1
|
Jaeger ACH, Hartmann M, Conz RF, Six J, Solly EF. Prolonged water limitation shifts the soil microbiome from copiotrophic to oligotrophic lifestyles in Scots pine mesocosms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13211. [PMID: 37991154 PMCID: PMC10866073 DOI: 10.1111/1758-2229.13211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023]
Abstract
Reductions in soil moisture due to prolonged episodes of drought can potentially affect whole forest ecosystems, including soil microorganisms and their functions. We investigated how the composition of soil microbial communities is affected by prolonged episodes of water limitation. In a mesocosm experiment with Scots pine saplings and natural forest soil maintained at different levels of soil water content over 2 years, we assessed shifts in prokaryotic and fungal communities and related these to changes in plant development and soil properties. Prolonged water limitation induced progressive changes in soil microbial community composition. The dissimilarity between prokaryotic communities at different levels of water limitation increased over time regardless of the recurrent seasons, while fungal communities were less affected by prolonged water limitation. Under low soil water contents, desiccation-tolerant groups outcompeted less adapted, and the lifestyle of prokaryotic taxa shifted from copiotrophic to oligotrophic. While the abundance of saprotrophic and ligninolytic groups increased alongside an accumulation of dead plant material, the abundance of symbiotic and nutrient-cycling taxa decreased, likely impairing the development of the trees. Overall, prolonged episodes of drought appeared to continuously alter the structure of microbial communities, pointing to a potential loss of critical functions provided by the soil microbiome.
Collapse
Affiliation(s)
- Astrid C. H. Jaeger
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Martin Hartmann
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Rafaela Feola Conz
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Johan Six
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Emily F. Solly
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
- Helmholtz Centre for Environmental Research—UFZLeipzigGermany
| |
Collapse
|
2
|
Park S, Kim I, Chhetri G, So Y, Jung Y, Woo H, Seo T. Alteromonas gilva sp. nov. and Erythrobacter fulvus sp. nov., isolated from a tidal mudflat. Int J Syst Evol Microbiol 2023; 73. [PMID: 37676705 DOI: 10.1099/ijsem.0.006032] [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: 09/08/2023] Open
Abstract
Strains chi3T and sf7T were collected from a tidal mudflat around Dongmak beach in Ganghwa, Republic of Korea. Both strains were Gram-stain-negative, aerobic or facultatively anaerobic, and rod-shaped. Results of phylogenetic tree analysis based on 16S rRNA and whole-genome sequences suggested that strains chi3T and sf7T belong to the genera Alteromonas and Erythrobacter, respectively. The cells of strain chi3T were non-motile and grew at 15-45 °C (optimum, 38 °C), at pH 6.0-10.0 (optimum, pH 8.0) and in the presence of 0-9.0 % (w/v) NaCl (optimum, 2.0 %). The cells of strain sf7T were motile as they had flagella and grew at 20-48 °C (optimum, 38 °C), at pH 6.0-10.0 (optimum, pH 9.0) and in the presence of 0-5.0 % (w/v) NaCl (optimum, 1.0 %). Strains chi3T and sf7T have average nucleotide identity values (70.0-70.4% and 78.9-81.7 %) and digital DNA-DNA hybridization values (21.8-22.3% and 21.0-25.6 %) with reference strains in the genera Alteromonas and Erythrobacter, respectively. Data from digital DNA-DNA hybridization, as well as phylogenetic, biochemical and physiological analyses, indicated the distinction of the two strains from the genera Alteromonas and Erythrobacter, respectively, and we thus propose the names Alteromonas gilva sp. nov. (type strain chi3T=KACC 22866T=TBRC 16612T) and Erythrobacter fulvus sp. nov. (type strain sf7T=KACC 22865T=TBRC 16611T).
Collapse
Affiliation(s)
- Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Haejin Woo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| |
Collapse
|
3
|
Doane MP, Johnson CJ, Johri S, Kerr EN, Morris MM, Desantiago R, Turnlund AC, Goodman A, Mora M, Lima LFO, Nosal AP, Dinsdale EA. The Epidermal Microbiome Within an Aggregation of Leopard Sharks (Triakis semifasciata) Has Taxonomic Flexibility with Gene Functional Stability Across Three Time-points. MICROBIAL ECOLOGY 2023; 85:747-764. [PMID: 35129649 PMCID: PMC9957878 DOI: 10.1007/s00248-022-01969-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/17/2022] [Indexed: 05/06/2023]
Abstract
The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein-rich mucus that collectively, influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiome of the Triakis semifasciata (leopard shark) at three time-points collected across 4 years to identify links between microbial groups and host metabolism. Our aims include (1) describing the variation of microbiome taxa over time and identifying recurrent microbiome members (present across all time-points); (2) investigating the relationship between the recurrent and flexible taxa (those which are not found consistently across time-points); (3) describing the functional compositions of the microbiome which may suggest links with the host metabolism; and (4) identifying whether metabolic processes are shared across microbial genera or are unique to specific taxa. Microbial members of the microbiome showed high similarity between all individuals (Bray-Curtis similarity index = 82.7, where 0 = no overlap, 100 = total overlap) with the relative abundance of those members varying across sampling time-points, suggesting flexibility of taxa in the microbiome. One hundred and eighty-eight genera were identified as recurrent, including Pseudomonas, Erythrobacter, Alcanivorax, Marinobacter, and Sphingopxis being consistently abundant across time-points, while Limnobacter and Xyella exhibited switching patterns with high relative abundance in 2013, Sphingobium and Sphingomona in 2015, and Altermonas, Leeuwenhoekiella, Gramella, and Maribacter in 2017. Of the 188 genera identified as recurrent, the top 19 relatively abundant genera formed three recurrent groups. The microbiome also displayed high functional similarity between individuals (Bray-Curtis similarity index = 97.6) with gene function composition remaining consistent across all time-points. These results show that while the presence of microbial genera exhibits consistency across time-points, their abundances do fluctuate. Microbial functions however remain stable across time-points; thus, we suggest the leopard shark microbiomes exhibit functional redundancy. We show coexistence of microbes hosted in elasmobranch microbiomes that encode genes involved in utilizing nitrogen, but not fixing nitrogen, degrading urea, and resistant to heavy metal.
Collapse
Affiliation(s)
- Michael P. Doane
- College of Science and Engineering, Flinders University, Bedford Park, South Australia Australia
| | - Colton J. Johnson
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Shaili Johri
- Hopkins Marine Station, Stanford University, Pacific Grove, CA USA
| | - Emma N. Kerr
- College of Science and Engineering, Flinders University, Bedford Park, South Australia Australia
| | | | - Ric Desantiago
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Abigail C. Turnlund
- Australian Centre for Ecogenomics, University of Queensland, St Lucia, QLD Australia
| | - Asha Goodman
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Maria Mora
- Department of Biology, San Diego State University, San Diego, CA USA
| | | | - Andrew P. Nosal
- Department of Environmental and Ocean Sciences, University of San Diego, San Diego, CA USA
- Scripps Institution of Oceanography, University of California – San Diego, CA La Jolla, USA
| | | |
Collapse
|
4
|
Duarte B, Figueiredo A, Ramalhosa P, Canning-Clode J, Caçador I, Fonseca VF. Unravelling the Portuguese Coastal and Transitional Waters' Microbial Resistome as a Biomarker of Differential Anthropogenic Impact. TOXICS 2022; 10:613. [PMID: 36287893 PMCID: PMC9612280 DOI: 10.3390/toxics10100613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/10/2022] [Accepted: 10/14/2022] [Indexed: 05/14/2023]
Abstract
Portugal mainland and Atlantic archipelagos (Madeira and Azores) provide a wide array of coastal ecosystems with varying typology and degrees of human pressure, which shape the microbial communities thriving in these habitats, leading to the development of microbial resistance traits. The samples collected on the Portuguese northeast Atlantic coast waters show an unequivocal prevalence of Bacteria over Archaea with a high prevalence of Proteobacteria, Cyanobacteria, Bacteroidetes and Actinobacteria. Several taxa, such as the Vibrio genus, showed significant correlations with anthropogenic pollution. These anthropogenic pressures, along with the differences in species diversity among the surveyed sites, lead to observed differences in the presence and resistance-related sequences' abundance (set of all metal and antibiotic resistant genes and their precursors in pathogenic and non-pathogenic bacteria). Gene ontology terms such as antibiotic resistance, redox regulation and oxidative stress response were prevalent. A higher number of significant correlations were found between the abundance of resistance-related sequences and pollution, inorganic pressures and density of nearby population centres when compared to the number of significant correlations between taxa abundance at different phylogenetic levels and the same environmental traits. This points towards predominance of the environmental conditions over the sequence abundance rather than the taxa abundance. Our data suggest that the whole resistome profile can provide more relevant or integrative answers in terms of anthropogenic disturbance of the environment, either as a whole or grouped in gene ontology groups, appearing as a promising tool for impact assessment studies which, due to the ubiquity of the sequences across microbes, can be surveyed independently of the taxa present in the samples.
Collapse
Affiliation(s)
- Bernardo Duarte
- MARE—Marine and Environmental Sciences Centre and ARNET—Aquatic Research Infrastructure Network Associated Laboratory, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Andreia Figueiredo
- Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- BioISI—Biosystems and Integrative Sciences Institute, Plant Functional Genomics Group, Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Patrício Ramalhosa
- MARE—Marine and Environmental Sciences Centre and ARNET—Aquatic Research Infrastructure Network Associated Laboratory, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo Piso 0, Caminho da Penteada, 9020-105 Funchal, Portugal
- OOM—Oceanic Observatory of Madeira, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo Piso 0, Caminho da Penteada, 9020-105 Funchal, Portugal
| | - João Canning-Clode
- MARE—Marine and Environmental Sciences Centre and ARNET—Aquatic Research Infrastructure Network Associated Laboratory, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo Piso 0, Caminho da Penteada, 9020-105 Funchal, Portugal
- Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, MD 21037, USA
| | - Isabel Caçador
- MARE—Marine and Environmental Sciences Centre and ARNET—Aquatic Research Infrastructure Network Associated Laboratory, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Vanessa F. Fonseca
- MARE—Marine and Environmental Sciences Centre and ARNET—Aquatic Research Infrastructure Network Associated Laboratory, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| |
Collapse
|
5
|
Kim SJ, Kim M, Lee KE, Cha IT, Park SJ. Complete genome sequence of marine photoheterotophic bacterium Erythrobacter sp. JK5. Mar Genomics 2022; 63:100950. [DOI: 10.1016/j.margen.2022.100950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 10/18/2022]
|
6
|
Li X, Guo R, Zou X, Yao Y, Lu L. The First Cbk-Like Phage Infecting Erythrobacter, Representing a Novel Siphoviral Genus. Front Microbiol 2022; 13:861793. [PMID: 35620087 PMCID: PMC9127768 DOI: 10.3389/fmicb.2022.861793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
Erythrobacter is an important and widespread bacterial genus in the ocean. However, our knowledge about their phages is still rare. Here, a novel lytic phage vB_EliS-L02, infecting Erythrobacter litoralis DSM 8509, was isolated and purified from Sanggou Bay seawater, China. Morphological observation revealed that the phage belonged to Cbk-like siphovirus, with a long prolate head and a long tail. The host range test showed that phage vB_EliS-L02 could only infect a few strains of Erythrobacter, demonstrating its potential narrow-host range. The genome size of vB_EliS-L02 was 150,063 bp with a G+C content of 59.43%, encoding 231 putative open reading frames (ORFs), but only 47 were predicted to be functional domains. Fourteen auxiliary metabolic genes were identified, including phoH that may confer vB_EliS-L02 the advantage of regulating phosphate uptake and metabolism under a phosphate-limiting condition. Genomic and phylogenetic analyses indicated that vB_EliS-L02 was most closely related to the genus Lacusarxvirus with low similarity (shared genes < 30%, and average nucleotide sequence identity < 70%), distantly from other reported phages, and could be grouped into a novel viral genus cluster, in this study as Eliscbkvirus. Meanwhile, the genus Eliscbkvirus and Lacusarxvirus stand out from other siphoviral genera and could represent a novel subfamily within Siphoviridae, named Dolichocephalovirinae-II. Being a representative of an understudied viral group with manifold adaptations to the host, phage vB_EliS-L02 could improve our understanding of the virus–host interactions and provide reference information for viral metagenomic analysis in the ocean.
Collapse
Affiliation(s)
- Xuejing Li
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University (Xiang'an), Xiamen, China
| | - Ruizhe Guo
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiao Zou
- Qingdao Central Hospital, Qingdao, China
| | - Yanyan Yao
- Weihai Changqing Ocean Science Technology Co., Ltd., Weihai, China
| | - Longfei Lu
- Weihai Changqing Ocean Science Technology Co., Ltd., Weihai, China
| |
Collapse
|
7
|
Comparative Genomics Reveals Genetic Diversity and Metabolic Potentials of the Genus Qipengyuania and Suggests Fifteen Novel Species. Microbiol Spectr 2022; 10:e0126421. [PMID: 35446150 PMCID: PMC9241875 DOI: 10.1128/spectrum.01264-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Members of the genus Qipengyuania are heterotrophic bacteria frequently isolated from marine environments with great application potential in areas such as carotenoid production. However, the genomic diversity, metabolic function, and adaption of this genus remain largely unclear. Here, 16 isolates related to the genus Qipengyuania were recovered from coastal samples and their genomes were sequenced. The phylogenetic inference of these isolates and reference type strains of this genus indicated that the 16S rRNA gene was insufficient to distinguish them at the species level; instead, the phylogenomic reconstruction could provide the reliable phylogenetic relationships and confirm 15 new well-supported branches, representing 15 putative novel genospecies corroborated by the digital DNA-DNA hybridization and average nucleotide identity analyses. Comparative genomics revealed that the genus Qipengyuania had an open pangenome and possessed multiple conserved genes and pathways related to metabolic functions and environmental adaptation, despite the presence of divergent genomic features and specific metabolic potential. Genetic analysis and pigment detection showed that the members of this genus were identified as carotenoid producers, while some proved to be potentially aerobic anoxygenic photoheterotrophs. Collectively, the first insight into the genetic diversity and metabolic potentials of the genus Qipengyuania will contribute to better understanding of the speciation and adaptive evolution in natural environments. IMPORTANCE The deciphering of the phylogenetic diversity and metabolic features of the abundant bacterial taxa is critical for exploring their ecological importance and application potential. Qipengyuania is a genus of frequently isolated heterotrophic microorganisms with great industrial application potential. Numerous strains related to the genus Qipengyuania have been isolated from diverse environments, but their genomic diversity and metabolic functions remain unclear. Our study revealed a high degree of genetic diversity, metabolic versatility, and environmental adaptation of the genus Qipengyuania using comparative genomics. Fifteen novel species of this genus have been established using a polyphasic taxonomic approach, expanding the number of described species to almost double. This study provided an overall view of the genus Qipengyuania at the genomic level and will enable us to better uncover its ecological roles and evolutionary history.
Collapse
|
8
|
Matos A, Antunes A. Symbiotic Associations in Ascidians: Relevance for Functional Innovation and Bioactive Potential. Mar Drugs 2021; 19:370. [PMID: 34206769 PMCID: PMC8303170 DOI: 10.3390/md19070370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 12/22/2022] Open
Abstract
Associations between different organisms have been extensively described in terrestrial and marine environments. These associations are involved in roles as diverse as nutrient exchanges, shelter or adaptation to adverse conditions. Ascidians are widely dispersed marine invertebrates associated to invasive behaviours. Studying their microbiomes has interested the scientific community, mainly due to its potential for bioactive compounds production-e.g., ET-73 (trabectedin, Yondelis), an anticancer drug. However, these symbiotic interactions embrace several environmental and biological functions with high ecological relevance, inspiring diverse biotechnological applications. We thoroughly reviewed microbiome studies (microscopic to metagenomic approaches) of around 171 hosts, worldwide dispersed, occurring at different domains of life (Archaea, Bacteria, Eukarya), to illuminate the functions and bioactive potential of associated organisms in ascidians. Associations with Bacteria are the most prevalent, namely with Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria and Planctomycetes phyla. The microbiomes of ascidians belonging to Aplousobranchia order have been the most studied. The integration of worldwide studies characterizing ascidians' microbiome composition revealed several functions including UV protection, bioaccumulation of heavy metals and defense against fouling or predators through production of natural products, chemical signals or competition. The critical assessment and characterization of these communities is extremely valuable to comprehend their biological/ecological role and biotechnological potential.
Collapse
Affiliation(s)
- Ana Matos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal;
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal;
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| |
Collapse
|
9
|
You X, Yin S, Suo F, Xu Z, Chu D, Kong Q, Zhang C, Li Y, Liu L. Biochar and fertilizer improved the growth and quality of the ice plant (Mesembryanthemum crystallinum L.) shoots in a coastal soil of Yellow River Delta, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 775:144893. [PMID: 33618299 DOI: 10.1016/j.scitotenv.2020.144893] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
Coastal soil is an important land reserve that may be used to alleviate the shortage of cultivated land; however, this soil is stressed by saline conditions and nutrient deficiency. Biochar offers the potential to reclaim coastal soil, but the response of plant growth to biochar addition in salt-affected soil is species-dependent. In this study, the response of ice plant (Mesembryanthemum crystallinum L.), an economically valuable halophyte that grows in the coastal soil of the Yellow River Delta, to wood chip biochar (WBC) either alone or in combination with chemical fertilizer was investigated using a 90-day pot experiment. The WBC enhanced the growth of ice plants in the coastal soil, but combining it with chemical fertilizer did not increase its effect. The nutritional quality of the plants was improved by the addition of WBC, regardless of whether chemical fertilizer was applied; moreover, WBC amendment enhanced photosynthesis and reduced the oxidative stress of the plants. The ameliorated soil properties (e.g., soil organic matter and water holding capacity) and increased contents of available macronutrients (e.g., P and K) and micronutrients (e.g., Mg, Mn, B and Zn) resulting from soil amendment with WBC may have contributed to the enhanced growth and quality of the ice plants. Additionally, in soil modified with WBC, an increased abundance of beneficial taxa (e.g., Erythrobacter, Sphingomonas and Lysobacter) and a shift in the microbial community may also have helped to improve the growth and quality of the ice plants. The results of our study provide useful information for developing a biochar-based technology to use in combination with valuable halophytes to reclaim degraded coastal soil and enhance food security.
Collapse
Affiliation(s)
- Xiangwei You
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Shaojing Yin
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Fengyue Suo
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Zongchang Xu
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Depeng Chu
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Qingxian Kong
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Chengsheng Zhang
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Yiqiang Li
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Lei Liu
- Qingdao Bureau of Agriculture and Rural Affairs, Qingdao 266100, China
| |
Collapse
|
10
|
Cho SH, Jeong Y, Lee E, Ko SR, Ahn CY, Oh HM, Cho BK, Cho S. Assessment of Erythrobacter Species Diversity through Pan-Genome Analysis with Newly Isolated Erythrobacter sp. 3-20A1M. J Microbiol Biotechnol 2021; 31:601-609. [PMID: 33526758 PMCID: PMC9723273 DOI: 10.4014/jmb.2012.12054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/15/2022]
Abstract
Erythrobacter species are extensively studied marine bacteria that produce various carotenoids. Due to their photoheterotrophic ability, it has been suggested that they play a crucial role in marine ecosystems. It is essential to identify the genome sequence and the genes of the species to predict their role in the marine ecosystem. In this study, we report the complete genome sequence of the marine bacterium Erythrobacter sp. 3-20A1M. The genome size was 3.1 Mbp and its GC content was 64.8%. In total, 2998 genetic features were annotated, of which 2882 were annotated as functional coding genes. Using the genetic information of Erythrobacter sp. 3-20A1M, we performed pangenome analysis with other Erythrobacter species. This revealed highly conserved secondary metabolite biosynthesis-related COG functions across Erythrobacter species. Through subsequent secondary metabolite biosynthetic gene cluster prediction and KEGG analysis, the carotenoid biosynthetic pathway was proven conserved in all Erythrobacter species, except for the spheroidene and spirilloxanthin pathways, which are only found in photosynthetic Erythrobacter species. The presence of virulence genes, especially the plant-algae cell wall degrading genes, revealed that Erythrobacter sp. 3-20A1M is a potential marine plant-algae scavenger.
Collapse
Affiliation(s)
- Sang-Hyeok Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yujin Jeong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Eunju Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - So-Ra Ko
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Chi-Yong Ahn
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Hee-Mock Oh
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea,KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea,
B.-K. Cho E-mail:
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea,KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea,Corresponding authors S. Cho Phone: +82-42-350-2660 Fax: +82-42-350-5620 E-mail:
| |
Collapse
|
11
|
Abstract
As the most abundant bacteria in oceans, the Pelagibacterales order (here SAR11) plays an important role in the global carbon cycle, but the study of the evolutionary forces driving its evolution has lagged considerably due to the inherent difficulty of obtaining pure cultures. Multiple evolutionary models have been proposed to explain the diversification of distinct lineages within a population; however, the identification of many of these patterns in natural populations remains mostly enigmatic. We have used a metagenomic approach to explore microdiversity patterns in their natural habitats. Comparison with a collection of bacterial and archaeal groups from the same environments shows that SAR11 populations have a different evolutionary regime, where multiple genotypes coexist within the same population and remain stable over time. Widespread homologous recombination could be one of the main driving factors of this homogenization. The SAR11 clade of Alphaproteobacteria is the most abundant group of planktonic cells in the near-surface epipelagic waters of the ocean, but the mechanisms underlying its exceptional success have not been fully elucidated. Here, we applied a metagenomic approach to explore microdiversity patterns by measuring the accumulation of synonymous and nonsynonymous mutations as well as homologous recombination in populations of SAR11 from different aquatic habitats (marine epipelagic, bathypelagic, and surface freshwater). The patterns of mutation accumulation and recombination were compared to those of other groups of representative marine microbes with multiple ecological strategies that share the same marine habitat, namely, Cyanobacteria (Prochlorococcus and Synechococcus), Archaea (“Candidatus Nitrosopelagicus” and Marine Group II Thalassoarchaea), and some heterotrophic marine bacteria (Alteromonas and Erythrobacter). SAR11 populations showed widespread recombination among distantly related members, preventing divergence leading to a genetically stable population. Moreover, their high intrapopulation sequence diversity with an enrichment in synonymous replacements supports the idea of a very ancient divergence and the coexistence of multiple different clones. However, other microbes analyzed seem to follow different evolutionary dynamics where processes of diversification driven by geographic and ecological instability produce a higher number of nonsynonymous replacements and lower intrapopulation sequence diversity. Together, these data shed light on some of the evolutionary and ecological processes that lead to the large genomic diversity in SAR11. Furthermore, this approach can be applied to other similar microbes that are difficult to culture in the laboratory, but abundant in nature, to investigate the underlying dynamics of their genomic evolution. IMPORTANCE As the most abundant bacteria in oceans, the Pelagibacterales order (here SAR11) plays an important role in the global carbon cycle, but the study of the evolutionary forces driving its evolution has lagged considerably due to the inherent difficulty of obtaining pure cultures. Multiple evolutionary models have been proposed to explain the diversification of distinct lineages within a population; however, the identification of many of these patterns in natural populations remains mostly enigmatic. We have used a metagenomic approach to explore microdiversity patterns in their natural habitats. Comparison with a collection of bacterial and archaeal groups from the same environments shows that SAR11 populations have a different evolutionary regime, where multiple genotypes coexist within the same population and remain stable over time. Widespread homologous recombination could be one of the main driving factors of this homogenization.
Collapse
|
12
|
Xu L, Sun C, Fang C, Oren A, Xu XW. Genomic-based taxonomic classification of the family Erythrobacteraceae. Int J Syst Evol Microbiol 2020; 70:4470-4495. [PMID: 32726199 PMCID: PMC7660246 DOI: 10.1099/ijsem.0.004293] [Citation(s) in RCA: 290] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 06/01/2020] [Indexed: 12/22/2022] Open
Abstract
The family Erythrobacteraceae, belonging to the order Sphingomonadales, class Alphaproteobacteria, is globally distributed in various environments. Currently, this family consist of seven genera: Altererythrobacter, Croceibacterium, Croceicoccus, Erythrobacter, Erythromicrobium, Porphyrobacter and Qipengyuania. As more species are identified, the taxonomic status of the family Erythrobacteraceae should be revised at the genomic level because of its polyphyletic nature evident from 16S rRNA gene sequence analysis. Phylogenomic reconstruction based on 288 single-copy orthologous clusters led to the identification of three separate clades. Pairwise comparisons of average nucleotide identity, average amino acid identity (AAI), percentage of conserved protein and evolutionary distance indicated that AAI and evolutionary distance had the highest correlation. Thresholds for genera boundaries were proposed as 70 % and 0.4 for AAI and evolutionary distance, respectively. Based on the phylo-genomic and genomic similarity analysis, the three clades were classified into 16 genera, including 11 novel ones, for which the names Alteraurantiacibacter, Altericroceibacterium, Alteriqipengyuania, Alteripontixanthobacter, Aurantiacibacter, Paraurantiacibacter, Parerythrobacter, Parapontixanthobacter, Pelagerythrobacter, Tsuneonella and Pontixanthobacter are proposed. We reclassified all species of Erythromicrobium and Porphyrobacter as species of Erythrobacter. This study is the first genomic-based study of the family Erythrobacteraceae, and will contribute to further insights into the evolution of this family.
Collapse
Affiliation(s)
- Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Cong Sun
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Chen Fang
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Oceanography, Hohai University, Nanjing 210000, PR China
| | - Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, PR China
| |
Collapse
|
13
|
Zhang J, Liu R, Xi S, Cai R, Zhang X, Sun C. A novel bacterial thiosulfate oxidation pathway provides a new clue about the formation of zero-valent sulfur in deep sea. ISME JOURNAL 2020; 14:2261-2274. [PMID: 32457501 PMCID: PMC7608252 DOI: 10.1038/s41396-020-0684-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 11/09/2022]
Abstract
Zero-valent sulfur (ZVS) has been shown to be a major sulfur intermediate in the deep-sea cold seep of the South China Sea based on our previous work, however, the microbial contribution to the formation of ZVS in cold seep has remained unclear. Here, we describe a novel thiosulfate oxidation pathway discovered in the deep-sea cold seep bacterium Erythrobacter flavus 21–3, which provides a new clue about the formation of ZVS. Electronic microscopy, energy-dispersive, and Raman spectra were used to confirm that E. flavus 21–3 effectively converts thiosulfate to ZVS. We next used a combined proteomic and genetic method to identify thiosulfate dehydrogenase (TsdA) and thiosulfohydrolase (SoxB) playing key roles in the conversion of thiosulfate to ZVS. Stoichiometric results of different sulfur intermediates further clarify the function of TsdA in converting thiosulfate to tetrathionate (−O3S–S–S–SO3−), SoxB in liberating sulfone from tetrathionate to form ZVS and sulfur dioxygenases (SdoA/SdoB) in oxidizing ZVS to sulfite under some conditions. Notably, homologs of TsdA, SoxB, and SdoA/SdoB widely exist across the bacteria including in Erythrobacter species derived from different environments. This strongly indicates that this novel thiosulfate oxidation pathway might be frequently used by microbes and plays an important role in the biogeochemical sulfur cycle in nature.
Collapse
Affiliation(s)
- Jing Zhang
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Rui Liu
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Shichuan Xi
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,CAS Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Ruining Cai
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Xin Zhang
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,CAS Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Chaomin Sun
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China. .,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
| |
Collapse
|
14
|
Roush D, Garcia-Pichel F. Succession and Colonization Dynamics of Endolithic Phototrophs within Intertidal Carbonates. Microorganisms 2020; 8:microorganisms8020214. [PMID: 32033409 PMCID: PMC7074784 DOI: 10.3390/microorganisms8020214] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/31/2020] [Accepted: 02/04/2020] [Indexed: 02/01/2023] Open
Abstract
Photosynthetic endolithic communities are common in shallow marine carbonates, contributing significantly to their bioerosion. Cyanobacteria are well known from these settings, where a few are euendoliths, actively boring into the virgin substrate. Recently, anoxygenic phototrophs were reported as significant inhabitants of endolithic communities, but it is unknown if they are euendoliths or simply colonize available pore spaces secondarily. To answer this and to establish the dynamics of colonization, nonporous travertine tiles were anchored onto intertidal beach rock in Isla de Mona, Puerto Rico, and developing endolithic communities were examined with time, both molecularly and with photopigment biomarkers. By 9 months, while cyanobacterial biomass and diversity reached levels indistinguishable from those of nearby climax communities, anoxygenic phototrophs remained marginal, suggesting that they are secondary colonizers. Early in the colonization, a novel group of cyanobacteria (unknown boring cluster, UBC) without cultivated representatives, emerged as the most common euendolith, but by 6 months, canonical euendoliths such as Plectonema (Leptolyngbya) sp., Mastigocoleus sp., and Pleurocapsalean clades displaced UBC in dominance. Later, the proportion of euendolithic cyanobacterial biomass decreased, as nonboring endoliths outcompeted pioneers within the already excavated substrate. Our findings demonstrate that endolithic cyanobacterial succession within hard carbonates is complex but can attain maturity within a year’s time.
Collapse
Affiliation(s)
- Daniel Roush
- School of Life Sciences, Arizona State University, Tempe, AZ 85282, USA;
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85282, USA
| | - Ferran Garcia-Pichel
- School of Life Sciences, Arizona State University, Tempe, AZ 85282, USA;
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85282, USA
- Correspondence:
| |
Collapse
|
15
|
Hauptmann AL, Paulová P, Castro-Mejía JL, Hansen LH, Sicheritz-Pontén T, Mulvad G, Nielsen DS. The microbial composition of dried fish prepared according to Greenlandic Inuit traditions and industrial counterparts. Food Microbiol 2020; 85:103305. [DOI: 10.1016/j.fm.2019.103305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/14/2019] [Accepted: 08/12/2019] [Indexed: 01/19/2023]
|
16
|
Lin W, Chen Q, Liu Y, Jiao N, Zheng Q. Characteristics of two myoviruses induced from the coastal photoheterotrophic bacterium Porphyrobacter sp. YT40. FEMS Microbiol Lett 2019; 366:5707402. [PMID: 31977007 DOI: 10.1093/femsle/fnaa009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 01/15/2020] [Indexed: 01/01/2023] Open
Abstract
In this study, we characterized two induced myoviruses from one marine photoheterotrophic bacterium Porphyrobacter sp. YT40 belonging to the Sphingomonadales family in Alphaproteobacteria. The genome sequence of prophage A is ∼36.9 kb with an average GC content of 67.1%, and its core or functional genes are homologous to Mu or Mu-like phages. Furthermore, induced viral particles from prophage A show a knob-like neck structure, which is only found in bacteriophage Mu. The genome size of prophage B is ∼36.8 kb with an average GC content of 65.3%. Prophage B contains a conserved gene cluster Q-P-O-N-M-L, which is unique in P2 phages. Induced viral particles from prophage B display an icosahedral head with a diameter of ∼55 nm and a 130 ± 5 nm long contractile tail. To our knowledge, this is the first report that characterizes the induced P2-like phage in marine Alphaproteobacteria. Phylogeny analyses suggest that these two types of prophages are commonly found in sequenced bacteria of the Sphingomonadales family. This study sheds light on the ongoing interaction between marine bacteria and phages, and improves our understanding of bacterial genomic plasticity and evolution.
Collapse
Affiliation(s)
- Wenxin Lin
- State Key Laboratory for Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China.,Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, People's Republic of China
| | - Qi Chen
- State Key Laboratory for Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China.,Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, People's Republic of China
| | - Yanting Liu
- State Key Laboratory for Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China.,Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, People's Republic of China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China.,Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, People's Republic of China
| | - Qiang Zheng
- State Key Laboratory for Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China.,Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, People's Republic of China
| |
Collapse
|
17
|
Tang T, Sun X, Dong Y, Liu Q. Erythrobacter aureus sp. nov., a plant growth-promoting bacterium isolated from sediment in the Yellow Sea, China. 3 Biotech 2019; 9:430. [PMID: 31696035 PMCID: PMC6823416 DOI: 10.1007/s13205-019-1958-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/14/2019] [Indexed: 01/03/2023] Open
Abstract
The application of plant growth-promoting (PGP) bacterium in agriculture is expanding rapidly in recent years. With the development of microbial technology, new bacterial species effective in promoting plant growth have been identified. In this study, a PGP bacterium was isolated from marine sediments of the Yellow Sea in China. The confrontation culture test and pot experiments showed that strain YH-07T inhibited the growth of Fusarium oxysporum f. sp. lycopersici (a plant pathogenic fungus), benefiting plant growth and reducing disease incidence of tomato wilt. We used polyphasic approaches including phenotypic, chemotaxonomic and phylogenetic information to determine its taxonomic status. In addition to profiling general features of the YH-07T genome, we identified genes related to PGP traits and genes involved in environmental stress tolerance. Metabolic assays showed that strain YH-07T could produce siderophores, solubilize phosphate, resist to salinity, and grow well within a wide range of temperature and pH, which is a promising PGP bacterium for future agricultural applications. These results provide evidence that strain YH-07T is a novel species of the genus Erythrobacter, for which the name Erythrobacter aureus sp. nov. is proposed. The type strain is YH-07T (= CGMCC 1.16784T = DSM 107319T).
Collapse
Affiliation(s)
- Tongtong Tang
- Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 Jiangsu Province China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xing Sun
- School of Biological Science and Food Engineering, Chuzhou University, Chuzhou, 239000 China
| | - Yuanhua Dong
- Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 Jiangsu Province China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qin Liu
- Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 Jiangsu Province China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| |
Collapse
|
18
|
Characteristics and Evolutionary Analysis of Photosynthetic Gene Clusters on Extrachromosomal Replicons: from Streamlined Plasmids to Chromids. mSystems 2019; 4:4/5/e00358-19. [PMID: 31506262 PMCID: PMC6739100 DOI: 10.1128/msystems.00358-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aerobic anoxygenic photoheterotrophic bacteria (AAPB) represent a bacteriochlorophyll a-containing functional group. Substantial evidence indicates that highly conserved photosynthetic gene clusters (PGCs) of AAPB can be transferred between species, genera, and even phyla. Furthermore, analysis of recently discovered PGCs carried by extrachromosomal replicons (exPGCs) suggests that extrachromosomal replicons (ECRs) play an important role in the transfer of PGCs. In this study, 13 Roseobacter clade genomes from seven genera that harbored exPGCs were used to analyze the characteristics and evolution of PGCs. The identification of plasmid-like and chromid-like ECRs among PGC-containing ECRs revealed two different functions: the spread of PGCs among strains and the maintenance of PGCs within genomes. Phylogenetic analyses indicated two independent origins of exPGCs, corresponding to PufC-containing and PufX-containing puf operons. Furthermore, the two different types of operons were observed within different strains of the same Tateyamaria and Jannaschia genera. The PufC-containing and PufX-containing operons were also differentially carried by chromosomes and ECRs in the strains, respectively, which provided clear evidence for ECR-mediated PGC transfer. Multiple recombination events of exPGCs were also observed, wherein the majority of exPGCs were inserted by replication modules at the same genomic positions. However, the exPGCs of the Jannaschia strains comprised superoperons without evidence of insertion and therefore likely represent an initial evolutionary stage where the PGC was translocated from chromosomes to ECRs without further combinations. Finally, a scenario of PGC gain and loss is proposed that specifically focuses on ECR-mediated exPGC transfer to explain the evolution and patchy distribution of AAPB within the Roseobacter clade.IMPORTANCE The evolution of photosynthesis was a significant event during the diversification of biological life. Aerobic anoxygenic photoheterotrophic bacteria (AAPB) share physiological characteristics with chemoheterotrophs and represent an important group associated with bacteriochlorophyll-dependent phototrophy in the environment. Here, characterization and evolutionary analyses were conducted for 13 bacterial strains that contained photosynthetic gene clusters (PGCs) carried by extrachromosomal replicons (ECRs) to shed light on the evolution of chlorophototrophy in bacteria. This report advances our understanding of the importance of ECRs in the transfer of PGCs within marine photoheterotrophic bacteria.
Collapse
|
19
|
Finding a common core microbiota in two Brazilian dairies through culture and DNA metabarcoding studies. Journal of Food Science and Technology 2019; 56:5326-5335. [PMID: 31749480 DOI: 10.1007/s13197-019-04003-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 07/25/2019] [Accepted: 08/01/2019] [Indexed: 01/30/2023]
Abstract
Dairy foods are complex ecosystems composed of microorganisms from different origins that can affect flavor and safety of final products. The objective of this paper is to assess the in-house microbiota of two Brazilian dairies and to discuss the possible implications of the taxa determined for food protection. In total, 27 samples from dairies were cultured in selective (Baird Parker, de Man, Rogosa and Sharpe) and non-selective (Brain Heart Infusion) media, and the isolates were identified by Sanger sequencing. Moreover, metagenomic DNA was directly extracted from samples and the structure of the bacterial community was determined by massive DNA sequencing followed by bioinformatics analyses. The results showed the majority of isolates belonged to the group of lactic acid bacteria, but Enterobacteriaceae, Staphylococcacceae, Bacillaceae, Pseudomonadaceae and Moraxellaceae were also detected. From the reads obtained in metataxonomics analyses, a heatmap was constructed and the top 20 OTUs (operational taxonomic units) were determined. Besides, 12 most prevalent bacterial taxa were assigned to the core microbiota of the dairies evaluated, which included Thiomonas thermosulfata, Alkalibacillus salilacus, Pseudomonas clemancea, Erythrobacter aquimans, Tetragenococcus doogicus, Macrococcus brunensis, Pseudomonas ludensis, Streptococcus dentinousetti, Serratia entomophila, Vagococcus teuberi, Lactococcus fujiensis and Tolumonas auensis. In conclusion, the results reveal the presence of bacteria that may be related to spoilage and also foodborne diseases, in microbial niches that also present rare taxa, highlighting the importance to consider culture-independent results to evaluate and improve food safety.
Collapse
|
20
|
Fiebig A, Varesio LM, Alejandro Navarreto X, Crosson S. Regulation of the Erythrobacter litoralis DSM 8509 general stress response by visible light. Mol Microbiol 2019; 112:442-460. [PMID: 31125464 DOI: 10.1111/mmi.14310] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2019] [Indexed: 01/23/2023]
Abstract
Extracytoplasmic function (ECF) sigma factors are environmentally responsive transcriptional regulators. In Alphaproteobacteria, σEcfG activates general stress response (GSR) transcription and protects cells from multiple stressors. A phosphorylation-dependent protein partner switching mechanism, involving HWE/HisKA_2-family histidine kinases, underlies σEcfG activation. The identity of these sensor kinases and the signals that regulate them remain largely uncharacterized. We have developed the aerobic anoxygenic photoheterotroph (AAP), Erythrobacter litoralis DSM 8509, as a comparative genetic model to investigate GSR. Using this system, we sought to define the role of visible light and a photosensory HWE kinase, LovK, in regulation of GSR transcription. We identified three HWE kinase genes that collectively control GSR: gsrK and lovK are activators, while gsrP is a repressor. In wild-type cells, GSR transcription is activated in the dark and nearly off in the light, and the opposing activities of gsrK and gsrP are sufficient to modulate GSR transcription in response to illumination. In the absence of gsrK and gsrP, lovK alone is sufficient to activate GSR transcription. lovK is a more robust activator in the dark, and light-dependent regulation by LovK requires that its N-terminal LOV domain be photochemically active. Our studies establish a role for visible light and an ensemble of HWE kinases in light-dependent regulation of GSR transcription in E. litoralis.
Collapse
Affiliation(s)
- Aretha Fiebig
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Lydia M Varesio
- The Committee on Microbiology, The University of Chicago, Chicago, IL, 60637, USA
| | | | - Sean Crosson
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.,The Committee on Microbiology, The University of Chicago, Chicago, IL, 60637, USA
| |
Collapse
|
21
|
Zorz J, Willis C, Comeau AM, Langille MGI, Johnson CL, Li WKW, LaRoche J. Drivers of Regional Bacterial Community Structure and Diversity in the Northwest Atlantic Ocean. Front Microbiol 2019; 10:281. [PMID: 30846975 PMCID: PMC6393369 DOI: 10.3389/fmicb.2019.00281] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 02/04/2019] [Indexed: 11/29/2022] Open
Abstract
The fundamental role of bacteria in global biogeochemical cycles warrants a thorough understanding of the factors controlling bacterial community structure. In this study, the integrated effect of seasonal differences and spatial distribution on bacterial community structure and diversity were investigated at the regional scale. We conducted a comprehensive bacterial survey, with 451 samples of the Scotian Shelf sector of the Northwest Atlantic Ocean during spring and fall of 2014 and 2016, to analyze the effects of physicochemical gradients on bacterial community structure. Throughout the region, Pelagibacteraceae and Rhodobacteraceae were the most common in the free-living fraction, while Flavobacteriia and Deltaproteobacteria were more abundant in the particle-associated fraction. Overall, there was strong covariation of the microbial community diversity from the two size fractions. This relationship existed despite the statistically significant difference in community structure between the free-living and particle-associated size fractions. In both size fractions, distribution patterns of bacterial taxa, and species within taxa, displayed temporal and spatial preferences. Distinct bacterial assemblages specific to season and depth in the water column were identified. These distinct assemblages, consistent for both 2014 and 2016, suggested replicable patterns in microbial communities for spring and fall in this region. Over all sites, temperature and oxygen values were highly correlated with community similarity, and salinity and oxygen values were the most strongly positively- and negatively correlated with alpha diversity, respectively. However, the strengths of these correlations depended on the depth and season sampled. The bathymetry of the Scotian Shelf, the abrupt shelf break to the Scotian Slope and the major ocean currents dominating in the region led to the formation of distinct on-shelf and off-shelf bacterial communities both in spring and fall. The highest species richness was observed at the shelf break, where water masses from the two major currents meet. Our study establishes the baseline for assessing future changes in the bacterial community of the Scotian Shelf waters, a rapidly changing sector of the Atlantic Ocean.
Collapse
Affiliation(s)
- Jackie Zorz
- Department of Biology, Dalhousie University, Halifax, NS, Canada.,Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Ciara Willis
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - André M Comeau
- CGEB-Integrated Microbiome Resource, Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Morgan G I Langille
- CGEB-Integrated Microbiome Resource, Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Catherine L Johnson
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS, Canada
| | - William K W Li
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| |
Collapse
|
22
|
Meziti A, Tsementzi D, Rodriguez-R LM, Hatt JK, Karayanni H, Kormas KA, Konstantinidis KT. Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient. ISME JOURNAL 2018; 13:767-779. [PMID: 30397261 DOI: 10.1038/s41396-018-0307-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 09/26/2018] [Accepted: 10/02/2018] [Indexed: 12/31/2022]
Abstract
Recent diversity studies have revealed that microbial communities of natural environments are dominated by species-like, sequence-discrete populations. However, how stable the sequence and gene-content diversity are within these populations and especially in highly dynamic lotic habitats remain unclear. Here we quantified the dynamics of intra-population diversity in samples spanning two years and five sites in the Kalamas River (Northwest Greece). A significant positive correlation was observed between higher intra-population sequence diversity and longer persistence over time, revealing that more diverse populations tended to represent more autochthonous (vs. allochthonous) community members. Assessment of intra-population gene-content changes caused by strain replacement or gene loss over time revealed different profiles with the majority of populations exhibiting gene-content changes close to 10% of the total genes, while one population exhibited ~21% change. The variable genes were enriched in hypothetical proteins and mobile elements, and thus, were probably functionally neutral or attributable to phage predation. A few notable exceptions to this pattern were also noted such as phototrophy-related proteins in summer vs. winter populations. Taken together, these results revealed that some freshwater genomes are remarkably dynamic, even across short time and spatial scales, and have implications for the bacterial species concept and microbial source tracking.
Collapse
Affiliation(s)
- Alexandra Meziti
- Department of Biological Applications and Technology, University of Ioannina, 45110, Ioannina, Greece.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia
| | - Despina Tsementzi
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia
| | - Luis M Rodriguez-R
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia
| | - Hera Karayanni
- Department of Biological Applications and Technology, University of Ioannina, 45110, Ioannina, Greece
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, 38446, Volos, Greece
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia. .,School of Biological Sciences, Georgia Institute of Technology, Ford Environmental Sciences & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia.
| |
Collapse
|
23
|
Xu L, Wu YH, Cheng H, Sun C, Han BN, Xu XW. Complete genome sequence of Erythrobacter seohaensis SW-135 T sheds light on the ecological role of the genus Erythrobacter for phosphorus cycle in the marine environment. Mar Genomics 2018; 40:21-24. [PMID: 32420878 DOI: 10.1016/j.margen.2018.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/01/2018] [Accepted: 03/01/2018] [Indexed: 10/17/2022]
Abstract
Erythrobacter seohaensis SW-135T was isolated from inter sediments collected from an intertidal zone of the Yellow Sea in Korea. The genome of E. seohaensis SW-135T was sequenced and comprised of one circular chromosome with the size of 2,942,673 bp and DNA G + C content of 61.7%. It was reported that E. seohaensis SW-135T was positive for alkaline phosphatase activity by enzymatic test. Genomic annotation indicated that the genome of E. seohaensis SW-135T had two alkaline phosphatase-encoding genes, phoD and phoX, which products can dephosphorylate phosphoesters to more bioavailable dissolved inorganic phosphorus for microorganisms in the phosphorus limited condition. Comparative genomic analysis of marine Erythrobacter strains revealed that phoD and phoX were widely distributed in these strains, indicating the genus Erythrobacter may play an important role in the marine phosphorus cycle. This study broadens our understandings about ecological roles of the genus Erythrobacter participating in the marine phosphorus cycle, which is rarely investigated previously.
Collapse
Affiliation(s)
- Lin Xu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Yue-Hong Wu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Hong Cheng
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Cong Sun
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Bing-Nan Han
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China.
| |
Collapse
|
24
|
Imhoff JF, Rahn T, Künzel S, Neulinger SC. Photosynthesis Is Widely Distributed among Proteobacteria as Demonstrated by the Phylogeny of PufLM Reaction Center Proteins. Front Microbiol 2018; 8:2679. [PMID: 29472894 PMCID: PMC5810265 DOI: 10.3389/fmicb.2017.02679] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 12/22/2017] [Indexed: 12/01/2022] Open
Abstract
Two different photosystems for performing bacteriochlorophyll-mediated photosynthetic energy conversion are employed in different bacterial phyla. Those bacteria employing a photosystem II type of photosynthetic apparatus include the phototrophic purple bacteria (Proteobacteria), Gemmatimonas and Chloroflexus with their photosynthetic relatives. The proteins of the photosynthetic reaction center PufL and PufM are essential components and are common to all bacteria with a type-II photosynthetic apparatus, including the anaerobic as well as the aerobic phototrophic Proteobacteria. Therefore, PufL and PufM proteins and their genes are perfect tools to evaluate the phylogeny of the photosynthetic apparatus and to study the diversity of the bacteria employing this photosystem in nature. Almost complete pufLM gene sequences and the derived protein sequences from 152 type strains and 45 additional strains of phototrophic Proteobacteria employing photosystem II were compared. The results give interesting and comprehensive insights into the phylogeny of the photosynthetic apparatus and clearly define Chromatiales, Rhodobacterales, Sphingomonadales as major groups distinct from other Alphaproteobacteria, from Betaproteobacteria and from Caulobacterales (Brevundimonas subvibrioides). A special relationship exists between the PufLM sequences of those bacteria employing bacteriochlorophyll b instead of bacteriochlorophyll a. A clear phylogenetic association of aerobic phototrophic purple bacteria to anaerobic purple bacteria according to their PufLM sequences is demonstrated indicating multiple evolutionary lines from anaerobic to aerobic phototrophic purple bacteria. The impact of pufLM gene sequences for studies on the environmental diversity of phototrophic bacteria is discussed and the possibility of their identification on the species level in environmental samples is pointed out.
Collapse
Affiliation(s)
- Johannes F Imhoff
- Research Unit Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Tanja Rahn
- Research Unit Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | | |
Collapse
|
25
|
Isolation and characterization of the first phage infecting ecologically important marine bacteria Erythrobacter. Virol J 2017; 14:104. [PMID: 28592325 PMCID: PMC5463345 DOI: 10.1186/s12985-017-0773-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 06/01/2017] [Indexed: 11/24/2022] Open
Abstract
Background Erythrobacter comprises a widespread and ecologically significant genus of marine bacteria. However, no phage infecting Erythrobacter spp. has been reported to date. This study describes the isolation and characterization of phage vB_EliS-R6L from Erythrobacter. Methods Standard virus enrichment and double-layer agar methods were used to isolate and characterize the phage. Morphology was observed by transmission electron microscopy, and a one-step growth curve assay was performed. The phage genome was sequenced using the Illumina Miseq platform and annotated using standard bioinformatics tools. Phylogenetic analyses were performed based on the deduced amino acid sequences of terminase, endolysin, portal protein, and major capsid protein, and genome recruitment analysis was conducted using Jiulong River Estuary Virome, Pacific Ocean Virome and Global Ocean Survey databases. Results A novel phage, vB_EliS-R6L, from coastal waters of Xiamen, China, was isolated and found to infect the marine bacterium Erythrobacter litoralis DSM 8509. Morphological observation and genome analysis revealed that phage vB_EliS-R6L is a siphovirus with a 65.7-kb genome that encodes 108 putative gene products. The phage exhibits growth at a wide range of temperature and pH conditions. Genes encoding five methylase-related proteins were found in the genome, and recognition site predictions suggested its resistance to restriction-modification host systems. Genomic comparisons and phylogenetic analyses indicate that phage vB_EliS-R6L is distinct from other known phages. Metagenomic recruitment analysis revealed that vB_EliS-R6L-like phages are widespread in marine environments, with likely distribution in coastal waters. Conclusions Isolation of the first Erythrobacter phage (vB_EliS-R6L) will contribute to our understanding of host-phage interactions, the ecology of marine Erythrobacter and viral metagenome annotation efforts.
Collapse
|
26
|
Viswanathan V, Narjala A, Ravichandran A, Jayaprasad S, Siddaramappa S. Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales. Genome Biol Evol 2017; 9:646-658. [PMID: 28201618 PMCID: PMC5381585 DOI: 10.1093/gbe/evx024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/11/2017] [Accepted: 02/04/2017] [Indexed: 12/20/2022] Open
Abstract
The order Sphingomonadales, containing the families Erythrobacteraceae and Sphingomonadaceae, is a relatively less well-studied phylogenetic branch within the class Alphaproteobacteria. Prophage elements are present in most bacterial genomes and are important determinants of adaptive evolution. An “intact” prophage was predicted within the genome of Sphingomonas hengshuiensis strain WHSC-8 and was designated Prophage IWHSC-8. Loci homologous to the region containing the first 22 open reading frames (ORFs) of Prophage IWHSC-8 were discovered among the genomes of numerous Sphingomonadales. In 17 genomes, the homologous loci were co-located with an ORF encoding a putative superoxide dismutase. Several other lines of molecular evidence implied that these homologous loci represent an ancient temperate bacteriophage integration, and this horizontal transfer event pre-dated niche-based speciation within the order Sphingomonadales. The “stabilization” of prophages in the genomes of their hosts is an indicator of “fitness” conferred by these elements and natural selection. Among the various ORFs predicted within the conserved prophages, an ORF encoding a putative proline-rich outer membrane protein A was consistently present among the genomes of many Sphingomonadales. Furthermore, the conserved prophages in six Sphingomonas sp. contained an ORF encoding a putative spermidine synthase. It is possible that one or more of these ORFs bestow selective fitness, and thus the prophages continue to be vertically transferred within the host strains. Although conserved prophages have been identified previously among closely related genera and species, this is the first systematic and detailed description of orthologous prophages at the level of an order that contains two diverse families and many pigmented species.
Collapse
Affiliation(s)
| | - Anushree Narjala
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru 560100, Karnataka, India
| | - Aravind Ravichandran
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru 560100, Karnataka, India
| | - Suvratha Jayaprasad
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru 560100, Karnataka, India
| | - Shivakumara Siddaramappa
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru 560100, Karnataka, India
| |
Collapse
|