1
|
Wei Y, Wang SG, Xia PF. Blue valorization of lignin-derived monomers via reprogramming marine bacterium Roseovarius nubinhibens. Appl Environ Microbiol 2024:e0089024. [PMID: 38940564 DOI: 10.1128/aem.00890-24] [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: 05/06/2024] [Accepted: 06/07/2024] [Indexed: 06/29/2024] Open
Abstract
Biological valorization of lignin, the second most abundant biopolymer on Earth, is an indispensable sector to build a circular economy and net-zero future. However, lignin is recalcitrant to bioupcycling, demanding innovative solutions. We report here the biological valorization of lignin-derived aromatic carbon to value-added chemicals without requesting extra organic carbon and freshwater via reprogramming the marine Roseobacter clade bacterium Roseovarius nubinhibens. We discovered the unusual advantages of this strain for the oxidation of lignin monomers and implemented a CRISPR interference (CRISPRi) system with the lacI-Ptrc inducible module, nuclease-deactivated Cas9, and programmable gRNAs. This is the first CRISPR-based regulatory system in R. nubinhibens, enabling precise and efficient repression of genes of interest. By deploying the customized CRISPRi, we reprogrammed the carbon flux from a lignin monomer, 4-hydroxybenzoate, to achieve the maximum production of protocatechuate, a pharmaceutical compound with antibacterial, antioxidant, and anticancer properties, with minimal carbon to maintain cell growth and drive biocatalysis. As a result, we achieved a 4.89-fold increase in protocatechuate yield with a dual-targeting CRISPRi system, and the system was demonstrated with real seawater. Our work underscores the power of CRISPRi in exploiting novel microbial chassis and will accelerate the development of marine synthetic biology. Meanwhile, the introduction of a new-to-the-field lineage of marine bacteria unveils the potential of blue biotechnology leveraging resources from the ocean.IMPORTANCEOne often overlooked sector in carbon-conservative biotechnology is the water resource that sustains these enabling technologies. Similar to the "food-versus-fuel" debate, the competition of freshwater between human demands and bioproduction is another controversial issue, especially under global water scarcity. Here, we bring a new-to-the-field lineage of marine bacteria with unusual advantages to the stage of engineering biology for simultaneous carbon and water conservation. We report the valorization of lignin monomers to pharmaceutical compounds without requesting extra organic substrate (e.g., glucose) or freshwater by reprogramming the marine bacterium Roseovarius nubinhibens with a multiplex CRISPR interference system. Beyond the blue lignin valorization, we present a proof-of-principle of leveraging marine bacteria and engineering biology for a sustainable future.
Collapse
Affiliation(s)
- Ying Wei
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Shu-Guang Wang
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
- Sino-French Research Institute for Ecology and Environment, Shandong University, Qingdao, China
- Weihai Research Institute of Industrial Technology, Shandong University, Weihai, China
| | - Peng-Fei Xia
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
| |
Collapse
|
2
|
Wei Y, Feng LJ, Yuan XZ, Wang SG, Xia PF. Developing a Base Editing System for Marine Roseobacter Clade Bacteria. ACS Synth Biol 2023. [PMID: 37436915 DOI: 10.1021/acssynbio.3c00259] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
The Roseobacter clade bacteria are of great significance in marine ecology and biogeochemical cycles, and they are potential microbial chassis for marine synthetic biology due to their versatile metabolic capabilities. Here, we adapted a CRISPR-Cas-based system, base editing, with the combination of nuclease-deactivated Cas9 and deaminase for Roseobacter clade bacteria. Taking the model roseobacter Roseovarius nubinhibens as an example, we achieved precise and efficient genome editing at single-nucleotide resolution without generating double-strand breaks or requesting donor DNAs. Since R. nubinhibens can metabolize aromatic compounds, we interrogated the key genes in the β-ketoadipate pathway with our base editing system via the introduction of premature STOP codons. The essentiality of these genes was demonstrated, and for the first time, we determined PcaQ as a transcription activator experimentally. This is the first report of CRISPR-Cas-based genome editing in the entire clade of Roseobacter bacteria. We believe that our work provides a paradigm for interrogating marine ecology and biogeochemistry with direct genotype-and-phenotype linkages and potentially opens a new avenue for the synthetic biology of marine Roseobacter bacteria.
Collapse
Affiliation(s)
- Ying Wei
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Li-Juan Feng
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Xian-Zheng Yuan
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
- Sino-French Research Institute for Ecology and Environment, Shandong University, Qingdao 266237, China
| | - Shu-Guang Wang
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
- Sino-French Research Institute for Ecology and Environment, Shandong University, Qingdao 266237, China
| | - Peng-Fei Xia
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| |
Collapse
|
3
|
Matsui Y, Nagai M, Ying BW. Growth rate-associated transcriptome reorganization in response to genomic, environmental, and evolutionary interruptions. Front Microbiol 2023; 14:1145673. [PMID: 37032868 PMCID: PMC10073601 DOI: 10.3389/fmicb.2023.1145673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/02/2023] [Indexed: 04/11/2023] Open
Abstract
The genomic, environmental, and evolutionary interruptions caused the changes in bacterial growth, which were stringently associated with changes in gene expression. The growth and gene expression changes remained unclear in response to these interruptions that occurred combinative. As a pilot study, whether and how bacterial growth was affected by the individual and dual interruptions of genome reduction, environmental stress, and adaptive evolution were investigated. Growth assay showed that the presence of the environmental stressors, i.e., threonine and chloramphenicol, significantly decreased the growth rate of the wild-type Escherichia coli, whereas not that of the reduced genome. It indicated a canceling effect in bacterial growth due to the dual interruption of the genomic and environmental changes. Experimental evolution of the reduced genome released the canceling effect by improving growth fitness. Intriguingly, the transcriptome architecture maintained a homeostatic chromosomal periodicity regardless of the genomic, environmental, and evolutionary interruptions. Negative epistasis in transcriptome reorganization was commonly observed in response to the dual interruptions, which might contribute to the canceling effect. It was supported by the changes in the numbers of differentially expressed genes (DEGs) and the enriched regulons and functions. Gene network analysis newly constructed 11 gene modules, one out of which was correlated to the growth rate. Enrichment of DEGs in these modules successfully categorized them into three types, i.e., conserved, responsive, and epistatic. Taken together, homeostasis in transcriptome architecture was essential to being alive, and it might be attributed to the negative epistasis in transcriptome reorganization and the functional differentiation in gene modules. The present study directly connected bacterial growth fitness with transcriptome reorganization and provided a global view of how microorganisms responded to genomic, environmental, and evolutionary interruptions for survival from wild nature.
Collapse
|
4
|
Coastal Transient Niches Shape the Microdiversity Pattern of a Bacterioplankton Population with Reduced Genomes. mBio 2022; 13:e0057122. [PMID: 35880883 PMCID: PMC9426536 DOI: 10.1128/mbio.00571-22] [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] [Indexed: 12/01/2022] Open
Abstract
Globally dominant marine bacterioplankton lineages are often limited in metabolic versatility, owing to their extensive genome reductions, and thus cannot take advantage of transient nutrient patches. It is therefore perplexing how the nutrient-poor bulk seawater sustains the pelagic streamlined lineages, each containing numerous populations. Here, we sequenced the genomes of 33 isolates of the recently discovered CHUG lineage (~2.6 Mbp), which have some of the smallest genomes in the globally abundant Roseobacter group (commonly over 4 Mbp). These genome-reduced bacteria were isolated from a transient habitat: seawater surrounding the brown alga, Sargassum hemiphyllum. Population genomic analyses showed that: (i) these isolates, despite sharing identical 16S rRNA genes, were differentiated into several genetically isolated populations through successive speciation events; (ii) only the first speciation event led to the genetic separation of both core and accessory genomes; and (iii) populations resulting from this event are differentiated at many loci involved in carbon utilization and oxygen respiration, corroborated by BiOLOG phenotype microarray assays and oxygen uptake kinetics experiments, respectively. These differentiated traits match well with the dynamic nature of the macroalgal seawater, in which the quantity and quality of carbon sources and the concentration of oxygen likely vary spatially and temporally, though other habitats, like fresh organic aggregates, cannot be ruled out. Our study implies that transient habitats in the overall nutrient-poor ocean can shape the microdiversity and population structure of genome-reduced bacterioplankton lineages.
Collapse
|
5
|
Amenu SG, Wei N, Wu L, Oyebanji O, Hu G, Zhou Y, Wang Q. Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution. BMC PLANT BIOLOGY 2022; 22:88. [PMID: 35219317 PMCID: PMC8881883 DOI: 10.1186/s12870-022-03480-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 02/15/2022] [Indexed: 05/07/2023]
Abstract
BACKGROUND The large and diverse Coffeeae alliance clade of subfamily Ixoroideae (Rubiaceae) consists of 10 tribes, > 90 genera, and > 2000 species. Previous molecular phylogenetics using limited numbers of markers were often unable to fully resolve the phylogenetic relationships at tribal and generic levels. Also, the structural variations of plastomes (PSVs) within the Coffeeae alliance tribes have been poorly investigated in previous studies. To fully understand the phylogenetic relationships and PSVs within the clade, highly reliable and sufficient sampling with superior next-generation analysis techniques is required. In this study, 71 plastomes (40 newly sequenced and assembled and the rest from the GenBank) were comparatively analyzed to decipher the PSVs and resolve the phylogenetic relationships of the Coffeeae alliance using four molecular data matrices. RESULTS All plastomes are typically quadripartite with the size ranging from 153,055 to 155,908 bp and contained 111 unique genes. The inverted repeat (IR) regions experienced multiple contraction and expansion; five repeat types were detected but the most abundant was SSR. The size of the Coffeeae alliance clade plastomes and its elements are affected by the IR boundary shifts and the repeat types. However, the emerging PSVs had no taxonomic and phylogenetic implications. Eight highly divergent regions were identified within the plastome regions ndhF, ccsA, ndhD, ndhA, ndhH, ycf1, rps16-trnQ-UUG, and psbM-trnD. These highly variable regions may be potential molecular markers for further species delimitation and population genetic analyses for the clade. Our plastome phylogenomic analyses yielded a well-resolved phylogeny tree with well-support at the tribal and generic levels within the Coffeeae alliance. CONCLUSIONS Plastome data could be indispensable in resolving the phylogenetic relationships of the Coffeeae alliance tribes. Therefore, this study provides deep insights into the PSVs and phylogenetic relationships of the Coffeeae alliance and the Rubiaceae family as a whole.
Collapse
Affiliation(s)
- Sara Getachew Amenu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Neng Wei
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Lei Wu
- College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, Hunan, People's Republic of China
| | - Oyetola Oyebanji
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, People's Republic of China
- Department of Botany, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Guangwan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China
- Sino-Africa Joint Research Center (SAJOREC), Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China
| | - Yadong Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
- Sino-Africa Joint Research Center (SAJOREC), Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
| | - Qingfeng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
- Sino-Africa Joint Research Center (SAJOREC), Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
| |
Collapse
|
6
|
Kurokawa M, Nishimura I, Ying BW. Experimental Evolution Expands the Breadth of Adaptation to an Environmental Gradient Correlated With Genome Reduction. Front Microbiol 2022; 13:826894. [PMID: 35154062 PMCID: PMC8826082 DOI: 10.3389/fmicb.2022.826894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/06/2022] [Indexed: 11/28/2022] Open
Abstract
Whether and how adaptive evolution adjusts the breadth of adaptation in coordination with the genome are essential issues for connecting evolution with ecology. To address these questions, experimental evolution in five Escherichia coli strains carrying either the wild-type genome or a reduced genome was performed in a defined minimal medium (C0). The ancestral and evolved populations were subsequently subjected to fitness and chemical niche analyses across an environmental gradient with 29 combinations of eight chemical components of the minimal medium. The results showed that adaptation was achieved not only specific to the evolutionary condition (C0), but also generally, to the environmental gradient; that is, the breadth of adaptation to the eight chemical niches was expanded. The magnitudes of the adaptive improvement and the breadth increase were both correlated with genome reduction and were highly significant in two out of eight niches (i.e., glucose and sulfate). The direct adaptation-induced correlated adaptation to the environmental gradient was determined by only a few genome mutations. An additive increase in fitness associated with the stepwise fixation of mutations was consistently observed in the reduced genomes. In summary, this preliminary survey demonstrated that evolution finely tuned the breadth of adaptation correlated with genome reduction.
Collapse
Affiliation(s)
- Masaomi Kurokawa
- School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Issei Nishimura
- School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Bei-Wen Ying
- School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| |
Collapse
|
7
|
Luo D, Wang X, Feng X, Tian M, Wang S, Tang SL, Ang P, Yan A, Luo H. Population differentiation of Rhodobacteraceae along with coral compartments. THE ISME JOURNAL 2021; 15:3286-3302. [PMID: 34017056 PMCID: PMC8528864 DOI: 10.1038/s41396-021-01009-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 02/04/2023]
Abstract
Coral mucus, tissue, and skeleton harbor compositionally different microbiota, but how these coral compartments shape the microbial evolution remains unexplored. Here, we sampled bacteria inhabiting a prevalent coral species Platygyra acuta and sequenced genomes of 234 isolates comprising two populations in Rhodobacteraceae, an alphaproteobacterial lineage representing a significant but variable proportion (5-50%) of the coral microbiota. The Ruegeria population (20 genomes) contains three clades represented by eight, six, and six isolates predominantly sampled from the skeleton (outgroup), mucus (clade-M), and skeleton (clade-S), respectively. The clade-M possesses functions involved in the utilization of coral osmolytes abundant in the mucus (e.g., methylamines, DMSP, taurine, and L-proline), whereas the clade-S uniquely harbors traits that may promote adaptation to the low-energy and diurnally anoxic skeleton (e.g., sulfur oxidation and swimming motility). These between-clade genetic differences were largely supported by physiological assays. Expanded analyses by including genomes of 24 related isolates (including seven new genomes) from other marine environments suggest that clade-M and clade-S may have diversified in non-coral habitats, but they also consolidated a key role of distinct coral compartments in diversifying many of the above-mentioned traits. The unassigned Rhodobacteraceae population (214 genomes) varies only at a few dozen nucleotide sites across the whole genomes, but the number of between-compartment migration events predicted by the Slatkin-Maddison test supported that dispersal limitation between coral compartments is another key mechanism diversifying microbial populations. Collectively, our results suggest that different coral compartments represent ecologically distinct and microgeographically separate habitats that drive the evolution of the coral microbiota.
Collapse
Affiliation(s)
- Danli Luo
- grid.10784.3a0000 0004 1937 0482Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR ,grid.10784.3a0000 0004 1937 0482Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Xiaojun Wang
- grid.10784.3a0000 0004 1937 0482Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR ,grid.10784.3a0000 0004 1937 0482Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Xiaoyuan Feng
- grid.10784.3a0000 0004 1937 0482Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR ,grid.10784.3a0000 0004 1937 0482Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Mengdan Tian
- grid.194645.b0000000121742757School of Biological Sciences, The University of Hong Kong, Shatin, Hong Kong SAR
| | - Sishuo Wang
- grid.10784.3a0000 0004 1937 0482Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Sen-Lin Tang
- grid.506939.0Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Put Ang
- grid.10784.3a0000 0004 1937 0482Institute of Space and Earth Information Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Aixin Yan
- grid.194645.b0000000121742757School of Biological Sciences, The University of Hong Kong, Shatin, Hong Kong SAR
| | - Haiwei Luo
- grid.10784.3a0000 0004 1937 0482Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR ,grid.10784.3a0000 0004 1937 0482Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| |
Collapse
|
8
|
Abdullah, Mehmood F, Heidari P, Rahim A, Ahmed I, Poczai P. Pseudogenization of the chloroplast threonine (trnT-GGU) gene in the sunflower family (Asteraceae). Sci Rep 2021; 11:21122. [PMID: 34702873 PMCID: PMC8548347 DOI: 10.1038/s41598-021-00510-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 10/05/2021] [Indexed: 01/22/2023] Open
Abstract
The chloroplast genome evolves through the course of evolution. Various types of mutational events are found within the chloroplast genome, including insertions-deletions (InDels), substitutions, inversions, gene rearrangement, and pseudogenization of genes. The pseudogenization of the chloroplast threonine (trnT-GGU) gene was previously reported in Cryptomeria japonica (Cupressaceae), Pelargonium × hortorum (Geraniaceae), and Anaphalis sinica and Leontopodium leiolepis of the tribe Gnaphalieae (Asteroideae, Asteraceae). Here, we performed a broad analysis of the trnT-GGU gene among the species of 13 subfamilies of Asteraceae and found this gene as a pseudogene in core Asteraceae (Gymnarrhenoideae, Cichorioideae, Corymbioideae, and Asteroideae), which was linked to an insertion event within the 5' acceptor stem and is not associated with ecological factors such as habit, habitat, and geographical distribution of the species. The pseudogenization of trnT-GGU was not predicted in codon usage, indicating that the superwobbling phenomenon occurs in core Asteraceae in which a single transfer RNA (trnT-UGU) decodes all four codons of threonine. To the best of our knowledge, this is the first evidence of a complete clade of a plant species using the superwobbling phenomenon for translation.
Collapse
Affiliation(s)
- Abdullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Furrukh Mehmood
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Parviz Heidari
- Faculty of Agriculture, Shahrood University of Technology, 3619995161, Shahrood, Iran
| | - Abdur Rahim
- Government Degree College Nowshera, Abdul Wali Khan University, Mardan, KPK, Pakistan
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, 45710, Pakistan
| | - Peter Poczai
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, 00014, Helsinki, Finland.
- Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, 00065, Helsinki, Finland.
| |
Collapse
|
9
|
Feng X, Chu X, Qian Y, Henson MW, Lanclos VC, Qin F, Barnes S, Zhao Y, Thrash JC, Luo H. Mechanisms driving genome reduction of a novel Roseobacter lineage. ISME JOURNAL 2021; 15:3576-3586. [PMID: 34145391 DOI: 10.1038/s41396-021-01036-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 01/21/2023]
Abstract
Members of the marine Roseobacter group are key players in the global carbon and sulfur cycles. While over 300 species have been described, only 2% possess reduced genomes (mostly 3-3.5 Mbp) compared to an average roseobacter (>4 Mbp). These taxonomic minorities are phylogenetically diverse but form a Pelagic Roseobacter Cluster (PRC) at the genome content level. Here, we cultivated eight isolates constituting a novel Roseobacter lineage which we named 'CHUG'. Metagenomic and metatranscriptomic read recruitment analyses showed that CHUG members are globally distributed and active in marine pelagic environments. CHUG members possess some of the smallest genomes (~2.6 Mb) among all known roseobacters, but they do not exhibit canonical features of typical bacterioplankton lineages theorized to have undergone genome streamlining processes, like higher coding density, fewer paralogues and rarer pseudogenes. While CHUG members form a genome content cluster with traditional PRC members, they show important differences. Unlike other PRC members, neither the relative abundances of CHUG members nor their relative gene expression levels are correlated with chlorophyll a concentration across the global samples. CHUG members cannot utilize most phytoplankton-derived metabolites or synthesize vitamin B12, a key metabolite mediating the roseobacter-phytoplankton interactions. This combination of features is evidence for the hypothesis that CHUG members may have evolved a free-living lifestyle decoupled from phytoplankton. This ecological transition was accompanied by the loss of signature genes involved in roseobacter-phytoplankton symbiosis, suggesting that relaxation of purifying selection owing to lifestyle shift is likely an important driver of genome reduction in CHUG.
Collapse
Affiliation(s)
- Xiaoyuan Feng
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, SAR, Hong Kong.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Xiao Chu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, SAR, Hong Kong
| | - Yang Qian
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, SAR, Hong Kong
| | - Michael W Henson
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.,Department of Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - V Celeste Lanclos
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Fang Qin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Shelby Barnes
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, SAR, Hong Kong. .,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.
| |
Collapse
|