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Ivanova AA, Naumoff DG, Kulichevskaya IS, Rakitin AL, Mardanov AV, Ravin NV, Dedysh SN. Planctomycetes of the Genus Singulisphaera Possess Chitinolytic Capabilities. Microorganisms 2024; 12:1266. [PMID: 39065035 PMCID: PMC11279305 DOI: 10.3390/microorganisms12071266] [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: 05/29/2024] [Revised: 06/15/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
Planctomycetes of the genus Singulisphaera are common inhabitants of soils and peatlands. Although described members of this genus are characterized as possessing hydrolytic capabilities, the ability to degrade chitin has not yet been reported for these bacteria. In this study, a novel Singulisphaera representative, strain Ch08, was isolated from a chitinolytic enrichment culture obtained from a boreal fen in Northern European Russia. The 16S rRNA gene sequence of this isolate displayed 98.2% similarity to that of Singulisphaera acidiphila MOB10T. Substrate utilization tests confirmed that strain Ch08 is capable of growth on amorphous chitin. The complete genome of strain Ch08 determined in this study was 10.85 Mb in size and encoded two predicted chitinases, which were only distantly related to each other and affiliated with the glycoside hydrolase family GH18. One of these chitinases had a close homologue in the genome of S. acidiphila MOB10T. The experimental verification of S. acidiphila MOB10T growth on amorphous chitin was also positive. Transcriptome analysis performed with glucose- and chitin-growth cells of strain Ch08 showed upregulation of the predicted chitinase shared by strain Ch08 and S. acidiphila MOB10T. The gene encoding this protein was expressed in Escherichia coli, and the endochitinase activity of the recombinant enzyme was confirmed. The ability to utilize chitin, a major constituent of fungal cell walls and arthropod exoskeletons, appears to be one of the previously unrecognized ecological functions of Singulisphaera-like planctomycetes.
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Affiliation(s)
- Anastasia A. Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (A.A.I.); (D.G.N.); (I.S.K.)
| | - Daniil G. Naumoff
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (A.A.I.); (D.G.N.); (I.S.K.)
| | - Irina S. Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (A.A.I.); (D.G.N.); (I.S.K.)
| | - Andrey L. Rakitin
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (A.L.R.); (A.V.M.); (N.V.R.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (A.L.R.); (A.V.M.); (N.V.R.)
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (A.L.R.); (A.V.M.); (N.V.R.)
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia; (A.A.I.); (D.G.N.); (I.S.K.)
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Vido JJ, Wang X, Sale PWG, Celestina C, Shindler AE, Hayden HL, Tang C, Wood JL, Franks AE. Bacterial community shifts occur primarily through rhizosphere expansion in response to subsoil amendments. Environ Microbiol 2024; 26:e16587. [PMID: 38454741 DOI: 10.1111/1462-2920.16587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 01/22/2024] [Indexed: 03/09/2024]
Abstract
To comprehensively evaluate the impact of agricultural management practices on soil productivity, it is imperative to conduct a thorough analysis of soil bacterial ecology. Deep-banding nutrient-rich amendments is a soil management practice that aims to improve plant growth and soil structure by addressing the plant-growth constraints posed by dense-clay subsoils. However, the response of bacterial communities to deep-banded amendments has not been thoroughly studied. To address this knowledge gap, we conducted a controlled-environment column experiment to examine the effects of different types of soil amendments (poultry litter, wheat straw + chemical fertiliser and chemical fertiliser alone) on bacterial taxonomic composition in simulated dense-clay subsoils. We evaluated the bacterial taxonomic and ecological group composition in soils beside and below the amendment using 16S rRNA amplicon sequencing and robust statistical methods. Our results indicate that deep-banded amendments alter bacterial communities through direct and indirect mechanisms. All amendments directly facilitated a shift in bacterial communities in the absence of growing wheat. However, a combination of amendments with growing wheat led to a more pronounced bacterial community shift which was distinct from and eclipsed the direct impact of the amendments and plants alone. This indirect mechanism was evidenced to be mediated primarily by plant growth and hypothesised to result from an enhancement in wheat root distribution, density and rhizodeposition changes. Therefore, we propose that subsoil amendments regardless of type facilitated an expansion in the rhizosphere which engineered a substantial plant-mediated bacterial community response within the simulated dense-clay subsoils. Overall, our findings highlight the importance of considering the complex and synergistic interactions between soil physicochemical properties, plant growth and bacterial communities when assessing agricultural management strategies for improving soil and plant productivity.
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Affiliation(s)
- Joshua J Vido
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, Australia
| | - Xiaojuan Wang
- Department of Animal, Plant and Soil Sciences, AgriBio the Centre for AgriBiosciences, La Trobe University, Bundoora, Australia
- School of Agriculture Food, and Ecosystem Sciences, Faculty of Science, University of Melbourne, Melbourne, Australia
| | - Peter W G Sale
- Department of Animal, Plant and Soil Sciences, AgriBio the Centre for AgriBiosciences, La Trobe University, Bundoora, Australia
| | - Corinne Celestina
- Department of Animal, Plant and Soil Sciences, AgriBio the Centre for AgriBiosciences, La Trobe University, Bundoora, Australia
- School of Agriculture Food, and Ecosystem Sciences, Faculty of Science, University of Melbourne, Melbourne, Australia
| | - Anya E Shindler
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, Australia
| | - Helen L Hayden
- School of Agriculture Food, and Ecosystem Sciences, Faculty of Science, University of Melbourne, Melbourne, Australia
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, Bundoora, Australia
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, AgriBio the Centre for AgriBiosciences, La Trobe University, Bundoora, Australia
| | - Jennifer L Wood
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, Australia
- Centre for Future Landscapes, La Trobe University, Bundoora, Australia
| | - Ashley E Franks
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, Australia
- Centre for Future Landscapes, La Trobe University, Bundoora, Australia
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Wang S, Zhou T, Zhao H, Zhang K, Cui J. Temporal and spatial changes in rhizosphere bacterial diversity of mountain Rhododendron mucronulatum. Front Microbiol 2023; 14:1201274. [PMID: 37415822 PMCID: PMC10321304 DOI: 10.3389/fmicb.2023.1201274] [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: 04/06/2023] [Accepted: 06/05/2023] [Indexed: 07/08/2023] Open
Abstract
To better conserve the ecology of the wild Rhododendron mucronulatum range, we studied the rhizosphere microenvironment of R. mucronulatum in Beijing's Yunmeng Mountain National Forest Park. R. mucronulatum rhizosphere soil physicochemical properties and enzyme activities changed significantly with temporal and elevational gradients. The correlations between soil water content (SWC), electrical conductivity (EC), organic matter content (OM), total nitrogen content (TN), catalase activity (CAT), sucrose-converting enzyme activity (INV), and urease activity (URE) were significant and positive in the flowering and deciduous periods. The alpha diversity of the rhizosphere bacterial community was significantly higher in the flowering period than in the deciduous period, and the effect of elevation was insignificant. The diversity of the R. mucronulatum rhizosphere bacterial community changed significantly with the change in the growing period. A network analysis of the correlations revealed stronger linkages between the rhizosphere bacterial communities in the deciduous period than in the flowering period. Rhizomicrobium was the dominant genus in both periods, but its relative abundance decreased in the deciduous period. Changes in the relative abundance of Rhizomicrobium may be the main factor influencing the changes in the R. mucronulatum rhizosphere bacterial community. Moreover, the R. mucronulatum rhizosphere bacterial community and soil characteristics were significantly correlated. Additionally, the influence of soil physicochemical properties on the rhizosphere bacterial community was larger than that of enzyme activity on the bacterial community. We mainly analyzed the change patterns in the rhizosphere soil properties and rhizosphere bacterial diversity of R. mucronulatum during temporal and spatial variation, laying the foundation for further understanding of the ecology of wild R. mucronulatum.
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Affiliation(s)
- Sirui Wang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Tiantian Zhou
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Hewen Zhao
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Kezhong Zhang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Jinteng Cui
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
- Ancient Tree Health and Culture Engineering Technology Research Center, Beijing University of Agriculture, Beijing, China
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Conners EM, Rengasamy K, Bose A. The phototrophic bacteria Rhodomicrobium spp. are novel chassis for bioplastic production. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.17.541187. [PMID: 37292726 PMCID: PMC10245738 DOI: 10.1101/2023.05.17.541187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Polyhydroxybutyrate (PHB) is a bio-based, biodegradable alternative to petroleum-based plastics. PHB production at industrial scales remains infeasible, in part due to insufficient yields and high costs. Addressing these challenges requires identifying novel biological chassis for PHB production and modifying known biological chassis to enhance production using sustainable, renewable inputs. Here, we take the former approach and present the first description of PHB production by two prosthecate photosynthetic purple non-sulfur bacteria (PNSB), Rhodomicrobium vannielii and Rhodomicrobium udaipurense. We show that both species produce PHB across photoheterotrophic, photoautotrophic, photoferrotrophic, and photoelectrotrophic growth conditions. Both species show the greatest PHB titers during photoheterotrophic growth on butyrate with dinitrogen gas as a nitrogen source (up to 44.08 mg/L), while photoelectrotrophic growth demonstrated the lowest titers (up to 0.13 mg/L). These titers are both greater (photoheterotrophy) and less (photoelectrotrophy) than those observed previously in a related PNSB, Rhodopseudomonas palustris TIE-1. On the other hand, we observe the highest electron yields during photoautotrophic growth with hydrogen gas or ferrous iron electron donors, and these electron yields were generally greater than those observed previously in TIE-1. These data suggest that non model organisms like Rhodomicrobium should be explored for sustainable PHB production and highlights utility in exploring novel biological chassis.
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Blastopirellula sediminis sp. nov. a new member of Pirellulaceae isolated from the Andaman and Nicobar Islands. Antonie Van Leeuwenhoek 2023; 116:463-475. [PMID: 36867270 DOI: 10.1007/s10482-023-01818-z] [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: 11/07/2022] [Accepted: 02/22/2023] [Indexed: 03/04/2023]
Abstract
Two cream-coloured strains (JC732T, JC733) of Gram-stain negative, mesophilic, catalase and oxidase positive, aerobic bacteria which divide by budding, form crateriform structures, and cell aggregates were isolated from marine habitats of Andaman and Nicobar Islands, India. Both strains had genome size of 7.1 Mb and G + C content of 58.9%. Both strains showed highest 16S rRNA gene-based similarity with Blastopirellula retiformator Enr8T (98.7%). Strains JC732T and JC733 shared 100% identity of 16S rRNA gene and genome sequences. The coherence of both strains with the genus Blastopirellula was supported by the 16S rRNA gene based and the phylogenomic trees. Further, the chemo-taxonomic characters and the genome relatedness indices [ANI (82.4%), AAI (80.4%) and dDDH (25.2%)] also support the delineation at the species level. Both strains have the capability to degrade chitin and genome analysis shows the ability to fix N2. Based on the phylogenetic, phylogenomic, comparative genomic, morphological, physiological, and biochemical characteristics, strain JC732T is described as a new species of the genus Blastopirellula for which the name Blastopirellula sediminis sp. nov. is proposed, with strain JC733 as an additional strain.
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Contrasting Responses of Rhizosphere Fungi of
Scutellaria tsinyunensis
, an Endangered Plant in Southwestern China. Microbiol Spectr 2022; 10:e0022522. [PMID: 35863021 PMCID: PMC9430849 DOI: 10.1128/spectrum.00225-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Scutellaria tsinyunensis is an endangered species in southwest China, distributed sporadically in mountainous areas at an elevation of approximately 200 to 900 m. Rhizosphere soil properties and fungal communities play critical roles in plant survival and expansion. Nevertheless, understanding of soil properties and fungal communities in the S. tsinyunensis distribution areas is extremely limited. The present study examined soil properties and fungal communities in nearly all extant S. tsinyunensis populations at two altitudinal gradients (low and high groups). Our findings indicated that soil characteristics (i.e., soil pH, water content, and available phosphorus) were affected distinctively by altitudes (P < 0.05). In addition, the low altitude group harbored higher fungal richness and diversity than the high altitude. Co-occurrence network analysis identified six key genera that proved densely connected interactions with many genera. Further analysis represented that the low altitude group harbored three beneficial genera belonging to Ascomycota (Archaeorhizomyces, Dactylella, and Helotiales), whereas the high altitude showed more pathogenic fungi (Apiosporaceae, Colletotrichum, and Fusarium). Correlation analysis found that soil water content was highly correlated with Hydnodontaceae and Lophiostoma. Besides, plants’ canopy density was negatively correlated with four pathogenic fungi, indicating that the high abundance of the pathogen at high altitudes probably inhibited the survival of S. tsinyunensis. To sum up, this comprehensive analysis generates novel insights to explore the contrasting responses of S. tsinyunensis rhizosphere fungal communities and provides profound references for S. tsinyunensis habitat restoration and species conservation. IMPORTANCE Our study highlighted the importance of rhizosphere fungal communities in an endangered plant, S. tsinyunensis. Comparative analysis of soil samples in nearly all extant S. tsinyunensis populations identified that soil properties, especially soil water content, might play essential roles in the survival and expansion of S. tsinyunensis. Our findings proved that a series of fungal communities (e.g., Archaeorhizomyces, Dactylella, and Helotiales) could be essential indicators for S. tsinyunensis habitat restoration and protection for the first time. In addition, further functional and correlation analyses revealed that pathogenic fungi might limit the plant expansion into high altitudes. Collectively, our findings displayed a holistic picture of the rhizosphere microbiome and environmental factors associated with S. tsinyunensis.
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