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Sun D, Feng C, Zhan Y, Deng B, Mei D, Chen N, Hu W. Disentangling microbial coupled fillers mechanisms for the permeable layer optimization process in multi-soil-layering systems. J Environ Sci (China) 2025; 147:538-549. [PMID: 39003069 DOI: 10.1016/j.jes.2023.12.009] [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: 09/28/2023] [Revised: 12/04/2023] [Accepted: 12/04/2023] [Indexed: 07/15/2024]
Abstract
The multi-soil-layering (MSL) systems is an emerging solution for environmentally-friendly and cost-effective treatment of decentralized rural domestic wastewater. However, the role of the seemingly simple permeable layer has been overlooked, potentially holding the breakthroughs or directions to addressing suboptimal nitrogen removal performance in MSL systems. In this paper, the mechanism among diverse substrates (zeolite, green zeolite and biological ceramsite) coupled microorganisms in different systems (activated bacterial powder and activated sludge) for rural domestic wastewater purification was investigated. The removal efficiencies performed by zeolite coupled with microorganisms within 3 days were 93.8% for COD, 97.1% for TP, and 98.8% for NH4+-N. Notably, activated sludge showed better nitrification and comprehensive performance than specialized nitrifying bacteria powder. Zeolite attained an impressive 89.4% NH4+-N desorption efficiency, with a substantive fraction of NH4+-N manifesting as exchanged ammonium. High-throughput 16S rRNA gene sequencing revealed that aerobic and parthenogenetic anaerobic bacteria dominated the reactor, with anaerobic bacteria conspicuously absent. And the heterotrophic nitrification-aerobic denitrification (HN-AD) process was significant, with the presence of denitrifying phosphorus-accumulating organisms (DPAOs) for simultaneous nitrogen and phosphorus removal. This study not only raises awareness about the importance of the permeable layer and enhances comprehension of the HN-AD mechanism in MSL systems, but also provides valuable insights for optimizing MSL system construction, operation, and rural domestic wastewater treatment.
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Affiliation(s)
- Daxin Sun
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
| | - Chuanping Feng
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China.
| | - Yongheng Zhan
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
| | - Bingbing Deng
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
| | - Duoduo Mei
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
| | - Nan Chen
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
| | - Weiwu Hu
- Journal Center, China University of Geosciences (Beijing), Beijing 100083, China
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Seixas MH, Munroe JS, Eggleston EM. Bacterial diversity and geomicrobiology of Winter Wonderland ice cave, Utah, USA. Microbiologyopen 2024; 13:e1426. [PMID: 38995161 PMCID: PMC11241547 DOI: 10.1002/mbo3.1426] [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: 10/23/2023] [Revised: 06/19/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024] Open
Abstract
The Winter Wonderland ice cave, located at an elevation of 3140 m above sea level in the Uinta Mountains of northern Utah, USA, maintains a constant sub-zero temperature. Seasonal snowmelt and rain enter the cave, freeze on the surface of the existing ice, and contribute to a 3-m-thick layered ice mass. This ice mass contains organic matter and cryogenic cave carbonates (CCCs) that date back centuries. In this study, samples of ice, liquid water, and exposed CCCs were collected to examine the bacterial communities within the cave and to determine if these communities vary spatially and between sample types. Flow cytometry showed that cell counts are an order of magnitude higher in liquid water samples than in ice. Epifluorescence microscopy and scanning electron microscopy imaging revealed potential coccoid and bacillus microbial morphologies in water samples and putative cells or calcite spherules in the CCCs. The diversity of bacteria associated with soil, identified through sequence-based analysis, supports the hypothesis that water enters the cave by filtering through soil and bedrock. A differential abundance of bacterial taxa was observed between sample types, with the greatest diversity found in CCCs. This supports a geomicrobiological framework where microbes aggregate in the water, sink into a concentrated layer, and precipitate out of the ice with the CCCs, thereby reducing the cell counts in the ice. These CCCs may provide essential nutrients for the bacteria or could themselves be products of biomineralization.
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Affiliation(s)
- Miranda Herschel Seixas
- Department of Earth and Climate SciencesMiddlebury CollegeMiddleburyVermontUSA
- Biology DepartmentMiddlebury CollegeMiddleburyVermontUSA
| | - Jeffrey S. Munroe
- Department of Earth and Climate SciencesMiddlebury CollegeMiddleburyVermontUSA
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Toxqui-Rodríguez S, Holhorea PG, Naya-Català F, Calduch-Giner JÀ, Sitjà-Bobadilla A, Piazzon C, Pérez-Sánchez J. Differential Reshaping of Skin and Intestinal Microbiota by Stocking Density and Oxygen Availability in Farmed Gilthead Sea Bream ( Sparus aurata): A Behavioral and Network-Based Integrative Approach. Microorganisms 2024; 12:1360. [PMID: 39065128 PMCID: PMC11278760 DOI: 10.3390/microorganisms12071360] [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: 05/23/2024] [Revised: 06/21/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024] Open
Abstract
Fish were kept for six weeks at three different initial stocking densities and water O2 concentrations (low-LD, 8.5 kg/m3 and 95-70% O2 saturation; medium-MD, 17 kg/m3 and 55-75% O2 saturation; high-HD, 25 kg/m3 and 60-45% O2 saturation), with water temperature increasing from 19 °C to 26-27 °C. The improvement in growth performance with the decrease in stocking density was related to changes in skin and intestinal mucosal microbiomes. Changes in microbiome composition were higher in skin, with an increased abundance of Alteromonas and Massilia in HD fish. However, these bacteria genera were mutually exclusive, and Alteromonas abundance was related to a reactive behavior and systemic growth regulation via the liver Gh/Igf system, while Massilia was correlated to a proactive behavior and a growth regulatory transition towards muscle rather than liver. At the intestinal level, microbial abundance showed an opposite trend for two bacteria taxa, rendering in a low abundance of Reyranella and a high abundance of Prauserella in HD fish. This trend was correlated with up-regulated host gene expression, affecting the immune response, epithelial cell turnover, and abiotic stress response. Most of the observed responses are adaptive in nature, and they would serve to infer new welfare indicators for increased stress resilience.
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Affiliation(s)
- Socorro Toxqui-Rodríguez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain; (S.T.-R.); (P.G.H.); (F.N.-C.); (J.À.C.-G.)
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain; (A.S.-B.); (C.P.)
| | - Paul George Holhorea
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain; (S.T.-R.); (P.G.H.); (F.N.-C.); (J.À.C.-G.)
| | - Fernando Naya-Català
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain; (S.T.-R.); (P.G.H.); (F.N.-C.); (J.À.C.-G.)
| | - Josep Àlvar Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain; (S.T.-R.); (P.G.H.); (F.N.-C.); (J.À.C.-G.)
| | - Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain; (A.S.-B.); (C.P.)
| | - Carla Piazzon
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain; (A.S.-B.); (C.P.)
| | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS, CSIC), 12595 Castellón, Spain; (S.T.-R.); (P.G.H.); (F.N.-C.); (J.À.C.-G.)
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Sharavin DY, Belyaeva PG. Biotechnological potential of psychrotolerant methylobacteria isolated from biotopes of Antarctic oases. Arch Microbiol 2024; 206:323. [PMID: 38907777 DOI: 10.1007/s00203-024-04056-7] [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: 04/03/2024] [Accepted: 06/16/2024] [Indexed: 06/24/2024]
Abstract
Ten strains of psychrotolerant methylotrophic bacteria were isolated from the samples collected in Larsemann and Bunger Hills (Antarctica). Most of the isolates are assigned to the genus Pseudomonas, representatives of the genera Janthinobacterium, Massilia, Methylotenera and Flavobacterium were also found. Majority of isolates were able to grow on a wide range of sugars, methylamines and other substrates. Optimal growth temperatures for the isolated strains varied from 6 °C to 28 °C. The optimal concentration of NaCl was 0.5-2.0%. The optimal pH values of the medium were 6-7. It was found that three strains synthesized indole-3-acetic acid on a medium with L-tryptophan reaching 11-12 μg/ml. The values of intracellular carbohydrates in several strains exceeded 50 μg/ml. Presence of calcium-dependent and lanthanum-dependent methanol dehydrogenase have been shown for some isolates. Strains xBan7, xBan20, xBan37, xBan49, xPrg27, xPrg48, xPrg51 showed the presence of free amino acids. Bioprospection of Earth cryosphere for such microorganisms has a potential in biotechnology.
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Affiliation(s)
- Dmitry Yuryevich Sharavin
- Laboratory of Cellular Immunology and Nanobiotechnology, Institute of Ecology and Genetics of Microorganisms (IEGM), 13, Golev st., Perm, 614081, Russia.
| | - Polina Gennadievna Belyaeva
- Laboratory of Cellular Immunology and Nanobiotechnology, Institute of Ecology and Genetics of Microorganisms (IEGM), 13, Golev st., Perm, 614081, Russia
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Diao F, Jia B, Luo J, Ding S, Liu T, Guo W. Arbuscular mycorrhizal fungi drive bacterial community assembly in halophyte Suaeda salsa. Microbiol Res 2024; 282:127657. [PMID: 38422862 DOI: 10.1016/j.micres.2024.127657] [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: 11/29/2023] [Revised: 01/08/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024]
Abstract
Halophytes inhabit saline soils, wherein most plants cannot grow, therefore, their ecological value is outstanding. Arbuscular mycorrhizal (AM) fungi can reconstruct microbial communities to assist plants with stress tolerance. However, little information is available on the microbial community assembly of AM fungi in halophytes. A pot experiment was conducted to investigate the effects of AM fungi on rhizosphere bacterial community structure and soil physiochemical characteristics in the halophyte Suaeda salsa at 0, 100, and 400 mM NaCl. The results demonstrated that AM fungi increased soil alkaline phosphatase (ALP) activity at the three NaCl concentrations, and decreased available P, available K, and the activity of soil catalase (CAT) at 100 mM NaCl. AM fungi decreased the Shannon index of the community at 0 and 100 mM NaCl and increased Sobs index at 400 mM NaCl. Regarding the bacterial community structure, AM fungi substantially decreased the abundance of Acidobacteria phylum at 0 and 100 mM NaCl. AM fungi significantly increased the abundance of genus Ramlibacter, an oxyanion-reducing bacteria that can clean out reactive oxygen species (ROS). AM fungi recruited the genera Massilia and Arthrobacter at 0 and 100 mM NaCl, respectively. Some strains in the two genera have been ascribed to plant growth promoting bacteria (PGPB). AM fungi increased the dry weight and promoted halophyte growth at all three NaCl levels. This study supplements the understanding that AM fungi assemble rhizosphere bacterial communities in halophytes.
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Affiliation(s)
- Fengwei Diao
- Shanxi Institute of Organic Dryland Farming, Shanxi Agricultural University, Taiyuan 030031, China; Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Bingbing Jia
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Junqing Luo
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Shengli Ding
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Tai Liu
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Wei Guo
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China.
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Belykh E, Maystrenko T, Velegzhaninov I, Tavleeva M, Rasova E, Rybak A. Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review. Microorganisms 2024; 12:733. [PMID: 38674676 PMCID: PMC11051952 DOI: 10.3390/microorganisms12040733] [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: 03/08/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.
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Affiliation(s)
- Elena Belykh
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Tatiana Maystrenko
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Ilya Velegzhaninov
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Marina Tavleeva
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
- Department of Biology, Institute of Natural Sciences, Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky Prospekt, Syktyvkar 167001, Russia
| | - Elena Rasova
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Anna Rybak
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
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Ahmad W, Coffman L, Weerasooriya AD, Crawford K, Khan AL. The silicon regulates microbiome diversity and plant defenses during cold stress in Glycine max L. FRONTIERS IN PLANT SCIENCE 2024; 14:1280251. [PMID: 38269137 PMCID: PMC10805835 DOI: 10.3389/fpls.2023.1280251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 12/14/2023] [Indexed: 01/26/2024]
Abstract
Introduction With climate change, frequent exposure of bioenergy and food crops, specifically soybean (Glycine max L.), to low-temperature episodes is a major obstacle in maintaining sustainable plant growth at early growth stages. Silicon (Si) is a quasi-essential nutrient that can help to improve stress tolerance; however, how Si and a combination of cold stress episodes influence plant growth, plant physiology, and microbiome diversity has yet to be fully discovered. Methods The soybean plants were exposed to cold stress (8-10°C) with or without applying Si, and the different plant organs (shoot and root) and rhizospheric soil were subjected to microbiome analysis. The plant growth, physiology, and gene expression analysis of plant defenses during stress and Si were investigated. Results and discussion We showed that cold stress significantly retarded soybean plants' growth and biomass, whereas, Si-treated plants showed ameliorated negative impacts on plant growth at early seedling stages. The beneficial effects of Si were also evident from significantly reduced antioxidant activities - suggesting lower cold-induced oxidative stress. Interestingly, Si also downregulated critical genes of the abscisic acid pathway and osmotic regulation (9-cis-epoxy carotenoid dioxygenase and dehydration-responsive element binding protein) during cold stress. Si positively influenced alpha and beta diversities of bacterial and fungal microbiomes with or without cold stress. Results showed significant variation in microbiome composition in the rhizosphere (root and soil) and phyllosphere (shoot) in Si-treated plants with or without cold stress exposures. Among microbiome phyla, Proteobacteria, Bacteroidota, and Ascomycota were significantly more abundant in Si treatments in cold stress than in control conditions. For the core microbiome, we identified 179 taxa, including 88 unique bacterial genera in which Edaphobacter, Haliangium, and Streptomyces were highly abundant. Enhanced extracellular enzyme activities in the cold and Si+cold treatments, specifically phosphatase and glucosidases, also reflected the microbiome abundance. In conclusion, this work elucidates cold-mediated changes in microbiome diversity and plant growth, including the positive impact Si can have on cold tolerance at early soybean growth stages - a step toward understanding crop productivity and stress tolerance.
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Affiliation(s)
- Waqar Ahmad
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
- Department of Biology and Biochemistry, College of Natural Science & Mathematics, University of Houston, Houston, TX, United States
| | - Lauryn Coffman
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
| | - Aruna D Weerasooriya
- Cooperative Agricultural Research Center, College of Agriculture & Human Sciences, Prairie View A&M University, Prairie View, TX, United States
| | - Kerri Crawford
- Department of Biology and Biochemistry, College of Natural Science & Mathematics, University of Houston, Houston, TX, United States
| | - Abdul Latif Khan
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
- Department of Biology and Biochemistry, College of Natural Science & Mathematics, University of Houston, Houston, TX, United States
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Wang Y, Ge Y, Deng Y, Xu X, Zhang Y, Li L, Xu Z. DOM hydrophilic components of organic fertilizers increased the soil nitrogen retention capacity and succession of the microbial community. Front Microbiol 2023; 14:1320302. [PMID: 38125572 PMCID: PMC10730659 DOI: 10.3389/fmicb.2023.1320302] [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: 10/12/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction Application of organic fertilizers affects soil properties and microbial communities, which in turn alters soil N transformation processes. Unfortunately, it is not clear how the difference in the character of the organic fertilizer DOM affects the soil nitrogen retention capacity and its microbial processes. Methods According to the principle of equal nutrients, the treatments of chemical fertilizer alone (treatment CF), chemical fertilizer with organic fertilizer DOM hydrophilic components (treatment H), and chemical fertilizer with organic fertilizer DOM hydrophobic components (treatment P) were set up, where the characteristics of soil nitrogen transformation and changes in microbial community structure were studied with soil culture conditions for 24 days. Results It was discovered that the addition of organic fertilizer DOM components (H and P) slowed nitrification rate and increased protease activity resulting in a higher NH4+-N content compared to the CF treatment. The DOM addition (H and P) increased the microbial biomass nitrogen (MBN) levels in the soil and increased the soil nitrogen pool capacity. Conclusions Moreover, the carbon use efficiency of the hydrophilic components is higher than that of the hydrophobic components, resulting in its further increase in nitrogen reservoir capacity and higher nitrogen retention capacity. Network analysis showed that the addition of organic fertilizer DOM hydrophilic components increased network complexity and synergy between microorganisms. In combination with random forest analysis, it was shown that Sphingomonas and Massilia were key species influencing soil nitrogen retention capacity and nitrogen availability characteristics.
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Affiliation(s)
- Yuyun Wang
- College of Resources and Environmental Science, Yunnan Agricultural University, Kunming, China
| | - Yingtong Ge
- College of Resources and Environmental Science, Yunnan Agricultural University, Kunming, China
| | - Yaqin Deng
- College of Resources and Environmental Science, Yunnan Agricultural University, Kunming, China
| | - Xiang Xu
- College of Resources and Environmental Science, Yunnan Agricultural University, Kunming, China
| | - Yong Zhang
- College of Resources and Environmental Science, Yunnan Agricultural University, Kunming, China
| | - Lan Li
- College of Resources and Environmental Science, Yunnan Agricultural University, Kunming, China
| | - Zhi Xu
- College of Resources and Environmental Science, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Vegetable Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
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Zhao X, Qin X, Jing X, Wang T, Qiao Q, Li X, Yan P, Li Y. Key genes of electron transfer, the nitrogen cycle and tetracycline removal in bioelectrochemical systems. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:174. [PMID: 37974273 PMCID: PMC10652473 DOI: 10.1186/s13068-023-02430-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Soil microbial fuel cells (MFCs) can remove antibiotics and antibiotic resistance genes (ARGs) simultaneously, but their removal mechanism is unclear. In this study, metagenomic analysis was employed to reveal the functional genes involved in degradation, electron transfer and the nitrogen cycle in the soil MFC. RESULTS The results showed that the soil MFC effectively removed tetracycline in the overlapping area of the cathode and anode, which was 64% higher than that of the control. The ARGs abundance increased by 14% after tetracycline was added (54% of the amplified ARGs belonged to efflux pump genes), while the abundance decreased by 17% in the soil MFC. Five potential degraders of tetracycline were identified, especially the species Phenylobacterium zucineum, which could secrete the 4-hydroxyacetophenone monooxygenase encoded by EC 1.14.13.84 to catalyse deacylation or decarboxylation. Bacillus, Geobacter, Anaerolinea, Gemmatirosa kalamazoonesis and Steroidobacter denitrificans since ubiquinone reductase (encoded by EC 1.6.5.3), succinate dehydrogenase (EC 1.3.5.1), Coenzyme Q-cytochrome c reductase (EC 1.10.2.2), cytochrome-c oxidase (EC 1.9.3.1) and electron transfer flavoprotein-ubiquinone oxidoreductase (EC 1.5.5.1) served as complexes I, II, III, IV and ubiquinone, respectively, to accelerate electron transfer. Additionally, nitrogen metabolism-related gene abundance increased by 16% to support the microbial efficacy in the soil MFC, and especially EC 1.7.5.1, and coding the mutual conversion between nitrite and nitrate was obviously improved. CONCLUSIONS The soil MFC promoted functional bacterial growth, increased functional gene abundance (including nitrogen cycling, electron transfer, and biodegradation), and facilitated antibiotic and ARG removal. Therefore, soil MFCs have expansive prospects in the remediation of antibiotic-contaminated soil. This study provides insight into the biodegradation mechanism at the gene level in soil bioelectrochemical remediation.
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Affiliation(s)
- Xiaodong Zhao
- College of Biological Sciences and Technology, Taiyuan Normal University, Yuci, 030619, People's Republic of China
| | - Xiaorui Qin
- College of Biological Sciences and Technology, Taiyuan Normal University, Yuci, 030619, People's Republic of China
| | - Xiuqing Jing
- College of Biological Sciences and Technology, Taiyuan Normal University, Yuci, 030619, People's Republic of China
| | - Teng Wang
- Department of Life Science, Changzhi University, Changzhi, 046011, People's Republic of China
| | - Qingqing Qiao
- College of Biological Sciences and Technology, Taiyuan Normal University, Yuci, 030619, People's Republic of China
| | - Xiaojing Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA, Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin, 300191, People's Republic of China.
| | - Pingmei Yan
- College of Biological Sciences and Technology, Taiyuan Normal University, Yuci, 030619, People's Republic of China
| | - Yongtao Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, People's Republic of China
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Jeon D, Jiang L, Kim KH, Peng Y, Cho D, Jeong RD, Kim CY, Jeong JC, Lee J. Bioplastic (poly-3-hydroxybutyrate)-producing Massilia endophytica sp. nov., isolated from Cannabis sativa L. 'Cheungsam'. Sci Rep 2023; 13:17767. [PMID: 37853022 PMCID: PMC10584911 DOI: 10.1038/s41598-023-44976-w] [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: 05/09/2023] [Accepted: 10/14/2023] [Indexed: 10/20/2023] Open
Abstract
A rod-shaped, motile, Gram-negative bacterial strain named DM-R-R2A-13T was isolated from the plant Cannabis sativa L. 'Cheungsam'. The phylogenetic analysis of the 16S rRNA gene sequence revealed that strain DM-R-R2A-13T belongs to the family Oxalobacteraceae and is closely related to members of the genus Massilia, with Massilia flava (97.58% sequence similarity) and Massilia armeniaca (97.37% sequence similarity) being the closest members. The digital DNA-DNA hybridization (dDDH) values between strain DM-R-R2A-13T and Massilia flava CGMCC 1.10685T and Massilia armeniaca ZMN-3Twere 22.2% and 23.3%, while the average nucleotide identity (ANI) values were 78.85% and 79.63%, respectively. The DNA G+C content was measured to be 64.6 mol%. Moreover, the bacterium was found to contain polyhydroxyalkanoate (PHA) granules based on transmission electron microscopy, indicating its potential to produce bioplastic. Genome annotation revealed the presence of PHA synthase genes (phaC, phaR, phaP, and phaZ), and the biopolymer was identified as poly-3-hydroxybutyrate (PHB) based on nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy (FTIR) analyses. Using maltose as a carbon source, the strain produced PHB of up to 58.06% of its dry cell weight. Based on the phenotypic, chemotaxonomic, and phylogenetic characteristics, it has been determined that DM-R-R2A-13T represents a novel species belonging to the genus Massilia. As such, the name Massilia endophytica sp. nov. is proposed for this newly identified species. The type strain is DM-R-R2A-13T (= KCTC 92072T = GDMCC 1.2920T).
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Affiliation(s)
- Doeun Jeon
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
- Department of Applied Biology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Lingmin Jiang
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Ki-Hyun Kim
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Yuxin Peng
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Donghyun Cho
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
- Department of Applied Biology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Cha Young Kim
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Jae Cheol Jeong
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Jiyoung Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea.
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Yuseong, Daejeon, 34113, Republic of Korea.
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11
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Xia M, Wei Y, Lai M, Yang X, Gao Z, Zhao H, Jia H, Chang J, Ji X. Hydrogel-potassium humate composite alleviates cadmium toxicity of tobacco by regulating Cd bioavailability. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 263:115361. [PMID: 37597289 DOI: 10.1016/j.ecoenv.2023.115361] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/27/2023] [Accepted: 08/10/2023] [Indexed: 08/21/2023]
Abstract
Cadmium (Cd) removal from soil to reduce Cd accumulation in plants is essential for agroecology, food safety, and human health. Cd enters plants from soil and affects plant growth and development. Hydrogels can easily combine with Cd, thereby altering its bioavailability in soil. However, few studies have evaluated the effects of hydrogel on the complex phytotoxicity caused by Cd uptake in plants and the microbial community structure. Herein, a new poly (acrylic acid)-grafted starch and potassium humate composite (S/K/AA) hydrogel was added to soil to evaluate its impact on tobacco growth and the soil microenvironment. The results indicate that the addition of S/K/AA hydrogel can significantly improve the biomass, chlorophyll (Chl) content, and photosynthetic capacity of tobacco plants during Cd stress conditions, and decrease Cd concentration, probably by affecting Cd absorption through the expression of Cd absorption transporters (e.g., NRAMP5, NRAMP3, and IRT1). Moreover, the application of S/K/AA hydrogel not only reduced the accumulation of reactive oxygen species (ROS), but also reduced the antioxidant activities of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT), suggesting that S/K/AA hydrogel alleviates Cd toxicity via a non-antioxidant pathway. Notably, we further analyzed the effectiveness of the hydrogel on microbial communities in Cd-contaminated soil and found that it increased the Cd-tolerant microbial community (Arthrobacter, Massilia, Streptomyces), enhancing the remediation ability of Cd-contaminated soil and helping tobacco plants to alleviate Cd toxicity. Overall, our study provides primary insights into how S/K/AA hydrogel affects Cd bioavailability and alleviates Cd toxicity in plants.
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Affiliation(s)
- Maolin Xia
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Yuewei Wei
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Miao Lai
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaopeng Yang
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Ziting Gao
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Haojie Zhao
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Hongfang Jia
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of tobacco Science, Henan Agricultural University, Zhengzhou 450002, China.
| | - Jianbo Chang
- Sanmenxia Branch of Henan Provincial Tobacco Corporation, Sanmenxia 472000, China.
| | - Xiaoming Ji
- National Tobacco Cultivation & Physiology & Biochemistry Research Centre, College of tobacco Science, Henan Agricultural University, Zhengzhou 450002, China.
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12
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Bowman JP. Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37589187 DOI: 10.1099/ijsem.0.005991] [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] [Indexed: 08/18/2023] Open
Abstract
Based on genome-wide data, Massilia species belonging to the clade including Telluria mixta LMG 11547T should be entirely transferred to the genus Telluria owing to the nomenclatural priority of the type species Telluria mixta. This results in the transfer of 35 Massilia species to the genus Telluria. The presented data also supports the creation of two new genera since peripherally branching Massilia species are distinct from Telluria and other related genera. It is proposed that 13 Massilia species are transferred to Mokoshia gen. nov. with the type species designated Mokoshia eurypsychrophila comb. nov. The species Massilia arenosa is proposed to belong to the genus Zemynaea gen. nov. as the type species Zemynaea arenosa comb. nov. The genome-wide analysis was well supported by canonical ordination analysis of Enzyme Commission (EC) codes annotated from genomes via pannzer2. This new approach was performed to assess the conclusions of the genome-based data and reduce possible ambiguity in the taxonomic decision making. Cross-validation of EC code data compared within canonical plots validated the reclassifications and correctly visualized the expected genus-level taxonomic relationships. The approach is complementary to genome-wide methodology and could be used for testing sequence alignment based data across genetically related genera. In addition to the proposed broader reclassifications, invalidly described species 'Massilia antibiotica', 'Massilia aromaticivorans', 'Massilia cellulosiltytica' and 'Massilia humi' are described as Telluria antibiotica sp. nov., Telluria aromaticivorans sp. nov., Telluria cellulosilytica sp. nov. and Pseudoduganella humi sp. nov., respectively. In addition, Telluria chitinolytica is reclassified as Pseudoduganella chitinolytica comb. nov. The use of combined genome-wide and annotation descriptors compared using canonical ordination clarifies the taxonomy of Telluria and its sibling genera and provides another way to evaluate complex taxonomic data.
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Affiliation(s)
- John P Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Sandy Bay, Hobart, Tasmania, 7005, Australia
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13
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Xu A, Liu C, Zhao S, Song Z, Sun H. Dynamic distribution of Massilia spp. in sewage, substrate, plant rhizosphere/phyllosphere and air of constructed wetland ecosystem. Front Microbiol 2023; 14:1211649. [PMID: 37577432 PMCID: PMC10413979 DOI: 10.3389/fmicb.2023.1211649] [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: 04/25/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction Massilia bacteria are widely distributed and have various ecological functions. Preliminary studies have shown that Massilia is the dominant species in constructed wetland ecosystems, but its species composition and distribution in constructed wetlands are still unclear. Methods In this paper, the in-house-designed primers were used to construct a 16S rDNA clone library of Massilia. The RFLP sequence analysis method was used to analyze the diversity of Massilia clone library and the composition of Massilia in sewage, substrate, plant rhizosphere, plant phyllosphere and air in a constructed wetland sewage treatment system. Redundancy analysis (RDA) and canonical correspondence analysis (CCA) were used to analyze the correlation between environmental factors and the population characteristics of Massilia in the corresponding environment. The dominant species of Massilia were analyzed for differences. Results The results showed that the 16S rDNA clone library in primer 5 worked well. According to the clone library diversity index analysis, the richness of Massilia varied significantly in different environments in different seasons, where the overall summer and autumn richness was higher than that in the spring and winter. The relative abundance of 5 Massilia in the constructed wetland ecosystem was greater than 1% in all samples, which were M. alkalitolerans, M. albidiflava, M. aurea, M. brevitalea, and M. timonae. The seasonal variation of dominant genera was significantly correlated with environmental factors in constructed wetlands. Discussion The above results indicated that the species of Massilia were abundant and widely distributed in the constructed wetland ecosystem, and there were significant seasonal differences. In addition, the Massilia clone library of constructed wetland was constructed for the first time in this study and the valuable data of Massilia community structure were provided, which was conducive to the further study of microbial community in constructed wetland.
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Affiliation(s)
- Ailing Xu
- School of Environmental and Municipal Engineering, Qingdao Technological University, Qingdao, Shandong, China
| | - Congcong Liu
- School of Environmental and Municipal Engineering, Qingdao Technological University, Qingdao, Shandong, China
| | - Shuke Zhao
- Qingdao sub-Center, Shandong Water Transfer Project Operation and Maintenance Center, Qingdao, Shandong, China
| | - Zhiwen Song
- School of Environmental and Municipal Engineering, Qingdao Technological University, Qingdao, Shandong, China
| | - Hui Sun
- Qingdao sub-Center, Shandong Water Transfer Project Operation and Maintenance Center, Qingdao, Shandong, China
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14
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Yang H, Sherman ME, Koo CJ, Treaster LM, Smith JP, Gallaher SG, Goodlett DR, Sweet CR, Ernst RK. Structure Determination of Lipid A with Multiple Glycosylation Sites by Tandem MS of Lithium-Adducted Negative Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1047-1055. [PMID: 37184080 DOI: 10.1021/jasms.3c00014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
FLATn is a tandem mass spectrometric technique that can be used to rapidly generate spectral information applicable for structural elucidation of lipids like lipid A from Gram-negative bacterial species from a single bacterial colony. In this study, we extend the scope and capability of FLATn by tandem MS fragmentation of lithium-adducted molecular lipid A anions and fragments (FLATn-Li) that provides additional structural and diagnostic data from FLATn samples allowing for the discrimination of terminal phosphate modifications in a variety of pathogenic and environmental species. Using FLATn-Li, we elucidated the lipid A structure from several bacterial species, including novel structures from arctic bacterioplankton of the Duganella and Massilia genera that favor 4-amino-4-deoxy-l-arabinopyranose (Ara4N) modification at the 1-phosphate position and that demonstrate double glycosylation with Ara4N at the 1 and 4' phosphate positions simultaneously. The structures characterized in this work demonstrate that some environmental psychrophilic species make extensive use of this structural lipid A modification previously characterized as a pathogenic adaptation and the structural basis of resistance to cationic antimicrobial peptides. This observation extends the role of phosphate modification(s) in environmental species adaptation and suggests that Ara4N modification can functionally replace the positive charge of the phosphoethanolamine modification that is more typically found attached to the 1-phosphate position of modified lipid A.
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Affiliation(s)
- Hyojik Yang
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States of America
| | - Matthew E Sherman
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States of America
| | - Caitlyn J Koo
- Chemistry Department, United States Naval Academy, Annapolis, Maryland 21402, United States of America
- School of Medicine, Uniformed Services University, Bethesda, Maryland 20814, United States of America
| | - Logan M Treaster
- Chemistry Department, United States Naval Academy, Annapolis, Maryland 21402, United States of America
- School of Medicine, University of Kansas, Kansas City, Kansas 66160, United States of America
| | - Joseph P Smith
- Oceanography Department, United States Naval Academy, Annapolis, Maryland 21402, United States of America
| | - Shawn G Gallaher
- Oceanography Department, United States Naval Academy, Annapolis, Maryland 21402, United States of America
| | - David R Goodlett
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
- Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7Z8, Canada
| | - Charles R Sweet
- Chemistry Department, United States Naval Academy, Annapolis, Maryland 21402, United States of America
| | - Robert K Ernst
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States of America
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15
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Li Q, Wang P, Zou C, Ge F, Li F, Liu Y, Zhang D, Tian J. Dynamics of dominant rhizospheric microbial communities responsible for trichlorfon absorption and translocation in maize seedlings. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131096. [PMID: 36893602 DOI: 10.1016/j.jhazmat.2023.131096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
In this study, the available phosphorus (AP) and TCF concentrations in soils and maize (Zea mays) seedling tissues were measured in response to escalating TCF concentrations during 216 hr of culture. Maize seedlings growth considerably enhanced soil TCF degradation, reaching the highest of 73.2% and 87.4% at 216 hr in 50 and 200 mg/kg TCF treatments, respectively, and increased AP contents in all the seedling tissues. Soil TCF was majorly accumulated in seedling roots, reaching maximum concentration of 0.017 and 0.076 mg/kg in TCF-50 and TCF-200, respectively. The hydrophilicity of TCF might hinder its translocation to the aboveground shoot and leaf. Using bacterial 16 S rRNA gene sequencing, we found that TCF addition drastically lessened bacterial community interactions and hindered the complexity of their biotic networks in rhizosphere than in bulk soils, leading to the homogeneity of bacterial communities that were resistant or prone to TCF biodegradation. Mantel test and redundancy analysis suggested a significant enrichment of dominant species Massilia belonging to Proteobacteria phyla, which in turn affecting TCF translocation and accumulation in maize seedling tissues. This study provided new insight into the biogeochemical fate of TCF in maize seedling and the responsible rhizobacterial community in soil TCF absorption and translocation.
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Affiliation(s)
- Qiqiang Li
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan, China
| | - Peiying Wang
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan, China
| | - Caihua Zou
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan, China
| | - Fei Ge
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan, China
| | - Feng Li
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan, China
| | - Yun Liu
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan, China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun 130021, China; Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun 130021, China
| | - Jiang Tian
- Department of Environmental Science and Engineering, College of Environment and Resources, Xiangtan University, Xiangtan, China.
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16
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Jiao Y, An L, Wang W, Ma J, Wu C, Wu X. Microbial communities and their roles in the Cenozoic sulfurous oil reservoirs in the Southwestern Qaidam Basin, Western China. Sci Rep 2023; 13:7988. [PMID: 37198206 DOI: 10.1038/s41598-023-33978-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/21/2023] [Indexed: 05/19/2023] Open
Abstract
The latest discovery of sulfurous natural gas marked a breakthrough in the Cenozoic natural gas exploration in the southwestern margin of Qaidam Basin. The 16S rRNA analyses were performed on the crude oil samples from H2S-rich reservoirs in the Yuejin, Shizigou and Huatugou profiles, to understand the sulfurous gas origin, which was also integrated with carbon and hydrogen isotopes of alkane and sulfur isotopes of H2S collected from the Yingxiongling Area. Results show that the microorganisms in samples can survive in the hypersaline reservoirs, and can be classified into multiple phyla, including Proteobacteria, Planctomycetes, Firmicutes, Bacteroidetes, and Haloanaerobiaeota. Methanogens are abundant in all of the three profiles, while sulfate-reducing bacteria are abundant in Yuejin and Huatugou profiles, contributing to the methane and H2S components in the natural gas. The carbon, hydrogen and sulfur isotopes of sulfurous natural gas in the Yingxiongling Area show that the natural gas is a mixture of coal-type gas and oil-type gas, which was primarily derived from thermal degradation, and natural gas from the Yuejin and Huatugou profiles also originated from biodegradation. The isotopic analysis agrees well with the 16S rRNA results, i.e., H2S-rich natural gas from the Cenozoic reservoirs in the southwest margin of the Qaidam Basin was primarily of thermal genesis, with microbial genesis of secondary importance.
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Affiliation(s)
- Yue Jiao
- The Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Science, Peking University, Beijing, 100871, China
| | - Liyun An
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, China
| | - Wei Wang
- The No. 1 Oil Extraction Plant, Qinghai Oilfield Company, PetroChina, Haixi, 817000, Qinghai, China
| | - Jian Ma
- The Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Science, Peking University, Beijing, 100871, China
| | - Chaodong Wu
- The Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Science, Peking University, Beijing, 100871, China.
| | - Xiaolei Wu
- College of Engineering, Peking University, Beijing, 100871, China
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Shaffer JMC, Giddings LA, Samples RM, Mikucki JA. Genomic and phenotypic characterization of a red-pigmented strain of Massilia frigida isolated from an Antarctic microbial mat. Front Microbiol 2023; 14:1156033. [PMID: 37250028 PMCID: PMC10213415 DOI: 10.3389/fmicb.2023.1156033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/20/2023] [Indexed: 05/31/2023] Open
Abstract
The McMurdo Dry Valleys of Antarctica experience a range of selective pressures, including extreme seasonal variation in temperature, water and nutrient availability, and UV radiation. Microbial mats in this ecosystem harbor dense concentrations of biomass in an otherwise desolate environment. Microbial inhabitants must mitigate these selective pressures via specialized enzymes, changes to the cellular envelope, and the production of secondary metabolites, such as pigments and osmoprotectants. Here, we describe the isolation and characterization of a Gram-negative, rod-shaped, motile, red-pigmented bacterium, strain DJPM01, from a microbial mat within the Don Juan Pond Basin of Wright Valley. Analysis of strain DJMP01's genome indicates it can be classified as a member of the Massilia frigida species. The genome contains several genes associated with cold and salt tolerance, including multiple RNA helicases, protein chaperones, and cation/proton antiporters. In addition, we identified 17 putative secondary metabolite gene clusters, including a number of nonribosomal peptides and ribosomally synthesized and post-translationally modified peptides (RiPPs), among others, and the biosynthesis pathway for the antimicrobial pigment prodigiosin. When cultivated on complex agar, multiple prodiginines, including the antibiotic prodigiosin, 2-methyl-3-propyl-prodiginine, 2-methyl-3-butyl-prodiginine, 2-methyl-3-heptyl-prodiginine, and cycloprodigiosin, were detected by LC-MS. Genome analyses of sequenced members of the Massilia genus indicates prodigiosin production is unique to Antarctic strains. UV-A radiation, an ecological stressor in the Antarctic, was found to significantly decrease the abundance of prodiginines produced by strain DJPM01. Genomic and phenotypic evidence indicates strain DJPM01 can respond to the ecological conditions of the DJP microbial mat, with prodiginines produced under a range of conditions, including extreme UV radiation.
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Affiliation(s)
- Jacob M. C. Shaffer
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | | | - Robert M. Samples
- Department of Chemistry, Smith College, Northampton, MA, United States
| | - Jill A. Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
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18
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Huq MA, Ma J, Srinivasan S, Parvez MAK, Rahman MM, Naserkheil M, Abuhena M, Maitra P, Islam F, Nam K, Park JH, Akter S. Massilia agrisoli sp. nov., isolated from rhizospheric soil of banana. Int J Syst Evol Microbiol 2023; 73. [PMID: 37224056 DOI: 10.1099/ijsem.0.005897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
A Gram-stain-negative, aerobic, short rod-shaped and motile novel bacterial strain, designated MAHUQ-52T, was isolated from the rhizospheric soil of a banana plant. Colonies grew at 10-35 °C (optimum, 28 °C), pH 6.0-9.5 (optimum, pH 7.0-7.5), and in the presence of 0-1.0 % NaCl (optimum 0 %). The strain was positive for catalase and oxidase tests, as well as hydrolysis of gelatin, casein, starch and Tween 20. Based on the results of phylogenetic analysis using 16S rRNA gene and genome sequences, strain MAHUQ-52T clustered together within the genus Massilia. Strain MAHUQ-52T was closely related to Massilia soli R798T (98.6 %) and Massilia polaris RP-1-19T (98.3 %). The novel strain MAHUQ-52T has a draft genome size of 4 677 454 bp (25 contigs), annotated with 4193 protein-coding genes, 64 tRNA and 19 rRNA genes. The genomic DNA G+C content was 63.0 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAHUQ-52T and closely related type strains were ≤88.4 and 35.8 %, respectively. The only respiratory quinone was ubiquinone-8. The major fatty acids were identified as C16 : 0 and summed feature 3 (C15 : 0 iso 2-OH and/or C16 : 1 ω7c). Strain MAHUQ-52T contained phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol as the major polar lipids. On the basis of dDDH and ANI values, as well as genotypic, chemotaxonomic and physiological data, strain MAHUQ-52T represents a novel species within the genus Massilia, for which the name Massilia agrisoli sp. nov. is proposed, with MAHUQ-52T (=KACC 21999T=CGMCC 1.18577T) as the type strain.
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Affiliation(s)
- Md Amdadul Huq
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - Juncai Ma
- World Data Center for Microorganisms (WDCM); Institute of Microbiology, Chinese Academy of Sciences (IMCAS), PR China
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea
| | | | - M Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia-7003, Bangladesh
| | - Masoumeh Naserkheil
- Animal Breeding and Genetics Division, National Institute of Animal Science, Cheonan 31000, Republic of Korea
| | - Md Abuhena
- Department of Research & Development, Apex Biofertilizers & Biopesticides Limited, Gobindaganj-5740, Gaibandha, Bangladesh
| | - Pulak Maitra
- Institute of Dendrology, Polish Academy of Sciences, 62-035 Kórnik, Poland
| | - Fahadul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Kihong Nam
- Department of Horticultural Life Science, Hankyong National University, Anseong-si, Gyeonggi-do, 17579, Republic of Korea
| | - Jong-Hyun Park
- Department of Food Science and Biotechnology, Gachon University, Seongnam, 461-701, Republic of Korea
| | - Shahina Akter
- Department of Food Science and Biotechnology, Gachon University, Seongnam, 461-701, Republic of Korea
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Nováková D, Koublová V, Sedlář K, Staňková E, Králová S, Švec P, Neumann-Schaal M, Wolf J, Koudelková S, Barták M, Sedláček I. Pseudomonas petrae sp. nov. isolated from regolith samples in Antarctica. Syst Appl Microbiol 2023; 46:126424. [PMID: 37167755 DOI: 10.1016/j.syapm.2023.126424] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 04/06/2023] [Accepted: 04/23/2023] [Indexed: 05/13/2023]
Abstract
A polyphasic taxonomic approach was used to characterize the four strains P2653T, P2652, P2498, and P2647, isolated from Antarctic regolith samples. Initial genotype screening performed by PCR fingerprinting based on repetitive sequences showed that the isolates studied formed a coherent cluster separated from the other Pseudomonas species. Identification results based on 16S rRNA gene sequences showed the highest sequence similarity with Pseudomonas graminis (99.7%), which was confirmed by multilocus sequence analysis using the rpoB, rpoD, and gyrB genes. Genome sequence comparison of P2653T with the most related P. graminis type strain DSM 11363T revealed an average nucleotide identity of 92.1% and a digital DNA-DNA hybridization value of 46.6%. The major fatty acids for all Antarctic strains were C16:0, Summed Feature 3 (C16:1ω7c/C16:1ω6c) and Summed Feature 8 (C18:1ω7c/C18:1ω6c). The predominant respiratory quinone was Q-9, and the major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol. The regolith strains could be differentiated from related species by the absence of arginine dihydrolase, ornithine and lysine decarboxylase and by negative tyrosine hydrolysis. The results of this polyphasic study allowed the genotypic and phenotypic differentiation of four analysed strains from the closest related species, which confirmed that the strains represent a novel species within the genus Pseudomonas, for which the name Pseudomonas petrae sp. nov. is proposed with P2653T (CCM 8850T = DSM 112068T = LMG 30619T) as the type strain.
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Affiliation(s)
- Dana Nováková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
| | - Vendula Koublová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Karel Sedlář
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic; Department of Informatics, Ludwig-Maximilians-Universität München, Amalienstraße 17, 803 33 Munich, Germany
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Švec
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jacqueline Wolf
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Sylva Koudelková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Miloš Barták
- Department of Experimental Biology, Section of Experimental Plant Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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20
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Yue J, Yang F, Wang S, Yuan J, Li L, Liu L. Massilia phyllostachyos sp. nov., Isolated from the Roots of Moso Bamboo in China. Curr Microbiol 2022; 80:54. [PMID: 36585979 DOI: 10.1007/s00284-022-03163-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/22/2022] [Indexed: 01/01/2023]
Abstract
A Gram-negative, strictly aerobic, motile, and rod-shaped bacterial strain G4R7T was isolated from the roots of moso bamboo (Phyllostachys edulis) in Zhejiang, Hangzhou Province, China. After comparing 16S rRNA gene sequences, strain G4R7T exhibited the highest similarities with Massilia neuiana PTW21T (98.3%), followed by M. agri K-3-1T (98.3%), M. consociate CCUG 58010T (97.7%), M. niastensis 5516S-1T (97.7%) and M. yuzhufengensis ZD1-4T (97.6%). The phylogenetic analysis revealed that strain G4R7T belonged to the genus Massilia. The draft genome of strain G4R7T was 5.81 Mb, and the G+C content was 64.4%. The average nucleotide identity values between G4R7T and another related member of the genus Massilia ranged from 76.6 to 87.2%, and the digital DNA-DNA hybridization ranged from 20.7 to 27.9%. Strain G4R7T grew at 15-37 °C (optimum 25-30 °C) and pH 6.0-9.0 (optimum pH 7.0) in the presence of 0-3% (w/v) NaCl (optimum 0%). The respiratory quinone was Q-8, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and aminophospholipid. The major cellular fatty acids were C10:0 3OH, C12:0, C12:0 2OH, and C16:0, summed feature 3 (C16:1 ω6c and/or C16:1 ω7c). As per the data from chemotaxonomic, phylogenetic, and phenotypic evidence, strain G4R7T represents a new species of genus Massilia, for which the name Massilia phyllostachyos sp. nov. is proposed. The type strain is G4R7T (=ACCC 61911T=GDMCC 1.2961T=JCM 35225T).
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Affiliation(s)
- Jinjun Yue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, 311400, China
| | - Fu Yang
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Siyu Wang
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jinling Yuan
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, 311400, China
| | - Lubin Li
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Lei Liu
- Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
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21
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Studying Plant-Insect Interactions through the Analyses of the Diversity, Composition, and Functional Inference of Their Bacteriomes. Microorganisms 2022; 11:microorganisms11010040. [PMID: 36677331 PMCID: PMC9863603 DOI: 10.3390/microorganisms11010040] [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: 11/04/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
As with many other trophic interactions, the interchange of microorganisms between plants and their herbivorous insects is unavoidable. To test the hypothesis that the composition and diversity of the insect bacteriome are driven by the bacteriome of the plant, the bacteriomes of both the plant Datura inoxia and its specialist insect Lema daturaphila were characterised using 16S sRNA gene amplicon sequencing. Specifically, the bacteriomes associated with seeds, leaves, eggs, guts, and frass were described and compared. Then, the functions of the most abundant bacterial lineages found in the samples were inferred. Finally, the patterns of co-abundance among both bacteriomes were determined following a multilayer network approach. In accordance with our hypothesis, most genera were shared between plants and insects, but their abundances differed significantly within the samples collected. In the insect tissues, the most abundant genera were Pseudomonas (24.64%) in the eggs, Serratia (88.46%) in the gut, and Pseudomonas (36.27%) in the frass. In contrast, the most abundant ones in the plant were Serratia (40%) in seeds, Serratia (67%) in foliar endophytes, and Hymenobacter (12.85%) in foliar epiphytes. Indeed, PERMANOVA analysis showed that the composition of the bacteriomes was clustered by sample type (F = 9.36, p < 0.001). Functional inferences relevant to the interaction showed that in the plant samples, the category of Biosynthesis of secondary metabolites was significantly abundant (1.4%). In turn, the category of Xenobiotics degradation and metabolism was significantly present (2.5%) in the insect samples. Finally, the phyla Proteobacteria and Actinobacteriota showed a pattern of co-abundance in the insect but not in the plant, suggesting that the co-abundance and not the presence−absence patterns might be more important when studying ecological interactions.
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22
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Suyal DC, Joshi D, Kumar S, Bhatt P, Narayan A, Giri K, Singh M, Soni R, Kumar R, Yadav A, Devi R, Kaur T, Kour D, Yadav AN. Himalayan Microbiomes for Agro-environmental Sustainability: Current Perspectives and Future Challenges. MICROBIAL ECOLOGY 2022; 84:643-675. [PMID: 34647148 DOI: 10.1007/s00248-021-01849-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
The Himalayas are one of the most mystical, yet least studied terrains of the world. One of Earth's greatest multifaceted and diverse montane ecosystems is also one of the thirty-four global biodiversity hotspots of the world. These are supposed to have been uplifted about 60-70 million years ago and support, distinct environments, physiography, a variety of orogeny, and great biological diversity (plants, animals, and microbes). Microbes are the pioneer colonizer of the Himalayas that are involved in various bio-geological cycles and play various significant roles. The applications of Himalayan microbiomes inhabiting in lesser to greater Himalayas have been recognized. The researchers explored the applications of indigenous microbiomes in both agricultural and environmental sectors. In agriculture, microbiomes from Himalayan regions have been suggested as better biofertilizers and biopesticides for the crops growing at low temperature and mountainous areas as they help in the alleviation of cold stress and other biotic stresses. Along with alleviation of low temperature, Himalayan microbes also have the capability to enhance plant growth by availing the soluble form of nutrients like nitrogen, phosphorus, potassium, zinc, and iron. These microbes have been recognized for producing plant growth regulators (abscisic acid, auxin, cytokinin, ethylene, and gibberellins). These microbes have been reported for bioremediating the diverse pollutants (pesticides, heavy metals, and xenobiotics) for environmental sustainability. In the current perspectives, present review provides a detailed discussion on the ecology, biodiversity, and adaptive features of the native Himalayan microbiomes in view to achieve agro-environmental sustainability.
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Affiliation(s)
- Deep Chandra Suyal
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Sirmaur, Himachal Pradesh, India
| | - Divya Joshi
- Uttarakhand Pollution Control Board, Regional Office, Kashipur, Uttarakhand, India
| | - Saurabh Kumar
- Division of Crop Research, Research Complex for Eastern Region, Patna, Bihar, India
| | - Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Arun Narayan
- Forest Research Institute, Dehradun, 2480 06, India
| | - Krishna Giri
- Rain Forest Research Institute, Jorhat, 785 010, India
| | - Manali Singh
- Department of Biotechnology, Invertis Institute of Engineering and Technology (IIET), Invertis University, Bareilly, 243123, Uttar Pradesh, India
| | - Ravindra Soni
- Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwa Vidyalaya, Raipur, Chhattisgarh, India
| | - Rakshak Kumar
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Ashok Yadav
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Rubee Devi
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India
| | - Tanvir Kaur
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India
| | - Divjot Kour
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India
| | - Ajar Nath Yadav
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India.
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23
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Lu H, Song D, Deng T, Mei C, Xu M. Duganella vulcania sp. nov., Rugamonas fusca sp. nov., Rugamonas brunnea sp. nov. and Rugamonas apoptosis sp. nov., isolated from subtropical streams, and phylogenomic analyses of the genera Janthinobacterium, Duganella, Rugamonas, Pseudoduganella and Massilia. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (FT81WT, FT82W, FT107W, FT3ST, LX20WT and LX47WT) sharing high 16S rRNA gene sequence similarities with species of the genera
Janthinobacterium
(97.0–98.3 %),
Duganella
(96.3–98.8 %),
Rugamonas
(97.8–98.6 %),
Pseudoduganella
(96.8–97.5 %) and
Massilia
(94.5–98.6 %) were isolated from subtropical streams in PR China. The phylogenetic trees reconstructed using the 16S rRNA gene sequences indicated that the species of above five genera often mix together, indicating that the taxonomic statuses of some species were questionable. Phylogenomic reconstruction based on 369 single-copy orthologous clusters indicated that the species of the genus
Janthinobacterium
form a distinct cluster, strains FT81WT, FT82W and FT107W form a tight cluster with the species of the genus
Duganella
, and strains FT3ST, LX20WT and LX47WT form a tight cluster with the species of genus
Rugamonas
, and the species of genus
Pseudoduganella
form a tight cluster with
Massilia guangdongensis
,
Massilia ginsengisoli
,
Massilia rivuli
,
Massilia namucuonensis
,
Massilia aquatica
sensu Lu et al.,
Massilia buxea
,
Massilia armeniaca
,
Massilia plicata
,
Massilia flava
,
Massilia lurida
,
Massilia dura
,
Massilia lutea
,
Massilia umbonata
,
Massilia albidiflava
and
Massilia violacea
. It should be noted that
Massilia aquatica
Lu et al. 2020 non
Massilia aquatica
Holochová et al. 2020 is a later homonym and an illegitimate name. The GTDB Release 202 also supported the proposal that
M. guangdongensis
,
M. ginsengisoli
,
M. rivuli
,
M. namucuonensis
,
M. aquatica
sensu Lu et al.,
M. buxea
,
M. armeniaca
,
M. plicata
,
M. flava
,
M. lurida
,
M. dura
,
M. lutea
,
M. umbonata
,
M. albidiflava
and
M. violacea
should be transferred into the genus
Pseudoduganella
. The calculated pairwise orthologous average nucleotide identity by usearch (OrthoANIu) values were between 95.0 % and 95.6 % among strains FT81WT, FT82W and FT107W, but were less than 91.5 % among strains FT3ST, LX20WT, LX47WT and other related strains. Combining the results of phylogenomic analyses, phenotypic, biochemical and genotypic characteristics, strains FT81WT, FT82W and FT107W should represent a novel species of the genus
Duganella
, and strains FT3ST, LX20WT and LX47WT should represent three novel species of the genus
Rugamonas
, for which the names Duganella vulcania sp. nov. (type strain FT81WT=GDMCC 1.1679T =KACC 21471T), Rugamonas fusca sp. nov. (type strain FT3ST=GDMCC 1.1907T =KACC 21952T), Rugamonas brunnea sp. nov. (type strain LX20WT=GDMCC 1.1911T =KACC 21956T) and Rugamonas apoptosis sp. nov. (type strain LX47WT=GDMCC 1.1914T =KACC 21959T) are proposed.
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Affiliation(s)
- Huibin Lu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, PR China
- Yunnan Key Laboratory of Plateau Geographical Process and Environmental Changes, School of Tourism and Geography, Yunnan Normal University, Kunming, PR China
- Guangdong Open Laboratory of Applied Microbiology, Guangzhou, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, PR China
| | - Da Song
- Guangdong Open Laboratory of Applied Microbiology, Guangzhou, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, PR China
| | - Tongchu Deng
- Guangdong Open Laboratory of Applied Microbiology, Guangzhou, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, PR China
| | - Chengfang Mei
- Guangdong Open Laboratory of Applied Microbiology, Guangzhou, PR China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, PR China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, PR China
- Guangdong Open Laboratory of Applied Microbiology, Guangzhou, PR China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, PR China
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24
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Heo J, Won M, Lee D, Han BH, Hong SB, Kwon SW. Duganella dendranthematis sp. nov. and Massilia forsythiae sp. nov., isolated from flowers. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two aerobic, Gram-stain-negative, motile, mesophilic, rod-shaped and catalase-positive bacterial strains designated AF9R3T and GN2-R2T were isolated from flowers collected in the Republic of Korea. Strain AF9R3T grew at 4–33 °C, pH 4.0–9.0 and with 0–1 % NaCl (w/v), and strain GN2-R2T grew at 10–33 °C, pH 4.0–9.0 and with 0–1 % NaCl (w/v). Phylogenetic analysis on the basis of 16S rRNA gene sequences indicated that strains AF9R3T and GN2-R2T belonged to the genera
Duganella
and
Massilia
, respectively, showing high sequence similarity to
Duganella levis
CY42WT (99.4 %) and
Massilia putida
6 NM-7T (98.0 %), respectively. Both strains contained summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) and C16 : 0 as the major fatty acids, and ubiquinone Q-8 as the predominant quinone. Strain AF9R3T had diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and strain GN2-R2T comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as the major polar lipids. Orthologous average nucleotide identity and digital DNA–DNA hybridization values of strain AF9R3T to its closest relative
D. levis
CY42WT were 92.6 and 56.5 %, and those of strain GN2-R2T to its closest relative
M. putida
6 NM-7T were 81.4 and 24.8 %. Based on genotypic and phenotypic data, strains AF9R3T and GN2-R2T are considered to represent novel species of the genus
Duganella
and
Massilia
, respectively, for which the names Duganella dendranthematis sp. nov. (type strain AF9R3T=KACC 21258T=NBRC 114510T) and Massilia forsythiae sp. nov. (type strain GN2-R2T=KACC 21261T=NBRC 114511T) have been proposed.
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Affiliation(s)
- Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Miyoung Won
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Daseul Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Byeong-Hak Han
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Seung-Beom Hong
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
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25
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Sedláček I, Holochová P, Busse HJ, Koublová V, Králová S, Švec P, Sobotka R, Staňková E, Pilný J, Šedo O, Smolíková J, Sedlář K. Characterisation of Waterborne Psychrophilic Massilia Isolates with Violacein Production and Description of Massilia antarctica sp. nov. Microorganisms 2022; 10:microorganisms10040704. [PMID: 35456753 PMCID: PMC9028926 DOI: 10.3390/microorganisms10040704] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022] Open
Abstract
A group of seven bacterial strains producing blue-purple pigmented colonies on R2A agar was isolated from freshwater samples collected in a deglaciated part of James Ross Island and Eagle Island, Antarctica, from 2017–2019. The isolates were psychrophilic, oligotrophic, resistant to chloramphenicol, and exhibited strong hydrolytic activities. To clarify the taxonomic position of these isolates, a polyphasic taxonomic approach was applied based on sequencing of the 16S rRNA, gyrB and lepA genes, whole-genome sequencing, rep-PCR, MALDI-TOF MS, chemotaxonomy analyses and biotyping. Phylogenetic analysis of the 16S rRNA gene sequences revealed that the entire group are representatives of the genus Massilia. The closest relatives of the reference strain P8398T were Massilia atriviolacea, Massilia violaceinigra, Massilia rubra, Massilia mucilaginosa, Massilia aquatica, Massilia frigida, Massilia glaciei and Massilia eurypsychrophila with a pairwise similarity of 98.6–100% in the 16S rRNA. The subsequent gyrB and lepA sequencing results showed the novelty of the analysed group, and the average nucleotide identity and digital DNA–DNA hybridisation values clearly proved that P8398T represents a distinct Massilia species. After all these results, we nominate a new species with the proposed name Massilia antarctica sp. nov. The type strain is P8398T (= CCM 8941T = LMG 32108T).
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Affiliation(s)
- Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.H.); (V.K.); (S.K.); (P.Š.); (E.S.)
- Correspondence: ; Tel.: +420-549-496-922
| | - Pavla Holochová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.H.); (V.K.); (S.K.); (P.Š.); (E.S.)
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria;
| | - Vendula Koublová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.H.); (V.K.); (S.K.); (P.Š.); (E.S.)
| | - Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.H.); (V.K.); (S.K.); (P.Š.); (E.S.)
| | - Pavel Švec
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.H.); (V.K.); (S.K.); (P.Š.); (E.S.)
| | - Roman Sobotka
- Centrum Algatech, Institute of Microbiology, Czech Academy of Sciences, Opatovický mlýn, 379 01 Třeboň, Czech Republic; (R.S.); (J.P.)
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.H.); (V.K.); (S.K.); (P.Š.); (E.S.)
| | - Jan Pilný
- Centrum Algatech, Institute of Microbiology, Czech Academy of Sciences, Opatovický mlýn, 379 01 Třeboň, Czech Republic; (R.S.); (J.P.)
| | - Ondrej Šedo
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic;
| | - Jana Smolíková
- Department of Physical Geography and Geoecology, Faculty of Science, Charles University, Albertov 6, 128 00 Praha, Czech Republic;
| | - Karel Sedlář
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technická 12, 616 00 Brno, Czech Republic;
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, Amalienstraße 17, 803 33 Munich, Germany
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26
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Baek JH, Baek W, Ruan W, Jung HS, Lee SC, Jeon CO. Massilia soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005227] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, catalase- and oxidase-positive and aerobic bacterium, designated strain R798T, was isolated from soil in South Korea. Cells were motile rods by means of a single polar flagellum. Growth of strain R798T was observed at 15–35 °C (optimum, 25–30 °C), pH 5.0–8.0 (optimum, 6.0) and 0–1.5 % NaCl (optimum, 0.3 %). Strain R798T contained ubiquinone-8 as the sole isoprenoid quinone, summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) and C16 : 0 as the major fatty acids and phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The DNA G+C content of strain R798T calculated from the whole genome sequence was 63.3 mol%. Phylogenetic analyses based on the 16S rRNA gene and whole genome sequences revealed that strain R798T formed a distinct phyletic lineage within the genus
Massilia
. Strain R798T was most closely related to
Massilia eurypsychrophila
B528-3T with a 98.0 % 16S rRNA gene sequence similarity. Average nucleotide identity and digital DNA–DNA hybridization values between strain R798T and the type strain of
M. eurypsychrophila
were 79.2 and 22.7 %, respectively. Based on the phenotypic, chemotaxonomic and molecular analyses, strain R798T represents a novel species of the genus
Massilia
, for which the name Massilia soli sp. nov. is proposed. The type strain is R798T (=KACC 22114T=JCM 34601T).
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Affiliation(s)
- Ju Hye Baek
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Woonhee Baek
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Wenting Ruan
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hye Su Jung
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sung Chul Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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Abstract
To increase the genomic data available for antibiotic discovery, three independently isolated antibiotic-producing Massilia strains were sequenced. No more than 84% average nucleotide identity was shared with publicly available Massilia genomes, and a low similarity of predicted biosynthetic gene clusters to known clusters was found.
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Oren A, Garrity GM. List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication. Int J Syst Evol Microbiol 2020; 70:5596-5600. [DOI: 10.1099/ijsem.0.004484] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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