclear. Here, we collected 140 bulk and rhizosphere sediment samples of Phragmites australis from 14 lakeshore zones across a 510-km transect in the Middle-Lower Yangtze plain. We performed high-throughput sequencing to investigate the bacterial diversity, composition, spatial distribution and assembly processes of these samples. Bacterial communities in the rhizosphere sediment exhibited higher alpha diversity but lower beta diversity than those in the bulk sediment. Both bulk and rhizosphere sediment bacterial communities had significant distance-decay relationships, but spatial turnover of the rhizosphere sediment bacterial community was strikingly lower than that of bulk sediment. Despite variable selection dominating the assembly processes of bacterial communities in bulk sediment, the rhizosphere of P. australis enhanced the role of dispersal limitation in governing bacterial communities. The relative importance of different ecological processes in determining bacterial assembly presented distinct patterns of increasing or decreasing linearly with an increase of scale. This investigation highlights the convergent selection of the aquatic plant rhizosphere for surrounding bacterial communities and emphasizes the importance of different ecological processes on bacterial community assembly in sediment environments over different scales. Furthermore, we provide a preliminary framework for exploring the scale dependence of microbial community assembly in aquatic ecosystems.
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Affiliation(s)
- Rujia He
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.,Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Shuren Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.,Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.,Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China
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12
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Martos S, Busoms S, Pérez-Martín L, Llugany M, Cabot C, Poschenrieder C. Identifying the Specific Root Microbiome of the Hyperaccumulator Noccaea brachypetala Growing in Non-metalliferous Soils. Front Microbiol 2021; 12:639997. [PMID: 34054748 PMCID: PMC8160108 DOI: 10.3389/fmicb.2021.639997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/06/2021] [Indexed: 12/02/2022] Open
Abstract
Noccaea brachypetala is a close relative of Noccaea caerulescens, a model plant species used in metal hyperaccumulation studies. In a previous survey in the Catalan Pyrenees, we found two occidental and two oriental N. brachypetala populations growing on non-metalliferous soils, with accumulated high concentrations of Cd and Zn. Our hypothesis was that the microbiome companion of the plant roots may influence the ability of these plants to absorb metals. We performed high-throughput sequencing of the bacterial and fungal communities in the rhizosphere soil and rhizoplane fractions. The rhizobiomes and shoot ionomes of N. brachypetala plants were analyzed along with those from other non-hyperaccumulator Brassicaceae species found at the same sampling locations. The analyses revealed that microbiome richness and relative abundance tended to increase in N. brachypetala plants compared to non-hyperaccumulator species, regardless of plant location. We confirmed that the root compartment is a key factor in describing the community composition linked to the cohabiting Brassicaceae species, and the rhizoplane fraction contained the specific and rare taxa associated with each species. N. brachypetala plants harbored a similar relative abundance of fungi compared to the other plant hosts, but there was a notable reduction in some specific taxa. Additionally, we observed an enrichment in the hyperaccumulator rhizoplane of previously described metal-tolerant bacteria and bacteria involved in nitrogen cycling. The bacteria involved in the nitrogen cycle could contribute indirectly to the hyperaccumulator phenotype by improving soil quality and fertility. Our results indicate that N. brachypetala captures a particular prokaryotic community from the soil. This particular prokaryotic community may benefit the extraction of metal ions and/or improve plant nutrition. Our research identified satellite groups associated with the root niche of a hyperaccumulator plant that may assist in improving biological strategies in heavy metal remediation.
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Affiliation(s)
- Soledad Martos
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sílvia Busoms
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Laura Pérez-Martín
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Mercè Llugany
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Catalina Cabot
- Department of Biology, Universitat de les Illes Balears, Palma, Spain
| | - Charlotte Poschenrieder
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Bellaterra, Spain
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13
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Wails CN, Baker K, Blackburn R, Del Vallé A, Heise J, Herakovich H, Holthuijzen WA, Nissenbaum MP, Rankin L, Savage K, Vanek JP, Jones HP. Assessing changes to ecosystem structure and function following invasion by Spartina alterniflora and Phragmites australis: a meta-analysis. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02540-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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14
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Pirrello C, Zeilmaker T, Bianco L, Giacomelli L, Moser C, Vezzulli S. Mining Grapevine Downy Mildew Susceptibility Genes: A Resource for Genomics-Based Breeding and Tailored Gene Editing. Biomolecules 2021; 11:181. [PMID: 33525704 PMCID: PMC7912118 DOI: 10.3390/biom11020181] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/13/2022] Open
Abstract
Several pathogens continuously threaten viticulture worldwide. Until now, the investigation on resistance loci has been the main trend to understand the interaction between grapevine and the mildew causal agents. Dominantly inherited gene-based resistance has shown to be race-specific in some cases, to confer partial immunity, and to be potentially overcome within a few years since its introgression. Recently, on the footprint of research conducted in Arabidopsis, putative genes associated with downy mildew susceptibility have been discovered also in the grapevine genome. In this work, we deep-sequenced four putative susceptibility genes-namely VvDMR6.1, VvDMR6.2, VvDLO1, VvDLO2-in 190 genetically diverse grapevine genotypes to discover new sources of broad-spectrum and recessively inherited resistance. Identified Single Nucleotide Polymorphisms were screened in a bottleneck analysis from the genetic sequence to their impact on protein structure. Fifty-five genotypes showed at least one impacting mutation in one or more of the scouted genes. Haplotypes were inferred for each gene and two of them at the VvDMR6.2 gene were found significantly more represented in downy mildew resistant genotypes. The current results provide a resource for grapevine and plant genetics and could corroborate genomic-assisted breeding programs as well as tailored gene editing approaches for resistance to biotic stresses.
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Affiliation(s)
- Carlotta Pirrello
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Tieme Zeilmaker
- SciENZA Biotechnologies B.V., Sciencepark 904, 1098 XH Amsterdam, The Netherlands;
| | - Luca Bianco
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
| | - Lisa Giacomelli
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
- SciENZA Biotechnologies B.V., Sciencepark 904, 1098 XH Amsterdam, The Netherlands;
| | - Claudio Moser
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
| | - Silvia Vezzulli
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
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15
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Kolton M, Rolando JL, Kostka JE. Elucidation of the rhizosphere microbiome linked to Spartina alterniflora phenotype in a salt marsh on Skidaway Island, Georgia, USA. FEMS Microbiol Ecol 2020; 96:5813622. [PMID: 32227167 DOI: 10.1093/femsec/fiaa026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 03/23/2020] [Indexed: 01/04/2023] Open
Abstract
Smooth cordgrass, Spartina alterniflora, dominates salt marshes on the east coast of the United States. While the physicochemical cues affecting S. alterniflora productivity have been studied intensively, the role of plant-microbe interactions in ecosystem functioning remains poorly understood. Thus, in this study, the effects of S. alterniflora phenotype on the composition of archaeal, bacterial, diazotrophic and fungal communities were investigated. Overall, prokaryotic communities were more diverse and bacteria were more abundant in the areas colonized by the tall plant phenotype in comparison to those of short plant phenotype. Diazotrophic methanogens (Methanomicrobia) preferentially colonized the area of the short plant phenotype. Putative iron-oxidizing Zetaproteobacteria and sulfur-oxidizing Campylobacteria were identified as indicator species in the rhizosphere of tall and short plant phenotypes, respectively. Finally, while diazotrophic populations shaped microbial interactions in the areas colonized by the tall plant phenotype, fungal populations filled this role in the areas occupied by the short plant phenotype. The results here demonstrate that S. alterniflora phenotype and proximity to the root zone are selective forces dictating microbial community assembly. Results further reveal that reduction-oxidation chemistry is a major factor driving the selection of belowground microbial populations in salt marsh habitats.
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Affiliation(s)
- Max Kolton
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - José L Rolando
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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16
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Yang Y, Ding J, Chi Y, Yuan J. Characterization of bacterial communities associated with the exotic and heavy metal tolerant wetland plant Spartina alterniflora. Sci Rep 2020; 10:17985. [PMID: 33093514 PMCID: PMC7583234 DOI: 10.1038/s41598-020-75041-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/09/2020] [Indexed: 11/30/2022] Open
Abstract
Heavy metal pollution has seriously disrupted eco-balance and transformed estuaries into sewage depots. Quanzhou bay is a typical heavy metal-contaminated estuary, in which Spartina alterniflora has widely invaded. Plant-associated microbial communities are crucial for biogeochemical cycles, studies of which would be helpful to demonstrate the invasion mechanisms of plants. Meanwhile, they are indispensable to phytoremediation by enhancing the heavy metal tolerance of plants, facilitating heavy metal absorption rate and promoting growth of plants. In the present study, S. alterniflora-associated rhizo- and endobacterial communities from 3 experimental sites were investigated by 454-pyrosequencing. Heavy metal screening generated 16 culturable isolates, further biochemical assays suggested these clones possess various abilities such as phosphate solubilization, indole-3-acetic acid (IAA) production and 1-aminocyclopropane-1-carboxylate (ACC) deaminase production to accelerate heavy metal uptake and growth of the host. This study revealed the bacterial community structures and characterized the predominant resident bacterial strains of S. alterniflora-associated rhizo- and endobacteria under heavy metal stress, and isolated several bacterial species with potential ecological function.
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Affiliation(s)
- Ying Yang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, 362000, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Jian Ding
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
- Sunshine Guojian Pharmaceutical (Shanghai) Co., Ltd, Shanghai, China
| | - Yulang Chi
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, 362000, China.
| | - Jianjun Yuan
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, 362000, China.
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17
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Papik J, Folkmanova M, Polivkova-Majorova M, Suman J, Uhlik O. The invisible life inside plants: Deciphering the riddles of endophytic bacterial diversity. Biotechnol Adv 2020; 44:107614. [PMID: 32858117 DOI: 10.1016/j.biotechadv.2020.107614] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/14/2020] [Accepted: 08/15/2020] [Indexed: 10/25/2022]
Abstract
Endophytic bacteria often promote plant growth and protect their host plant against pathogens, herbivores, and abiotic stresses including drought, increased salinity or pollution. Current agricultural practices are being challenged in terms of climate change and the ever-increasing demand for food. Therefore, the rational exploitation of bacterial endophytes to increase the productivity and resistance of crops appears to be very promising. However, the efficient and larger-scale use of bacterial endophytes for more effective and sustainable agriculture is hindered by very little knowledge on molecular aspects of plant-endophyte interactions and mechanisms driving bacterial communities in planta. In addition, since most of the information on bacterial endophytes has been obtained through culture-dependent techniques, endophytic bacterial diversity and its full biotechnological potential still remain highly unexplored. In this study, we discuss the diversity and role of endophytic populations as well as complex interactions that the endophytes have with the plant and vice versa, including the interactions leading to plant colonization. A description of biotic and abiotic factors influencing endophytic bacterial communities is provided, along with a summary of different methodologies suitable for determining the diversity of bacterial endophytes, mechanisms governing the assembly and structure of bacterial communities in the endosphere, and potential biotechnological applications of endophytes in the future.
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Affiliation(s)
- Jakub Papik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Magdalena Folkmanova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Marketa Polivkova-Majorova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Jachym Suman
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic.
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18
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Contrasting Patterns in Diversity and Community Assembly of Phragmites australis Root-Associated Bacterial Communities from Different Seasons. Appl Environ Microbiol 2020; 86:AEM.00379-20. [PMID: 32385080 DOI: 10.1128/aem.00379-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/01/2020] [Indexed: 12/13/2022] Open
Abstract
The common reed (Phragmites australis), a cosmopolitan aquatic macrophyte, plays an important role in the structure and function of aquatic ecosystems. We compared bacterial community compositions (BCCs) and their assembly processes in the root-associated compartments (i.e., rhizosphere and endosphere) of reed and bulk sediment between summer and winter. The BCCs were analyzed using high-throughput sequencing of the bacterial 16S rRNA gene; meanwhile, null-model analysis was employed to characterize their assembly mechanisms. The sources of the endosphere BCCs were quantitatively examined using SourceTracker from bulk sediment, rhizosphere, and seed. We observed the highest α-diversity and the lowest β-diversity of BCCs in the rhizosphere in both seasons. We also found a significant increase in α- and β-diversity in summer compared to that in winter among the three compartments. It was demonstrated that rhizosphere sediments were the main source (∼70%) of root endosphere bacteria during both seasons. Null-model tests indicated that stochastic processes primarily affected endosphere BCCs, whereas both deterministic and stochastic processes dictated bacterial assemblages of the rhizosphere, with the relative importance of stochastic versus deterministic processes depending on the season. This study suggests that multiple mechanisms of bacterial selection and community assembly exist both inside and outside P. australis roots in different seasons.IMPORTANCE Understanding the composition and assembly mechanisms of root-associated microbial communities of plants is crucial for understanding the interactions between plants and soil. Most previous studies of the plant root-associated microbiome focused on model and economic plants, with fewer temporal or seasonal investigations. The assembly mechanisms of root-associated bacterial communities in different seasons remain poorly known, especially for the aquatic macrophytes. In this study, we compared the diversity, composition, and relative importance of two different assembly processes (stochastic and deterministic processes) of bacterial communities associated with bulk sediment and the rhizosphere and endosphere of Phragmites australis in summer and winter. While we found apparent differences in composition, diversity, and assembly processes of bacterial communities among different compartments, season played important roles in determining BCCs and their diversity patterns and assemblages. We also found that endosphere bacteria mainly originated from the rhizosphere. The results add new knowledge regarding the plant-microbe interactions in aquatic ecosystems.
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19
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Liu X, Yang C, Yu X, Yu H, Zhuang W, Gu H, Xu K, Zheng X, Wang C, Xiao F, Wu B, He Z, Yan Q. Revealing structure and assembly for rhizophyte-endophyte diazotrophic community in mangrove ecosystem after introduced Sonneratia apetala and Laguncularia racemosa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 721:137807. [PMID: 32179356 DOI: 10.1016/j.scitotenv.2020.137807] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 06/10/2023]
Abstract
Biological nitrogen fixation (BNF) mediated by diazotrophic communities is a major source of bioavailable nitrogen in mangrove wetlands, which plays important roles in maintaining the health and stability of mangrove ecosystems. Recent large-scale mangrove afforestation activities have drawn great attention due to introduced mangrove species and their potential impacts on bio-functionalities of local ecosystems. However, the effects of introduced mangrove species on diazotrophic communities remain unclear. Here, we analyzed rhizosphere and endosphere diazotrophic communities between native mangrove species (Avicennia marina) and introduced mangrove species (Sonneratia apetala and Laguncularia racemose) by sequencing nifH gene amplicons. Our results showed that S. apetala and L. racemose introduction significantly (P < 0.05) increased nutrition components (e.g., total carbon and total nitrogen) in rhizosphere, as well as the diazotrophs richness in rhizosphere and endosphere. The relative abundance of clusters III diazotrophs in the rhizosphere and Rhizobium in the endosphere were significantly increased with L. racemosa or S. apetala introduction. Fe and pH were the main environmental factors driving the divergence of endophyte-rhizophyte diazotrophs between native and introduced mangroves. The correlation-based network analyses indicated that the interaction among rhizophyte-endophyte diazotrophs is more harmonious in native mangrove, while there exist more competition in introduced mangroves. These findings expand our current understanding of BNF in mangrove afforestation, and providing new perspectives to sustainable management of mangrove ecosystem.
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Affiliation(s)
- Xingyu Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Chao Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Huang Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Wei Zhuang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Hang Gu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Kui Xu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Cheng Wang
- South China Sea Institution, Sun Yat-sen University, Zhuhai 519082, China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; South China Sea Institution, Sun Yat-sen University, Zhuhai 519082, China; College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.
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20
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Wang C, Masoudi A, Wang M, Yang J, Shen R, Man M, Yu Z, Liu J. Community structure and diversity of the microbiomes of two microhabitats at the root-soil interface: implications of meta-analysis of the root-zone soil and root endosphere microbial communities in Xiong'an New Area. Can J Microbiol 2020; 66:605-622. [PMID: 32526152 DOI: 10.1139/cjm-2020-0061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The diversity of the microbial compositions of the root-zone soil (the rhizosphere-surrounding soil) and root endosphere (all inner root tissues) of Pinus tabulaeformis Carr. and Ginkgo biloba L. were evaluated in Xiong'an New Area using high-throughput sequencing; the influence of the soil edaphic parameters on microbial community compositions was also evaluated. Our results showed that both the taxonomic and phylogenetic diversities of the root endosphere were lower than those of the root-zone soil, but the variation in the endosphere microbial community structure was remarkably higher than that of the root-zone soil. Spearman correlation analysis showed that the soil organic matter, total nitrogen, total phosphate, total potassium, ratio of carbon to nitrogen, and pH significantly explained the α-diversity of the bacterial community and that total nitrogen differentially contributed to the α-diversity of the fungal community. Variation partitioning analysis showed that plant species had a greater influence on microbial composition variations than did any other soil property, although soil chemical parameters explained more variation when integrated. Together, our results suggest that both plant species and soil chemical parameters played a critical role in shaping the microbial community composition.
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Affiliation(s)
- Can Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Abolfazl Masoudi
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Min Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Jia Yang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Ruowen Shen
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Meng Man
- Library of Hebei Normal University, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
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21
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Yang A, Akhtar SS, Fu Q, Naveed M, Iqbal S, Roitsch T, Jacobsen SE. Burkholderia Phytofirmans PsJN Stimulate Growth and Yield of Quinoa under Salinity Stress. PLANTS 2020; 9:plants9060672. [PMID: 32466435 PMCID: PMC7355930 DOI: 10.3390/plants9060672] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/16/2020] [Accepted: 05/18/2020] [Indexed: 12/17/2022]
Abstract
One of the major challenges in agriculture is to ensure sufficient and healthy food availability for the increasing world population in near future. This requires maintaining sustainable cultivation of crop plants under varying environmental stresses. Among these stresses, salinity is the second most abundant threat worldwide after drought. One of the promising strategies to mitigate salinity stress is to cultivate halotolerant crops such as quinoa. Under high salinity, performance can be improved by plant growth promoting bacteria (PGPB). Among PGPB, endophytic bacteria are considered better in stimulating plant growth compared to rhizosphere bacteria because of their ability to colonize both in plant rhizosphere and plant interior. Therefore, in the current study, a pot experiment was conducted in a controlled greenhouse to investigate the effects of endophytic bacteria i.e., Burkholderia phytofirmans PsJN on improving growth, physiology and yield of quinoa under salinity stress. At six leaves stage, plants were irrigated with saline water having either 0 (control) or 400 mM NaCl. The results indicated that plants inoculated with PsJN mitigated the negative effects of salinity on quinoa resulting in increased shoot biomass, grain weight and grain yield by 12%, 18% and 41% respectively, over un-inoculated control. Moreover, inoculation with PsJN improved osmotic adjustment and ion homeostasis ability. In addition, leaves were also characterized for five key reactive oxygen species (ROS) scavenging enzyme in response to PsJN treatment. This showed higher activity of catalase (CAT) and dehydroascobate reductase (DHAR) in PsJN-treated plants. These findings suggest that inoculation of quinoa seeds with Burkholderia phytofirmans PsJN could be used for stimulating growth and yield of quinoa in highly salt-affected soils.
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Affiliation(s)
- Aizheng Yang
- School of Water Conservancy and Civil Engineering, Northeast Agriculture University, Harbin 150030, China;
| | - Saqib Saleem Akhtar
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Højbakkegård Allé 13, DK-2630 Tåstrup, Denmark; (S.S.A.); (T.R.)
- Dansk Agro Aps, Snubbekorsvej 20 C, DK-2630 Tåstrup, Denmark
| | - Qiang Fu
- School of Water Conservancy and Civil Engineering, Northeast Agriculture University, Harbin 150030, China;
- Correspondence: (Q.F.); (S.-E.J.)
| | - Muhammad Naveed
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
| | - Shahid Iqbal
- Department of Agronomy, Muhammad Nawaz Shareef University of Agriculture, Multan 66000, Pakistan;
| | - Thomas Roitsch
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Højbakkegård Allé 13, DK-2630 Tåstrup, Denmark; (S.S.A.); (T.R.)
- Department of Adaptive Biotechnologies, Global Change Research Institute, CAS, 603 00 Brno, Czech Republic
| | - Sven-Erik Jacobsen
- Quinoa Quality ApS, DK-4420 Regstrup, Denmark
- Correspondence: (Q.F.); (S.-E.J.)
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22
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Shyntum DY, Nkomo NP, Shingange NL, Gricia AR, Bellieny-Rabelo D, Moleleki LN. The Impact of Type VI Secretion System, Bacteriocins and Antibiotics on Bacterial Competition of Pectobacterium carotovorum subsp. brasiliense and the Regulation of Carbapenem Biosynthesis by Iron and the Ferric-Uptake Regulator. Front Microbiol 2019; 10:2379. [PMID: 31681235 PMCID: PMC6813493 DOI: 10.3389/fmicb.2019.02379] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/30/2019] [Indexed: 12/17/2022] Open
Abstract
The complexity of plant microbial communities provides a rich model for investigating biochemical and regulatory strategies involved in interbacterial competition. Within these niches, the soft rot Enterobacteriaceae (SRE) represents an emerging group of plant-pathogens causing soft rot/blackleg diseases resulting in economic losses worldwide in a variety of crops. A preliminary screening using next-generation sequencing of 16S rRNA comparatively analyzing healthy and diseased potato tubers, identified several taxa from Proteobacteria to Firmicutes as potential potato endophytes/plant pathogens. Subsequent to this, a range of molecular and computational techniques were used to determine the contribution of antimicrobial factors such as bacteriocins, carbapenem and type VI secretion system (T6SS), found in an aggressive SRE (Pectobacterium carotovorum subsp. brasiliense strain PBR1692 - Pcb1692) against these endophytes/plant pathogens. The results showed growth inhibition of several Proteobacteria by Pcb1692 depends either on carbapenem or pyocin production. Whereas for targeted Firmicutes, only the Pcb1692 pyocin seems to play a role in growth inhibition. Furthermore, production of carbapenem by Pcb1692 was observably dependent on the presence of environmental iron and oxygen. Additionally, upon deletion of fur, slyA and expI regulators, carbapenem production ceased, implying a complex regulatory mechanism involving these three genes. Finally, the results demonstrated that although T6SS confers no relevant advantage during in vitro competition, a significant attenuation in competition by the mutant strain lacking a functional T6SS was observed in planta. IMPORTANCE Soft rot Enterobacteriaceae (SRE) represents important phytopathogens causing soft rot/blackleg diseases in a variety of crops leading to huge economic losses worldwide. These pathogens have been isolated alongside other bacteria from different environments such as potato tubers, stems, roots and from the soil. In these environments, SREs coexist with other bacteria where they have to compete for scarce nutrients and other resources. In this report, we show that Pectobacterium carotovorum subsp. brasiliense strain PBR1692 - Pcb1692, which represents one of the SREs, inhibits growth of several different bacteria by producing different antimicrobial compounds. These antimicrobial compounds can be secreted inside or outside the plant host, allowing Pcb1692 to effectively colonize different types of ecological niches. By analyzing the genome sequences of several SREs, we show that other SREs likely deploy similar antimicrobials to target other bacteria.
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Affiliation(s)
- Divine Yufetar Shyntum
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Ntombikayise Precious Nkomo
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Ntwanano Luann Shingange
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Alessandro Rino Gricia
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Daniel Bellieny-Rabelo
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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23
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Chen L, Fang K, Zhou J, Yang ZP, Dong XF, Dai GH, Zhang HB. Enrichment of soil rare bacteria in root by an invasive plant Ageratina adenophora. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 683:202-209. [PMID: 31132698 DOI: 10.1016/j.scitotenv.2019.05.220] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/15/2019] [Accepted: 05/15/2019] [Indexed: 05/24/2023]
Abstract
The assembly of the root-associated microbiome provides mutual benefits for the host plant and bacteria in soils. It is interesting how invasive plants interact with the local soil microbial community and establish the soil bacterial community in the endosphere of these plants in the short term. In this study, we compared the bacterial community in the rhizosphere with that in the root endosphere of an invasive plant, Ageratina adenophora, using high-throughput sequencing. The results showed that the roots of A. adenophora selectively accumulated the genera Clostridium and Enterobacter, which are rarely distributed in the rhizosphere. This selective accumulation caused a switch in the bacterial composition at the phylum level from Bacteroidetes predominant in the rhizosphere to Proteobacteria dominant in the root endosphere of A. adenophora. Our data indicated the potential existence of a highly conserved signal recognition in which hosts, either invasive or native, enrich the endosphere bacteria, such as Clostridium, Enterobacter, etc., from the rhizosphere. Moreover, the accumulated bacteria were physiologically and genetically different at the strain level and displayed distinct roles in growth between invasive and native plants. The assembly of the bacterial community in the roots may be an advantageous strategy for A. adenophora in competition with native plants.
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Affiliation(s)
- Lin Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; School of Life Sciences, Yunnan University, Kunming 650091, China; School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Kai Fang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; School of Life Sciences, Yunnan University, Kunming 650091, China; School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Jie Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Zhi-Ping Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Xing-Fan Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Guang-Hui Dai
- Institute of Ecology and Geobotany, School of Ecology and Environment Science, Yunnan University, Kunming 650091, China
| | - Han-Bo Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; School of Life Sciences, Yunnan University, Kunming 650091, China; School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China.
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24
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Nguyen PM, Afzal M, Ullah I, Shahid N, Baqar M, Arslan M. Removal of pharmaceuticals and personal care products using constructed wetlands: effective plant-bacteria synergism may enhance degradation efficiency. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:21109-21126. [PMID: 31134537 DOI: 10.1007/s11356-019-05320-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 04/30/2019] [Indexed: 06/09/2023]
Abstract
Post-industrial era has witnessed significant advancements at unprecedented rates in the field of medicine and cosmetics, which has led to affluent use of pharmaceuticals and personal care products (PPCPs). However, this has exacerbated the influx of various pollutants in the environment affecting living organisms through multiple routes. Thousands of PPCPs of various classes-prescription and non-prescription drugs-are discharged directly into the environment. In this review, we have surveyed literature investigating plant-based remediation practices to remove PPCPs from the environment. Our specific aim is to highlight the importance of plant-bacteria interplay for sustainable remediation of PPCPs. The green technologies not only are successfully curbing organic pollutants but also have displayed certain limitations. For example, the presence of biologically active compounds within plant rhizosphere may affect plant growth and hence compromise the phytoremediation potential of constructed wetlands. To overcome these hindrances, combined use of plants and beneficial bacteria has been employed. The microbes (both rhizo- and endophytes) in this type of system not only degrade PPCPs directly but also accelerate plant growth by producing growth-promoting enzymes and hence remediation potential of constructed wetlands.
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Affiliation(s)
- Phuong Minh Nguyen
- Department of Environmental Technology, Faculty of Environmental Sciences, VNU University of Science, Vietnam National University, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam.
| | - Muhammad Afzal
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan
| | - Inaam Ullah
- International Join laboratory for Global Climate Change Ecology, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Naeem Shahid
- Department System Ecotoxicology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, Leipzig, 04318, Germany
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari Campus, Islamabad, Pakistan
| | - Mujtaba Baqar
- Sustainable Development Study Centre, Government College University Lahore, Lahore, 54000, Pakistan
| | - Muhammad Arslan
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan.
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany.
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25
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Zhang Q, Acuña JJ, Inostroza NG, Mora ML, Radic S, Sadowsky MJ, Jorquera MA. Endophytic Bacterial Communities Associated with Roots and Leaves of Plants Growing in Chilean Extreme Environments. Sci Rep 2019; 9:4950. [PMID: 30894597 PMCID: PMC6426880 DOI: 10.1038/s41598-019-41160-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/01/2019] [Indexed: 12/21/2022] Open
Abstract
Several studies have demonstrated the relevance of endophytic bacteria on the growth and fitness of agriculturally-relevant plants. To our knowledge, however, little information is available on the composition, diversity, and interaction of endophytic bacterial communities in plants struggling for existence in the extreme environments of Chile, such as the Atacama Desert (AD) and Patagonia (PAT). The main objective of the present study was to analyze and compare the composition of endophytic bacterial communities associated with roots and leaves of representative plants growing in Chilean extreme environments. The plants sampled were: Distichlis spicate and Pluchea absinthioides from the AD, and Gaultheria mucronata and Hieracium pilosella from PAT. The abundance and composition of their endophytic bacterial communities was determined by quantitative PCR and high–throughput sequencing of 16S rRNA, respectively. Results indicated that there was a greater abundance of 16S rRNA genes in plants from PAT (1013 to 1014 copies g−1 DNA), compared with those from AD (1010 to 1012 copies g−1 DNA). In the AD, a greater bacterial diversity, as estimated by Shannon index, was found in P. absinthioides, compared with D. spicata. In both ecosystems, the greater relative abundances of endophytes were mainly attributed to members of the phyla Proteobacteria (14% to 68%), Firmicutes (26% to 41%), Actinobacteria (6 to 23%) and Bacteroidetes (1% to 21%). Our observations revealed that most of operational taxonomic units (OTUs) were not shared between tissue samples of different plant species in both locations, suggesting the effect of the plant genotype (species) on the bacterial endophyte communities in Chilean extreme environments, where Bacillaceae and Enterobacteriacea could serve as keystone taxa as revealed our linear discriminant analysis.
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Affiliation(s)
- Qian Zhang
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA
| | - Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Nitza G Inostroza
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - María Luz Mora
- Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Sergio Radic
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad de Magallanes, Ave. Bulnes 01855, Punta Arenas, Chile
| | - Michael J Sadowsky
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA.,Department of Soil, Water, and Climate, and Department of Plant and Microbial Biology, University of Minnesota, 439 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile. .,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.
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26
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Ren F, Dong W, Yan DH. Endophytic bacterial communities of Jingbai Pear trees in north China analyzed with Illumina sequencing of 16S rDNA. Arch Microbiol 2018; 201:199-208. [PMID: 30506399 DOI: 10.1007/s00203-018-1597-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/05/2018] [Accepted: 11/16/2018] [Indexed: 01/08/2023]
Abstract
Plant endophytes play a crucial role in plant growth, health and ecological function. Jingbai pear (the best quality cultivar of Pyrus ussuriensi Maxim. ex Rupr.) has important ecological and economic value in north China. Conversation of its genetics has great meanings to pear genus (Pyrus L.). However, the bacterial community associated with the cultivar remains unknown. In this study, the structure of endophytic bacterial communities associated with different tissues and soil of Jingbai Pear trees was analyzed with Illumina Miseq sequencing of bacterial 16S rDNA. This is the first report on bacterial microbiome associated with Jingbai pear. Our results demonstrated that different tissues harbored a unique bacterial assemblage. Interestingly, Cyanobacteria was the most abundant phylum, followed by Proteobacteria and Actinobacteria. Samples from three different sites (soils) had significant differences in microbial communities structure. Redundancy analysis (RDA) showed that the bacterial community structure correlated significantly with soil properties-temperature, pH, nitrogen and carbon contents. The conclusion could facilitate to understand the interaction and ecological function of endophytic bacteria with host Jingbai pear trees, so as to benefit the pear variety genetic resource conservation and protection.
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Affiliation(s)
- Fei Ren
- Forestry Experiment Center in North China, Chinese Academy of Forestry, Beijing, 102300, China.
| | - Wei Dong
- China Electric Power Research Institute, Beijing, 100192, China
| | - Dong-Hui Yan
- The Key Laboratory of Forest Protection Affiliated to State Forestry Administration of China, Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, 100091, China.
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27
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Haldar S, Nazareth SW. Taxonomic diversity of bacteria from mangrove sediments of Goa: metagenomic and functional analysis. 3 Biotech 2018; 8:436. [PMID: 30306005 DOI: 10.1007/s13205-018-1441-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/24/2018] [Indexed: 12/12/2022] Open
Abstract
The present study compared the taxonomic diversity and evaluated the functional attributes of the bacterial species from Mandovi and Zuari mangrove sediments, Goa, using paired-end amplicon sequencing of 16S rDNA and culture-based analyses, respectively. 16S rDNA sequencing revealed Proteobacteria, Firmicutes, and Actinobacteria as the dominant phyla in both the sediments. However, the abundance of these phyla significantly differed between the samples. Bacteroidetes from Mandovi sediment, and Acidobacteria and Gemmatimonadetes from Zuari sediment were the other exclusive major phyla. Chloroflexi, Cyanobacteria, Nitrospirae, Planctomycetes, Verrucomicrobia, and WS3 were the minor phyla observed in both. However, a significant difference in the distribution of minor phyla and lower bacterial taxa under each phylum was noted between the sediments, indicating that the resident microbial flora completely differed between them. This was further validated by high values from distance matrix analyses between the samples. In addition, the pathogenic Vibrio sp. was recorded exclusively in Mandovi sediment, while higher abundance of ecologically important bacterial classes including Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, and Bacilli was observed in Zuari sediment. Taken together, the data indicated that Zuari sediment was taxonomically richer than Mandovi sediment, while a greater incidence of anthropogenic activities occurred in the latter. This observation was further validated by non-parametric richness estimators which were found to be higher for Zuari sediment. The cultured bacterial isolates, all identified as Firmicutes, were tested for activities related to biofertilization and production of enzymes to be used for bioremediation and chemotherapeutic applications. Higher number of bacterial isolates from Mandovi was found to produce indole-acetic-acid, tannase, xylanase, and glutaminase enzymes, and could solubilize phosphate. In contrast, higher proportion of bacterial isolates from Zuari sediment were capable of producing amylase, cellulase, gelatinase, laccase, lipase, protease, and asparaginase enzymes, emphasizing the fact that the Zuari mangrove sediment is a rich reservoir for economically and biotechnologically important bacterial species.
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Affiliation(s)
- Shyamalina Haldar
- Department of Microbiology, Goa University, Taleigao Plateau, Taleigão, Goa 403206 India
| | - Sarita W Nazareth
- Department of Microbiology, Goa University, Taleigao Plateau, Taleigão, Goa 403206 India
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28
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Zhang H, Zhang S, Meng X, Li M, Mu L, Lei J, Sui X. Conversion from natural wetlands to forestland and farmland alters the composition of soil fungal communities in Sanjiang Plain, Northeast China. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1459208] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Huihui Zhang
- College of Resources and Environment, Northeast Agricultural University, Harbin, PR China
| | - Siyu Zhang
- College of Resources and Environment, Northeast Agricultural University, Harbin, PR China
| | - Xiangxinyue Meng
- College of Resources and Environment, Northeast Agricultural University, Harbin, PR China
| | - Mengsha Li
- Department of Bioresources, Institute of Nature & Ecology, Heilongjiang Academy of Sciences, Harbin, PR China
- Department of Forest Plant Resource, College of Forestry, Northeast Forestry University, Harbin, PR China
| | - Liqiang Mu
- Department of Forest Plant Resource, College of Forestry, Northeast Forestry University, Harbin, PR China
| | - Jingpin Lei
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, PR China
| | - Xin Sui
- Department of Restoration Ecology, College of Life Science, Heilongjiang University, Harbin, PR China
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29
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Zogg GP, Travis SE, Brazeau DA. Strong associations between plant genotypes and bacterial communities in a natural salt marsh. Ecol Evol 2018; 8:4721-4730. [PMID: 29760911 PMCID: PMC5938472 DOI: 10.1002/ece3.4105] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 03/24/2018] [Indexed: 01/06/2023] Open
Abstract
Although microbial communities have been shown to vary among plant genotypes in a number of experiments in terrestrial ecosystems, relatively little is known about this relationship under natural conditions and outside of select model systems. We reasoned that a salt marsh ecosystem, which is characterized by twice‐daily flooding by tides, would serve as a particularly conservative test of the strength of plant–microbial associations, given the high degree of abiotic regulation of microbial community assembly resulting from alternating periods of inundation and exposure. Within a salt marsh in the northeastern United States, we characterized genotypes of the foundational plant Spartina alterniflora using microsatellite markers, and bacterial metagenomes within marsh soil based on pyrosequencing. We found significant differences in bacterial community composition and diversity between bulk and rhizosphere soil, and that the structure of rhizosphere communities varied depending on the growth form of, and genetic variation within, the foundational plant S. alterniflora. Our results indicate that there are strong plant–microbial associations within a natural salt marsh, thereby contributing to a growing body of evidence for a relationship between plant genotypes and microbial communities from terrestrial ecosystems and suggest that principles of community genetics apply to this wetland type.
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Affiliation(s)
- Gregory P Zogg
- Department of Biology University of New England Biddeford Maine
| | - Steven E Travis
- Department of Biology University of New England Biddeford Maine
| | - Daniel A Brazeau
- Department of Biomedical Sciences University of New England Biddeford Maine
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30
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Zuo L, Yang R, Zhen Z, Liu J, Huang L, Yang M. A 5-year field study showed no apparent effect of the Bt transgenic 741 poplar on the arthropod community and soil bacterial diversity. Sci Rep 2018; 8:1956. [PMID: 29386632 PMCID: PMC5792429 DOI: 10.1038/s41598-018-20322-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/15/2018] [Indexed: 12/02/2022] Open
Abstract
China is currently the only country that has commercialized genetically engineered tree species, and this has attracted worldwide attention. As a perennial tree species, transgenic poplar has a long growth cycle and needs to be tested for long-term ecological risks. The main purpose of this study was to explore the ecological safety of perennial transgenic poplars in arthropod community, physical and chemical properties of soil, gene flow, and soil microbial diversity. The study found transgenic poplars could effectively inhibit the number of pests. Moreover, transgenic poplar 741 did not affect the stability of the arthropod community. Studies on the microbial diversity of poplar showed that transgenic poplars did not affect the physical and chemical properties of the soil and the soil microbial community structure. Furthermore, the microbial community structure was obviously affected by location and season. The results showed that a 5-year-old transgenic 741 poplar did not pose an ecological risk, and did not affect the microbial community structure or functional diversity. This study provides a reference for the ecological security evaluation of transgenic poplars, and provides a theoretical basis for promoting the commercialization of transgenic poplars.
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Affiliation(s)
- Lihui Zuo
- Institute of Forest Biotechnology, Forestry College, Agricultural University of Hebei, 071000, Baoding, PR China.,Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, PR China
| | - Runlei Yang
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, PR China.,College of life science, Hebei University, 071000, Baoding, PR China
| | - Zhixian Zhen
- Institute of Forest Biotechnology, Forestry College, Agricultural University of Hebei, 071000, Baoding, PR China.,Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, PR China
| | - Junxia Liu
- Institute of Forest Biotechnology, Forestry College, Agricultural University of Hebei, 071000, Baoding, PR China.,Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, PR China
| | - Lisha Huang
- BiomicsTech Co.L td, 100083, Beijing, PR China
| | - Minsheng Yang
- Institute of Forest Biotechnology, Forestry College, Agricultural University of Hebei, 071000, Baoding, PR China. .,Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, PR China.
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31
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Liu M, Yu Z, Yu X, Xue Y, Huang B, Yang J. Invasion by Cordgrass Increases Microbial Diversity and Alters Community Composition in a Mangrove Nature Reserve. Front Microbiol 2017; 8:2503. [PMID: 29326666 PMCID: PMC5737034 DOI: 10.3389/fmicb.2017.02503] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 12/01/2017] [Indexed: 11/13/2022] Open
Abstract
Invasion by exotic plant species can alter ecosystem function and reduce native plant diversity, but relatively little is known about their effects on belowground microbial communities. Here we investigated the effects of exotic cordgrass (Spartina alterniflora) invasion on the distribution of soil bacterial communities in a mangrove nature reserve of the Jiulong River Estuary, southeast China using high-throughput sequencing of 16S rRNA gene and multivariate statistical analysis. Our results showed that S. alterniflora invasion altered soil properties, and significantly increased soil bacterial taxa richness, primarily by stimulating an increase in conditionally rare or rare taxa, and changes in community composition and function. Abundant, conditionally rare and rare subcommunities exhibited similar response patterns to environment changes, with both conditionally rare and rare taxa showing a stronger response than abundant ones. Habitat generalists were detected among abundant, conditionally rare and rare taxa, whereas habitat specialists were only identified among conditionally rare taxa and rare taxa. In addition, we found that vegetation was the key factor driving these patterns. However, our comparative analysis indicated that both environmental selection, and neutral process, significantly contributed to soil bacterial community assembly. These results could improve the understanding of the microbial processes and mechanisms of cordgrass invasion, and offer empirical data of use in the restoration and management of the mangrove wetlands.
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Affiliation(s)
- Min Liu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China.,College of Environment and Ecology, Xiamen University, Xiamen, China
| | - Zheng Yu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,Department of Chemical Engineering, University of Washington, Seattle, WA, United States
| | - Xiaoqing Yu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yuanyuan Xue
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China.,College of Environment and Ecology, Xiamen University, Xiamen, China
| | - Bangqin Huang
- College of Environment and Ecology, Xiamen University, Xiamen, China
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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32
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Wang M, Li E, Liu C, Jousset A, Salles JF. Functionality of Root-Associated Bacteria along a Salt Marsh Primary Succession. Front Microbiol 2017; 8:2102. [PMID: 29163397 PMCID: PMC5670159 DOI: 10.3389/fmicb.2017.02102] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/13/2017] [Indexed: 01/23/2023] Open
Abstract
Plant-associated bacteria are known for their high functional trait diversity, from which many are likely to play a role in primary and secondary succession, facilitating plant establishment in suboptimal soils conditions. Here we used an undisturbed salt marsh chronosequence that represents over 100 years of soil development to assess how the functional traits of plant associated bacteria respond to soil type, plant species and plant compartment. We isolated and characterized 808 bacterial colonies from the rhizosphere soil and root endosphere of two salt marsh plants, Limonium vulgare and Artemisia maritima, along the chronosequence. From these, a set of 59 strains (with unique BOX-PCR patterns, 16S rRNA sequence and unique to one of the treatments) were further screened for their plant growth promoting traits (siderophore production, IAA production, exoprotease production and biofilm formation), traits associated with bacterial fitness (antibiotic and abiotic stress resistance - pH, osmotic and oxidative stress, and salinity) and metabolic potential. An overall view of functional diversity (multivariate analysis) indicated that the distributional pattern of bacterial functional traits was driven by soil type. Samples from the late succession (Stage 105 year) showed the most restricted distribution, harboring strains with relatively low functionalities, whereas the isolates from intermediate stage (35 year) showed a broad functional profiles. However, strains with high trait performance were largely from stage 65 year. Grouping the traits according to category revealed that the functionality of plant endophytes did not vary along the succession, thus being driven by plant rather than soil type. In opposition, the functionality of rhizosphere isolates responded strongly to variations in soil type as observed for antibiotic resistance (P = 0.014). Specifically, certain Pseudomonas sp. and Serratia sp. strains revealed high resistance against abiotic stress and antibiotics and produce more siderophores, confirming the high plant-growth promoting activity of these two genera. Overall, this study contributes to a better understanding of the functional diversity and adaptation of the microbiome at typical salt marsh plant species across soil types. Specifically, soil type was influential only in the rhizosphere but not on the endosphere, indicating a strong plant-driven effect on the functionality of endophytes.
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Affiliation(s)
- Miao Wang
- Research Group of Microbial Community Ecology, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Erqin Li
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Chen Liu
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, Netherlands
| | | | - Joana F. Salles
- Research Group of Microbial Community Ecology, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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33
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Illumina-based analysis of endophytic bacterial diversity of tree peony (Paeonia Sect. Moutan) roots and leaves. Braz J Microbiol 2017; 48:695-705. [PMID: 28606427 PMCID: PMC5628320 DOI: 10.1016/j.bjm.2017.02.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 01/26/2017] [Accepted: 02/01/2017] [Indexed: 11/22/2022] Open
Abstract
Diverse communities of bacteria inhabit plant tissues and those bacteria play a crucial role for plant health and growth. Tree peony (Paeonia Sect. Moutan) is known for its excellent ornamental and medicinal values as Chinese traditional plant, but little is known about its associated bacterial community under natural conditions. To examine how endophytic bacteria in tree peony vary across tissues and cultivars, PCR-based Illumina was applied to reveal the diversity of endophytic bacteria in tree peony. A total of 149,842 sequences and 21,463 operational taxonomic units (OTUs) were obtained. The OTU abundance of roots was higher than leaves across other three cultivars except for ‘Kinkaku’ and ‘Luoyanghong’. The community was composed of five dominant groups (Proteobacteria, Firmicutes, Bacteroidetes, Acidobacteria and Actinobacteria) in all samples. Endophytic bacteria community structures had changed in leaves and roots. Sequences of Pseudomonas and Enterobacteriaceae were prevalent in root samples, whereas Succinivibrio and Acinetobacter were the dominant genus in leaf samples. Otherwise, the distribution of each dominant genus among the 5 cultivars was either varied. These findings suggested that both plant genotype and tissues contribute to the shaping of the bacterial communities associated with tree peony.
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34
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Mitter EK, de Freitas JR, Germida JJ. Bacterial Root Microbiome of Plants Growing in Oil Sands Reclamation Covers. Front Microbiol 2017; 8:849. [PMID: 28559882 PMCID: PMC5432656 DOI: 10.3389/fmicb.2017.00849] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/25/2017] [Indexed: 12/22/2022] Open
Abstract
Oil sands mining in northern Alberta impacts a large footprint, but the industry is committed to reclaim all disturbed land to an ecologically healthy state in response to environmental regulations. However, these newly reconstructed landscapes may be limited by several factors that include low soil nutrient levels and reduced microbial activity. Rhizosphere microorganisms colonize plant roots providing hosts with nutrients, stimulating growth, suppressing disease and increasing tolerance to abiotic stress. High-throughput sequencing techniques can be used to provide a detailed characterization of microbial community structure. This study used 16S rRNA amplicon sequencing to characterize the bacterial root microbiome associated with annual barley (Hordeum vulgare) and sweet clover (Melilotus albus) growing in an oil sands reclamation area. Our results indicate that Proteobacteria dominated the endosphere, whereas other phyla such as Acidobacteria and Gemmatimonadetes were restricted to the rhizosphere, suggesting that plants have the ability to select for certain soil bacterial consortia. The bacterial community in the endosphere compartments were less rich and diverse compared to the rhizosphere. Furthermore, it was apparent that sweet clover plants were more selective, as the community exhibited a lower richness and diversity compared to barley. Members of the family Rhizobiaceae, such as Sinorhizobium and Rhizobium were mainly associated with clover, whereas Acholeplasma (wall-less bacteria transmitted by insects) was unique to barley. Genera from the Enterobacteriaceae family, such as Yersinia and Lentzea were also mostly detected in barley, while other genera such Pseudomonas and Pantoea were able to successfully colonize both plants. Endophytic bacterial profiles varied within the same plant species at different sampling locations; however, these differences were driven by factors other than slope positions or cover management. Our results suggest that bacterial endophytic communities of plants growing in land reclamation systems are a subset of the rhizosphere community and selection is driven by plant factors.
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Affiliation(s)
- Eduardo K Mitter
- Department of Food and Bioproduct Sciences, University of Saskatchewan, SaskatoonSK, Canada
| | | | - James J Germida
- Department of Soil Science, University of Saskatchewan, SaskatoonSK, Canada
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35
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Ma ZP, Lao YM, Jin H, Lin GH, Cai ZH, Zhou J. Diverse Profiles of AI-1 Type Quorum Sensing Molecules in Cultivable Bacteria from the Mangrove ( Kandelia obovata) Rhizosphere Environment. Front Microbiol 2016; 7:1957. [PMID: 27994584 PMCID: PMC5136546 DOI: 10.3389/fmicb.2016.01957] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/22/2016] [Indexed: 11/25/2022] Open
Abstract
Mangrove rhizosphere environment harbors diverse populations of microbes, and some evidence showed that rhizobacteria behavior was regulated by quorum sensing (QS). Investigating the diverse profiles of QS molecules in mangrove ecosystems may shed light on the bacterial roles and lead to a better understanding of the symbiotic interactions between plants and microbes. The aims of the current study focus on identifying AI-1 type QS signals, i.e., acyl homoserine lactones (AHLs), in Kandelia obovata rhizosphere environment. Approximately 1200 rhizobacteria were screened and 184 strains (15.3%) tested were positive. Subsequent 16s rRNA gene sequencing and dereplication analyses identified 24 species from the positive isolates, which were affiliated to three different phyla, including Proteobacteria, Firmicutes, and Actinobacteria. Thin-layer chromatography separation of extracts revealed diverse AHL profiles and detected at least one active compound in the supernatant of these 24 cultivable AHL-producers. The active extracts from these bacterial isolates were further evaluated by ultra performance liquid chromatography-mass spectrometry, and the carbon side chain length ranged from C4 to C14. This is the first report on the diversity of AI-1 type auto-inducers in the mangrove plant K. obovata, and it is imperative to expand our knowledge of plant-bacteria interactions with respect to the maintenance of wetland ecosystem health.
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Affiliation(s)
- Zhi P Ma
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China; Shenzhen Public Platform for Screening and Application of Marine Microbial ResourcesShenzhen, China
| | - Yong M Lao
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China; Shenzhen Public Platform for Screening and Application of Marine Microbial ResourcesShenzhen, China
| | - Hui Jin
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China; Shenzhen Public Platform for Screening and Application of Marine Microbial ResourcesShenzhen, China
| | - Guang H Lin
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua University Shenzhen, China
| | - Zhong H Cai
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China; Shenzhen Public Platform for Screening and Application of Marine Microbial ResourcesShenzhen, China
| | - Jin Zhou
- The Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua UniversityShenzhen, China; Shenzhen Public Platform for Screening and Application of Marine Microbial ResourcesShenzhen, China
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