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Da Silva CGN, Monteiro EDC, Diniz PP, Terra LA, Schwab S, Reis VM, Simoes-Araujo JL, Urquiaga S. Designing and validation of specific primers for the quantitative detection of bacteria in sugarcane inoculant. Braz J Microbiol 2023; 54:2627-2640. [PMID: 37843794 PMCID: PMC10689644 DOI: 10.1007/s42770-023-01144-6] [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: 10/02/2021] [Accepted: 10/02/2023] [Indexed: 10/17/2023] Open
Abstract
Endophytic diazotrophic plant growth-promoting bacteria Herbaspirillum rubrisubalbicans (HCC103), Herbaspirillum seropedicae (HRC54), Paraburkholderia tropica (Ppe8T), Gluconacetobacter diazotrophicus (Pal5T), and Nitrospirillum amazonense (CBAmC) have been used as inoculants for sugarcane. The genome sequences of these strains were used to design a set of specific primers for the real-time PCR (qPCR) assay. Primer specificity was confirmed by conventional PCR using the genomic DNAs of 25 related bacterial species and the five target strains. The qPCR assays were conducted using root and shoot samples from two sugarcane varieties (RB867515 and RB92579). These samples were collected both with and without inoculation, using the target strains specified in this study. The sugarcane plants were grown in a greenhouse, utilizing a substrate composed of sterile sand and vermiculite in a 2:1 ratio, for a duration of 55 days. The primers designed for this study successfully amplified target DNA fragments from each of the bacterial species, enabling their differentiation at the species level. The total bacterial population present in the sugarcane quantified using qPCR was on average 105.2 cells g-1 of fresh tissue. Across both evaluated varieties, it was observed that the population of inoculated bacteria tended to decrease over time and became more concentrated in the sugarcane roots compared to the aerial parts. The qPCR results suggest that both the host and the microbes influence the endophytic population and the bacterial number decreases with plant age.
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Affiliation(s)
- Cleudison Gabriel Nascimento Da Silva
- Instituto de Agronomia, Programa de Pós Graduação em Fitotecnia, Universidade Federal Rural Do Rio de Janeiro (UFRRJ), Km 07, BR 465, 23890-000, Seropédica, Rio de Janeiro, Brazil.
| | - Edevaldo de Castro Monteiro
- Instituto de Agronomia, Programa de Pós Graduação em Agronomia - Ciência Do Solo, UFRRJ, Km 07, BR 465, 23890-000, Seropédica, Rio de Janeiro, Brazil
| | - Priscila Pereira Diniz
- Instituto de Agronomia, Programa de Pós Graduação em Agronomia - Ciência Do Solo, UFRRJ, Km 07, BR 465, 23890-000, Seropédica, Rio de Janeiro, Brazil
| | - Leonardo Araujo Terra
- Instituto de Agronomia, Programa de Pós Graduação em Ciência, Tecnologia e Inovação Agropecuária, UFRRJ, Km 07, BR 465, 23890-000, Seropédica, Rio de Janeiro, Brazil
| | - Stefan Schwab
- Embrapa Agrobiologia, Km 07, BR 465, 23891-000, Seropédica, Rio de Janeiro, Brazil
| | | | | | - Segundo Urquiaga
- Embrapa Agrobiologia, Km 07, BR 465, 23891-000, Seropédica, Rio de Janeiro, Brazil
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Beccaccioli M, Moricca C, Faino L, Reale R, Mineo M, Reverberi M. The Neolithic site "La Marmotta": DNA metabarcoding to identify the microbial deterioration of waterlogged archeological wood. Front Microbiol 2023; 14:1129983. [PMID: 37032892 PMCID: PMC10079079 DOI: 10.3389/fmicb.2023.1129983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/03/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction The evaluation of biological degradation of waterlogged archeological wood is crucial to choose the conservative and protective treatments to be applied to the wooden material. The waterlogged environmental conditions are characterized by oxygen scarcity, only allowing the growth of adapted microbes capable to degrade the organic wooden material, mainly erosion bacteria and soft-rot fungi. In this work, we characterized and evaluated the biodegradation state and the microbial communities of wooden fragments preserved in storage tanks. These were preserved by waterlogging within the Neolithic village "La Marmotta," currently found under the Bracciano Lake (Lazio, Italy). Methods The waterlogged wood samples were first identified taxonomically with an optical microscope, also allowing an evaluation of their preservation state. The microbial community was then evaluated through the sequencing of Internal Transcribed Spacer sequences for fungi and 16S for bacteria with the Oxford Nanopore Technologies (ONT) MinION platform. Results The identified microbial community appears to be consistent with the waterlogged samples, as many bacteria attributable to the erosion of wood and ligninolytic fungi have been sequenced. Discussion The reported results highlight the first use of targeted metabarcoding by ONT applied to study the biodeterioration of waterlogged archeological wood.
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Affiliation(s)
- Marzia Beccaccioli
- Department of Environmental Biology, “Sapienza” University of Rome, Rome, Italy
- *Correspondence: Marzia Beccaccioli,
| | - Claudia Moricca
- Department of Environmental Biology, “Sapienza” University of Rome, Rome, Italy
| | - Luigi Faino
- Department of Environmental Biology, “Sapienza” University of Rome, Rome, Italy
| | - Rita Reale
- Chemistry Applied to Restoration, A. Galli Academy, Via Petrarca, Como, Italy
| | - Mario Mineo
- Department of Environmental Biology, “Sapienza” University of Rome, Rome, Italy
| | - Massimo Reverberi
- Department of Environmental Biology, “Sapienza” University of Rome, Rome, Italy
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Blumberg K, Miller M, Ponsero A, Hurwitz B. Ontology-driven analysis of marine metagenomics: what more can we learn from our data? Gigascience 2022; 12:giad088. [PMID: 37941395 PMCID: PMC10632069 DOI: 10.1093/gigascience/giad088] [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: 03/01/2023] [Revised: 06/30/2023] [Accepted: 09/28/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND The proliferation of metagenomic sequencing technologies has enabled novel insights into the functional genomic potentials and taxonomic structure of microbial communities. However, cyberinfrastructure efforts to manage and enable the reproducible analysis of sequence data have not kept pace. Thus, there is increasing recognition of the need to make metagenomic data discoverable within machine-searchable frameworks compliant with the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles for data stewardship. Although a variety of metagenomic web services exist, none currently leverage the hierarchically structured terminology encoded within common life science ontologies to programmatically discover data. RESULTS Here, we integrate large-scale marine metagenomic datasets with community-driven life science ontologies into a novel FAIR web service. This approach enables the retrieval of data discovered by intersecting the knowledge represented within ontologies against the functional genomic potential and taxonomic structure computed from marine sequencing data. Our findings highlight various microbial functional and taxonomic patterns relevant to the ecology of prokaryotes in various aquatic environments. CONCLUSIONS In this work, we present and evaluate a novel Semantic Web architecture that can be used to ask novel biological questions of existing marine metagenomic datasets. Finally, the FAIR ontology searchable data products provided by our API can be leveraged by future research efforts.
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Affiliation(s)
- Kai Blumberg
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Matthew Miller
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Alise Ponsero
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Bonnie Hurwitz
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
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Analysis of multipartite bacterial genomes using alignment free and alignment-based pipelines. Arch Microbiol 2022; 205:25. [PMID: 36515719 DOI: 10.1007/s00203-022-03354-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 11/18/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022]
Abstract
Since the discovery of second chromosome in Rhodobacter sphaeroides 2.4.1 in 1989, multipartite genomes have been reported in over three hundred bacterial species under nine different phyla. This has shattered the unipartite (single chromosome) genome dogma in bacteria. Since then, many questions on various aspects of multipartite genomes in bacteria have been addressed. However, our understanding of how multipartite genomes emerge and evolve is still lacking. Importantly, the knowledge of genetic factors underlying the differences in multipartite and single-chromosome genomes is lacking. In this work, we have performed comparative evolutionary and functional genomics analyses to identify molecular factors that discriminate multipartite from unipartite bacteria, with the goal to decipher taxon-specific factors, and those that are prevalent across the taxa, underlying these traits. We assessed the roles of evolutionary mechanisms, specifically gene gain, in driving the divergence of bacteria with single and multiple chromosomes. In addition, we performed functional genomic analysis to garner support for our findings from comparative evolutionary analysis. We found genes such as those encoding conserved hypothetical proteins in Deinococcus radiodurans R1, and putative phage phi-C31 gp36 major capsid like and hypothetical proteins in Rhodobacter sphaeroides 2.4.1, which are located on accessory chromosomes in these bacteria but were not found in the inferred ancestral sequences, and on the primary chromosomes, as well as were not found in their closest relatives with single chromosome within the same clade. Our study shines a new light on the potential roles of the secondary chromosomes in helping bacteria with multipartite genomes to adapt to specialized environments or growth conditions.
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Li M, Liu R, Li Y, Wang C, Ma W, Zheng L, Zhang K, Fu X, Li X, Su Y, Huang G, Zhong Y, Liao H. Functional Investigation of Plant Growth Promoting Rhizobacterial Communities in Sugarcane. Front Microbiol 2022; 12:783925. [PMID: 35058904 PMCID: PMC8763851 DOI: 10.3389/fmicb.2021.783925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/30/2021] [Indexed: 11/24/2022] Open
Abstract
Plant microbiota are of great importance for host nutrition and health. As a C4 plant species with a high carbon fixation capacity, sugarcane also associates with beneficial microbes, though mechanisms underlying sugarcane root-associated community development remain unclear. Here, we identify microbes that are specifically enriched around sugarcane roots and report results of functional testing of potentially beneficial microbes propagating with sugarcane plants. First, we analyzed recruitment of microbes through analysis of 16S rDNA enrichment in greenhouse cultured sugarcane seedlings growing in field soil. Then, plant-associated microbes were isolated and assayed for beneficial activity, first in greenhouse experiments, followed by field trials for selected microbial strains. The promising beneficial microbe SRB-109, which quickly colonized both roots and shoots of sugarcane plants, significantly promoted sugarcane growth in field trials, nitrogen and potassium acquisition increasing by 35.68 and 28.35%, respectively. Taken together, this report demonstrates successful identification and utilization of beneficial plant-associated microbes in sugarcane production. Further development might facilitate incorporation of such growth-promoting microbial applications in large-scale sugarcane production, which may not only increase yields but also reduce fertilizer costs and runoff.
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Affiliation(s)
- Mingjia Li
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ran Liu
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanjun Li
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cunhu Wang
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenjing Ma
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lei Zheng
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kefei Zhang
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xing Fu
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinxin Li
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yachun Su
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guoqiang Huang
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongjia Zhong
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hong Liao
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
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Han G, Mannaa M, Kim N, Jeon HW, Jung H, Lee HH, Kim J, Park J, Park AR, Kim JC, Seo YS. Response of Pine Rhizosphere Microbiota to Foliar Treatment with Resistance-Inducing Bacteria against Pine Wilt Disease. Microorganisms 2021; 9:microorganisms9040688. [PMID: 33810444 PMCID: PMC8065550 DOI: 10.3390/microorganisms9040688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 11/19/2022] Open
Abstract
In this study, two bacterial strains, IRP7 and IRP8, were selected to induce resistance against pine wilt disease (PWD). Foliar application with these strains to nematode-inoculated pine seedlings significantly reduced PWD severity. The effect of nematode inoculation and bacterial treatment on the rhizosphere bacterial community was investigated. The results indicated that the rhizosphere of nematode-inoculated seedlings contained a lower relative abundance of beneficial microbes such as Paraburkholderia, Bradyrhizobium, Rhizobacter, Lysobacter, and Caballeronia. Bacterial treatment resulted in significant changes in the microbes that were represented in relatively low relative abundance. Treatment with IRP7 resulted in an increase in the relative abundance of Nitrospirillum, Bacillus, and Luteibacter, which might be useful for protection against infection. Treatment with IRP8 resulted in an increase in the relative abundance of obligate bacterial predators of the Bdellovibrio genus that were previously shown to control several bacterial phytopathogens and may have a role in the management of nematode-carried bacteria. The selected bacteria were identified as Pseudomonas koreensis IRP7 and Lysobacter enzymogenes IRP8 and are suggested as a potential treatment for induced resistance against PWD. To our knowledge, this is the first report on the effect of foliar treatment with resistance-inducing bacteria on the rhizosphere microbiota.
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Affiliation(s)
- Gil Han
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
| | - Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
- Department of Plant Pathology, Cairo University, Giza 12613, Egypt
| | - Namgyu Kim
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
| | - Hee Won Jeon
- Division of Applied Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea; (H.W.J.); (A.R.P.)
| | - Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
| | - Hyun-Hee Lee
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
| | - Junheon Kim
- Forest Insect Pests and Diseases Division, National Institute of Forest Science, Seoul 02455, Korea;
| | - Jungwook Park
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
- Environmental Microbiology Research Team, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju 37242, Korea
| | - Ae Ran Park
- Division of Applied Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea; (H.W.J.); (A.R.P.)
| | - Jin-Cheol Kim
- Division of Applied Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea; (H.W.J.); (A.R.P.)
- Correspondence: (J.-C.K.); (Y.-S.S.)
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (G.H.); (M.M.); (N.K.); (H.J.); (H.-H.L.); (J.P.)
- Correspondence: (J.-C.K.); (Y.-S.S.)
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