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Zhou X, Zhang X, Ma C, Wu F, Jin X, Dini-Andreote F, Wei Z. Biochar amendment reduces cadmium uptake by stimulating cadmium-resistant PGPR in tomato rhizosphere. CHEMOSPHERE 2022; 307:136138. [PMID: 36002065 DOI: 10.1016/j.chemosphere.2022.136138] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 08/06/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Biochar amendment in the soil can exert a positive effect in reducing heavy metal toxicity in plants. However, it remains unclear the extent to which this effect is associated with the modulation of plant growth-promoting rhizobacteria (PGPR). Here, we initially conducted a pot experiment using tomato (Solanum lycopersicum L.) as a model plant grown in soil spiked with cadmium. First, we found biochar amendment to result in reduced cadmium uptake in tomato plants and trackable changes in the tomato rhizosphere microbiome. Then, a rhizosphere transplant experiment validated the importance of this microbiome modulation for cadmium-toxicity amelioration. Sequence-based analyses targeted the isolation of representative isolates of PGPR, including Bacillus and Flavisolibacter spp. that displayed in vitro cadmium tolerance and biosorption capabilities (in addition to abilities to solubilize phosphate and produce indole acetic acid). Last, we performed a soil inoculation experiment and confirmed the effectiveness of these isolates in reducing cadmium toxicity in tomato plants. Besides, we found the inoculation of these taxa as single inoculant and in combination to result in increased activities of specific antioxidant enzymes in tomato tissues. Taken together, this study revealed the ecological and physiological mechanisms by which biochar amendment indirectly alleviate cadmium toxicity in tomato plants, in this case, via the modulation and activity of specific PGPR populations. This study provides new insights into strategies able to promote beneficial PGPR in the rhizosphere with potential application to ameliorate heavy metal toxicity in plants.
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Affiliation(s)
- Xingang Zhou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, Harbin, 150030, PR China
| | - Xianhong Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, Harbin, 150030, PR China
| | - Changli Ma
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, Harbin, 150030, PR China
| | - Fengzhi Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, Harbin, 150030, PR China
| | - Xue Jin
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, Harbin, 150030, PR China.
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China.
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Ravinath R, Das AJ, Usha T, Ramesh N, Middha SK. Targeted metagenome sequencing reveals the abundance of Planctomycetes and Bacteroidetes in the rhizosphere of pomegranate. Arch Microbiol 2022; 204:481. [PMID: 35834016 DOI: 10.1007/s00203-022-03100-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/24/2022] [Indexed: 11/25/2022]
Abstract
Agricultural productivity of pomegranate can be enhanced by identifying the crop-associated microbial diversity in the rhizosphere region with respect to plant growth promoters and other beneficial organisms. Traditional culture methods have limitations in microbial screening as only 1-2% of these organisms can be cultured. In the present study, 16S rRNA amplicon-based metagenomics approach using MinION Oxford Nanopore platform was employed to explore the microbial diversity in the rhizosphere of pomegranate Bhagwa variety, across variable soil depths from 0 to 5 cms (R2), 5-10 cms (R4) and 10-15 cms (R6), using bulk soil as the control. Across all the three layers, significant variations in pH, nitrogen content and total fungal count were observed. 16S rRNA analysis showed the abundance of planctomycetes, Pirellula staleyi, followed by bacteroidetes, Flavisolibacter LC59 and Niastella koreensis across the various soil depths in the rhizospheric soil samples. Pathway prediction analysis indicated arginine and proline metabolism (gamma-glutamyl putrescine oxidase) and hydrogen sulfide biosynthesis as the most abundant pathway hits. Comparative abundance analysis across layers showed the R6 layer with the maximum microbial diversity in terms of highest dimension of variation (79.2%) followed by R4 and R2 layers (p < 0.01). Our analysis shows the significant influence of root zone in shaping microbial diversity. This study has reported the presence of Planctomycetes, Pirellula staleyi for the first time in the pomegranate field.
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Affiliation(s)
- Renuka Ravinath
- School of Applied Sciences, REVA University, Rukmini Knowledge Park, Bangalore, 560064, Karnataka, India
| | - Anupam J Das
- School of Applied Sciences, REVA University, Rukmini Knowledge Park, Bangalore, 560064, Karnataka, India
- Basesolve Informatics Private Limited, Ellisbridge, Ahmedabad, 380006, Gujarat, India
| | - Talambedu Usha
- Department of Biotechnology, Maharani Lakshmi Ammani College for Women, Bangalore, 560012, Karnataka, India
| | - Nijalingappa Ramesh
- School of Applied Sciences, REVA University, Rukmini Knowledge Park, Bangalore, 560064, Karnataka, India
| | - Sushil Kumar Middha
- Department of Biotechnology, Maharani Lakshmi Ammani College for Women, Bangalore, 560012, Karnataka, India.
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Choi GM, Liu Q, Liu Q, Jun MO, Choi WJ, Yong Kim S, Wee JH, Im WT. Hanamia caeni gen. nov., sp. nov., a Member of the Family Chitinophagaceae Isolated from Activated Sludge in Korea. Curr Microbiol 2022; 79:134. [PMID: 35294641 DOI: 10.1007/s00284-022-02814-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/17/2022] [Indexed: 11/03/2022]
Abstract
A novel Gram-stain-negative, aerobic, yellowish-pigmented, non-motile, rod-shaped bacterial strain, designated strain BO-59T, was isolated from the activated sludge of a wastewater treatment plant in Hanam City, South Korea. Phylogenetic study based on the 16S rRNA gene sequence positioned BO-59T in a distinct lineage in the family Chitinophagaceae, sharing less than 92.8% sequence similarity with members of the closely related genera Ferruginibacter, Flavitalea, Pseudoflavitalea, Flavisolibacter, Niastella, and Terrimonas. Phylogenomic- and genomic relatedness analyses revealed that strain BO-59T is clearly distinguished from other genera in the family Chitinophagaceae by average nucleotide identity < 66.9%) and the genome-to-genome distance (< 29.5%) values. The strain BO-59T contained MK-7 as the predominant quinone, and iso-C15:0, iso-C17:0 3OH, and iso-C15:1 G as major fatty acids (> 10%). The DNA G + C content was 39.1 mol% based on genome sequence analysis. The polar lipids of strain BO-59T were phosphatidylethanolamine, an unidentified aminophospholipid and three unidentified polar lipids. 16S rRNA gene sequence similarity, physiological, and biochemical characteristics indicated that strain BO-59T represents a novel species of a new genus, for which the name Hanamia caeni gen. nov., sp. nov. is proposed. The type strain is BO-59T (= KACC 19646T = LMG 30865 T).
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Affiliation(s)
- Gyu-Min Choi
- Department of Biotechnology, Hankyong National University, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea.,AceEMzyme Co., Ltd., Academic Industry Cooperation, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea
| | - Qingmei Liu
- Department of Biotechnology, Hankyong National University, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea.,AceEMzyme Co., Ltd., Academic Industry Cooperation, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea.,HK Ginseng Research Center, Hankyong National University, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea
| | - Qingzhen Liu
- Department of Biotechnology, Hankyong National University, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea.,AceEMzyme Co., Ltd., Academic Industry Cooperation, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea
| | - Min Ok Jun
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, 56212, Jeollabuk-do, Republic of Korea
| | - Won Jung Choi
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, 56212, Jeollabuk-do, Republic of Korea
| | - Sang Yong Kim
- Department of Food Science & Bio Technology, Shinansan University, Ansan, Republic of Korea
| | - Ji-Hyang Wee
- Department of Food Science & Bio Technology, Shinansan University, Ansan, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyong National University, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea. .,AceEMzyme Co., Ltd., Academic Industry Cooperation, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea. .,HK Ginseng Research Center, Hankyong National University, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea.
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Hymenobacter negativus sp. nov., bacteria isolated from mountain soil collected in South Korea. Antonie van Leeuwenhoek 2021; 114:1025-1031. [PMID: 33948755 DOI: 10.1007/s10482-021-01573-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/01/2021] [Indexed: 10/21/2022]
Abstract
Two novel Gram-negative bacterial strains BT442T and BT584 were isolated from dry soil collected in mountains Busan and Guri, Korea during wintertime. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains BT442T and BT584 both belong to a distinct lineage within the genus Hymenobacter (family Hymenobacteraceae, order Cytophagales, class Cytophagia). Strain BT442T was closely related to Hymenobacter soli PB17T (98.0% 16S rRNA gene similarity) and Hymenobacter terrae POA9T (97.6%). No other recognized bacterial species showed more than 97% 16S rRNA gene sequence similarity to strains BT442T. The genome size of strain BT442T was 5,143,362 bp. Bacterial growth was observed at 10-30 °C (optimum 25 °C), pH 6.0-8.0 (optimum pH 6.0) in R2A agar and in the presence up to 1% NaCl. The major cellular fatty acids of strains BT442T and BT584 were iso-C15:0, anteiso-C15:0 and summed feature 3 (C16:1 ω6c / C16:1 ω7c). In addition, their predominant respiratory quinone was MK-7. The major polar lipids of strains BT442T and BT584 were identified to be phosphatidylethanolamine, aminophospholipid, and aminolipid. Based on the biochemical, chemotaxonomic, and phylogenetic analyses, strains BT442T and BT584 are novel bacterial species within the genus Hymenobacter, and the proposed name is Hymenobacter negativus. The strain type of Hymenobacter negativus is BT442T (= KCTC 72902T = NBRC XXXXT).
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Maeng S, Park Y, Lee SE, Han JH, Bai J, Kim MK. Flavisolibacter longurius sp. nov., isolated from soil. Arch Microbiol 2021; 203:2825-2830. [PMID: 33742220 DOI: 10.1007/s00203-021-02236-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/09/2020] [Accepted: 02/11/2021] [Indexed: 11/29/2022]
Abstract
A novel Gram-negative bacterial strain BT320T was isolated from soil collected in Uijeongbu city, Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BT320T belong to a distinct lineage within the genus Flavisolibacter (family Chitinophagaceae, order Chitinophagales, class Chitinophagia). The strain BT320T was closely related to Flavisolibacter galbus 17J28-26T (97.6% 16S rRNA gene similarity), Flavisolibacter nicotianae X7XT (96.7%), Flavisolibacter ginsengiterrae Gsoil 492T (96.2%), and Flavisolibacter ginsengisoli Gsoil 643 T (96.1%). The genome size of strain BT320T was 5,664,094 bp. Bacterial growth was observed at 10-37 °C (optimum 25 °C) and pH 6.0-8.0 (optimum pH 7.0) on R2A agar. The major cellular fatty acids of strain BT320T were iso-C15:0, summed feature 3 (C16:1 ω6c/C16:1 ω7c), and summed feature 1 (iso-C15:1 H/C13:0 3OH). Its predominant respiratory quinone was MK-7. The major polar lipid of strain BT320T was identified to be phosphatidylethanolamine (PE). Based on the biochemical, chemotaxonomic, and phylogenetic analysis, strain BT320T can be suggested as a novel bacterial species within the genus Flavisolibacter and the proposed name is Flavisolibacter longurius. The type strain of Flavisolibacter longurius is BT320T (= KCTC 72422T = NBRC 114375T).
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Affiliation(s)
- Soohyun Maeng
- Department of Bio and Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 139-774, Korea
| | - Yuna Park
- Department of Bio and Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 139-774, Korea
| | - Sang Eun Lee
- Department of Bio and Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 139-774, Korea
| | - Joo Hyun Han
- Department of Bio and Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 139-774, Korea
| | - Jaewoo Bai
- Department of Food Science and Technology, Division of Applied Food System, Seoul Women's University, Seoul, 139-774, Korea.
| | - Myung Kyum Kim
- Department of Bio and Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 139-774, Korea.
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