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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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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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Daussin A, Vannier P, Daboussy L, Šantl-Temkiv T, Cockell C, Marteinsson VÞ. Atmospheric dispersal shapes rapid bacterial colonization of Icelandic Lava Rocks. FEMS MICROBES 2024; 5:xtae016. [PMID: 38873337 PMCID: PMC11173176 DOI: 10.1093/femsmc/xtae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 04/02/2024] [Accepted: 05/23/2024] [Indexed: 06/15/2024] Open
Abstract
Microorganisms released into the atmosphere by various disturbances can travel significant distances before depositing, yet their impact on community assembly remains unclear. To address this, we examined atmospheric and lithospheric bacterial communities in 179 samples collected at two distinct Icelandic volcanic sites: a small volcanic island Surtsey, and a volcanic highland Fimmvörðuháls using 16S rRNA amplicon sequencing. Airborne microbial communities were similar between sites while significant differences emerged in the communities on lava rocks after 1-year exposure. SourceTracker analysis revealed distinct bacterial populations in the atmosphere and the lava rocks with surrounding soil contributed more significantly to lava rock microbial composition. Nevertheless, shared genera among air, rocks, and local sources, suggested potential exchange between these environments. The prevalent genera shared between rocks and potential sources exhibited stress-resistant properties, likely helping their survival during air transportation and facilitating their colonization of the rocks. We hypothesize that the atmosphere serves as a conduit for locally sourced microbes and stress-resistant distant-sourced microbes. Additionally, bacterial communities on the lava rocks of Fimmvörðuháls showed remarkable similarity after 1 and 9 years of exposure, suggesting rapid establishment. Our study reveals that atmospheric deposition significantly influences bacterial community formation, potentially influencing ecosystem dynamics and microbial communities' resilience.
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Affiliation(s)
- Aurélien Daussin
- Faculty of Food Science and Nutrition, University of Iceland, Sæmundargatu 2, 102 Reykjavík, Iceland
- MATIS, Department of Research and Innovation, Vinlandsleið 12, 113 Reykjavík, Iceland
| | - Pauline Vannier
- MATIS, Department of Research and Innovation, Vinlandsleið 12, 113 Reykjavík, Iceland
- Université de Toulon, MAPIEM, SeaTech, Bâtiment X, Avenue de l'Université, 83130 La Garde, France
| | - Lola Daboussy
- University of Technology of Compiègne, CS 60319, 60203 Compiègne, France
| | - Tina Šantl-Temkiv
- Department of Biology, Aarhus University, Ny Munkegade 114, 8000 Aarhus, Denmark
- Department of Biology, Arctic Research Center, Aarhus University, Ole Worms Allé 1, 8000 Aarhus, Denmark
- Department of Environmental Science, iCLIMATE Aarhus University Interdisciplinary Centre for Climate Change, Aarhus University, Ny Munkegade 116, 8000 Aarhus, Denmark
| | - Charles Cockell
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, Scotland
| | - Viggó Þór Marteinsson
- Faculty of Food Science and Nutrition, University of Iceland, Sæmundargatu 2, 102 Reykjavík, Iceland
- MATIS, Department of Research and Innovation, Vinlandsleið 12, 113 Reykjavík, Iceland
- The Agricultural University of Iceland, Hvanneyri, 311 Borgabyggð, Iceland
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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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Yang J, Ding D, Zhang X, Gu H. A comparative analysis of soil physicochemical properties and microbial community structure among four shelterbelt species in the northeast China plain. Microbiol Spectr 2024; 12:e0368323. [PMID: 38376351 PMCID: PMC10986494 DOI: 10.1128/spectrum.03683-23] [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: 10/18/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Conducting studies that focus on the alterations occurring in the soil microbiome within protection forests in the northeast plain is of utmost importance in evaluating the ecological rehabilitation of agricultural lands in the Mollisols region. Nevertheless, the presence of geographic factors contributes to substantial disparities in the microbiomes, and thus, addressing this aspect of influence becomes pivotal in ensuring the credibility of the collected data. Consequently, the objective is to compare the variations in soil physicochemical properties and microbial community structure within the understory of diverse shelterbelt species. In this study, we analyzed the understory soils of Juglans mandshurica (Jm), Fraxinus mandschurica (Fm), Acer mono (Am), and Betula platyphylla (Bp) from the same locality. We employed high-throughput sequencing technology and soil physicochemical data to investigate the impact of these different tree species on soil microbial communities, chemical properties, and enzyme activities in Mollisols areas. Significant variations in soil nutrients and enzyme activities were observed among tree species, with soil organic matter content ranging from 49.1 to 67.7 g/kg and cellulase content ranging from 5.3 to 524.0 μg/d/g. The impact of tree species on microbial diversities was found to be more pronounced in the bacterial community (Adnoism: R = 0.605) compared to the fungal community (Adnoism: R = 0.433). The linear discriminant analysis effect size (LEfSe) analysis revealed a total of 5 (Jm), 3 (Bp), and 6 (Am) bacterial biomarkers, as well as 2 (Jm), 6 (Fm), 4 (Bp), and 1 (Am) fungal biomarker at the genus level (LDA3). The presence of various tree species was observed to significantly alter the relative abundance of specific microbial community structures, specifically in Gammaproteobacteria, Ascomycota, and Basidiomycota. Furthermore, environmental factors, such as pH, total potassium, and available phosphorus were important factors influencing changes in bacterial communities. We propose that Fm be utilized as the primary tree species for establishing farmland protection forests in the northeastern region, owing to its superior impact on enhancing soil quality. IMPORTANCE The focal point of this study lies in the implementation of a controlled experiment conducted under field conditions. In this experiment, we deliberately selected four shelterbelts within the same field, characterized by identical planting density, and planting year. This deliberate selection effectively mitigated the potential impact of extraneous factors on the three microbiomes, thereby enhancing the reliability and validity of our findings.
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Affiliation(s)
- Jia Yang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Dang Ding
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Xiuru Zhang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Huiyan Gu
- School of Forestry, Northeast Forestry University, Harbin, China
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Huang X, Qi S, Song W, Yu X, Zhang H, Xiang W, Zhao J, Wang X. Massilia luteola sp. nov., a novel indole-producing and cellulose-degrading bacterium isolated from soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 38619981 DOI: 10.1099/ijsem.0.006331] [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: 04/17/2024] Open
Abstract
A Gram-stain-negative, rod-shaped, indole-producing, and cellulose-degrading bacterial strain, designated NEAU-G-C5T, was isolated from soil collected from a forest in Dali city, Yunnan province, south China. 16S rRNA gene sequence analysis showed that strain NEAU-G-C5T was assigned to the genus Massilia and showed high sequence similarities to Massilia phosphatilytica 12-OD1T (98.32 %) and Massilia putida 6 NM-7T (98.41 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-G-C5T formed a lineage related to M. phosphatilytica 12-OD1T and M. putida 6 NM-7T. The major fatty acids of the strain were C16 : 0, C16 : 1 ω7c, and C17 : 0 cyclo. The respiratory quinone was Q-8. The polar lipid profile of the strain showed the presence of diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. In addition, the average nucleotide identity values between strain NEAU-G-C5T and its reference strains M. phosphatilytica 12-OD1T, M. putida 6 NM-7T, M. norwichensis NS9T, and M. kyonggiensis TSA1T were 89.7, 88.2, 81.3, and 88.0 %, respectively, and the levels of digital DNA-DNA hybridization between them were found to be 58.5 % (54.9-62.0 %), 53.2 % (49.8-56.7 %), 31.9 % (28.6-35.5 %), and 57.7 % (54.1-61.2 %), respectively, which were lower than the accepted threshold values of 95-96 % and 70 %, respectively. The DNA G+C content of strain NEAU-G-C5T was 66.5 mol%. The strain could produce indoleacetic acid and cellulase. On the basis of the phenotypic, genotypic, and chemotaxonomic characteristics, we conclude that strain NEAU-G-C5T represents a novel species of the genus Massilia, for which the name Massilia luteola sp. nov. is proposed. The type strain is NEAU-G-C5T (=MCCC 1K08668T=KCTC 8080T).
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Affiliation(s)
- Xinbing Huang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District,Harbin 150030, PR China
| | - Shengtao Qi
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District,Harbin 150030, PR China
| | - Wenshuai Song
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District,Harbin 150030, PR China
| | - Xiaoxin Yu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District,Harbin 150030, PR China
| | - Haifeng Zhang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District,Harbin 150030, PR China
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District,Harbin 150030, PR China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests,Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Junwei Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District,Harbin 150030, PR China
| | - Xiangjing Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District,Harbin 150030, PR China
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Prado T, Magalhães MGP, Moreira DA, Brandão ML, Fumian TM, Ferreira FC, Chame M, Leomil L, Degrave WMS, Leite JPG, Miagostovich MP. Microbiome and virome on indoor surfaces of an Antarctic research ship. Mem Inst Oswaldo Cruz 2023; 118:e230084. [PMID: 37672426 PMCID: PMC10481937 DOI: 10.1590/0074-02760230084] [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: 05/13/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND Few studies have focused on microbial diversity in indoor environments of ships, as well as the role of the microbiome and its ecological interconnections. In this study, we investigated the microbiome and virome present on the internal surfaces of a polar ship in different stages (beginning, during, and at the end) of the Brazilian Antarctic expedition in order to evaluate abundance of microorganisms in different periods. OBJECTIVES AND METHODS We used shotgun metagenomic analysis on pooled samples from sampling surfaces in the ship's interior to track the microbial diversity. FINDINGS Considering the total fraction of the microbiome, the relative abundance of bacteria, eukaryotes, viruses, and archaea was 83.7%, 16.2%, 0.04%, and 0.002%, respectively. Proteobacteria was the most abundant bacterial phyla, followed by Firmicutes, Actinobacteria, and Bacteroidetes. Concerning the virome, the greatest richness of viral species was identified during the middle of the trip, including ten viral families after de novo assembly: Autographiviridae, Chrysoviridae, Genomoviridae, Herelleviridae, Myoviridae, Partitiviridae, Podoviridae, Potyviridae, Siphoviridae, and Virgaviridae. MAIN CONCLUSIONS This study contributed to the knowledge of microbial diversity in naval transportation facilities, and variations in the abundance of microorganisms probably occurred due to factors such as the number of passengers and activities on the ship.
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Affiliation(s)
- Tatiana Prado
- Fundação Oswaldo Cruz-Fiocruz, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro, RJ, Brasil
- Fundação Oswaldo Cruz-Fiocruz, Laboratório de Genômica Aplicada e BioInovações, Rio de Janeiro, RJ, Brasil
| | | | - Daniel Andrade Moreira
- Fundação Oswaldo Cruz-Fiocruz, Laboratório de Genômica Aplicada e BioInovações, Rio de Janeiro, RJ, Brasil
| | - Martha Lima Brandão
- Fundação Oswaldo Cruz-Fiocruz, Projeto FioAntar/VPPIS, Rio de Janeiro, RJ, Brasil
| | - Tulio Machado Fumian
- Fundação Oswaldo Cruz-Fiocruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro, RJ, Brasil
| | - Fernando Cesar Ferreira
- Fundação Oswaldo Cruz-Fiocruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro, RJ, Brasil
| | - Marcia Chame
- Fundação Oswaldo Cruz-Fiocruz, Plataforma Institucional para Biodiversidade e Saúde Animal, Rio de Janeiro, RJ, Brasil
| | - Luciana Leomil
- Serviço Nacional de Aprendizagem Industrial, Centro Tecnológico para Indústria Química e Têxtil, Biotecnologia, Parque Tecnológico da Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | | | - José Paulo Gagliardi Leite
- Fundação Oswaldo Cruz-Fiocruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro, RJ, Brasil
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Ma T, Xue H, Piao C, Jiang N, Li Y. Genome-based analyses of family Oxalobacteraceae reveal the taxonomic classification. Res Microbiol 2023; 174:104076. [PMID: 37137377 DOI: 10.1016/j.resmic.2023.104076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/05/2023]
Abstract
Family Oxalobacteraceae is known for the indicator of bacterial diversity in the environment and many of which are important beneficial bacteria. Previous studies on the taxonomic structure of family Oxalobacteraceae mostly relied on 16S rRNA gene analysis, or core-genome phylogeny of a limited number of species and resulted in taxonomic confusion within several genera. Developments in sequencing technologies have allowed more genome sequences to be obtained, enabling the revision of family Oxalobacteraceae. Here, we report a comprehensive analysis of phylogenomic trees, concatenated protein and up-to-date bacterial core gene phylogenetic trees, and genomic metrics for genus demarcation on 135 genomes of Oxalobacteraceae species to elucidate their interrelationships. Following this framework for classification of species in family Oxalobacteraceae, all the proposed genera formed monophyletic lineages in the phylogenomic trees and could also be clearly separated from others in the genomic similarity indexes of average amino acid identity, percentage of conserved proteins and core-proteome average amino acid identity.
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Affiliation(s)
- Tengfei Ma
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China.
| | - Han Xue
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China.
| | - Chungen Piao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China.
| | - Ning Jiang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China.
| | - Yong Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China.
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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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Tanunchai B, Ji L, Schröder O, Gawol SJ, Geissler A, Wahdan SFM, Buscot F, Kalkhof S, Schulze ED, Noll M, Purahong W. Fate of a biodegradable plastic in forest soil: Dominant tree species and forest types drive changes in microbial community assembly, influence the composition of plastisphere, and affect poly(butylene succinate-co-adipate) degradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162230. [PMID: 36796697 DOI: 10.1016/j.scitotenv.2023.162230] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Poly(butylene succinate-co-adipate) (PBSA) degradation and its plastisphere microbiome in cropland soils have been studied; however, such knowledge is limited in the case of forest ecosystems. In this context, we investigated: i) the impact of forest types (conifer and broadleaved forests) on the plastisphere microbiome and its community assembly, ii) their link to PBSA degradation, and iii) the identities of potential microbial keystone taxa. We determined that forest type significantly affected microbial richness (F = 5.26-9.88, P = 0.034 to 0.006) and fungal community composition (R2 = 0.38, P = 0.001) of the plastisphere microbiome, whereas its effects on microbial abundance and bacterial community composition were not significant. The bacterial community was governed by stochastic processes (mainly homogenizing dispersal), whereas the fungal community was driven by both stochastic and deterministic processes (drift and homogeneous selection). The highest molar mass loss was found for PBSA degraded under Pinus sylvestris (26.6 ± 2.6 to 33.9 ± 1.8 % (mean ± SE) at 200 and 400 days, respectively), and the lowest molar mass loss was found under Picea abies (12.0 ± 1.6 to 16.0 ± 0.5 % (mean ± SE) at 200 and 400 days, respectively). Important fungal PBSA decomposers (Tetracladium) and atmospheric dinitrogen (N2)-fixing bacteria (symbiotic: Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium and Methylobacterium and non-symbiotic: Mycobacterium) were identified as potential keystone taxa. The present study is among the first to determine the plastisphere microbiome and its community assembly processes associated with PBSA in forest ecosystems. We detected consistent biological patterns in the forest and cropland ecosystems, indicating a potential mechanistic interaction between N2-fixing bacteria and Tetracladium during PBSA biodegradation.
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Affiliation(s)
- Benjawan Tanunchai
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany; Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany; Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, 95440 Bayreuth, Germany
| | - Li Ji
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany; School of Forestry, Central South of Forestry and Technology, 410004 Changsha, PR China
| | - Olaf Schröder
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany
| | - Susanne Julia Gawol
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany
| | - Andreas Geissler
- Department of Macromolecular Chemistry and Paper Chemistry, Technical University of Darmstadt, Darmstadt D-64287, Germany
| | - Sara Fareed Mohamed Wahdan
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany; Department of Botany and Microbiology, Faculty of Science, Suez Canal University, 41522 Ismailia, Egypt
| | - François Buscot
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Stefan Kalkhof
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany; Department of Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany
| | - Ernst-Detlef Schulze
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Matthias Noll
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany; Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, 95440 Bayreuth, Germany.
| | - Witoon Purahong
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany.
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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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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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Yuan YH, Liu LX, Wang L, Dong GZ, Liu YG. Effects of different seasons on bacterial community structure in rose rhizosphere soil. Appl Microbiol Biotechnol 2022; 107:405-417. [DOI: 10.1007/s00253-022-12290-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/31/2022] [Accepted: 11/04/2022] [Indexed: 11/25/2022]
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Oren A, Garrity GM. Validation List no. 206. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005422] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] 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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