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Hilário S, Gonçalves MFM, Matos I, Rangel LF, Sousa JA, Santos MJ, Ayra-Pardo C. Comparative genomics reveals insights into the potential of Lysinibacillus irui as a plant growth promoter. Appl Microbiol Biotechnol 2024; 108:370. [PMID: 38861018 PMCID: PMC11166776 DOI: 10.1007/s00253-024-13210-6] [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: 03/05/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
Members of the genus Lysinibacillus attract attention for their mosquitocidal, bioremediation, and plant growth-promoting abilities. Despite this interest, comprehensive studies focusing on genomic traits governing plant growth and stress resilience in this genus using whole-genome sequencing are still scarce. Therefore, we sequenced and compared the genomes of three endophytic Lysinibacillus irui strains isolated from Canary Island date palms with the ex-type strain IRB4-01. Overall, the genomes of these strains consist of a circular chromosome with an average size of 4.6 Mb and a GC content of 37.2%. Comparative analysis identified conserved gene clusters within the core genome involved in iron acquisition, phosphate solubilization, indole-3-acetic acid biosynthesis, and volatile compounds. In addition, genome analysis revealed the presence of genes encoding carbohydrate-active enzymes, and proteins that confer resistance to oxidative, osmotic, and salinity stresses. Furthermore, pathways of putative novel bacteriocins were identified in all genomes. This illustrates possible common plant growth-promoting traits shared among all strains of L. irui. Our findings highlight a rich repertoire of genes associated with plant lifestyles, suggesting significant potential for developing inoculants to enhance plant growth and resilience. This study is the first to provide insights into the overall genomic signatures and mechanisms of plant growth promotion and biocontrol in the genus Lysinibacillus. KEY POINTS: • Pioneer study in elucidating plant growth promoting in L. irui through comparative genomics. • Genome mining identified biosynthetic pathways of putative novel bacteriocins. • Future research directions to develop L. irui-based biofertilizers for sustainable agriculture.
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Affiliation(s)
- Sandra Hilário
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
- GreenUPorto, Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences, University of Porto, Campus de Vairão, 747, 4485-646, Vila do Conde, Portugal.
| | - Micael F M Gonçalves
- Department of Biology, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Inês Matos
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - Luis F Rangel
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - José A Sousa
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, FC4, 4169-007, Porto, Portugal
| | - Maria J Santos
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, FC4, 4169-007, Porto, Portugal
| | - Camilo Ayra-Pardo
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
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Sudheer NS, Biju IF, Balasubramanian CP, Panigrahi A, Kumar TS, Kumar S, Mandal B, Das S, De D. Probiotic potential of a novel endophytic Streptomyces griseorubens CIBA-NS1 isolated from Salicornia sp. against Vibrio campbellii infection in shrimp. Microb Pathog 2024; 191:106677. [PMID: 38705217 DOI: 10.1016/j.micpath.2024.106677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/28/2024] [Accepted: 05/03/2024] [Indexed: 05/07/2024]
Abstract
A novel endophytic Streptomyces griseorubens CIBA-NS1 was isolated from a salt marsh plant Salicornia sp. The antagonistic effect of S. griseorubens against Vibrio campbellii, was studied both in vitro and in vivo. The strain was validated for its endophytic nature and characterized through scanning electron microscopy, morphological and biochemical studies and 16SrDNA sequencing. The salinity tolerance experiment has shown that highest antibacterial activity was at 40‰ (16 ± 1.4 mm) and lowest was at 10 ‰ salinity (6.94 ± 0.51 mm). In vivo exclusion of Vibrio by S. griseorubens CIBA-NS1 was studied in Penaeus indicus post larvae and evaluated for its ability to improve growth and survival of P. indicus. After 20 days administration of S. griseorubens CIBA-NS1, shrimps were challenged with V. campbellii. The S. griseorubens CIBA-NS1 reduced Vibrio population in test group when compared to control, improved survival (60.5 ± 6.4%) and growth, as indicated by weight gain (1.8 ± 0.05g). In control group survival and growth were 48.4 ± 3.5% and 1.4 ± 0.03 g respectively. On challenge with V. campbellii, the S. griseorubens CIBA-NS1 administered group showed better survival (85.6 ± 10%) than positive control (64.3 ± 10%). The results suggested that S. griseorubens CIBA-NS1 is antagonistic to V. campbellii, reduce Vibrio population in the culture system and improve growth and survival. This is the first report on antagonistic activity of S. griseorubens isolated from salt marsh plant Salicornia sp, as a probiotic candidate to prevent V. campbellii infection in shrimps.
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Affiliation(s)
- N S Sudheer
- Kakdwip Research Centre of ICAR-CIBA, Kakdwip, South 24 Parganas, West Bengal, India.
| | - I F Biju
- Kakdwip Research Centre of ICAR-CIBA, Kakdwip, South 24 Parganas, West Bengal, India
| | - C P Balasubramanian
- ICAR-Central Institute of Brackishwater Aquaculture, Chennai, Tamil Nadu, India
| | - A Panigrahi
- ICAR-Central Institute of Brackishwater Aquaculture, Chennai, Tamil Nadu, India
| | - T Sathish Kumar
- ICAR-Central Institute of Brackishwater Aquaculture, Chennai, Tamil Nadu, India
| | - Sujeet Kumar
- ICAR-Central Institute of Brackishwater Aquaculture, Chennai, Tamil Nadu, India
| | - Babita Mandal
- Kakdwip Research Centre of ICAR-CIBA, Kakdwip, South 24 Parganas, West Bengal, India
| | - S Das
- Kakdwip Research Centre of ICAR-CIBA, Kakdwip, South 24 Parganas, West Bengal, India
| | - D De
- Kakdwip Research Centre of ICAR-CIBA, Kakdwip, South 24 Parganas, West Bengal, India
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Nguyen NL, Van Dung V, Van Tung N, Nguyen TKL, Quan ND, Giang TTH, Ngan NTT, Hien NT, Nguyen HH. Draft genome sequencing of halotolerant bacterium Salinicola sp. DM10 unravels plant growth-promoting potentials. 3 Biotech 2023; 13:416. [PMID: 38009164 PMCID: PMC10667196 DOI: 10.1007/s13205-023-03833-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/24/2023] [Indexed: 11/28/2023] Open
Abstract
In this study, strain DM10 was isolated from mangrove roots and characterized as a halotolerant plant growth-promoting bacterium. Strain DM10 exhibited the ability to solubilize phosphate, produce siderophore, show 1-aminocyclopropane-1-carboxylic acid deaminase activity, and hydrolyze starch. The rice plants subjected to a treatment of NaCl (200 mM) and inoculated with strain DM10 showed an improvement in the shoot length, root length, and dried weight, when compared to those exposed solely to saline treatment. The comprehensive genome sequencing of strain DM10 revealed a genome spanning of 4,171,745 bp, harboring 3626 protein coding sequences. Within its genome, strain DM10 possesses genes responsible for both salt-in and salt-out strategies, indicative of a robust genetic adaptation aimed at fostering salt tolerance. Additionally, the genome encodes genes involved in phosphate solubilization, such as the synthesis of gluconic acid, high-affinity phosphate transport systems, and alkaline phosphatase. In the genome of DM10, we identified the acdS gene, responsible for encoding 1-aminocyclopropane-1-carboxylate deaminase, as well as the amy1A gene, which encodes α-amylase. Furthermore, the genome of DM10 contains sequences associated with the iron (3+)-hydroxamate and iron uptake clusters, responsible for siderophore production. Such data provide a deep understanding of the mechanism employed by strain DM10 to combat osmotic and salinity stress, facilitate plant growth, and elucidate its molecular-level behaviors.
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Affiliation(s)
- Ngoc-Lan Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
- Graduate of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Vu Van Dung
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
- Graduate of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Nguyen Van Tung
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
- Graduate of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Thi Kim Lien Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Nguyen Duc Quan
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Tran Thi Huong Giang
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Nguyen Thi Thanh Ngan
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
- Graduate of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Nguyen Thanh Hien
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Huy-Hoang Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
- Graduate of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
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Petrosyan K, Thijs S, Piwowarczyk R, Ruraż K, Kaca W, Vangronsveld J. Diversity and potential plant growth promoting capacity of seed endophytic bacteria of the holoparasite Cistanche phelypaea (Orobanchaceae). Sci Rep 2023; 13:11835. [PMID: 37481658 PMCID: PMC10363106 DOI: 10.1038/s41598-023-38899-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/17/2023] [Indexed: 07/24/2023] Open
Abstract
Salt marshes are highly dynamic, biologically diverse ecosystems with a broad range of ecological functions. We investigated the endophytic bacterial community of surface sterilized seeds of the holoparasitic Cistanche phelypaea growing in coastal salt marshes of the Iberian Peninsula in Portugal. C. phelypaea is the only representative of the genus Cistanche that was reported in such habitat. Using high-throughput sequencing methods, 23 bacterial phyla and 263 different OTUs on genus level were found. Bacterial strains belonging to phyla Proteobacteria and Actinobacteriota were dominating. Also some newly classified or undiscovered bacterial phyla, unclassified and unexplored taxonomic groups, symbiotic Archaea groups inhabited the C. phelypaea seeds. γ-Proteobacteria was the most diverse phylogenetic group. Sixty-three bacterial strains belonging to Bacilli, Actinomycetes, α-, γ- and β-Proteobacteria and unclassified bacteria were isolated. We also investigated the in vitro PGP traits and salt tolerance of the isolates. Among the Actinobacteria, Micromonospora spp. showed the most promising endophytes in the seeds. Taken together, the results indicated that the seeds were inhabited by halotolerant bacterial strains that may play a role in mitigating the adverse effects of salt stress on the host plant. In future research, these bacteria should be assessed as potential sources of novel and unique bioactive compounds or as novel bacterial species.
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Affiliation(s)
- Kristine Petrosyan
- Department of Microbiology, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406, Kielce, Poland.
- Environmental Biology Research Group, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium.
| | - Sofie Thijs
- Environmental Biology Research Group, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
| | - Renata Piwowarczyk
- Department of Environmental Biology, Center for Research and Conservation of Biodiversity, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406, Kielce, Poland
| | - Karolina Ruraż
- Department of Environmental Biology, Center for Research and Conservation of Biodiversity, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406, Kielce, Poland
| | - Wiesław Kaca
- Department of Microbiology, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406, Kielce, Poland
| | - Jaco Vangronsveld
- Environmental Biology Research Group, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
- Department of Plant Physiology and Biophysics, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka, 19, 20-033, Lublin, Poland
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Qian F, Huang X, Bao Y. Heavy metals reshaping the structure and function of phylloplane bacterial community of native plant Tamarix ramosissima from Pb/Cd/Cu/Zn smelting regions. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 251:114495. [PMID: 36640572 DOI: 10.1016/j.ecoenv.2022.114495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Heavy metal (HM) is noxious element that cannot be biodegraded, thus accumulating in the environment and posing a serious threat to the ecology. Plant phylloplane harbors diverse microbial communities that profoundly influence ecosystem functioning and host health. With more HM accumulating around smelters, native plants and microbes in various habitats tend to suffer from HM. However, the response of phylloplane bacteria of native plants to HM remains unclear. Thus, this study aimed to explain the response of Tamarix ramosissima, a phylloplane bacterial community to HM as well as the effect of the process on host growth in situ by investigating the potential source of HM and bacterial community shift. Results showed that, in most cases, the contaminated site with high HM level caused more accumulation of HM in phylloplane and leaves. Moreover, HM in the phylloplane was not from the internal transport of the plant but it could be due to the wind action or rains. Bacteria in phylloplane may have come from the soil due to their strong positive correlation with corresponding soil at the genus level. High HM level inhibited the relative abundance of dominant bacteria, increased the diversity and species richness of bacterial community in phylloplane, and induced more special bacteria to maintain higher productivity of the host plant, for which, Cu and Pb were the major contributors. Meanwhile, bacteria in phylloplane showed a universal positive correlation in the co-occurrence network, which showed less stability than that in corresponding soil in the smelting region, and it is helpful to regulate the growth of plants more rapidly. Nearly 25% of KEGG pathways were modulated by high HM level and bacterial function tended to stabilize HM to avoid the potential process of leaf absorption. The study illustrated that HM in phylloplane played an important role in shaping the bacterial community of phylloplane as compared to HM in leaves or phyllosphere, and the resulting increase of diversity and richness of bacterial community and special bacteria further maintained the growth of the host plant suffering from HM stress.
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Affiliation(s)
- Fanghan Qian
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xinjian Huang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yanyu Bao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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Pérez-Inocencio J, Iturriaga G, Aguirre-Mancilla CL, Ramírez-Pimentel JG, Vásquez-Murrieta MS, Álvarez-Bernal D. Identification of Halophilic and Halotolerant Bacteria from the Root Soil of the Halophyte Sesuvium verrucosum Raf. PLANTS (BASEL, SWITZERLAND) 2022; 11:3355. [PMID: 36501394 PMCID: PMC9740589 DOI: 10.3390/plants11233355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/14/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Soil salinity is a condition that limits crop growth and productivity, and soil-dwelling bacteria from halophytic plant roots may be a viable strategy to cope with low productivity due to salt stress. Halophilic and halotolerant bacteria of the root soil of Sesuvium verrucosum were analyzed in this study as there is little evidence regarding its associated microbiology. Soil was sampled from the roots of Sesuvium verrucosum to obtain the cultivable bacteria. Their morphological characteristics were identified and they were molecularly identified by the 16S sequence. The growth capacity of the bacteria was determined at different levels of pH and salinity, and several growth promotion characteristics were identified, such as phosphorus solubilization, indole acetic acid production by the tryptophan-dependent (AIAt) and tryptophan-independent (IAA) pathways, ammonium production from organic sources, solubilization of carbonates, and zinc and sodium capture capacity. In addition, the bacteria that presented the best characteristics for germination variables of Solanum lycopersicum were evaluated. A total of 20 bacteria from root soil of Sesuvium verrucosum Raf. belonging to the phyla Proteobacteria (50%), Firmicutes (45%) and Actinobacteria (5%) were identified, with each one having different morphological characteristics. Among the bacterial isolates, 45% had the ability to resist different levels of salinity and pH, ranging from 0 to 20% of NaCl, and pH between 5 and 11. Moreover, these bacteria had the capacity to solubilize carbonates, phosphorus and zinc, capture sodium, produce ammonium from organic substrates and IAA (indole acetic acid), and promote enzymatic activity of amylases, proteases, lipases and cellulases. The bacteria evaluated on the germination of Solanum lycopersicum had an influence on germination at different salinity levels, with greater influence at 100 mM NaCl. This demonstrated that halophilic bacteria belonging to the rhizosphere of Sesuvium verrucosum have the ability to promote growth in extreme salinity conditions, making them candidates for the recovery of productivity in saline soils.
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Affiliation(s)
| | | | | | | | | | - Dioselina Álvarez-Bernal
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional Unidad Michoacán (CIIDIR-Michoacán), Jiquilpan 59510, Mexico
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Maldonado JE, Gaete A, Mandakovic D, Aguado-Norese C, Aguilar M, Gutiérrez RA, González M. Partners to survive: Hoffmannseggia doellii root-associated microbiome at the Atacama Desert. THE NEW PHYTOLOGIST 2022; 234:2126-2139. [PMID: 35274744 DOI: 10.1111/nph.18080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
The discovery and characterization of plant species adapted to extreme environmental conditions have become increasingly important. Hoffmannseggia doellii is a perennial herb endemic to the Chilean Atacama Desert that grows in the western Andes between 2800 and 3600 m above sea level. Its growing habitat is characterized by high radiation and low water and nutrient availability. Under these conditions, H. doellii can grow, reproduce, and develop an edible tuberous root. We characterized the H. doellii soil-associated microbiomes to understand the biotic factors that could influence their surprising ability to survive. We found an increased number of observed species and higher phylogenetic diversity of bacteria and fungi on H. doellii root soils compared with bare soil (BS) along different sites and to soil microbiomes of other plant species. Also, the H. doellii-associated microbiome had a higher incidence of overall positive interactions and fungal within-kingdom interactions than their corresponding BS network. These findings suggest a microbial diversity soil modulation mechanism that may be a characteristic of highly tolerant plants to diverse and extreme environments. Furthermore, since H. doellii is related to important cultivated crops, our results create an opportunity for future studies on climate change adaptation of crop plants.
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Affiliation(s)
- Jonathan E Maldonado
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Departamento de Genética Molecular y Microbiología, ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 7500565, Chile
- Laboratorio de Multiómica Vegetal y Bioinformática, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile
| | - Alexis Gaete
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, 7830490, Chile
| | - Dinka Mandakovic
- GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Santiago, 8580745, Chile
| | - Constanza Aguado-Norese
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, 7830490, Chile
| | - Melissa Aguilar
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Departamento de Genética Molecular y Microbiología, ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 7500565, Chile
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Departamento de Genética Molecular y Microbiología, ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 7500565, Chile
| | - Mauricio González
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, 7830490, Chile
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Araújo S, Azenha SR, Henriques I, Tacão M. qnrA gene diversity in Shewanella spp. MICROBIOLOGY (READING, ENGLAND) 2021; 167. [PMID: 34914577 DOI: 10.1099/mic.0.001118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Members of Shewanella are ubiquitous in aquatic environments, some of which have been implicated in human infections. The progenitors of antibiotic resistance genes with clinical relevance, such as qnrA genes, have been identified in Shewanella. qnrA code for a pentapeptide repeat protein that protects type II topoisomerases, decreasing susceptibility to quinolones and fluoroquinolones. In this study, 248 genomes of 49 Shewanella species were analysed as well as 33 environmental isolates belonging to 10 Shewanella species. The presence of the qnrA gene was detected in 22.9% of the genomes and 15.2% of the isolates. The gene was more often detected in Shewanella algae, but was also detected in Shewanella carassii, Shewanella chilikensis, Shewanella haliotis and Shewanella indica. The identified genes encoded the previously described variants QnrA3 (in 22 genomes of one species), QnrA2 (eight genomes and three species), QnrA1 (six genomes and two species), QnrA7 (five genomes and two species), QnrA10 (two genomes of one species) and QnrA4 (one genome). In addition, 11 novel variants with 3 to 7 amino acid substitutions were identified (in 13 genomes and one environmental isolate). The presence of this gene appears to be species-specific although within some species several variants were detected. The study presents a previously unknown diversity of qnrA in Shewanella, highlighting the role of this genus as progenitor and reservoir of these genes. Further studies are needed to determine the phenotypes conferred by the new variants and the mechanisms that may mediate the transfer of these genes to new hosts.
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Affiliation(s)
- S Araújo
- Biology Department, University of Aveiro, Aveiro, Portugal.,CESAM, University of Aveiro, Aveiro, Portugal
| | - S R Azenha
- Biology Department, University of Aveiro, Aveiro, Portugal
| | - I Henriques
- Biology Department, University of Aveiro, Aveiro, Portugal.,CESAM, University of Aveiro, Aveiro, Portugal.,University of Coimbra, Department of Life Sciences, Faculty of Sciences and Technology, Coimbra, Portugal
| | - M Tacão
- Biology Department, University of Aveiro, Aveiro, Portugal.,CESAM, University of Aveiro, Aveiro, Portugal
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9
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Tarquinio F, Attlan O, Vanderklift MA, Berry O, Bissett A. Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds. Front Microbiol 2021; 12:703014. [PMID: 34621247 PMCID: PMC8491609 DOI: 10.3389/fmicb.2021.703014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Seagrasses are marine angiosperms that can live completely or partially submerged in water and perform a variety of significant ecosystem services. Like terrestrial angiosperms, seagrasses can reproduce sexually and, the pollinated female flower develop into fruits and seeds, which represent a critical stage in the life of plants. Seed microbiomes include endophytic microorganisms that in terrestrial plants can affect seed germination and seedling health through phytohormone production, enhanced nutrient availability and defence against pathogens. However, the characteristics and origins of the seagrass seed microbiomes is unknown. Here, we examined the endophytic bacterial community of six microenvironments (flowers, fruits, and seeds, together with leaves, roots, and rhizospheric sediment) of the seagrass Halophila ovalis collected from the Swan Estuary, in southwestern Australia. An amplicon sequencing approach (16S rRNA) was used to characterize the diversity and composition of H. ovalis bacterial microbiomes and identify core microbiome bacteria that were conserved across microenvironments. Distinct communities of bacteria were observed within specific seagrass microenvironments, including the reproductive tissues (flowers, fruits, and seeds). In particular, bacteria previously associated with plant growth promoting characteristics were mainly found within reproductive tissues. Seagrass seed-borne bacteria that exhibit growth promoting traits, the ability to fix nitrogen and anti-pathogenic potential activity, may play a pivotal role in seed survival, as is common for terrestrial plants. We present the endophytic community of the seagrass seeds as foundation for the identification of potential beneficial bacteria and their selection in order to improve seagrass restoration.
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Affiliation(s)
- Flavia Tarquinio
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia.,Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Océane Attlan
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia.,Sciences et Technologies, Université de la Réunion, Saint-Denis, France
| | - Mathew A Vanderklift
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Oliver Berry
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Hobart, TAS, Australia
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10
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Mitra M, Nguyen KMAK, Box TW, Berry TL, Fujita M. Isolation and characterization of a heavy metal- and antibiotic-tolerant novel bacterial strain from a contaminated culture plate of Chlamydomonas reinhardtii, a green micro-alga. F1000Res 2021; 10:533. [PMID: 34540203 PMCID: PMC8424464 DOI: 10.12688/f1000research.53779.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/24/2021] [Indexed: 11/04/2023] Open
Abstract
Background:Chlamydomonas reinhardtii, a green micro-alga, is normally cultured in laboratories in Tris-Acetate Phosphate (TAP), a medium which contains acetate as the sole carbon source. Acetate in TAP can lead to occasional bacterial and fungal contamination. We isolated a yellow-pigmented bacterium from a Chlamydomonas TAP plate. It was named Clip185 based on the Chlamydomonas strain plate it was isolated from. In this article we present our work on the isolation, taxonomic identification and physiological and biochemical characterizations of Clip185. Methods: We measured sensitivities of Clip185 to five antibiotics and performed standard microbiological tests to characterize it. We partially sequenced the 16S rRNA gene of Clip185. We identified the yellow pigment of Clip185 by spectrophotometric analyses. We tested tolerance of Clip185 to six heavy metals by monitoring its growth on Lysogeny Broth (LB) media plates containing 0.5 mM -10 mM concentrations of six different heavy metals. Results: Clip185 is an aerobic, gram-positive rod, oxidase-negative, mesophilic, alpha-hemolytic bacterium. It can ferment glucose, sucrose and mannitol. It is starch hydrolysis-positive. It is very sensitive to vancomycin but resistant to penicillin and other bacterial cell membrane- and protein synthesis-disrupting antibiotics. Clip185 produces a C50 carotenoid, decaprenoxanthin, which is a powerful anti-oxidant with a commercial demand. Decaprenoxanthin production is induced in Clip185 under light. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of Clip185 revealed a 99% sequence identity to that of Microbacterium binotii strain PK1-12M and Microbacterium sp. strain MDP6. Clip185 is able to tolerate toxic concentrations of six heavy metals. Conclusions: Our results show that Clip185 belongs to the genus Microbacterium. In the future, whole genome sequencing of Clip185 will clarify if Clip185 is a new Microbacterium species or a novel strain of Microbacterium binotii, and will reveal its genes involved in antibiotic-resistance, heavy-metal tolerance and regulation of decaprenoxanthin biosynthesis.
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Affiliation(s)
- Mautusi Mitra
- Department of Mathematics, Sciences and Technology, University of West Georgia, Carrollton, Georgia, 30118, USA
| | - Kevin Manoap-Anh-Khoa Nguyen
- Department of Mathematics, Sciences and Technology, University of West Georgia, Carrollton, Georgia, 30118, USA
- Department of Mechanical Engineering, Kennesaw State University, Marietta, Georgia, 30060, USA
| | - Taylor Wayland Box
- Department of Mathematics, Sciences and Technology, University of West Georgia, Carrollton, Georgia, 30118, USA
| | - Taylor Lynne Berry
- Carrollton High School, Carrollton, Georgia, 30117, USA
- Department of Chemistry and Biochemistry, University of North Georgia, Dahlonega, Georgia, 30597, USA
| | - Megumi Fujita
- Department of Mathematics, Sciences and Technology, University of West Georgia, Carrollton, Georgia, 30118, USA
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11
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Mitra M, Nguyen KMAK, Box TW, Berry TL, Fujita M. Isolation and characterization of a heavy metal- and antibiotic-tolerant novel bacterial strain from a contaminated culture plate of Chlamydomonas reinhardtii, a green micro-alga. F1000Res 2021; 10:533. [PMID: 34540203 PMCID: PMC8424464 DOI: 10.12688/f1000research.53779.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/27/2021] [Indexed: 11/20/2022] Open
Abstract
Background:Chlamydomonas reinhardtii, a green micro-alga, is normally cultured in laboratories in Tris-Acetate Phosphate (TAP), a medium which contains acetate as the sole carbon source. Acetate in TAP can lead to occasional bacterial and fungal contamination. We isolated a yellow-pigmented bacterium from a Chlamydomonas TAP plate. It was named Clip185 based on the Chlamydomonas strain plate it was isolated from. In this article we present our work on the isolation, taxonomic identification and physiological and biochemical characterizations of Clip185. Methods: We measured sensitivities of Clip185 to five antibiotics and performed standard microbiological tests to characterize it. We partially sequenced the 16S rRNA gene of Clip185. We identified the yellow pigment of Clip185 by spectrophotometric analyses. We tested tolerance of Clip185 to six heavy metals by monitoring its growth on Lysogeny Broth (LB) media plates containing 0.5 mM -10 mM concentrations of six different heavy metals. Results: Clip185 is an aerobic, gram-positive rod, oxidase-negative, mesophilic, alpha-hemolytic bacterium. It can ferment glucose, sucrose and mannitol. It is starch hydrolysis-positive. It is very sensitive to vancomycin but resistant to penicillin and other bacterial cell membrane- and protein synthesis-disrupting antibiotics. Clip185 produces a C50 carotenoid, decaprenoxanthin, which is a powerful anti-oxidant with a commercial demand. Decaprenoxanthin production is induced in Clip185 under light. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of Clip185 revealed a 99% sequence identity to that of Microbacterium binotii strain PK1-12M and Microbacterium sp. strain MDP6. Clip185 is able to tolerate toxic concentrations of six heavy metals. Conclusions: Our results show that Clip185 belongs to the genus Microbacterium. In the future, whole genome sequencing of Clip185 will clarify if Clip185 is a new Microbacterium species or a novel strain of Microbacterium binotii, and will reveal its genes involved in antibiotic-resistance, heavy-metal tolerance and regulation of decaprenoxanthin biosynthesis.
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Affiliation(s)
- Mautusi Mitra
- Department of Mathematics, Sciences and Technology, University of West Georgia, Carrollton, Georgia, 30118, USA
| | - Kevin Manoap-Anh-Khoa Nguyen
- Department of Mathematics, Sciences and Technology, University of West Georgia, Carrollton, Georgia, 30118, USA
- Department of Mechanical Engineering, Kennesaw State University, Marietta, Georgia, 30060, USA
| | - Taylor Wayland Box
- Department of Mathematics, Sciences and Technology, University of West Georgia, Carrollton, Georgia, 30118, USA
| | - Taylor Lynne Berry
- Carrollton High School, Carrollton, Georgia, 30117, USA
- Department of Chemistry and Biochemistry, University of North Georgia, Dahlonega, Georgia, 30597, USA
| | - Megumi Fujita
- Department of Mathematics, Sciences and Technology, University of West Georgia, Carrollton, Georgia, 30118, USA
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12
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Wang H, Narsing Rao MP, Gao Y, Li X, Gao R, Xie Y, Li Q, Li W. Insights into the endophytic bacterial community comparison and their potential role in the dimorphic seeds of halophyte Suaeda glauca. BMC Microbiol 2021; 21:143. [PMID: 33980153 PMCID: PMC8114534 DOI: 10.1186/s12866-021-02206-1] [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: 01/22/2021] [Accepted: 04/19/2021] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Seed dimorphism has been thought to be a bet-hedging strategy that helps plants survive in the disturbed environment and has been widely studied for its ecological adaptation mechanism. Many studies showed that seed-associated microorganisms play an important role in enhancing plant fitness, but information regarding endophytic bacteria associated with dimorphic seeds is limited. This study explores the influence of seed coat structure and seed phytochemical properties on the community composition and diversity of endophytic bacteria of dimorphic seeds of Suaeda glauca. In this study, we used 16S rRNA high-throughput gene sequencing method to compare the community composition and bacterial diversity between brown and black seeds of Suaeda glauca. RESULTS A significant difference was observed in seed coat structure and phytochemical properties between brown and black seeds of S. glauca. Total 9 phyla, 13 classes, 31 orders, 53 families, 102 genera were identified in the dimorphic seeds. The dominant phyla were Proteobacteria, Firmicutes, and Actinobacteria. The results showed that seed dimorphism had little impact on the diversity and richness of endophytic bacterial communities but significantly differs in the relative abundance of the bacterial community between brown and black seeds. At the phylum level, Actinobacteria tend to be enriched significantly in brown seeds. At the genus level, Rhodococcus, Ralstonia, Pelomonas and Bradyrhizobium tend to be enriched significantly in brown seeds, while Marinilactibacillus was mainly found in black seeds. Besides, brown seeds harbored a large number of bacteria with plant-growth-promoting traits, whereas black seeds presented bacteria with enzyme activities (i.e., pectinase, cellulolytic and xylanolytic activities). CONCLUSION The endophytic bacterial community compositions were significantly different between dimorphic seeds of Suaeda glauca, and play an important role in the ecological adaptation of dimorphic seeds by performing different biological function roles. The endophytic bacterial communities of the dimorphic seeds may be influenced mainly by the seed coat structureand partly by the seed phytochemical characteristics. These findings provide valuable information for better understanding of the ecological adaptation strategy of dimorphic seeds in the disturbed environment.
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Affiliation(s)
- Hongfei Wang
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, No.1 Liushu South Street, Dalian, 650081, China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yanli Gao
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, No.1 Liushu South Street, Dalian, 650081, China
| | - Xinyang Li
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, No.1 Liushu South Street, Dalian, 650081, China
| | - Rui Gao
- Dandong Forestry and Grassland Development Service Center, Dandong, 118000, China
| | - Yuanguo Xie
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qiuli Li
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, No.1 Liushu South Street, Dalian, 650081, China.
| | - Wenjun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China. .,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
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13
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Yamamoto K, Matsutani M, Shiwa Y, Ishige T, Sakamoto H, Saitoh H, Tsushima S. Comparative Analysis of Bacterial Diversity and Community Structure in the Rhizosphere and Root Endosphere of Two Halophytes, Salicornia europaea and Glaux maritima, Collected from Two Brackish Lakes in Japan. Microbes Environ 2021; 35. [PMID: 32893195 PMCID: PMC7511784 DOI: 10.1264/jsme2.me20072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Microbial community structures associated with halophytes and their compositions among different habitats, particularly natural saline sites, have not yet been investigated in detail. In the present study, we examined the diversity and composition of the rhizosphere and root endosphere bacteria of two halophytes, Salicornia europaea L. and Glaux maritima L., collected from two adjacent brackish lakes, Lake Notoro and Lake Tofutsu, in Japan. The bacterial species richness and diversity indices of the two halophytes collected from both lakes showed no significant differences in the rhizosphere or root endosphere. In contrast, beta diversity and taxonomic analyses revealed significant differences in the bacterial communities from each halophyte between the two lakes even though the two locations were natural saline sites, indicating that the bacterial communities for S. europaea and G. maritima both fluctuated in a manner that depended on the geographical location. Common and abundant genera associated with each halophyte across the two lakes were then identified to verify the bacterial genera specifically inhabiting each plant species. The results obtained showed that the composition of abundant genera inhabiting each halophyte across two lakes was distinct from that reported previously in other saline soil areas. These results suggest that each halophyte in different geographical sites had an individual complex bacterial community.
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Affiliation(s)
- Kosuke Yamamoto
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture
| | | | - Yuh Shiwa
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture.,NODAI Genome Research Center, Tokyo University of Agriculture
| | - Taichiro Ishige
- NODAI Genome Research Center, Tokyo University of Agriculture
| | - Hikaru Sakamoto
- Department of Northern Biosphere Agriculture, Faculty of Bioindustry, Tokyo University of Agriculture
| | - Hiromasa Saitoh
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture
| | - Seiya Tsushima
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture
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14
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Singh S, Ghadge VA, Kumar P, Mathew DE, Dhimmar A, Sahastrabudhe H, Nalli Y, Rathod MR, Shinde PB. Biodiversity and antimicrobial potential of bacterial endophytes from halophyte Salicornia brachiata. Antonie Van Leeuwenhoek 2021; 114:591-608. [PMID: 33674993 DOI: 10.1007/s10482-021-01544-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/13/2021] [Indexed: 12/01/2022]
Abstract
Extreme natural habitats like halophytes, marsh land, and marine environment are suitable arena for chemical ecology between plants and microbes having environmental impact. Endophytes are an ecofriendly option for the promotion of plant growth and to serve as sustainable resource of novel bioactive natural products. The present study, focusing on biodiversity of bacterial endophytes from Salicornia brachiata, led to isolation of around 336 bacterial endophytes. Phylogenetic analysis of 63 endophytes revealed 13 genera with 27 different species, belonging to 3 major groups: Firmicutes, Proteobacteria, and Actinobacteria. 30% endophytic isolates belonging to various genera demonstrated broad-spectrum antibacterial and antifungal activities against a panel of human, plant, and aquatic infectious agents. An endophytic isolate Bacillus amyloliquefaciens 5NPA-1, exhibited strong in-vitro antibacterial activity against human pathogen Staphylococcus aureus and phytopathogen Xanthomonas campestris. Investigation through LC-MS/MS-based molecular networking and bioactivity-guided purification led to the identification of three bioactive compounds belonging to lipopeptide class based on 1H-, 13C-NMR and MS analysis. To our knowledge, this is the first report studying bacterial endophytic biodiversity of Salicornia brachiata and the isolation of bioactive compounds from its endophyte. Overall, the present study provides insights into the diversity of endophytes associated with the plants from the extreme environment as a rich source of metabolites with remarkable agricultural applications and therapeutic properties.
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Affiliation(s)
- Sanju Singh
- Natural Products and Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vishal A Ghadge
- Natural Products and Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pankaj Kumar
- Natural Products and Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Doniya Elze Mathew
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.,Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India
| | - Asmita Dhimmar
- Natural Products and Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Harshal Sahastrabudhe
- Natural Products and Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Yedukondalu Nalli
- Natural Products and Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India
| | - Mina R Rathod
- Natural Products and Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India
| | - Pramod B Shinde
- Natural Products and Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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15
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The Root Microbiome of Salicornia ramosissima as a Seedbank for Plant-Growth Promoting Halotolerant Bacteria. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11052233] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Root−associated microbial communities play important roles in the process of adaptation of plant hosts to environment stressors, and in this perspective, the microbiome of halophytes represents a valuable model for understanding the contribution of microorganisms to plant tolerance to salt. Although considered as the most promising halophyte candidate to crop cultivation, Salicornia ramosissima is one of the least-studied species in terms of microbiome composition and the effect of sediment properties on the diversity of plant-growth promoting bacteria associated with the roots. In this work, we aimed at isolating and characterizing halotolerant bacteria associated with the rhizosphere and root tissues of S. ramosissima, envisaging their application in saline agriculture. Endophytic and rhizosphere bacteria were isolated from wild and crop cultivated plants, growing in different estuarine conditions. Isolates were identified based on 16S rRNA sequences and screened for plant-growth promotion traits. The subsets of isolates from different sampling sites were very different in terms of composition but consistent in terms of the plant-growth promoting traits represented. Bacillus was the most represented genus and expressed the wider range of extracellular enzymatic activities. Halotolerant strains of Salinicola, Pseudomonas, Oceanobacillus, Halomonas, Providencia, Bacillus, Psychrobacter and Brevibacterium also exhibited several plant-growth promotion traits (e.g., 3-indole acetic acid (IAA), 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, siderophores, phosphate solubilization). Considering the taxonomic diversity and the plant-growth promotion potential of the isolates, the collection represents a valuable resource that can be used to optimize the crop cultivation of Salicornia under different environmental conditions and for the attenuation of salt stress in non-halophytes, considering the global threat of arable soil salinization.
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16
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Yang SH, Park MJ, Kwon KK. Oricola thermophila sp. nov., a marine bacterium isolated from tidal flat sediment and emended description of the genus Oricola Hameed et al. 2015. Int J Syst Evol Microbiol 2020; 71. [PMID: 33263513 DOI: 10.1099/ijsem.0.004574] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, facultatively anaerobic, rod-shaped (1.8-4.4×0.5-0.7 µm) and motile marine bacterium, designated as MEBiC13590T, was isolated from tidal flat sediment sampled at Incheon City, on the west coast of the Republic of Korea. The 16S rRNA gene sequence analysis revealed that strain MEBiC13590T showed high similarity to Oricola cellulosilytica CC-AMH-0T (98.2 %), followed by Oceaniradius stylonematis StC1T (97.5 %); however, it clustered with Oricola cellulosilytica. The phylogenomic tree inferred by the up-to-date bacterial core gene set suggested that strain MEBiC13590T shared a phyletic line with Oricola cellulosilytica. Average nucleotide identity and digital DNA-DNA hybridization values (75.0 and 19.3 %, respectively) between strain MEBiC13590T and Oricola cellulosilytica CC-AMH-0T were below the respective species delineation cutoffs. Growth was observed at 22-50 °C (optimum, 45 °C), at pH 5-9 (optimum, pH 7) and with 1-6 % (optimum, 3 %) NaCl. The predominant cellular fatty acids were C16 : 0 (7.6 %), C18 : 0 (12.2 %), 11-methyl C18 : 1 ω7c (5.7 %), C19 : 0 cyclo ω6c and summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c; 38 %). The DNA G+C content was 63.5 mol%. The major respiratory quinone was Q-10. Several phenotypic characteristics such as growth temperature, oxygen requirement, enzyme activities of urease, gelatinase, lipase (C14), α-chymotrypsin, acid phosphatase, β-galactosidase, β-glucosidase etc. differentiate strain MEBiC13590T from Oricola cellulosilytica CC-AMH-0T. Based on this polyphasic taxonomic data, strain MEBiC13590T should be classified as representing a novel species in the genus Oricola for which the name Oricola thermophila sp. nov. is proposed . The type strain is MEBiC13590T (=KCCM 43313T=JCM 33661T).
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Affiliation(s)
- Sung-Hyun Yang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, 385, Haeyang-ro, Yeongdo-gu, Busan, Republic of Korea
| | - Mi-Jeong Park
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, 385, Haeyang-ro, Yeongdo-gu, Busan, Republic of Korea
| | - Kae Kyoung Kwon
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, 385, Haeyang-ro, Yeongdo-gu, Busan, Republic of Korea
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17
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Corretto E, Antonielli L, Sessitsch A, Höfer C, Puschenreiter M, Widhalm S, Swarnalakshmi K, Brader G. Comparative Genomics of Microbacterium Species to Reveal Diversity, Potential for Secondary Metabolites and Heavy Metal Resistance. Front Microbiol 2020; 11:1869. [PMID: 32903828 PMCID: PMC7438953 DOI: 10.3389/fmicb.2020.01869] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/16/2020] [Indexed: 12/11/2022] Open
Abstract
Microbacterium species have been isolated from a wide range of hosts and environments, including heavy metal-contaminated sites. Here, we present a comprehensive analysis on the phylogenetic distribution and the genetic potential of 70 Microbacterium belonging to 20 different species isolated from heavy metal-contaminated and non-contaminated sites with particular attention to secondary metabolites gene clusters. The analyzed Microbacterium species are divided in three main functional clades. They share a small core genome (331 gene families covering basic functions) pointing to high genetic diversity. The most common secondary metabolite gene clusters encode pathways for the production of terpenoids, type III polyketide synthases and non-ribosomal peptide synthetases, potentially responsible of the synthesis of siderophore-like compounds. In vitro tests showed that many Microbacterium strains produce siderophores, ACC deaminase, auxins (IAA) and are able to solubilize phosphate. Microbacterium isolates from heavy metal contaminated sites are on average more resistant to heavy metals and harbor more genes related to metal homeostasis (e.g., metalloregulators). On the other hand, the ability to increase the metal mobility in a contaminated soil through the secretion of specific molecules seems to be widespread among all. Despite the widespread capacity of strains to mobilize several metals, plants inoculated with selected Microbacterium isolates showed only slightly increased iron concentrations, whereas concentrations of zinc, cadmium and lead were decreased.
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Affiliation(s)
- Erika Corretto
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Livio Antonielli
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Angela Sessitsch
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Christoph Höfer
- Institute of Soil Research, Department of Forest- and Soil Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Markus Puschenreiter
- Institute of Soil Research, Department of Forest- and Soil Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Siegrid Widhalm
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | | | - Günter Brader
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
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18
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De Hita D, Fuentes M, Zamarreño AM, Ruiz Y, Garcia-Mina JM. Culturable Bacterial Endophytes From Sedimentary Humic Acid-Treated Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:837. [PMID: 32636861 PMCID: PMC7316998 DOI: 10.3389/fpls.2020.00837] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 05/25/2020] [Indexed: 05/14/2023]
Abstract
The global decrease in soil fertility leads to a new agricultural scenario where eco-friendly solutions play an important role. The plant growth promotion through the use of microbes, especially endophytes and rhizosphere microbiota, has been proposed as a useful solution. Several studies have shown that humic substances are suitable vehicles for the inoculation of plant growth promoting bacteria, and that this combination has an enhanced effect on the stimulation of plant development. In this work, cucumber plants grown hydroponically have been pre-treated with a sedimentary humic acid (SHA) with known plant growth-enhancing effects, and culturable bacterial endophytes have been isolated from these plants. The hypothesis was that this pre-treatment with SHA could lead to the isolation of certain endophytic taxa whose proliferation within the plant could have been promoted as a result of the effects of the treatment with SHA, and that could eventually reinforce a potential synergistic effect of a combined application of those endophytic bacteria and SHA. The culturable endophytes that have been isolated from humic acid-treated cucumber plants have been identified as members of four main phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Isolates were characterized according to the following plant growth-promoting traits: nitrogen fixation/scavenging, phosphate solubilization, siderophore production and plant hormone production. Most of the isolates were able to fix/scavenge nitrogen and to produce plant hormones (indole-3-acetic acid and several cytokinins), whereas few isolates were able to solubilize phosphate and/or produce siderophores. The most promising endophyte isolates for its use in futures investigations as plant growth-promoting bacterial inocula were Pseudomonas sp. strains (that showed all traits), Sphingomonas sp., Stenotrophomonas sp. strains, or some Arthrobacter sp. and Microbacterium sp. isolates.
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Affiliation(s)
- David De Hita
- Department of Environmental Biology, Biological and Agricultural Chemistry Group (BACh), University of Navarra, Pamplona, Spain
| | - Marta Fuentes
- Department of Environmental Biology, Biological and Agricultural Chemistry Group (BACh), University of Navarra, Pamplona, Spain
| | - Angel M. Zamarreño
- Department of Environmental Biology, Biological and Agricultural Chemistry Group (BACh), University of Navarra, Pamplona, Spain
| | - Yaiza Ruiz
- Department of Environmental Biology, Biological and Agricultural Chemistry Group (BACh), University of Navarra, Pamplona, Spain
| | - Jose M. Garcia-Mina
- Department of Environmental Biology, Biological and Agricultural Chemistry Group (BACh), University of Navarra, Pamplona, Spain
- Centre Mondial de I’lnnovation (CMI) – Groupe Roullier, Saint-Malo, France
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19
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Mariano C, Mello IS, Barros BM, da Silva GF, Terezo AJ, Soares MA. Mercury alters the rhizobacterial community in Brazilian wetlands and it can be bioremediated by the plant-bacteria association. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:13550-13564. [PMID: 32030584 DOI: 10.1007/s11356-020-07913-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/28/2020] [Indexed: 06/10/2023]
Abstract
This study examined how soil mercury contamination affected the structure and functionality of rhizobacteria communities from Aeschynomene fluminensis and Polygonum acuminatum and how rhizobacteria mediate metal bioremediation. The strains were isolated using culture-dependent methods, identified through 16S rDNA gene sequencing, and characterized with respect to their functional traits related to plant growth promotion and resistance to metals and antibiotics. The bioremediation capacity of the rhizobacteria was determined in greenhouse using corn plants. The isolated bacteria belonged to the phyla Actinobacteria, Deinococcus-Thermus, Firmicutes, and Proteobacteria, with great abundance of the species Microbacterium trichothecenolyticum. The rhizobacteria abundance, richness, and diversity were greater in mercury-contaminated soils. Bacteria isolated from contaminated environments had higher minimum inhibitory concentration values, presented plasmids and the merA gene, and were multi-resistant to metals and antibiotics. Enterobacter sp._C35 and M. trichothecenolyticum_C34 significantly improved (Dunnett's test, p < 0.05) corn plant growth in mercury-contaminated soil. These bacteria helped to reduce up to 87% of the mercury content in the soil, and increased the mercury bioaccumulation factor by up to 94%. Mercury bioremediation mitigated toxicity of the contaminated substrate. Enterobacter sp._C35, Bacillus megaterium_C28, and Bacillus mycoides_C1 stimulated corn plant growth and could be added to biofertilizers produced in research and related industries.
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Affiliation(s)
- Caylla Mariano
- Laboratory of Biotechnology and Microbial Ecology, Institute of Biosciences, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Ivani Souza Mello
- Laboratory of Biotechnology and Microbial Ecology, Institute of Biosciences, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Breno Martins Barros
- Laboratory of Biotechnology and Microbial Ecology, Institute of Biosciences, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | | | - Ailton Jose Terezo
- Central Analytical of Fuels, Department of Chemistry, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Marcos Antônio Soares
- Laboratory of Biotechnology and Microbial Ecology, Institute of Biosciences, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil.
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20
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Yang X, Jiang Z, Zhang J, Zhou X, Zhang X, Wang L, Yu T, Wang Z, Bei J, Dong B, Dai Z, Yang Q, Chen Z. Mesorhizobium alexandrii sp. nov., isolated from phycosphere microbiota of PSTs-producing marine dinoflagellate Alexandrium minutum amtk4. Antonie Van Leeuwenhoek 2020; 113:907-917. [PMID: 32193664 DOI: 10.1007/s10482-020-01400-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/04/2020] [Indexed: 11/26/2022]
Abstract
An aerobic, Gram-stain-negative, motile and rod-shaped bacterial strain, designated as Z1-4T, was isolated from the phycosphere microbiota of marine dinoflagellate Alexandrium minutum that produces paralytic shellfish poisoning toxins. Phylogenetic analysis based on 16S rRNA gene sequences showed that the new isolate belongs to the genus Mesorhizobium, and it was closely related to Mesorhizobium waimense LMG 28228T and Mesorhizobium amorphae LMG 18977T with both 16S rRNA gene sequence similarities of 97.3%. The values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) relatedness between strain Z1-4T and its relatives are both well below the thresholds used for the delineation of a new species. A genome-based phylogenetic tree constructed by up-to-date bacterial core gene set (UBCG) indicates that strain Z1-4T forms an independent branch within the genus Mesorhizobium. The respiratory quinone of strain Z1-4T was Q-10. The major fatty acids were similar to other members of the genus Mesorhizobium containing the summed feature 8, C16:0, C19:0cycloω8c, C17:0 and summed feature 3. The polar lipids are phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, five glycolipids and seven unknown polar lipids. The DNA G + C content was determined to be 62.1 mol % based on its genomic sequence. Combined evidences based on the genotypic, chemotaxonomic and phenotypic characteristics clearly indicates that strain Z1-4T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobium alexandrii sp. nov. is proposed. The type strain is Z1-4T (= KCTC 72512T = CCTCC AB 2019101T).
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Affiliation(s)
- Xi Yang
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Zhiwei Jiang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316021, Zhejiang, People's Republic of China
| | - Jing Zhang
- Comprehensive Technology Service Center of Zhoushan Customs, Zhoushan, 316021, Zhejiang, People's Republic of China
| | - Xin Zhou
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316021, Zhejiang, People's Republic of China
| | - Xiaoling Zhang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316021, Zhejiang, People's Republic of China
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan Municipal Center for Disease Control and Prevention, Zhoushan, 316021, Zhejiang, People's Republic of China
| | - Lei Wang
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Ting Yu
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Zhilin Wang
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Jinlong Bei
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Bo Dong
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Zhangyan Dai
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Qiao Yang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316021, Zhejiang, People's Republic of China.
| | - Zhuang Chen
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China.
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21
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Yang Q, Jiang Z, Zhou X, Zhang R, Wu Y, Lou L, Ma Z, Wang D, Ge Y, Zhang X, Yu X. Nioella ostreopsis sp. nov. , isolated from toxic dinoflagellate, Ostreopsis lenticularis. Int J Syst Evol Microbiol 2020; 70:759-765. [PMID: 31833831 DOI: 10.1099/ijsem.0.003816] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A novel short-rod-shaped bacterial strain with poly-β-hydroxybutyric acid granules inside, designated as Z7-4T, was isolated from a culture of a marine dinoflagellate with palytoxin-producing capacity, Ostreopsis lenticularis OS06, collected from the East China Sea. Cells of Z7-4T were Gram-stain-negative, non-motile, strictly aerobic, 0.9-1.2 µm wide and 2.0-3.9 µm long. Growth occurred in 1-4 % (w/v) NaCl, at 15-37 °C and at pH 5.0-10.0, with optimum growth in 3.5 % (w/v) NaCl, at 30 °C and at pH 7.0. Analysis of 16S rRNA gene sequence revealed that Z7-4T shared the highest 16S rRNA gene sequence similarities with Nioella aestuarii JCM 30752T (98.8 %), followed by Nioella sediminis KCTC 42144T (98.6 %) and Nioella nitratireducens KCTC 32417T (96.9 %). Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that Z7-4T clearly represented a member of the genus Nioella within the family Rhodobacteraceae. The respiratory quinone of Z7-4T was identified as Q-10. Polar lipids of Z7-4T were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, three unidentified aminophospholipids and one unidentified phospholipid. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The DNA G+C content of Z7-4T was 63.0 mol%. DNA-DNA hybridization values of the isolate against the closely related type strains were far below the 70 % limit for species delineation. The average nucleotide identity and in silico DNA-DNA genome hybridization relatedness between Z7-4T and the closely related members of the genus Nioella, N. sediminis KCTC 42144T and N. nitratireducens KCTC 32417T, were 91.1 and 46.3 %, and 79.3 and 19.4 %, respectively. On the basis of the results of polyphasic analysis, Z7-4T is proposed to represent a novel species of the genus Nioella, for which the name Nioella ostreopsis sp. nov. is proposed. The type strain of Nioella ostreopsis is Z7-4T (=KCTC 62459T=CCTCC AB 2017231T).
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Affiliation(s)
- Qiao Yang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Zhiwei Jiang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Xin Zhou
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Ruonan Zhang
- Center of Research in Life Sciences and Environmental Sciences, Harbin University of Commerce, Harbin 150076, PR China.,ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Yiru Wu
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Linghao Lou
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Zetao Ma
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Dongfang Wang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Yaming Ge
- Innovation and Application Research Institute, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Xiaoling Zhang
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan Municipal Center For Disease Control and Prevention, Zhoushan 316021, PR China.,ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Xinwei Yu
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan Municipal Center For Disease Control and Prevention, Zhoushan 316021, PR China
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22
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Yang Q, Jiang Z, Zhou X, Zhang R, Xie Z, Zhang S, Wu Y, Ge Y, Zhang X. Haliea alexandrii sp. nov., isolated from phycosphere microbiota of the toxin-producing dinoflagellate Alexandrium catenella. Int J Syst Evol Microbiol 2019; 70:1133-1138. [PMID: 31751199 DOI: 10.1099/ijsem.0.003890] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacterium, named strain LZ-16-2T, was isolated from the phycosphere microbiota of the paralytic shellfish poisoning toxin-producing marine dinoflagellate Alexandrium catenella LZT09. Strain LZ-16-2T grew optimally at 28 °C at pH 6.5 and with 3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain LZ-16-2T fell within the genus Haliea and was most closely related to Haliea salexigens DSM 19537T, with which the new isolate exhibited 98.5 % 16S rRNA gene sequence similarity. The major respiratory quinone was Q-8. The predominant cellular fatty acids were C17 : 1 ω8c, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C17 : 1 ω6c, C11 : 0 3-OH and C17 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The average nucleotide identity and in silico DNA-DNA genome hybridization relatedness values between strain LZ-16-2T and its closest relative, H. salexigens DSM 19537T, were 92.8 and 55.1 %, respectively. The DNA G+C content was 61.3 mol%. Differential phenotypic properties and phylogenetic distinctiveness distinguished strain LZ-16-2T from all other members of the genus Haliea. On the basis of the polyphasic characterization, strain LZ-16-2T represents a novel species of the genus Haliea, for which the name Haliea alexandrii sp. nov. is proposed. The type strain is LZ-16-2T (=KCTC 62344T=CCTCC AB2017229T).
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Affiliation(s)
- Qiao Yang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Zhiwei Jiang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Xin Zhou
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Ruonan Zhang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
- Center of Research in Life Sciences & Environmental Sciences, Harbin University of Commerce, Harbin 150076, PR China
| | - Zhangxian Xie
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361005, PR China
| | - Shuo Zhang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Yiru Wu
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Yaming Ge
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361005, PR China
- Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Xiaoling Zhang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan Municipal Center For Disease Control and Prevention, Zhoushan 316021, PR China
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23
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Yang Q, Jiang Z, Zhou X, Xie Z, Wang Y, Wang D, Feng L, Yang G, Ge Y, Zhang X. Saccharospirillum alexandrii sp. nov., isolated from the toxigenic marine dinoflagellate Alexandrium catenella LZT09. Int J Syst Evol Microbiol 2019; 70:820-826. [PMID: 31671052 DOI: 10.1099/ijsem.0.003832] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic, non-motile and non-pigmented spirillum, designated strain LZ-5T, was isolated from cultures of the paralytic shellfish poisoning (PSP) toxin-producing marine dinoflagellate Alexandrium catenella LZT09 collected from the Zhoushan sea area in the East China Sea during an algal bloom. The isolate grew at 4-40 °C (optimum, 25-33 °C) and pH 5.0-9.0 (optimum, 7.5) in the presence of 0.5-10 % (w/v) NaCl (optimum, 4.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain LZ-5T clearly belonged to the genus Saccharospirillum of the family Saccharospirillaceae. Strain LZ-5T shared highest 16S rRNA gene sequence similarity with Saccharospirillum impatiens EL-105T (98.9 %), Saccharospirillum mangrovi HK-33T (97.2 %), Saccharospirillum correiae CPA1T (96.8 %), Saccharospirillum salsuginis YIM-Y25T (96.8 %) and Saccharospirillum aestuarii IMCC 4453T (95.1 %). The average nucleotide identity and in silico DNA-DNA hybridization between strain LZ-5T and the two most closely related Saccharospirillum strains, S. impatiens EL-105T and S. mangrovi HK-33T, were 82.2 and 19.3 %, and 72.2 and 13.2 %, respectively. The predominant respiratory quinone of strain LZ-5T was Q-8, and the major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipids of strain LZ-5T were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), glycolipid (GL), two unidentified glycophospholipids (GPLs), three unidentified aminophospholipids (APLs) and two unidentified lipids. The genomic DNA G+C content was 57.2 mol%. On the basis of this polyphasic characterization, strain LZ-5T represents a novel species of the genus Saccharospirillum, for which the name Saccharospirillum alexandrii sp. nov. is proposed. The type strain is LZ-5T (=KCTC 62460T=CCTCC AB2017232T).
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Affiliation(s)
- Qiao Yang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Zhiwei Jiang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Xin Zhou
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Zhangxian Xie
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361005, PR China
| | - Ying Wang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Dongfang Wang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Lijuan Feng
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Guangfeng Yang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Yaming Ge
- Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan 316021, PR China
| | - Xiaoling Zhang
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan Municipal Center for Disease Control and Prevention, Zhoushan 316021, PR China.,ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316021, PR China
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24
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Draft Genome Sequence of Marinobacter sp. Strain LZ-6, Isolated from the Toxic Dinoflagellate Alexandrium catenella. Microbiol Resour Announc 2019; 8:8/37/e00795-19. [PMID: 31515344 PMCID: PMC6742795 DOI: 10.1128/mra.00795-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Here, we report the draft genome sequence of Marinobacter sp. strain LZ-6, isolated from the cell culture of a toxic marine dinoflagellate, Alexandrium catenella LZT09. A total of 4,405 predicted protein-coding genes were revealed, including those associated with initial biosynthesis of the key intermediate of paralytic shellfish poisoning toxins (PSTs), namely saxitoxin, and with toxic compound extrusion.
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26
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Furtado BU, Gołębiewski M, Skorupa M, Hulisz P, Hrynkiewicz K. Bacterial and Fungal Endophytic Microbiomes of Salicornia europaea. Appl Environ Microbiol 2019; 85:e00305-19. [PMID: 31003988 PMCID: PMC6581177 DOI: 10.1128/aem.00305-19] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/14/2019] [Indexed: 01/21/2023] Open
Abstract
We examined Salicornia europaea, a nonmycorrhizal halophyte associated with specific and unique endophytic bacteria and fungi. The microbial community structure was analyzed at two sites differing in salinization history (anthropogenic and naturally saline site), in contrasting seasons (spring and fall) and in two plant organs (shoots and roots) via 16S rRNA and internal transcribed spacer amplicon sequencing. We observed distinct communities at the two sites, and in shoots and roots, while the season was of no importance. The bacterial community was less diverse in shoot libraries than in roots, regardless of the site and season, whereas no significant differences were observed for the fungal community. Proteobacteria and Bacteroidetes dominated bacterial assemblages, and Ascomycetes were the most frequent fungi. A root core microbiome operational taxonomic unit belonging to the genus Marinimicrobium was identified. We detected a significant influence of the Salicornia bacterial community on the fungal one by means of cocorrespondence analysis. In addition, pathways and potential functions of the bacterial community in Salicornia europaea were inferred and discussed. We can conclude that bacterial and fungal microbiomes of S. europaea are determined by the origin of salinity at the sites. Bacterial communities seemed to influence fungal ones, but not the other way around, which takes us closer to understanding of interactions between the two microbial groups. In addition, the plant organs of the halophyte filter the microbial community composition.IMPORTANCE Endophytes are particularly fascinating because of their multifaceted lifestyle, i.e., they may exist as either free-living soil microbes or saprobic ones or pathogens. Endophytic communities of halophytes may be different than those in other plants because salinity acts as an environmental filter. At the same time, they may contribute to the host's adaptation to adverse environmental conditions, which may be of importance in agriculture.
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Affiliation(s)
- Bliss Ursula Furtado
- Department of Microbiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Toruń, Poland
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Toruń, Poland
| | - Marcin Gołębiewski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Toruń, Poland
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Toruń, Poland
| | - Monika Skorupa
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Toruń, Poland
| | - Piotr Hulisz
- Department of Soil Science and Landscape Management, Faculty of Earth Sciences, Nicolaus Copernicus University, Toruń, Poland
| | - Katarzyna Hrynkiewicz
- Department of Microbiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Toruń, Poland
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Toruń, Poland
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Alves M, Pereira A, Vicente C, Matos P, Henriques J, Lopes H, Nascimento F, Mota M, Correia A, Henriques I. The role of bacteria in pine wilt disease: insights from microbiome analysis. FEMS Microbiol Ecol 2019; 94:4987203. [PMID: 29718181 DOI: 10.1093/femsec/fiy077] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 04/24/2018] [Indexed: 01/18/2023] Open
Abstract
Pine Wilt Disease (PWD) has a significant impact on Eurasia pine forests. The microbiome of the nematode (the primary cause of the disease), its insect vector, and the host tree may be relevant for the disease mechanism. The aim of this study was to characterize these microbiomes, from three PWD-affected areas in Portugal, using Denaturing Gradient Gel Electrophoresis, 16S rRNA gene pyrosequencing, and a functional inference-based approach (PICRUSt). The bacterial community structure of the nematode was significantly different from the infected trees but closely related to the insect vector, supporting the hypothesis that the nematode microbiome might be in part inherited from the insect. Sampling location influenced mostly the tree microbiome (P < 0.05). Genes related both with plant growth promotion and phytopathogenicity were predicted for the tree microbiome. Xenobiotic degradation functions were predicted in the nematode and insect microbiomes. Phytotoxin biosynthesis was also predicted for the nematode microbiome, supporting the theory of a direct contribution of the microbiome to tree-wilting. This is the first study that simultaneously characterized the nematode, tree and insect-vector microbiomes from the same affected areas, and overall the results support the hypothesis that the PWD microbiome plays an important role in the disease's development.
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Affiliation(s)
- Marta Alves
- Departamento de Biologia e Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, 3810-193, Portugal
| | - Anabela Pereira
- Departamento de Biologia e Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, 3810-193, Portugal
| | - Cláudia Vicente
- NemaLab/ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas & Departamento de Biologia, Universidade de Évora, Núcleo de Mitra, Ap. 94, 7002-554 Évora, Portugal
| | - Patrícia Matos
- Departamento de Biologia e Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, 3810-193, Portugal
| | - Joana Henriques
- UEIS Sistemas Agrários e Florestais e Sanidade Vegetal, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, IP), Oeiras, 2780-159, Portugall
| | - Helena Lopes
- Departamento de Biologia e Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, 3810-193, Portugal
| | - Francisco Nascimento
- NemaLab/ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas & Departamento de Biologia, Universidade de Évora, Núcleo de Mitra, Ap. 94, 7002-554 Évora, Portugal.,Departamento de Microbiologia, Laboratório de Microbiologia do Solo, Universidade de Santa Catarina, Florianópolis, Brasil
| | - Manuel Mota
- NemaLab/ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas & Departamento de Biologia, Universidade de Évora, Núcleo de Mitra, Ap. 94, 7002-554 Évora, Portugal.,Departamento de Ciências da Vida, Universidade Lusófona de Humanidades e Tecnologias, EPCV, C. Grande 376, 1749-024 Lisboa, Portugal
| | - António Correia
- Departamento de Biologia e Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, 3810-193, Portugal
| | - Isabel Henriques
- Departamento de Biologia e Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, 3810-193, Portugal
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28
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Plant beneficial endophytic bacteria: Mechanisms, diversity, host range and genetic determinants. Microbiol Res 2019; 221:36-49. [DOI: 10.1016/j.micres.2019.02.001] [Citation(s) in RCA: 258] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 12/11/2018] [Accepted: 02/01/2019] [Indexed: 12/13/2022]
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29
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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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30
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Yamamoto K, Shiwa Y, Ishige T, Sakamoto H, Tanaka K, Uchino M, Tanaka N, Oguri S, Saitoh H, Tsushima S. Bacterial Diversity Associated With the Rhizosphere and Endosphere of Two Halophytes: Glaux maritima and Salicornia europaea. Front Microbiol 2018; 9:2878. [PMID: 30555434 PMCID: PMC6282094 DOI: 10.3389/fmicb.2018.02878] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 11/09/2018] [Indexed: 12/22/2022] Open
Abstract
Root-associated microbial communities are very important in the adaptation of halophytes to coastal environments. However, little has been reported on microbial community structures related to halophytes, or on comparisons of their compositions among halophytic plant species. Here, we studied the diversity and community structure of both rhizosphere and root endosphere bacteria in two halophytic plants: Glaux maritima and Salicornia europaea. We sampled the rhizosphere, the root endosphere, and bulk control soil samples, and performed bacterial 16S rRNA sequencing using the Illumina MiSeq platform to characterize the bacterial community diversities in the rhizosphere and root endosphere of both halophytes. Among the G. maritima samples, the richness and diversity of bacteria in the rhizosphere were higher than those in the root endosphere but were lower than those of the bulk soil. In contrast for S. europaea, the bulk soil, the rhizosphere, and the root endosphere all had similar bacterial richness and diversity. The number of unique operational taxonomic units within the root endosphere, the rhizosphere, and the bulk soil were 181, 366, and 924 in G. maritima and 126, 416, and 596 in S. europaea, respectively, implying habitat-specific patterns for each halophyte. In total, 35 phyla and 566 genera were identified. The dominant phyla across all samples were Proteobacteria and Bacteroidetes. Actinobacteria was extremely abundant in the root endosphere from G. maritima. Beneficial bacterial genera were enriched in the root endosphere and rhizosphere in both halophytes. Rhizobium, Actinoplanes, and Marinomonas were highly abundant in G. maritima, whereas Sulfurimonas and Coleofasciculus were highly abundant in S. europaea. A principal coordinate analysis demonstrated significant differences in the microbiota composition associated with the plant species and type of sample. These results strongly indicate that there are clear differences in bacterial community structure and diversity between G. maritima and S. europaea. This is the first report to characterize the root microbiome of G. maritima, and to compare the diversity and community structure of rhizosphere and root endosphere bacteria between G. maritima and S. europaea.
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Affiliation(s)
- Kosuke Yamamoto
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
| | - Yuh Shiwa
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan.,NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Taichiro Ishige
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Hikaru Sakamoto
- Department of Northern Biosphere Agriculture, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Masataka Uchino
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
| | - Naoto Tanaka
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
| | - Suguru Oguri
- Department of Northern Biosphere Agriculture, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido, Japan
| | - Hiromasa Saitoh
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
| | - Seiya Tsushima
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
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31
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Fidalgo C, Proença DN, Morais PV, Henriques I, Alves A. The endosphere of the salt marsh plant Halimione portulacoides is a diversity hotspot for the genus Salinicola: description of five novel species Salinicola halimionae sp. nov., Salinicola aestuarinus sp. nov., Salinicola endophyticus sp. nov., Salinicola halophyticus sp. nov. and Salinicola lusitanus sp. nov. Int J Syst Evol Microbiol 2018; 69:46-62. [PMID: 30418109 DOI: 10.1099/ijsem.0.003061] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven endophytic strains were isolated from the halophyte Halimione portulacoides, collected from Ria de Aveiro, Portugal. To determine their exact taxonomic position, comparative analyses were performed with these strains and closely related type strains of Salinicola species. Genome sequencing and comparison indicated that five of the seven isolated strains comprised distinct and novel species (average nucleotide identity <0.95; in silico DNA-DNA hybridization <70 %; G+C difference >1 %). Multilocus sequence analysis was performed using gyrB, rpoD and 16S rRNA gene sequences from the novel and type strains to determine their phylogenetic positions. The novel strains are facultative anaerobes, mesophilic, facultative alkaliphic and halophilic, test positive for catalase and oxidase activities, for hydrolysis of Tween 20 and phosphate, for production of indole-3-acetic acid, but do not produce H2S. Ubiquinone UQ-9 is present in major amounts in all strains. The major fatty acids include C16 : 0 and the summed feature containing C18 : 1ω7c and/or C18 : 1ω6c. The DNA G+C content ranges from 60.6 to 65.8 mol%. Five strains were confirmed as new species belonging to the genus Salinicola, for which the names Salinicolahalimionae sp. nov. (type strain CPA60T=CECT 9338T=LMG 30107T), Salinicolaaestuarinus sp. nov. (type strain CPA62T=CECT 9339T=LMG 30108T), Salinicolaendophyticus sp. nov. (type strain CPA92T=CECT 9340T=LMG 30109T), Salinicolahalophyticus sp. nov. (type strain CR45T=CECT 9341T=LMG 30105T) and Salinicola lusitanus sp. nov. (type strain CR50T=CECT 9342T=LMG 30106T) are proposed.
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Affiliation(s)
- Cátia Fidalgo
- 1Department of Biology & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | | | - Paula V Morais
- 2CEMMPRE, University of Coimbra, 3030-788 Coimbra, Portugal
- 3Department of Life Sciences, FCTUC, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Isabel Henriques
- 1Department of Biology & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Artur Alves
- 1Department of Biology & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
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32
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Syranidou E, Thijs S, Avramidou M, Weyens N, Venieri D, Pintelon I, Vangronsveld J, Kalogerakis N. Responses of the Endophytic Bacterial Communities of Juncus acutus to Pollution With Metals, Emerging Organic Pollutants and to Bioaugmentation With Indigenous Strains. FRONTIERS IN PLANT SCIENCE 2018; 9:1526. [PMID: 30405664 PMCID: PMC6200866 DOI: 10.3389/fpls.2018.01526] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/28/2018] [Indexed: 05/23/2023]
Abstract
Plants and their associated bacteria play a crucial role in constructed wetlands. In this study, the impact of different levels of pollution and bioaugmentation with indigenous strains individually or in consortia was investigated on the composition of the endophytic microbial communities of Juncus acutus. Five treatments were examined and compared in where the wetland plant was exposed to increasing levels of metal pollution (Zn, Ni, Cd) and emerging pollutants (BPA, SMX, CIP), enriched with different combinations of single or mixed endophytic strains. High levels of mixed pollution had a negative effect on alpha diversity indices of the root communities; moreover, the diversity indices were negatively correlated with the increasing metal concentrations. It was demonstrated that the root communities were separated depending on the level of mixed pollution, while the family Sphingomonadaceae exhibited the higher relative abundance within the root endophytic communities from high and low polluted treatments. This study highlights the effects of pollution and inoculation on phytoremediation efficiency based on a better understanding of the plant microbiome community composition.
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Affiliation(s)
- Evdokia Syranidou
- School of Environmental Engineering, Technical University of Crete, Chania, Greece
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Sofie Thijs
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Marina Avramidou
- School of Environmental Engineering, Technical University of Crete, Chania, Greece
| | - Nele Weyens
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Danae Venieri
- School of Environmental Engineering, Technical University of Crete, Chania, Greece
| | - Isabel Pintelon
- Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | - Jaco Vangronsveld
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Nicolas Kalogerakis
- School of Environmental Engineering, Technical University of Crete, Chania, Greece
- Department of Chemical Engineering, American University of Sharjah, Sharjah, United Arab Emirates
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33
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Leite L, Jude-Lemeilleur F, Raymond N, Henriques I, Garabetian F, Alves A. Phylogenetic diversity and functional characterization of the Manila clam microbiota: a culture-based approach. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:21721-21732. [PMID: 28766142 DOI: 10.1007/s11356-017-9838-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/26/2017] [Indexed: 06/07/2023]
Abstract
According to the hologenome theory, the microbiota contributes to the fitness of the holobiont having an important role in its adaptation, survival, development, health, and evolution. Environmental stress also affects the microbiota and its capability to assist the holobiont in coping with stress factors. Here, we analyzed the diversity of cultivable bacteria associated with Manila clam tissues (mantle, gills, hemolymph) in two non-contaminated sites (Portugal and France) and one metal-contaminated site (Portugal). A total of 240 isolates were obtained. Representative isolates (n = 198) of the overall diversity were identified by 16S rDNA sequencing and subjected to functional characterization. Isolates affiliated with Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Proteobacteria (mostly Pseudoalteromonadaceae and Vibrionaceae) were dominant in non-contaminated sites while Actinobacteria (mostly Microbacteriaceae) dominated in the metal-contaminated site. The main factor affecting the microbiota composition was contamination. No significant differences were observed between clam tissues and geographic regions. Several isolates tested positive for antibacterial activity, biofilm formation, protease, and siderophore production. The results show that the Manila clam harbors a diverse microbiota that may contribute to clam protection and overall fitness, as well as to its adaptation to stressful environments. In addition, the Manila clam microbiota is revealed as a promising source of novel probiotics with potential application in aquaculture.
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Affiliation(s)
- Laura Leite
- Departamento de Biologia, CESAM, Campus de Santiago, Universidade de Aveiro, 3810-193, Aveiro, Portugal
- Université de Bordeaux, UMR 5805 EPOC, 33120, Arcachon, France
- CNRS, UMR 5805 EPOC, 33120, Arcachon, France
| | - Florence Jude-Lemeilleur
- Université de Bordeaux, UMR 5805 EPOC, 33120, Arcachon, France
- CNRS, UMR 5805 EPOC, 33120, Arcachon, France
| | - Natalie Raymond
- Université de Bordeaux, UMR 5805 EPOC, 33120, Arcachon, France
- CNRS, UMR 5805 EPOC, 33120, Arcachon, France
| | - Isabel Henriques
- Departamento de Biologia, CESAM, Campus de Santiago, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - Frédéric Garabetian
- Université de Bordeaux, UMR 5805 EPOC, 33120, Arcachon, France
- CNRS, UMR 5805 EPOC, 33120, Arcachon, France
| | - Artur Alves
- Departamento de Biologia, CESAM, Campus de Santiago, Universidade de Aveiro, 3810-193, Aveiro, Portugal.
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34
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Fidalgo C, Rocha J, Martins R, Proença DN, Morais PV, Henriques I, Alves A. Altererythrobacter halimionae sp. nov. and Altererythrobacter endophyticus sp. nov., two endophytes from the salt marsh plant Halimione portulacoides. Int J Syst Evol Microbiol 2017; 67:3057-3062. [DOI: 10.1099/ijsem.0.002079] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Cátia Fidalgo
- Departamento de Biologia, CESAM, Universidade de Aveiro, Aveiro, Portugal
| | - Jaqueline Rocha
- Departamento de Biologia, CESAM, Universidade de Aveiro, Aveiro, Portugal
| | - Ricardo Martins
- Departamento de Biologia, CESAM, Universidade de Aveiro, Aveiro, Portugal
| | | | - Paula V. Morais
- Department of Life Sciences, FCTUC, University of Coimbra, 3000-456 Coimbra, Portugal
- CEMUC, University of Coimbra, 3030-788 Coimbra, Portugal
| | - Isabel Henriques
- Departamento de Biologia, CESAM, Universidade de Aveiro, Aveiro, Portugal
| | - Artur Alves
- Departamento de Biologia, CESAM, Universidade de Aveiro, Aveiro, Portugal
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35
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Fidalgo C, Martins R, Proença DN, Morais PV, Alves A, Henriques I. Zunongwangia endophytica sp. nov., an endophyte isolated from the salt marsh plant, Halimione portulacoides, and emended description of the genus Zunongwangia. Int J Syst Evol Microbiol 2017; 67:3004-3009. [PMID: 28853694 DOI: 10.1099/ijsem.0.002069] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Cátia Fidalgo
- Departamento de Biologia, CESAM, Universidade de Aveiro, Aveiro, Portugal
| | - Ricardo Martins
- Departamento de Biologia, CESAM, Universidade de Aveiro, Aveiro, Portugal
| | | | - Paula V. Morais
- Department of Life Sciences, FCTUC, University of Coimbra, 3000-456 Coimbra, Portugal
- CEMUC, University of Coimbra, 3030-788 Coimbra, Portugal
| | - Artur Alves
- Departamento de Biologia, CESAM, Universidade de Aveiro, Aveiro, Portugal
| | - Isabel Henriques
- Departamento de Biologia, CESAM, Universidade de Aveiro, Aveiro, Portugal
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Tacão M, Araújo S, Vendas M, Alves A, Henriques I. Shewanella species as the origin of bla OXA-48 genes: insights into gene diversity, associated phenotypes and possible transfer mechanisms. Int J Antimicrob Agents 2017; 51:340-348. [PMID: 28666748 DOI: 10.1016/j.ijantimicag.2017.05.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 05/15/2017] [Accepted: 05/27/2017] [Indexed: 11/30/2022]
Abstract
Chromosome-encoded beta-lactamases of Shewanella spp. have been indicated as probable progenitors of blaOXA-48-like genes. However, these have been detected in few Shewanella spp. and dissemination mechanisms are unclear. Thus, our main objective was to confirm the role of Shewanella species as progenitors of blaOXA-48-like genes. In silico analysis of Shewanella genomes was performed to detect blaOXA-48-like genes and context, and 43 environmental Shewanella spp. were characterised. Clonal relatedness was determined by BOX-PCR. Phylogenetic affiliation was assessed by 16S rDNA and gyrB sequencing. Antibiotic susceptibility phenotypes were determined. The blaOXA-48-like genes and genetic context were inspected by PCR, hybridisation and sequence analysis. Gene variants were cloned in Escherichia coli and MICs were determined. Shewanella isolates were screened for integrons, plasmids and insertion sequences. Analysis of Shewanella spp. genomes showed that putative blaOXA-48-like is present in the majority and in an identical context. Isolates presenting unique BOX profiles affiliated with 11 Shewanella spp. blaOXA-48-like genes were detected in 22 isolates from 6 species. Genes encoded enzymes identical to OXA-48, OXA-204, OXA-181, and 7 new variants differing from OXA-48 from 2 to 82 amino acids. IS1999 was detected in 24 isolates, although not in the vicinity of blaOXA-48 genes. Recombinant E. coli strains presented altered MICs. The presence/absence of blaOXA-48-like genes was species-related. Gene variants encoded enzymes with hydrolytic spectra similar to OXA-48-like from non-shewanellae. From the mobile elements previously described in association with blaOXA-48-like genes, only the IS1999 was found in Shewanella, which indicates its relevance in blaOXA-48-like genes transfer to other hosts.
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Affiliation(s)
- Marta Tacão
- Biology Department & CESAM, University of Aveiro, Aveiro, Portugal.
| | - Susana Araújo
- Biology Department & CESAM, University of Aveiro, Aveiro, Portugal
| | - Maria Vendas
- Biology Department & CESAM, University of Aveiro, Aveiro, Portugal
| | - Artur Alves
- Biology Department & CESAM, University of Aveiro, Aveiro, Portugal
| | - Isabel Henriques
- Biology Department & CESAM, University of Aveiro, Aveiro, Portugal
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Fidalgo C, Rocha J, Proença DN, Morais PV, Alves A, Henriques I. Saccharospirillum correiae sp. nov., an endophytic bacterium isolated from the halophyte Halimione portulacoides. Int J Syst Evol Microbiol 2017; 67:2026-2030. [PMID: 28675353 DOI: 10.1099/ijsem.0.001914] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Cátia Fidalgo
- Departamento de Biologia, CESAM, Universidade de Aveiro, Aveiro, Portugal
| | - Jaqueline Rocha
- Departamento de Biologia, CESAM, Universidade de Aveiro, Aveiro, Portugal
| | | | - Paula Vasconcelos Morais
- CEMUC, University of Coimbra, 3030-788 Coimbra, Portugal
- Department of Life Sciences, FCTUC, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Artur Alves
- Departamento de Biologia, CESAM, Universidade de Aveiro, Aveiro, Portugal
| | - Isabel Henriques
- Departamento de Biologia, CESAM, Universidade de Aveiro, Aveiro, Portugal
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Teixeira P, Tacão M, Alves A, Henriques I. Antibiotic and metal resistance in a ST395 Pseudomonas aeruginosa environmental isolate: A genomics approach. MARINE POLLUTION BULLETIN 2016; 110:75-81. [PMID: 27371958 DOI: 10.1016/j.marpolbul.2016.06.086] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
We analyzed the resistome of Pseudomonas aeruginosa E67, an epiphytic isolate from a metal-contaminated estuary. The aim was to identify genetic determinants of resistance to antibiotics and metals, assessing possible co-selection mechanisms. Identification was based on phylogenetic analysis and average nucleotide identity value calculation. MLST affiliated E67 to ST395, previously described as a high-risk clone. Genome analysis allowed identifying genes probably involved in resistance to antibiotics (e.g. beta-lactams, aminoglycosides and chloramphenicol) and metals (e.g. mercury and copper), consistent with resistance phenotypes. Several genes associated with efflux systems, as well as genetic determinants contributing to gene motility, were identified. Pseudomonas aeruginosa E67 possesses an arsenal of resistance determinants, probably contributing to adaptation to a polluted ecosystem. Association to mobile structures highlights the role of these platforms in multi-drug resistance. Physical links between metal and antibiotic resistance genes were not identified, suggesting a predominance of cross-resistance associated with multidrug efflux pumps.
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Affiliation(s)
- Pedro Teixeira
- Biology Department, CESAM & IBIMED, University of Aveiro, Aveiro, Portugal
| | - Marta Tacão
- Biology Department, CESAM & IBIMED, University of Aveiro, Aveiro, Portugal.
| | - Artur Alves
- Biology Department, CESAM, University of Aveiro, Aveiro, Portugal
| | - Isabel Henriques
- Biology Department, CESAM & IBIMED, University of Aveiro, Aveiro, Portugal
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39
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Fidalgo C, Riesco R, Henriques I, Trujillo ME, Alves A. Microbacterium diaminobutyricum sp. nov., isolated from Halimione portulacoides, which contains diaminobutyric acid in its cell wall, and emended description of the genus Microbacterium. Int J Syst Evol Microbiol 2016; 66:4492-4500. [PMID: 27498827 DOI: 10.1099/ijsem.0.001379] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three actinobacterial strains were isolated from roots of the salt-marsh plant Halimione portulacoides collected in Ria de Aveiro, Portugal. Molecular typing using enterobacterial repetitive intergenic consensus ERIC-PCR fingerprinting showed the strains to be highly similar. Phylogenetic analyses based on the 16S rRNA gene sequence and multilocus sequence analysis (MLSA) using gyrB, rpoB, recA and ppk and 16S rRNA genes sequences showed that the strains represented a member of the genus Microbacterium, with Microbacterium lacus DSM 18910T as the closest phylogenetic relative. DNA-DNA hybridization between strain RZ63T and its closest relative was below 70 %, supporting the hypothesis that it represented a distinct genomic species. Chemotaxonomic analyses of the novel strains and their DNA G+C contents confirmed their affiliation to the genus Microbacterium, however, the peptidoglycan of RZ63T contained diaminobutyric acid as the diagnostic diamino acid. In addition, physiological and fatty acid analyses revealed differences between these strains and their phylogenetic relatives, reinforcing their status as a distinct species. Based on the physiological, genetic and chemotaxonomic characterisation it is proposed that the strains studied represent a novel species of the genus Microbacterium for which the name Microbacterium diaminobutyricum sp. nov. is proposed (type strain RZ63T=DSM 27101T=CECT 8355T).
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Affiliation(s)
- Cátia Fidalgo
- Departamento de Biologia, CESAM, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.,Departamento de Biologia, iBiMED, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Raúl Riesco
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 214, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Isabel Henriques
- Departamento de Biologia, CESAM, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.,Departamento de Biologia, iBiMED, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 214, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Artur Alves
- Departamento de Biologia, CESAM, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
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40
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Rocha J, Tacão M, Fidalgo C, Alves A, Henriques I. Diversity of endophytic Pseudomonas in Halimione portulacoides from metal(loid)-polluted salt marshes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:13255-13267. [PMID: 27023813 DOI: 10.1007/s11356-016-6483-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 03/15/2016] [Indexed: 06/05/2023]
Abstract
Phytoremediation assisted by bacteria is seen as a promising alternative to reduce metal contamination in the environment. The main goal of this study was to characterize endophytic Pseudomonas isolated from Halimione portulacoides, a metal-accumulator plant, in salt marshes contaminated with metal(loid)s. Phylogenetic analysis based on 16S rRNA and gyrB genes showed that isolates affiliated with P. sabulinigri (n = 16), P. koreensis (n = 10), P. simiae (n = 5), P. seleniipraecipitans (n = 2), P. guineae (n = 2), P. migulae (n = 1), P. fragi (n = 1), P. xanthomarina (n = 1), and Pseudomonas sp. (n = 1). Most of these species have never been described as endophytic. The majority of the isolates were resistant to three or more metal(loid)s. Antibiotic resistance was frequent among the isolates but most likely related to species-intrinsic features. Common acquired antibiotic resistance genes and integrons were not detected. Plasmids were detected in 43.6 % of the isolates. Isolates that affiliated with different species shared the same plasmid profile but attempts to transfer metal resistance to receptor strains were not successful. Phosphate solubilization and IAA production were the most prevalent plant growth promoting traits, and 20 % of the isolates showed activity against phytopathogenic bacteria. Most isolates produced four or more extracellular enzymes. Preliminary results showed that two selected isolates promote Arabidopsis thaliana root elongation. Results highlight the diversity of endophytic Pseudomonas in H. portulacoides from contaminated sites and their potential to assist phytoremediation by acting as plant growth promoters and as environmental detoxifiers.
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Affiliation(s)
- Jaqueline Rocha
- Biology Department and CESAM, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Marta Tacão
- Biology Department, CESAM and iBiMED, University of Aveiro, Aveiro, Portugal
| | - Cátia Fidalgo
- Biology Department, CESAM and iBiMED, University of Aveiro, Aveiro, Portugal
| | - Artur Alves
- Biology Department and CESAM, University of Aveiro, 3810-193, Aveiro, Portugal.
| | - Isabel Henriques
- Biology Department, CESAM and iBiMED, University of Aveiro, Aveiro, Portugal
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