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Vu MT, Geraldi A, Do HDK, Luqman A, Nguyen HD, Fauzia FN, Amalludin FI, Sadila AY, Wijaya NH, Santoso H, Manuhara YSW, Bui LM, Hariyanto S, Wibowo AT. Soil Mineral Composition and Salinity Are the Main Factors Regulating the Bacterial Community Associated with the Roots of Coastal Sand Dune Halophytes. BIOLOGY 2022; 11:biology11050695. [PMID: 35625422 PMCID: PMC9138652 DOI: 10.3390/biology11050695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/15/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022]
Abstract
Soil salinity and mineral deficiency are major problems in agriculture. Many studies have reported that plant-associated microbiota, particularly rhizosphere and root microbiota, play a crucial role in tolerance against salinity and mineral deficiency. Nevertheless, there are still many unknown parts of plant–microbe interaction, especially regarding their role in halophyte adaptation to coastal ecosystems. Here, we report the bacterial community associated with the roots of coastal sand dune halophytes Spinifex littoreus and Calotropis gigantea, and the soil properties that affect their composition. Strong correlations were observed between root bacterial diversity and soil mineral composition, especially with soil Calcium (Ca), Titanium (Ti), Cuprum (Cu), and Zinc (Zn) content. Soil Ti and Zn content showed a positive correlation with bacterial diversity, while soil Ca and Cu had a negative effect on bacterial diversity. A strong correlation was also found between the abundance of several bacterial species with soil salinity and mineral content, suggesting that some bacteria are responsive to changes in soil salinity and mineral content. Some of the identified bacteria, such as Bacillus idriensis and Kibdelosporangium aridum, are known to have growth-promoting effects on plants. Together, the findings of this work provided valuable information regarding bacterial communities associated with the roots of sand dune halophytes and their interactions with soil properties. Furthermore, we also identified several bacterial species that might be involved in tolerance against stresses. Further work will be focused on isolation and transplantation of these potential microbes, to validate their role in plant tolerance against stresses, not only in their native hosts but also in crops.
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Affiliation(s)
- Minh Thiet Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam; (M.T.V.); (H.D.K.D.); (H.D.N.)
| | - Almando Geraldi
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
- Biotechnology of Tropical Medicinal Plants Research Group, Airlangga University, Surabaya 60115, Indonesia
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam; (M.T.V.); (H.D.K.D.); (H.D.N.)
| | - Arif Luqman
- Biology Department, Institut Teknologi Sepuluh Nopember, Surabaya 60111, Indonesia;
| | - Hoang Danh Nguyen
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam; (M.T.V.); (H.D.K.D.); (H.D.N.)
| | - Faiza Nur Fauzia
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
| | - Fahmi Ikhlasul Amalludin
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
| | - Aliffa Yusti Sadila
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
| | - Nabilla Hapsari Wijaya
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
| | - Heri Santoso
- Generasi Biologi Indonesia (Genbinesia) Foundation, Gresik 61171, Indonesia;
| | - Yosephine Sri Wulan Manuhara
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
- Biotechnology of Tropical Medicinal Plants Research Group, Airlangga University, Surabaya 60115, Indonesia
| | - Le Minh Bui
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
- Department of Biotechnology, NTT Hi-tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam
| | - Sucipto Hariyanto
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
- Correspondence: (S.H.); (A.T.W.)
| | - Anjar Tri Wibowo
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
- Biotechnology of Tropical Medicinal Plants Research Group, Airlangga University, Surabaya 60115, Indonesia
- Correspondence: (S.H.); (A.T.W.)
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Casanova M, Pasotti L, Zucca S, Politi N, Massaiu I, Calvio C, Cusella De Angelis MG, Magni P. A BioBrick™-Compatible Vector for Allelic Replacement Using the XylE Gene as Selection Marker. Biol Proced Online 2016; 18:6. [PMID: 26877712 PMCID: PMC4752771 DOI: 10.1186/s12575-016-0036-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/08/2016] [Indexed: 01/10/2023] Open
Abstract
Background Circular plasmid-mediated homologous recombination is commonly used for marker-less allelic replacement, exploiting the endogenous recombination machinery of the host. Common limitations of existing methods include high false positive rates due to mutations in counter-selection genes, and limited applicability to specific strains or growth media. Finally, solutions compatible with physical standards, such as the BioBrick™, are not currently available, although they proved to be successful in the design of other replicative or integrative plasmids. Findings We illustrate pBBknock, a novel BioBrick™-compatible vector for allelic replacement in Escherichia coli. It includes a temperature-sensitive replication origin and enables marker-less genome engineering via two homologous recombination events. Chloramphenicol resistance allows positive selection of clones after the first event, whereas a colorimetric assay based on the xylE gene provides a simple way to screen clones in which the second recombination event occurs. Here we successfully use pBBknock to delete the lactate dehydrogenase gene in E. coli W, a popular host used in metabolic engineering. Conclusions Compared with other plasmid-based solutions, pBBknock has a broader application range, not being limited to specific strains or media. We expect that pBBknock will represent a versatile solution both for practitioners, also among the iGEM competition teams, and for research laboratories that use BioBrick™-based assembly procedures. Electronic supplementary material The online version of this article (doi:10.1186/s12575-016-0036-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michela Casanova
- Department of Electrical, Computer and Biomedical Engineering, Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, University of Pavia, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, 27100 Pavia, Italy
| | - Lorenzo Pasotti
- Department of Electrical, Computer and Biomedical Engineering, Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, University of Pavia, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, 27100 Pavia, Italy
| | - Susanna Zucca
- Department of Electrical, Computer and Biomedical Engineering, Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, University of Pavia, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, 27100 Pavia, Italy
| | - Nicolò Politi
- Department of Electrical, Computer and Biomedical Engineering, Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, University of Pavia, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, 27100 Pavia, Italy
| | - Ilaria Massaiu
- Department of Electrical, Computer and Biomedical Engineering, Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, University of Pavia, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, 27100 Pavia, Italy
| | - Cinzia Calvio
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, 27100 Pavia, Italy
| | | | - Paolo Magni
- Department of Electrical, Computer and Biomedical Engineering, Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, University of Pavia, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, 27100 Pavia, Italy
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