1
|
Xie J, Yin D, Ou J, Lu B, Liao S, Yang D, Zhang H, Shen N. A new strain of Rhodococcus indonesiensis T22.7.1 T and its functional potential for deacetylation of chitin and chitooligsaccharides. Front Microbiol 2024; 15:1427143. [PMID: 39113839 PMCID: PMC11303147 DOI: 10.3389/fmicb.2024.1427143] [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: 05/03/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024] Open
Abstract
Introduction Chitin, abundant in marine environments, presents significant challenges in terms of transformation and utilization. A strain, T22.7.1T, with notable chitin deacetylation capabilities, was isolated from the rhizosphere of Acanthus ebracteatus in the North Sea of China. Comparative 16S rDNA sequence analysis showed that the new isolate had the highest sequence similarity (99.79%) with Rhodococcus indonesiensis CSLK01-03T, followed by R. ruber DSM 43338T, R. electrodiphilus JC435T, and R. aetherivorans 10bc312T (98.97%, 98.81%, and 98.83%, respectively). Subsequent genome sequencing and phylogenetic analysis confirmed that strain T22.7.1T belongs to the R. indonesiensis species. However, additional taxonomic characterization identified strain T22.7.1T as a novel type strain of R. indonesiensis distinct from CSLK01-03T. Methods This study refines the taxonomic description of R. indonesiensis and investigates its application in converting chitin into chitosan. The chitin deacetylase (RiCDA) activity of strain T22.7.1T was optimized, and the enzyme was isolated and purified from the fermentation products. Results Through optimization, the RiCDA activity of strain T22.7.1T reached 287.02 U/mL, which is 34.88 times greater than the original enzyme's activity (8.0 U/mL). The natural CDA enzyme was purified with a purification factor of 31.83, and the specific activity of the enzyme solution reached 1200.33 U/mg. RiCDA exhibited good pH and temperature adaptability and stability, along with a wide range of substrate adaptabilities, effectively deacetylating chitin, chitooligosaccharides, N-acetylglucosamine, and other substrates. Discussion Product analysis revealed that RiCDA treatment increased the deacetylation degree (DD) of natural chitin to 83%, surpassing that of commercial chitosan. Therefore, RiCDA demonstrates significant potential as an efficient deacetylation tool for natural chitin and chitooligosaccharides, highlighting its applicability in the biorefining of natural polysaccharides.
Collapse
Affiliation(s)
- Junjie Xie
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Doudou Yin
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Junchao Ou
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Bo Lu
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, China
| | - Siming Liao
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, China
| | - Dengfeng Yang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, China
| | - Hongyan Zhang
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Naikun Shen
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| |
Collapse
|
2
|
Younker IT, Molnar N, Scorza K, Weed R, Light SH, Pfister CA. Bacteria on the foundational kelp in kelp forest ecosystems: Insights from culturing, whole genome sequencing and metabolic assays. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13270. [PMID: 38778582 PMCID: PMC11112141 DOI: 10.1111/1758-2229.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 04/06/2024] [Indexed: 05/25/2024]
Abstract
In coastal marine ecosystems, kelp forests serve as a vital habitat for numerous species and significantly influence local nutrient cycles. Bull kelp, or Nereocystis luetkeana, is a foundational species in the iconic kelp forests of the northeast Pacific Ocean and harbours a complex microbial community with potential implications for kelp health. Here, we report the isolation and functional characterisation of 16 Nereocystis-associated bacterial species, comprising 13 Gammaproteobacteria, 2 Flavobacteriia and 1 Actinomycetia. Genome analyses of these isolates highlight metabolisms potentially beneficial to the host, such as B vitamin synthesis and nitrogen retention. Assays revealed that kelp-associated bacteria thrive on amino acids found in high concentrations in the ocean and in the kelp (glutamine and asparagine), generating ammonium that may facilitate host nitrogen acquisition. Multiple isolates have genes indicative of interactions with key elemental cycles in the ocean, including carbon, nitrogen and sulphur. We thus report a collection of kelp-associated microbial isolates that provide functional insight for the future study of kelp-microbe interactions.
Collapse
Affiliation(s)
- Isaac T. Younker
- Committee on MicrobiologyThe University of ChicagoChicagoIllinoisUSA
| | - Nichos Molnar
- The CollegeThe University of ChicagoChicagoIllinoisUSA
| | - Kaylie Scorza
- The CollegeThe University of ChicagoChicagoIllinoisUSA
| | - Roo Weed
- The Graduate Program in Biophysical SciencesThe University of ChicagoChicagoIllinoisUSA
| | - Samuel H. Light
- Department of MicrobiologyThe University of ChicagoChicagoIllinoisUSA
| | | |
Collapse
|
3
|
Deng TH, Zhang Y, Zhang WW, Su Y, Gao JW, Ying JJ, Xu L, Xia XM, Sun C. Marinobacter albus sp. nov., Isolated from Sand Sediment in a Coastal Intertidal Zone. Curr Microbiol 2024; 81:138. [PMID: 38609554 DOI: 10.1007/s00284-024-03676-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 03/24/2024] [Indexed: 04/14/2024]
Abstract
A Gram-stain-negative bacterium with a rod-to-ovoid shape, named strain M216T, was isolated from sand sediment from the coastal intertidal zone of Huludao, Liaoning Province, China. Growth was observed at 8-40 °C (optimal, 30 °C), pH 5.5-9.5 (optimal, pH 6.5) and 0.5-14.0% (w/v) NaCl (optimal, 6%). Strain M216T possessed ubiquinone-9 as its sole respiratory quinone and phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, one unidentified aminophosphoglycolipid, one unidentified aminophospholipid, two unidentified phosphoglycolipids, three unidentified phospholipids and three unidentified glycolipids as the main polar lipids. C12:0, C16:0, C12:0 3-OH, C16:1 ω9c, C18:1 ω9c and summed features 3 (C16:1 ω7c and/or C16:1 ω6c) were the major fatty acids (> 5%). The 16S rRNA gene sequence of strain M216T exhibited high similarity to those of 'Marinobacter arenosus' CAU 1620T and Marinobacter adhaerens HP15T (99.3% and 98.5%, respectively) and less than 98.5% similarity to those of the other type strains. The ANI and dDDH values between the strain M216T and 'Marinobacter arenosus' CAU 1620T were 87.4% and 33.3%, respectively; these values were the highest among the other type strains but lower than the species threshold. The G+C content of strain M216T was 58.3%. Genomic analysis revealed that strain M216T harbors the major CAZymes of GH13, GH23, GH73, and PL5, which are responsible for polysaccharide degradation and the potential ability to reduce nitrate to ammonia. Through phenotypic, genotypic, and chemotaxonomic analyses, we proposed the name Marinobacter albus sp. nov., a novel species in the genus Marinobacter, with its type strain M216T (= MCCC 1K08600T = KCTC 82894T).
Collapse
Affiliation(s)
- Tai-Hang Deng
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd., Shaoxing, 312369, People's Republic of China
| | - Yu Zhang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd., Shaoxing, 312369, People's Republic of China
| | - Wen-Wu Zhang
- Trend Biotech Co., Ltd., Hangzhou, 311121, People's Republic of China
| | - Yue Su
- Trend Biotech Co., Ltd., Hangzhou, 311121, People's Republic of China
| | - Jia-Wei Gao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd., Shaoxing, 312369, People's Republic of China
| | - Jun-Jie Ying
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd., Shaoxing, 312369, People's Republic of China
| | - Lin Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd., Shaoxing, 312369, People's Republic of China
| | - Xiao-Ming Xia
- Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China
| | - Cong Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd., Shaoxing, 312369, People's Republic of China.
| |
Collapse
|
4
|
Dong Z, Liu Z, Xu Y, Tan B, Sun W, Ai Q, Yang Z, Zeng J. Potential for the development of Taraxacum mongolicum aqueous extract as a phytogenic feed additive for poultry. Front Immunol 2024; 15:1354040. [PMID: 38529273 PMCID: PMC10961442 DOI: 10.3389/fimmu.2024.1354040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/27/2024] [Indexed: 03/27/2024] Open
Abstract
Introduction Taraxacum mongolicum (TM) is a kind of medicinal and edible homologous plant which is included in the catalogue of feed raw materials in China. It is rich in polyphenols, flavonoids, polysaccharides and other active substances, and shows many benefits to livestock, poultry and aquatic products. The study aimed to assess the potential of TM aqueous extract (TMAE) as a substitute for poultry AGPs. Methods A total of 240 one-day-old Arbor Acker broilers were randomly assigned to four groups and fed a basal diet (Con) supplemented with 500, 1000, and 2000 mg/kg TMAE (Low, Medium, and High groups). The growth performance of the broilers was measured on day 21 and day 42. At the end of the trial, the researchers measured slaughter performance and collected serum, liver, spleen, ileum, and intestinal contents to investigate the effects of TMAE on serum biochemistry, antioxidant capacity, immune function, organ coefficient, intestinal morphology, flora composition, and short-chain fatty acids (SCFAs). Results The results showed that broilers treated with TMAE had a significantly higher average daily gain from 22 to 42 days old compared to the Con group. Various doses of TMAE resulted in different levels of improvement in serum chemistry. High doses increased serum alkaline phosphatase and decreased creatinine. TMAE also increased the antioxidant capacity of serum, liver, and ileum in broilers. Additionally, middle and high doses of TMAE enhanced the innate immune function of the liver (IL-10) and ileum (Occludin) in broilers. Compared to the control group, the TMAE treatment group exhibited an increase in the ratio of villi length to villi crypt in the duodenum. TMAE increased the abundance of beneficial bacteria, such as Alistipes and Lactobacillus, while reducing the accumulation of harmful bacteria, such as Colidextracter and Sellimonas. The cecum's SCFAs content increased with a medium dose of TMAE. Supplementing broiler diets with TMAE at varying doses enhanced growth performance and overall health. The most significant benefits were observed at a dose of 1000 mg/kg, including improved serum biochemical parameters, intestinal morphology, antioxidant capacity of the liver and ileum, immune function of the liver and ileum, and increased SCFAs content. Lactobacillus aviarius, norank_f_norank_o__Clostridia_UCG-014, and Flavonifractor are potentially dominant members of the intestinal microflora. Conclusion In conclusion, TMAE is a promising poultry feed additive and 1000 mg/kg is an effective reference dose.
Collapse
Affiliation(s)
- Zhen Dong
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
- Hunan Province Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Zhiqin Liu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
- Hunan Province Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Yufeng Xu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
- Hunan Province Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Bin Tan
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
- Hunan Province Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Wenqing Sun
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
- Hunan Province Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Qin Ai
- DHN Business Division, Wens Foodstuff Group Co., Ltd., Zhaoqing, China
| | - Zihui Yang
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
- Hunan Province Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Jianguo Zeng
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
- Hunan Province Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| |
Collapse
|
5
|
Wang J, Wang Y, Zhang Q, Kong D, Xing Z, Zhang W, Ruan Z. Chryseobacterium pyrolae sp. nov., isolated from the rhizosphere soil of Pyrola calliantha H. Int J Syst Evol Microbiol 2023; 73. [PMID: 38054475 DOI: 10.1099/ijsem.0.006068] [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: 12/07/2023] Open
Abstract
A novel Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, designated pc2-12T, was isolated from the rhizosphere soil of the herb Pyrola calliantha collected from arid areas of Tibet. The strain grew most vigorously with 1 % (w/v) NaCl, at pH 7.0 and at 25 °C. According to the results of 16S rRNA gene sequence analysis, pc2-12T was closely related to the members of the genus Chryseobacterium, with highest levels of sequence similarity to Chryseobacterium viscerum 687B-08T (98.42 %), Chryseobacterium oncorhynchi 701B-08T (98.11 %) and Chryseobacterium ureilyticum DSM 18017T (97.98 %). The average nucleotide identity values between pc2-12T and C. viscerum 687B-08T, C. oncorhynchi 701B-08T and C. ureilyticum DSM 18017T were 79.71, 79.49 and 79.26 %, respectively. The in silico DNA-DNA hybridisation values between pc2-12T and C. viscerum 687B-08T, C. oncorhynchi 701B-08T and C. ureilyticum DSM 18017T were 23.30, 23.00 and 22.90 %, respectively. The draft genome sequence of pc2-12T was 4.64 Mb long, with DNA G+C content of 37.0 mol%. The fatty acids contained in the cells of pc2-12T were mainly composed of iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The main polar lipid was phosphatidylethanolamine. MK-6 was the sole respiratory quinone. On the basis of the results of analysis of all the data described, pc2-12T is considered to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium pyrolae sp. nov., is proposed. The type strain is pc2-12T (=GDMCC 1.3256T= JCM 35712T).
Collapse
Affiliation(s)
- Jie Wang
- College of Life Science, Xinjiang Normal University, Urumqi 830054, PR China
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Yan Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, PR China
| | - Qi Zhang
- Xinjiang Urumqi Maternal and Child Care Hospital, Urumqi 830001, PR China
| | - Delong Kong
- College of Life Science, Xinjiang Normal University, Urumqi 830054, PR China
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Zhen Xing
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, PR China
| | - Wei Zhang
- College of Life Science, Xinjiang Normal University, Urumqi 830054, PR China
| | - Zhiyong Ruan
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, PR China
- College of Life Sciences, Yantai University, Yantai 264005, PR China
| |
Collapse
|
6
|
Kan Y, Zhang L, Wang Y, Ma Q, Zhou Y, Jiang X, Zhang W, Ruan Z. Endophytic Bacterium Flexivirga meconopsidis sp. nov. with Plant Growth-Promoting Function, Isolated from the Seeds of Meconopsis integrifolia. Microorganisms 2023; 11:2899. [PMID: 38138043 PMCID: PMC10745605 DOI: 10.3390/microorganisms11122899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/25/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Strain Q11T of an irregular coccoid Gram-positive bacterium, aerobic and non-motile, was isolated from Meconopsis integrifolia seeds. Strain Q11T grew optimally in 1% (w/v) NaCl, pH 7, at 30 °C. Strain Q11T is most closely related to Flexivirga, as evidenced by 16S rRNA gene analysis, and shares the highest similarity with Flexivirga aerilata ID2601ST (99.24%). Based on genome sequence analysis, the average nucleotide identity and digital DNA-DNA hybridization values of strains Q11T and D2601ST were 88.82% and 36.20%, respectively. Additionally, strain Q11T showed the abilities of nitrogen fixation and indole acetic acid production and was shown to promote maize growth under laboratory conditions. Its genome contains antibiotic resistance genes (the vanY gene in the vanB cluster and the vanW gene in the vanI cluster) and extreme environment tolerance genes (ectoine biosynthetic gene cluster). Shotgun proteomics also detected antibiotic resistance proteins (class A beta-lactamases, D-alanine ligase family proteins) and proteins that improve plant cold tolerance (multispecies cold shock proteins). Strain Q11T was determined to be a novel species of the genus Flexivirga, for which the name Flexivirga meconopsidis sp. nov. is proposed. The strain type is Q11T (GDMCC 1.3002T = JCM 36020 T).
Collapse
Affiliation(s)
- Yongtao Kan
- College of Life Sciences, Xinjiang Normal University, Urumqi 830017, China;
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (Q.M.); (Y.Z.); (X.J.)
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Li Zhang
- College of Life Sciences, Yantai University, Yantai 264005, China;
| | - Yan Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (Q.M.); (Y.Z.); (X.J.)
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China
| | - Qingyun Ma
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (Q.M.); (Y.Z.); (X.J.)
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiqing Zhou
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (Q.M.); (Y.Z.); (X.J.)
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Jiang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (Q.M.); (Y.Z.); (X.J.)
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Zhang
- College of Life Sciences, Xinjiang Normal University, Urumqi 830017, China;
| | - Zhiyong Ruan
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (Q.M.); (Y.Z.); (X.J.)
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| |
Collapse
|
7
|
Yin QJ, Tang HZ, Zhu FC, Liu X, Xing YZ, Tang LC, Li XG. Complete genome of Rossellomorea sp. DA94, an agarolytic and orange-pigmented bacterium isolated from mangrove sediment of the South China Sea. Mar Genomics 2023; 71:101059. [PMID: 37620055 DOI: 10.1016/j.margen.2023.101059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/10/2023] [Indexed: 08/26/2023]
Abstract
Rossellomorea sp. DA94, isolated from mangrove sediment in the South China Sea (Beihai, Guangxi province), is an agarolytic and orange-pigmented bacterium. Here, we present the complete genome sequence of strain DA94, which comprises 4.63 Mb sequences with 43.5% GC content. In total, 4589 CDSs, 33 rRNA genes and 110 tRNA genes were obtained. Genomic analysis of strain DA94 revealed that 108 CAZymes were organized in 4578 PULs involved in polysaccharides degradation, transport, and regulation. Further, we performed the diversity of CAZymes and PULs comparison among Rossellomorea strains. Less CAZymes were organized more PULs, indicating highly efficiently polysaccharides utilization in Rossellomorea. Meanwhile, PUL0459, PUL0460 and PUL0316 related to agar degradation, and exolytic beta-agarase GH50, endo-type beta-agarase GH86 and arylsulfatase were identified in the genome of strain DA94. We verified that strain DA94 can degrade agar to form a bright clear zone around the bacterial colonies in the laboratory. Moreover, the carotenoid biosynthetic pathways were proposed, which may be responsible for orange-pigment of Rossellomorea sp. DA94. This study represents a thorough genomic characterization of CAZymes repertoire and carotenoid biosynthetic pathways of Rossellomorea, provides insight into diversity of related enzymes and their potential biotechnological applications.
Collapse
Affiliation(s)
- Qun-Jian Yin
- Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China; Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China; Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai, China.
| | - Hong-Zhi Tang
- Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Fang-Chao Zhu
- Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China; Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China; Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai, China
| | - Xin Liu
- Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China; Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China; Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai, China
| | - Yong-Ze Xing
- Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China; Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China; Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai, China
| | - Li-Chang Tang
- Beihai Public Inspection and Testing Centre, Beihai, China
| | - Xue-Gong Li
- Laboratory of Deep-sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
| |
Collapse
|
8
|
Zhu DH, Nie FH, Song QL, Wei W, Zhang M, Hu Y, Lin HY, Kang DJ, Chen ZB, Chen JJ. Isolation and genomic characterization of Klebsiella Lw3 with polychlorinated biphenyl degradability. ENVIRONMENTAL TECHNOLOGY 2023; 44:3656-3666. [PMID: 35441572 DOI: 10.1080/09593330.2022.2068381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
Bioremediation of sediment organic pollution has been intensely investigated, but the degradation of complex organic compounds, pesticide residues, and polychlorinated biphenyls (PCBs) remains poorly studied. In this study, sediments were collected from Zhanjiang Mangrove Reserve and inoculated in an inorganic salt medium using only biphenyl (BP) and PCBs as the carbon sources to obtain a PCB-degrading strain. A gram-negative bacterium that metabolized PCBs was isolated and identified as Klebsiella Lw3 by 16S rDNA phylogenetic analysis. Genomic sequencing showed that this bacterium possessed genes related to BP/PCB degradation, and its GC content was 58.2%; we identified 3326 cellular pathways. Gas chromatography-mass spectrometry was employed to test the PCB degrading ability; the results showed that the strain had a good degradation effect on PCB3 at concentrations of 5, 10, 20, 40, and 60 mg/L and that the final degradation rate was higher than 97% after 96 h. Interestingly, this strain showed good biodegradability of PCBs despite having no classical PCB degradation pathway, providing a new direction for Klebsiella research with practical significance for in situ bioremediation of PCB contamination. Overall, this study provides valuable insights into the genetic structure of PCB-degrading strains as well as eco-friendly and low-cost PCB degradation and lays a foundation for the discovery of new degradation pathways.
Collapse
Affiliation(s)
- Di-Hua Zhu
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Fang-Hong Nie
- College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Qing-Lang Song
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Wan Wei
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Min Zhang
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Yao Hu
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Hong-Ying Lin
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Dan-Ju Kang
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Zhi-Bao Chen
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Jin-Jun Chen
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| |
Collapse
|
9
|
Gao JW, He DY, Zhang WW, Wang YR, Su Y, Ying JJ, Wu ZC, Qu W, Xu L, Sun C. Aestuariibaculum lutulentum sp. nov., a marine bacterium isolated from coastal sediment in Beihai. Arch Microbiol 2023; 205:187. [PMID: 37043022 DOI: 10.1007/s00203-023-03535-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/01/2023] [Indexed: 04/13/2023]
Abstract
A Gram-stain negative, strictly aerobic, and rod-shaped bacterium, designated as strain L182T, was isolated from coastal sediment in Beihai, Guangxi Province, PR China. Colonies of strain L182T were yellow, 2 mm in diameter, round, opaque, smooth and convex after incubation on marine ager at 30 °C for 3 days. Cells were catalase-positive but oxidase-negative. Growth of strain L182T was observed at 4-40 °C (optimum, 25 °C), pH 5.5-10.0 (optimum, pH 5.5-8.0) and with 0-6% (w/v) NaCl (optimum, 0.5-4.0%). The G + C content based on the genome sequence was 36.0%. The only respiratory quinone was MK-6. The main polar lipids included phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid, one unidentified glycolipids, four unidentified aminolipids and six unidentified lipids. The major fatty acids (> 10%) were iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH. The 16S rRNA gene sequence similarity between strain L182T and Aestuariibaculum suncheonense SC17T was 98.2%, and the similarities with other type strains of the genus Aestuariibaculum were 96.1-97.2%. The average nucleotide identity and in silicon DNA-DNA hybridization values between the strain L182T and its closely related Aestuariibaculum species were 80.8-85.2% and 22.0-29.5%. According to the above results, Aestuariibaculum lutulentum sp. nov. was proposed as a novel species. The type strain is L182T (= MCCC 1K08065T = KCTC 92530T).
Collapse
Affiliation(s)
- Jia-Wei Gao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd., Shaoxing, 312369, People's Republic of China
| | - Dong-Yan He
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Wen-Wu Zhang
- Trend Biotech Co., Ltd., Hangzhou, 311121, People's Republic of China
| | - Yu-Ruo Wang
- Zhejiang Development and Planning Institute, Hangzhou, 310012, People's Republic of China
| | - Yue Su
- Trend Biotech Co., Ltd., Hangzhou, 311121, People's Republic of China
| | - Jun-Jie Ying
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd., Shaoxing, 312369, People's Republic of China
| | - Zhi-Cheng Wu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China
| | - Wu Qu
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316000, People's Republic of China
| | - Lin Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd., Shaoxing, 312369, People's Republic of China
| | - Cong Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd., Shaoxing, 312369, People's Republic of China.
| |
Collapse
|
10
|
Lozada M, Diéguez MC, García PE, Dionisi HM. Microbial communities associated with kelp detritus in temperate and subantarctic intertidal sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159392. [PMID: 36240919 DOI: 10.1016/j.scitotenv.2022.159392] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Kelp forests, among the most productive ecosystems on Earth, cover large areas of the South Atlantic coast. Sediment heterotrophic bacteria have a pivotal role in the degradation of kelp biomass, however, the response of sediment microbial communities to periodic kelp biomass inputs is mostly unknown. Here, we show that kelp biomass induced rapid changes in overlying water chemistry and shifts in sediment microbial communities, which differed in the experimental systems containing Macrocystis pyrifera (M) and Undaria pinnatifida (U) with sediments of the respective regions. We observed results compatible with the degradation of labile, high molecular weight compounds into smaller and more refractory compounds towards the end of the incubations. The capability of microbial communities to degrade alginate, the major component of kelp cell walls, significantly increased with respect to controls after kelp biomass addition (Absorbance at 235 nm 1.2 ± 0.3 and 1.0 ± 0.2 for M and U, respectively, controls <0.2, t = 4 days). Shifts in microbial community structure (based on 16S rRNA gene amplicon sequencing) were tightly related to the kelp treatment and, to a lesser extent, to the sediment provenance (Principal Coordinates Analysis, 80 % of variation explained in the first two axes). Dissolved oxygen, pH, salinity, alginolytic potential, Absorbance at 235 and 600 nm, total N, total C, and SUVA index correlated significantly with community structure. Differentially abundant populations between kelp-amended treatments and controls included members of the Flavobacteriia class (Algibacter and Polaribacter), and Gammaproteobacteria (Psychromonas and Marinomonas), among others. Metagenomes of M and U-amended sediments contained sequences from 18 of the 19 enzyme families related to alginate or fucoidan degradation. Specific taxonomic groups were associated with enzyme classes targeting different substrates, suggesting niche differentiation. This work expands our knowledge on the patterns of microbial assemblages from intertidal sediments in response to kelp biomass inputs.
Collapse
Affiliation(s)
- Mariana Lozada
- Laboratorio de Microbiología Ambiental (CESIMAR-CONICET/IBIOMAR-CONICET), Puerto Madryn, Argentina.
| | - María C Diéguez
- Grupo de Ecología de Sistemas Acuáticos a Escala de Paisaje (GESAP, INIBIOMA-CONICET-UNComa), Bariloche, Argentina
| | - Patricia E García
- Grupo de Ecología de Sistemas Acuáticos a Escala de Paisaje (GESAP, INIBIOMA-CONICET-UNComa), Bariloche, Argentina
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental (CESIMAR-CONICET/IBIOMAR-CONICET), Puerto Madryn, Argentina
| |
Collapse
|
11
|
Park J, Davis K, Lajoie G, Parfrey LW. Alternative approaches to identify core bacteria in Fucus distichus microbiome and assess their distribution and host-specificity. ENVIRONMENTAL MICROBIOME 2022; 17:55. [PMID: 36384808 PMCID: PMC9670562 DOI: 10.1186/s40793-022-00451-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Identifying meaningful ecological associations between host and components of the microbiome is challenging. This is especially true for hosts such as marine macroalgae where the taxonomic composition of the microbiome is highly diverse and variable in space and time. Identifying core taxa is one way forward but there are many methods and thresholds in use. This study leverages a large dataset of microbial communities associated with the widespread brown macroalga, Fucus distichus, across sites and years on one island in British Columbia, Canada. We compare three different methodological approaches to identify core taxa at the amplicon sequence variant (ASV) level from this dataset: (1) frequency analysis of taxa on F. distichus performed over the whole dataset, (2) indicator species analysis (IndVal) over the whole dataset that identifies frequent taxa that are enriched on F. distichus in comparison to the local environment, and (3) a two-step IndVal method that identifies taxa that are consistently enriched on F. distichus across sites and time points. We then investigated a F. distichus time-series dataset to see if those core taxa are seasonally consistent on another remote island in British Columbia, Canada. We then evaluate host-specificity of the identified F. distichus core ASVs using comparative data from 32 other macroalgal species sampled at one of the sites. RESULTS We show that a handful of core ASVs are consistently identified by both frequency analysis and IndVal approaches with alternative definitions, although no ASVs were always present on F. distichus and IndVal identified a diverse array of F. distichus indicator taxa across sites on Calvert Island in multiple years. Frequency analysis captured a broader suit of taxa, while IndVal was better at identifying host-specific microbes. Finally, two-step IndVal identified hundreds of indicator ASVs for particular sites/timepoints but only 12 that were indicators in a majority (> 6 out of 11) of sites/timepoints. Ten of these ASVs were also indicators on Quadra Island, 250 km away. Many F. distichus-core ASVs are generally found on multiple macroalgal species, while a few ASVs are highly specific to F. distichus. CONCLUSIONS Different methodological approaches with variable set thresholds influence core identification, but a handful of core taxa are apparently identifiable as they are widespread and temporally associated with F. distichus and enriched in comparison to the environment. Moreover, we show that many of these core ASVs of F. distichus are found on multiple macroalgal hosts, indicating that most occupy a macroalgal generalist niche rather than forming highly specialized associations with F. distichus. Further studies should test whether macroalgal generalists or specialists are more likely to engage in biologically important exchanges with host.
Collapse
Affiliation(s)
- Jungsoo Park
- Department of Botany, Biodiversity Research Centre, University of British Columbia, Vancouver, BC Canada
| | - Katherine Davis
- Department of Botany, Biodiversity Research Centre, University of British Columbia, Vancouver, BC Canada
| | - Geneviève Lajoie
- Department of Botany, Biodiversity Research Centre, University of British Columbia, Vancouver, BC Canada
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, QC Canada
| | - Laura Wegener Parfrey
- Department of Botany, Biodiversity Research Centre, University of British Columbia, Vancouver, BC Canada
- Department of Zoology, University of British Columbia, Vancouver, BC Canada
| |
Collapse
|
12
|
Li Z, Du Z, Li H, Chen Y, Zheng M, Jiang Z, Du X, Ni H, Zhu Y. Characterisation of marine bacterium Microbulbifer sp. ALW1 with Laminaria japonica degradation capability. AMB Express 2022; 12:139. [DOI: 10.1186/s13568-022-01482-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 10/23/2022] [Indexed: 11/07/2022] Open
Abstract
AbstractMarine bacterium Microbulbifer sp. ALW1 was revealed to be able to effectively degrade Laminaria japonica thallus fragments into fine particles. Polysaccharide substrate specificity analysis indicated that ALW1 could produce extracellular alginate lyase, laminarinase, fucoidanase and cellulase. Based on alignment of the 16 S rRNA sequence with other reference relatives, ALW1 showed the closest relationship with Microbulbifer aggregans CCB-MM1T. The cell morphology and some basic physiological and biochemical parameters of ALW1 cells were characterised. ALW1 is a Gram-negative, rod- or oval-shaped, non-spore-forming and non-motile bacterium. The DNA–DNA relatedness values of ALW1 with type strains of M. gwangyangensis (JCM 17,800), M. aggregans (JCM 31,875), M. maritimus (JCM 12,187), M. okinawensis (JCM 16,147) and M. rhizosphaerae (DSM 28,920) were 28.9%, 43.3%, 41.2%, 35.4% and 45.6%, respectively. The major cell wall sugars of ALW1 were determined to be ribose and galactose, which differed from other closely related species. These characteristics indicated that ALW1 could be assigned to a separate species of the genus Microbulbifer. The complete genome of ALW1 contained one circular chromosome with 4,682,287 bp and a GC content of 56.86%. The putative encoded proteins were categorised based on their functional annotations. Phenotypic, physiological, biochemical and genomic characterisation will provide insights into the many potential industrial applications of Microbulbifer sp. ALW1.Key points.
Collapse
|
13
|
Whole-genome sequencing and functional analysis of a novel chitin-degrading strain Rhodococcus sp. 11-3. J Biosci Bioeng 2022; 134:167-173. [PMID: 35644796 DOI: 10.1016/j.jbiosc.2022.04.010] [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: 09/28/2021] [Revised: 04/08/2022] [Accepted: 04/22/2022] [Indexed: 11/24/2022]
Abstract
Chitin is the second most abundant polysaccharide in nature. Therefore, how to utilize the resource is an important issue. Rhodococcus sp. 11-3 is a strain with high chitin deacetylase (CDA) activity. In the present study, we used a combined Illumina and PacBio sequencing strategy to assemble the whole genome sequence of this strain. The genome of Rhodococcus sp. 11-3 was 5,627,661 bp in size and contained 5983 coding genes, of which 5983, 4040, 4648, 4914, 4174, 2350, and 173 genes were annotated in the Non-Redundant Protein Database (NR), Swiss-Prot, Pfam, Clusters of Orthologous Groups of proteins (COG), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-active enzymes (CAZymes) databases, respectively. The genome was annotated to a chitin deacetylase gene (RhoCDA) and a chitinase gene (RhoChi). They were not very similar to the previously reported chitin deacetylase and chitinase. This made it possible to investigate the genes associated with chitin degradation and would provide an important reference for subsequent gene cloning, functional research, development and application. Therefore, the Rhodococcus sp. 11-3 strain has great potential in the development of chitin resources.
Collapse
|
14
|
Kong D, Wang Y, Li Q, Zhou Y, Jiang X, Xing Z, Wang Z, Ruan Z. Chryseobacterium subflavum sp. nov., isolated from soil. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005345] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, designated LAMRS1T, was isolated from a soil sample collected in Hebei Province, PR China. Strain LAMRS1T was able to grow optimally in the presence of 0.5 % (w/v) NaCl, at pH 7.5 and at 30 °C. On the basis of 16S rRNA gene sequence analysis, strain LAMRS1T was closely related to members of the genus
Chryseobacterium
, with highest levels of sequence similarity to
Chryseobacterium soli
DSM 19298T (97.9 %),
Chryseobacterium soldanellicola
DSM 17072T (97.6%) and
Chryseobacterium piperi
CTMT (97.5 %). The average nucleotide identity and digital DNA–DNA hybridization values between LAMRS1T and the closely related species of
C. soli
DSM 19298T,
C. soldanellicola
DSM 17072T and
C. piperi
CTMT were 78.1, 78.2 and 80.7 %, and 21.7, 22.0 and 23.7 %, respectively. The draft genome sequence of LAMRS1T was 4.61 Mb, with DNA G+C content of 36.2 mol%. The major isoprenoid quinone was menaquinone-6 and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1
ω6c and/or C16 : 1
ω7c) constituted the major cellular fatty acids. The main polar lipids were phosphatidylethanolamine, four aminolipids, three glycolipids and seven unidentified lipids. On the basis of evidence presented in this study, strain LAMRS1T represents a novel species of the genus
Chryseobacterium
, for which the name Chryseobacterium subflavum sp. nov. is proposed. The type strain is LAMRS1T (=JCM 33868T=KCTC 72823T).
Collapse
Affiliation(s)
- Delong Kong
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, PR China
| | - Yan Wang
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, PR China
| | - Qingqing Li
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Yanzheng Zhou
- Jining Academy of Agricultural Sciences, Jining 272000, PR China
| | - Xu Jiang
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Zhen Xing
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, PR China
| | - Zhiye Wang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou 730000, PR China
| | - Zhiyong Ruan
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, PR China
- College of Life Sciences, Yantai University, Yantai 264005, PR China
| |
Collapse
|
15
|
Kong D, Li Q, Zhou Y, Wang Y, Jiang X, Wang Z, Ruan Z. Pseudomonas tumuqii sp. nov., isolated from greenhouse soil. Arch Microbiol 2022; 204:249. [PMID: 35396979 DOI: 10.1007/s00203-022-02869-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 11/02/2022]
Abstract
A Gram-stain-negative, aerobic, rod-shaped and motile bacterium, named LAMW06T, was isolated from greenhouse soil in Beijing, China. In the 16S rRNA gene sequence comparison, strain LAMW06T had the highest similarity with Pseudomonas cuatrocienegasensis 1NT. Phylogenetic analysis based on the 16S rRNA and three housekeeping gene sequences (gyrB, rpoB and rpoD) indicated that strain represented a member of the genus Pseudomonas. The genome sequence size of the isolate was 5.5 Mb, with a DNA G + C content of 63.5 mol%. The average nucleotide identity and DNA-DNA hybridization values between strain LAMW06T and closely related members of Pseudomonas borbori R-20821T, Pseudomonas taeanensis MS-3T and P. cuatrocienegasensis 1NT were 90.9%, 82.4%, 81.5% and 43.0%, 25.9%, 24.6% respectively. The major fatty acids contained summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), C18:1 ω7c and C16:0. The primary respiratory quinone was ubiquinone-9. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, six aminophospholipids, six phospholipids, one aminolipid and one glycolipid. According to the genotypic, phylogenetic and chemotaxonomic data, strain LAMW06T represents a novel species within the genus Pseudomonas, for which the name Pseudomonas tumuqii sp. nov. is proposed. The type strain is LAMW06T (= GDMCC 1.2003T = KCTC 72829T).
Collapse
Affiliation(s)
- Delong Kong
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Qingqing Li
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Yanzheng Zhou
- Jining Academy of Agricultural Sciences, Jining, 272000, People's Republic of China
| | - Yan Wang
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.,College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi, 860000, People's Republic of China
| | - Xu Jiang
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Zhiye Wang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China
| | - Zhiyong Ruan
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China. .,College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi, 860000, People's Republic of China. .,College of Life Sciences, Yantai University, Yantai, 264005, People's Republic of China.
| |
Collapse
|
16
|
Kong D, Xia Z, Gao Y, Zhou Y, Jiang X, Xu P, Guo W, Ruan Z. Sporosarcina jiandibaonis sp. nov., isolated from saline soil. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005244] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic, motile, rod-shaped bacterium, designated strain LAM9210T, was isolated from a saline soil sample collected from Lingxian County, Shandong Province, PR China. Analysis of the 16S rRNA gene sequence of the isolate revealed highest sequence similarities to the type strain of
Sporosarcina pasteurii
NCIMB 8841T (97.6 % sequence similarity). The genomic G+C content was 40.4 mol%. The average nucleotide identity and in silico DNA–DNA hybridization values between strain LAM9210T and the type strain of the most closely related species
S. pasteurii
NCIMB 8841T were 73.6 and 20.6 %, respectively. Strain LAM9210T was found to grow at 10–40 °C (optimum, 30 °C), at pH 6.0–10.0 (optimum, pH 9.0) and with 0–6 % (w/v) NaCl (optimum, 0.5 %), respectively. The major fatty acids were anteiso-C15 : 0 and iso-C14 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and one unidentified phospholipid. Menaquinone-7 was detected as the predorminant respiratory quinone. Strain LAM9210T contained glycine, lysine, alanine and glutamic acid as the diagnostic amino acids in the cell-wall peptidoglycan. On the basis of phenotypic, phylogenetic and genotypic data, strain LAM9210T is considered to represent a novel species of the genus
Sporosarcina
, for which the name Sporosarcina jiandibaonis sp. nov. is proposed. The type strain is LAM9210T (=CGMCC 1.18607T=GDMCC 1.2002T=JCM 32514T).
Collapse
Affiliation(s)
- Delong Kong
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
- College of Life Science, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, Alar 843300, PR China
| | - Zhanfeng Xia
- College of Life Science, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, Alar 843300, PR China
| | - Yan Gao
- Institute of Applied Microbiology, Xinjiang Academy of Agriculture Science/Xinjiang Special Environmental Microbiology Laboratory, Urumqi 830091, PR China
| | - Yiqing Zhou
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Xu Jiang
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Piao Xu
- Guangxi Jiandibao Bio-Technology Limited, Nanning 530105, PR China
| | - Wei Guo
- Graduate School of Chinese Academy of Agriculture Sciences, Beijing 100081, PR China
| | - Zhiyong Ruan
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000 Tibet, PR China
| |
Collapse
|
17
|
He XY, Liu NH, Lin CY, Sun ML, Chen XL, Zhang YZ, Zhang YQ, Zhang XY. Description of Aureibaculum luteum sp. nov. and Aureibaculum flavum sp. nov. isolated from Antarctic intertidal sediments. Antonie van Leeuwenhoek 2022; 115:391-405. [PMID: 35022928 DOI: 10.1007/s10482-021-01702-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/14/2021] [Indexed: 10/19/2022]
Abstract
Two Gram-stain-negative, aerobic, non-motile, and rod-shaped bacterial strains, designated SM1352T and A20T, were isolated from intertidal sediments collected from King George Island, Antarctic. They shared 99.8% 16S rRNA gene sequence similarity with each other and had the highest sequence similarity of 98.1% to type strain of Aureibaculum marinum but < 93.4% sequence similarity to those of other known bacterial species. The genomes of strains SM1352T and A20T consisted of 5,108,092 bp and 4,772,071 bp, respectively, with the G + C contents both being 32.0%. They respectively encoded 4360 (including 37 tRNAs and 6 rRNAs) and 4032 (including 36 tRNAs and 5 rRNAs) genes. In the phylogenetic trees based on 16S rRNA gene and single-copy orthologous clusters (OCs), both strains clustered with Aureibaculum marinum and together formed a separate branch within the family Flavobacteriaceae. The ANI and DDH values between the two strains and Aureibaculum marinum BH-SD17T were all below the thresholds for species delineation. The major cellular fatty acids (> 10%) of the two strains included iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH. Their polar lipids predominantly included phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified aminolipid, and two unidentified lipids. Genomic comparison revealed that both strains possessed much more glycoside hydrolases and sulfatase-rich polysaccharide utilization loci (PULs) than Aureibaculum marinum BH-SD17T. Based on the above polyphasic evidences, strains SM1352T and A20T represent two novel species within the genus Aureibaculum, for which the names Aureibaculum luteum sp. nov. and Aureibaculum flavum sp. nov. are proposed. The type strains are SM1352T (= CCTCC AB 2014243 T = JCM 30335 T) and A20T (= CCTCC AB 2020370 T = KCTC 82503 T), respectively.
Collapse
Affiliation(s)
- Xiao-Yan He
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Ning-Hua Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Chao-Yi Lin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Mei-Ling Sun
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
| | - Yu-Qiang Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| |
Collapse
|
18
|
Geng ZQ, Qian DK, Hu ZY, Wang S, Yan Y, van Loosdrecht MCM, Zeng RJ, Zhang F. Identification of Extracellular Key Enzyme and Intracellular Metabolic Pathway in Alginate-Degrading Consortia via an Integrated Metaproteomic/Metagenomic Analysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:16636-16645. [PMID: 34860015 DOI: 10.1021/acs.est.1c05289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Uronic acid in extracellular polymeric substances is a primary but often ignored factor related to the difficult hydrolysis of waste-activated sludge (WAS), with alginate as a typical polymer. Previously, we enriched alginate-degrading consortia (ADC) in batch reactors that can enhance methane production from WAS, but the enzymes and metabolic pathway are not well documented. In this work, two chemostats in series were operated to enrich ADC, in which 10 g/L alginate was wholly consumed. Based on it, the extracellular alginate lyase (∼130 kD, EC 4.2.2.3) in the cultures was identified by metaproteomic analysis. This enzyme offers a high specificity to convert alginate to disaccharides over other mentioned hydrolases. Genus Bacteroides (>60%) was revealed as the key bacterium for alginate conversion. A new Entner-Doudoroff pathway of alginate via 5-dehydro-4-deoxy-d-glucuronate (DDG) and 3-deoxy-d-glycerol-2,5-hexdiulosonate (DGH) as the intermediates to 2-keto-3-deoxy-gluconate (KDG) was constructed based on the metagenomic and metaproteomic analysis. In summary, this work documented the core enzymes and metabolic pathway for alginate degradation, which provides a good paradigm when analyzing the degrading mechanism of unacquainted substrates. The outcome will further contribute to the application of Bacteroides-dominated ADC on WAS methanogenesis in the future.
Collapse
Affiliation(s)
- Zi-Qian Geng
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Ding-Kang Qian
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zhi-Yi Hu
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Shuai Wang
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yang Yan
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands
| | - Raymond Jianxiong Zeng
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Fang Zhang
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| |
Collapse
|
19
|
Zhang J, Zhang Y, Liu R, Cai R, Liu F, Sun C. Iocasia fonsfrigidae NS-1 gen. nov., sp. nov., a Novel Deep-Sea Bacterium Possessing Diverse Carbohydrate Metabolic Pathways. Front Microbiol 2021; 12:725159. [PMID: 34899621 PMCID: PMC8652127 DOI: 10.3389/fmicb.2021.725159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Resolving metabolisms of deep-sea microorganisms is crucial for understanding ocean energy cycling. Here, a strictly anaerobic, Gram-negative strain NS-1 was isolated from the deep-sea cold seep in the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain NS-1 was most closely related to the type strain Halocella cellulosilytica DSM 7362T (with 92.52% similarity). A combination of phylogenetic, genomic, and physiological traits with strain NS-1, was proposed to be representative of a novel genus in the family Halanaerobiaceae, for which Iocasia fonsfrigidae NS-1 was named. It is noteworthy that I. fonsfrigidae NS-1 could metabolize multiple carbohydrates including xylan, alginate, starch, and lignin, and thereby produce diverse fermentation products such as hydrogen, lactate, butyrate, and ethanol. The expressions of the key genes responsible for carbohydrate degradation as well as the production of the above small molecular substrates when strain NS-1 cultured under different conditions, were further analyzed by transcriptomic methods. We thus predicted that part of the ecological role of Iocasia sp. is likely in the fermentation of products from the degradation of diverse carbohydrates to produce hydrogen as well as other small molecules, which are in turn utilized by other members of cold seep microbes.
Collapse
Affiliation(s)
- Jing Zhang
- CAS Key Laboratory of Experimental Marine Biology and 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 for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,School of Life Sciences, Hebei University, Baoding, China
| | - Yuechao Zhang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Rui Liu
- CAS Key Laboratory of Experimental Marine Biology and 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 for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Ruining Cai
- CAS Key Laboratory of Experimental Marine Biology and 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 for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Fanghua Liu
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Chaomin Sun
- CAS Key Laboratory of Experimental Marine Biology and 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 for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| |
Collapse
|
20
|
Sun C, Fang YC, Li H, Chen J, Ye YL, Ni LF, Xu L, Han BN, Wu M, Wang CS, Xu XW. Complete genome sequence of marine Roseobacter lineage member Monaibacterium sp. ALG8 with six plasmids isolated from seawater around brown algae. Mar Genomics 2021; 60:100878. [PMID: 34006489 DOI: 10.1016/j.margen.2021.100878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/09/2021] [Accepted: 05/10/2021] [Indexed: 11/26/2022]
Abstract
Monaibacterium sp. ALG8 (=MCCC 1 K04733) was isolated from seawater around brown algae. The genome of Monaibacterium sp. ALG8 was sequenced, one circular 3,036,380 bp chromosome and six circular plasmids ranging from 12,229 to 151,263 bp were found after assembly. The results of genomic annotation showed that Monaibacterium sp. ALG8 lacks the ability to degrade alginate, indicating its ecological role may not be directly related to the degradation of brown algae. The comparison of genomic features in the plasmids showed that almost all of these plasmids, except pALG4, were horizontally recruited from donors, not ancestors. Based on predicted functions, the existence of plasmids may provide strain ALG8 with advantages including nitrate reduction, tolerance of osmotic stress via glycine betaine, resistance to heavy metal stress such as mercury and cobalt, degradation of benzoate metabolites such as p-cumate, transformation of the swim-or-stick lifestyle and improvement of the immune system with two CRISPR-Cas systems. This study provides evidence for the carbon metabolic patterns of Monaibacterium sp. ALG8 and predicts the functions and donors of six plasmids in this strain, broadening our understanding of the ecological roles of bacteria in the environment around brown algae and the functions and evolutionary patterns of plasmids in marine Roseobacter lineage members.
Collapse
Affiliation(s)
- Cong Sun
- Key Laboratory of Marine Ecosystem Dynamics, 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
| | - Yuan-Chun Fang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Hao Li
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Jie Chen
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Yong-Lian Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Ling-Fang Ni
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, 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
| | - Bing-Nan Han
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Chun-Sheng Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China.
| |
Collapse
|
21
|
Yin Q, Liang J, Zheng X, Wang Y, Song ZM, Zhang Y, Xu Y. Algibacter onchidii sp. nov., a symbiotic bacterium isolated from a marine invertebrate. Int J Syst Evol Microbiol 2021; 71. [PMID: 34788209 DOI: 10.1099/ijsem.0.005102] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel symbiotic bacterium, designated strain XY-114T, was isolated from the cerata of an Onchidium marine invertebrate species collected in the South China Sea. Strain XY-114T was an aerobic, Gram-stain-negative, non-motile and short rod-shaped bacterium (0.5-0.8 µm wide and 1.0-1.5 µm long) without flagellum. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain XY-114T belonged to the genus Algibacter with the highest similarity of 97.2 % to the closest phylogenetic relative Algibacter aestuarii KYW371T. Cells grew at 15-37 °C (optimum, 30 °C), at pH 5.5-9.0 (optimum 7.0-8.0) and at NaCl concentrations of 0.5-5.0 % (w/v; optimum 1.5-3.0 %). The major fatty acids (>10 %) were summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The predominant polar lipid was phosphatidylethanolamine. The predominant respiratory quinone was MK-6. Flexirubin-type pigments were absent. The genome size of strain XY-114T was 3.4 Mbp, with 34.9 mol% of DNA G+C content. The average nucleotide identity, digital DNA-DNA hybridization and amino acid identity values between strain XY-114T and A. aestuarii KYW371T were 74.5 %, 17.0±1.8 % and 73.9 %. Characterization based on phylogenetic, phenotypic, chemotaxonomic and genomic evidence demonstrated that strain XY-114T represents a novel species of the genus Algibacter, for which the name Algibacter onchidii sp. nov. is proposed. The type strain is XY-114T (=KCTC 72217T=MCCC 1K03606T).
Collapse
Affiliation(s)
- Qi Yin
- School of Public Health and Management, Chongqing Medical University, Chongqing 400016, PR China
| | - Jinyou Liang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University,, Shenzhen 518060, PR China
| | - Xiaoli Zheng
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University,, Shenzhen 518060, PR China
| | - Yu Wang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University,, Shenzhen 518060, PR China
| | - Zhi-Man Song
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University,, Shenzhen 518060, PR China
| | - Yu Zhang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University,, Shenzhen 518060, PR China
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University,, Shenzhen 518060, PR China
| |
Collapse
|
22
|
Ying JJ, Fang YC, Ye YL, Wu ZC, Xu L, Han BN, Sun C. Marinomonas vulgaris sp. nov., a marine bacterium isolated from seawater in a coastal intertidal zone of Zhoushan island. Arch Microbiol 2021; 203:5133-5139. [PMID: 34319420 DOI: 10.1007/s00203-021-02500-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/01/2021] [Accepted: 07/19/2021] [Indexed: 10/20/2022]
Abstract
A Marinomonas-like, Gram-stain-negative, strictly aerobic and rod to ovoid-shaped bacterium, designated as strain A79T, was isolated from the seawater mixtures of oyster shells and brown algae in a coastal intertidal zone of Zhoushan, China. The strain was positive for oxidase and catalase. Colonies grown on marine agar for 48 h were round, milky white, smooth and moist with the diameter of 2-3 mm. Growth was observed at 15-30 °C (optimum, 25℃), pH 5.5-9.5 (optimum, pH 8.5) and with 0.5-8% (w/v) NaCl (optimum, 2-2.5%). The G + C content based on the genome sequence was 46.0%. The only respiratory quinone was Q-8. The main polar lipids contained phosphatidylglycerol, phosphatidylethanolamine, unidentified glycolipids, unidentified phospholipid and three unidentified lipids. The major fatty acids (> 10%) were C16:0, Summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c) and summed feature 8 (comprising C18:1 ω6c and/or C18:1 ω7c). The 16S rRNA gene sequence similarity between strain A79T and Marinomonas pollencensis IVIA-Po-185T was 97.4%, the similarities with other type strains of the genus Marinomonas were 93.8-96.7%. Based on the results, Marinomonas vulgaris sp. nov. was proposed as a novel species. The type strain is A79T (= MCCC 1K05799T = KCTC 82519T = JCM 34473T).
Collapse
Affiliation(s)
- Jun-Jie Ying
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Yuan-Chun Fang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Yong-Lian Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Zhi-Cheng Wu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China.,Ocean College, Zhejiang University, Zhoushan, 316021, People's Republic of China
| | - Lin Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.,Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China
| | - Bing-Nan Han
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Cong Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China. .,Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China.
| |
Collapse
|
23
|
Phylogenomic Analyses of a Clade Within the Family Flavobacteriaceae Suggest Taxonomic Reassignments of Species of the Genera Algibacter, Hyunsoonleella, Jejuia, and Flavivirga, and the Proposal of Pseudalgibacter gen. nov. and Pseudalgibacter alginicilyticus comb. nov. Curr Microbiol 2021; 78:3277-3284. [PMID: 34081182 DOI: 10.1007/s00284-021-02559-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/28/2021] [Indexed: 10/21/2022]
Abstract
The family Flavobacteriaceae forms a major branch within the phylum Bacteroidetes. Whole-genome sequence-based analysis could significantly improve the accuracy of taxonomic assignments. In this study, phylogenomic analyses were carried out to revisit the taxonomic status of a clade of the family Flavobacteriaceae. Taking genome-based phylogeny as the primary guideline and average amino acid identity and phenotypic information as supplements, the following taxonomic proposals were put forward: Arenitalea lutea should be reclassified into the genus Algibacter; Algibacter aquaticus should be reclassified into the genus Flavivirga; Jejuia pallidilutea and Algibacter aestuarii should be reclassified into the genus Hyunsoonleella; Algibacter alginicilyticus should be reclassified into the novel genus Pseudalgibacter gen. nov. This study builds up a solid framework for taxonomic decisions of a clade of the family Flavobacteriaceae and will contribute to further insights into the evolution of this family.
Collapse
|
24
|
Chernysheva N, Bystritskaya E, Likhatskaya G, Nedashkovskaya O, Isaeva M. Genome-Wide Analysis of PL7 Alginate Lyases in the Genus Zobellia. Molecules 2021; 26:2387. [PMID: 33924031 PMCID: PMC8073546 DOI: 10.3390/molecules26082387] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/15/2021] [Indexed: 12/04/2022] Open
Abstract
We carried out a detailed investigation of PL7 alginate lyases across the Zobellia genus. The main findings were obtained using the methods of comparative genomics and spatial structure modeling, as well as a phylogenomic approach. Initially, in order to elucidate the alginolytic potential of Zobellia, we calculated the content of polysaccharide lyase (PL) genes in each genome. The genus-specific PLs were PL1, PL6, PL7 (the most abundant), PL14, PL17, and PL40. We revealed that PL7 belongs to subfamilies 3, 5, and 6. They may be involved in local and horizontal gene transfer and gene duplication processes. Most likely, an individual evolution of PL7 genes promotes the genetic variability of the Alginate Utilization System across Zobellia. Apparently, the PL7 alginate lyases may acquire a sub-functionalization due to diversification between in-paralogs.
Collapse
Affiliation(s)
| | | | | | | | - Marina Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, 690022 Vladivostok, Russia; (N.C.); (E.B.); (G.L.); (O.N.)
| |
Collapse
|
25
|
Aestuariibaculum sediminum sp. nov., a marine bacterium isolated from a tidal flat in Zhoushan. Arch Microbiol 2021; 203:2953-2960. [PMID: 33770231 DOI: 10.1007/s00203-021-02262-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 10/21/2022]
Abstract
A Gram-staining-negative, non-motile, strictly aerobic bacterium, designated as strain TT11T, was isolated from a sediment sample of a tidal flat connected in Zhoushan, China. Cells of strain TT11T are spherical, halotolerant, catalase- and oxidase-positive, and produce carotenoid-like pigments. Colonies were 0.5-1.0 mm diameter, smooth, round, convex and orange-yellow after growth on marine agar at 30 °C for 24 h. Growth of the strain TT11T was observed at 10-40 °C (optimum, 35 °C), at pH 6.0-9.5 (optimum, pH 6.5), and in the presence of 0-8.0% (w/v) NaCl (optimum, 0.5-1.0%). The results of 16S rRNA gene sequence analysis revealed that strain TT11T represents a member of the genus Aestuariibaculum and was closely related to Aestuariibaculum suncheonense SC17T (97.2%) and Aestuariibaculum marinum IP7T (96.8%). The G + C content of the genome was 34.6%. The only respiratory quinone was MK-6. The major fatty acids (> 10%) were iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH. The major polar lipids contained phosphatidylethanolamine, phosphoglycolipid, four unidentified aminolipids, four unidentified lipids and two unidentified glycolipids. On the basis of these genomic, chemotaxonomic and phenotypic characteristics, we propose a novel species Aestuariibaculum sediminum sp. nov. with the type strain TT11T (= KCTC 82195T = MCCC 1K04734T).
Collapse
|
26
|
Li M, Ma Q, Kong D, Han X, Che J, Zhou Y, Jiang X, Ruan Z, Zhang Q. Pseudomonas nicosulfuronedens sp. nov., a nicosulfuron degrading bacterium, isolated from a microbial consortium. Int J Syst Evol Microbiol 2021; 71. [PMID: 33411665 DOI: 10.1099/ijsem.0.004632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, motile, short-rod-shaped bacterium with nicosulfuron-degrading ability, designated strain LAM1902T, was isolated from a microbial consortium enriched with nicosulfuron as a sole nitrogen and energy source. The optimal temperature and pH for growth of strain LAM1902T were 30 °C and pH 6.0, respectively. Strain LAM1902T could grow in the presence of NaCl with concentration up to 4.0 % (w/v). Comparative analysis of 16S rRNA gene sequences revealed that LAM1902T was closely related to the members of the family Pseudomonadaceae to the genus Pseudomonas, with the highest similarity to Pseudomonas nitroreducens DSM 14399T (99.6 %), Pseudomonas nitritireducens WZBFD3-5A2T (99.3 %) and Pseudomonas panipatensis Esp-1T (98.8 %). Multi-locus sequence analysis based on both concatenated sequences of the 16S rRNA gene and three housekeeping genes (gyrB, rpoB and rpoD) further confirmed the intrageneric phylogenetic position of strain LAM1902T. The genomic DNA G+C content of LAM1902T was 64.8 mol%. The low values of in silico DNA-DNA hybridization (less than 43.7 %) and average nucleotide identity (less than 90.9 %) also showed that the strain was distinctly different from known species of the genus Pseudomonas. The major fatty acids were C16 : 0, C17 : 0 cyclo and anteiso C15 : 0. Ubiquinone Q-9 was detected as the predorminant respiratory quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. Based on phylogenetic, phenotypic and chemotaxonomic analyses and genome comparisons, we conclude that strain LAM1902T represents a novel species, for which the name Pseudomonas nicosulfuronedens sp. nov. is proposed. The type strain is LAM1902T (=JCM 33860T=KCTC 72830T).
Collapse
Affiliation(s)
- Miaomiao Li
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China.,College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Qingyun Ma
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Delong Kong
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Xiaoyan Han
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China.,College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Juan Che
- College of Life Science, Xinjiang Normal University, Urumqi, XinJiang, 830046, PR China.,Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Yiqing Zhou
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Xu Jiang
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Zhiyong Ruan
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China.,College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, Tibet, PR China
| | - Qinghua Zhang
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| |
Collapse
|
27
|
Liu A, Wang H, Yang YY, Xue QJ, Li XZ. Reclassification of Algibacter wandonensis as a Later Heterotypic Synonym of Algibacter lectus Based on Whole-Genome Sequence Analysis. Curr Microbiol 2021; 78:1034-1038. [PMID: 33527165 DOI: 10.1007/s00284-021-02356-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/10/2021] [Indexed: 11/28/2022]
Abstract
The genus Algibacter belongs to the family Flavobacteriaceae of the Bacteroidetes, and all members of this genus were isolated from marine environments. Among the Algibacter species, two members, Algibacter lectus KMM 3902T and Algibacter wandonensis WS-MY22T, were isolated from green algae and sediment around a brown algae respectively. The 16S rRNA gene sequences of these two type strains possess 99.4% sequence similarity. In this study, further studies were undertaken to clarify the taxonomic assignments of the two species. Whole-genome sequence analysis showed that the similarities for other phylogenetic markers are also very high (i.e. 99.9% for gyrB, 99.6% for recA and 99.9% for rpoD). Average nucleotide identity, average amino acids identity and digital DNA-DNA hybridization value between A. lectus KMM 3902T and A. wandonensis WS-MY22T are 98.3%, 98.6% and 89.4% respectively, all clearly exceed suggested species delineation thresholds. Furthermore, phylogenetic trees based on sequences of 16S rRNA gene and up-to-date bacterial core gene set (UBCG) consisting of 92 genes provided additional evidence that A. lectus KMM 3902T and A. wandonensis WS-MY22T are very closely related. In addition, a review of their profiles indicated that A. lectus KMM 3902T and A. wandonensis WS-MY22T did not present pronounced differences at phenotypic and chemotaxonomic levels. Based on these evidence, we propose that A. wandonensis should be reclassified as later heterotypic synonyms of A. lectus.
Collapse
Affiliation(s)
- Ang Liu
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, Jining, Shandong, 272067, P. R. China
| | - Hui Wang
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, Jining, Shandong, 272067, P. R. China
| | - Yuan-Yuan Yang
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, Jining, Shandong, 272067, P. R. China
| | - Qing-Jie Xue
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, Jining, Shandong, 272067, P. R. China
| | - Xiu-Zhen Li
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, Jining, Shandong, 272067, P. R. China.
| |
Collapse
|
28
|
Cha QQ, Wang XJ, Ren XB, Li D, Wang P, Li PY, Fu HH, Zhang XY, Chen XL, Zhang YZ, Xu F, Qin QL. Comparison of Alginate Utilization Pathways in Culturable Bacteria Isolated From Arctic and Antarctic Marine Environments. Front Microbiol 2021; 12:609393. [PMID: 33584613 PMCID: PMC7874173 DOI: 10.3389/fmicb.2021.609393] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/07/2021] [Indexed: 11/13/2022] Open
Abstract
Alginate, mainly derived from brown algae, is an important carbon source that can support the growth of marine microorganisms in the Arctic and Antarctic regions. However, there is a lack of systematic investigation and comparison of alginate utilization pathways in culturable bacteria from both polar regions. In this study, 88 strains were isolated from the Arctic and Antarctic regions, of which 60 strains could grow in the medium with alginate as the sole carbon source. These alginate-utilizing strains belong to 9 genera of the phyla Proteobacteria and Bacteroidetes. The genomes of 26 alginate-utilizing strains were sequenced and genomic analyses showed that they all contain the gene clusters related to alginate utilization. The alginate transport systems of Proteobacteria differ from those of Bacteroidetes and there may be unique transport systems among different genera of Proteobacteria. The biogeographic distribution pattern of alginate utilization genes was further investigated. The alginate utilization genes are found to cluster according to bacterial taxonomy rather than geographic location, indicating that the alginate utilization genes do not evolve independently in both polar regions. This study systematically illustrates the alginate utilization pathways in culturable bacteria from the Arctic and Antarctic regions, shedding light into the distribution and evolution of alginate utilization pathways in polar bacteria.
Collapse
Affiliation(s)
- Qian-Qian Cha
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Juan Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xue-Bing Ren
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Dong Li
- Department of Molecular Biology, Qingdao Vland Biotech Group Inc., Qingdao, China
| | - Peng Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hui-Hui Fu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Fei Xu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| |
Collapse
|
29
|
Arthrobacter sulfonylureivorans sp. nov., isolated from a sulfonylurea herbicides degrading consortium enriched with birch forest soil. Arch Microbiol 2020; 203:1039-1045. [PMID: 33140141 DOI: 10.1007/s00203-020-02097-2] [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: 03/10/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 10/23/2022]
Abstract
A gram-stain positive, aerobic, motile, rod-shaped bacterium, designated strain LAM7117T, was isolated from a sulfonylurea herbicides degrading consortium enriched with birch forest soil. The optimal temperature and pH for the growth of strain LAM7117T were 35 °C and 7.5, respectively. Strain LAM7117T could grow in the presence of NaCl with concentration up to 9% (w/v). Strain LAM7117T formed a distinct phylogenetic subclade within the genus Arthrobacter in the phylogenetic trees built with 16S rRNA gene sequences and shared the highest similarity with A. crystallopoietes JCM 2522T (97.7%). The values of digital DNA-DNA relatedness and Avery Nucleotide Identity based on the genome sequences between LAM7117T and A. crystallopoietes JCM 2522T were 21.4 and 77.4%, respectively. The genomic DNA G + C content was 65.9 mol%. The major cellular fatty acids were anteiso-C15:0, iso-C16:0 and anteiso-C17:0. The cell wall peptidoglycan contained the amino acids as glycine, lysine, alanine and glutamic acid. The major polar lipids present in strain LAM7117T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidyl inositol, two unidentified glycolipids and one unidentified lipid. The predominant menaquinones of strain LAM7117T were MK-8 and MK-9. Based on the phenotypic characteristics, chemotaxonomic data and genotypic analyses, strain LAM7117T should be classified as a novel species of genus Arthrobacter, for which the name Arthrobacter sulfonylureivorans sp. nov. is proposed. The type strain is LAM7117T (= JCM 32824T = CGMCC 1.16681T).
Collapse
|
30
|
Ulva lactuca as a functional ingredient and water bioremediator positively influences the hepatopancreas and water microbiota in the rearing of Litopenaeus vannamei. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.102040] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
31
|
Gotteland M, Riveros K, Gasaly N, Carcamo C, Magne F, Liabeuf G, Beattie A, Rosenfeld S. The Pros and Cons of Using Algal Polysaccharides as Prebiotics. Front Nutr 2020; 7:163. [PMID: 33072794 PMCID: PMC7536576 DOI: 10.3389/fnut.2020.00163] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
Macroalgae stand out for their high content of dietary fiber (30–75%) that include soluble, sulfated (fucoidan, agaran, carrageenan, and ulvan) and non-sulfated (laminaran and alginate) polysaccharides. Many studies indicate that these compounds exert varied biological activities and health-promoting effects and for this reason, there is a growing interest for using them in food products. The aim of this review was to critically evaluate prebiotic properties of algal polysaccharides, i.e., their ability to exert biological activities by modulating the composition and/or diversity of gut microbiota (GM). Pre-clinical studies show that the non-sulfated alginate and laminaran are well-fermented by GM, promoting the formation of short chain fatty acids (SCFAs) including butyrate, and preventing that of harmful putrefactive compounds (NH3, phenol, p-cresol, indole and H2S). Alginate increases Bacteroides, Bifidobacterium, and Lactobacillus species while laminaran mostly stimulates Bacteroides sp. Results with sulfated polysaccharides are more questionable. Agarans are poorly fermentable but agarose-oligosaccharides exhibit an interesting prebiotic potential, increasing butyrate-producing bacteria and SCFAs. Though carrageenan-oligosaccharides are also fermented, their use is currently limited due to safety concerns. Regarding fucoidan, only one study reports SCFAs production, suggesting that it is poorly fermented. Its effect on GM does not indicate a clear pattern, making difficult to conclude whether it is beneficial or not. Notably, fucoidan impact on H2S production has not been evaluated, though some studies report it increases sulfate-reducing bacteria. Ulvan is badly fermented by GM and some studies show that part of its sulfate is dissimilated to H2S, which could affect colonic mitochondrial function. Accordingly, these results support the use of laminaran, alginate and agaro-oligosaccharides as prebiotics while more studies are necessary regarding that of fucoidan, carrageenan and ulvan. However, the realization of clinical trials is necessary to confirm such prebiotic properties in humans.
Collapse
Affiliation(s)
- Martin Gotteland
- Department of Nutrition, Faculty of Medicine, University of Chile, Santiago, Chile.,Department of Human Nutrition, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile.,Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| | - Karla Riveros
- Department of Nutrition, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Naschla Gasaly
- Department of Nutrition, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Constanza Carcamo
- Department of Nutrition, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Fabien Magne
- Microbiology and Mycology Program, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, University of Chile, Santiago, Chile
| | - Gianella Liabeuf
- Department of Nutrition, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Alejandra Beattie
- Laboratorio de Ecosistemas Marinos Antárticos y Subantárticos, Universidad de Magallanes, Punta Arenas, Chile.,Centro de Investigación para la Conservación de Ecosistemas Australes, Punta Arenas, Chile
| | - Sebastián Rosenfeld
- Laboratorio de Ecosistemas Marinos Antárticos y Subantárticos, Universidad de Magallanes, Punta Arenas, Chile.,Laboratorio de Ecología Molecular, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Instituto de Ecología y Biodiversidad, Santiago, Chile
| |
Collapse
|
32
|
Comparative Genomic Study of Polar Lichen-Associated Hymenobacter sp. PAMC 26554 and Hymenobacter sp. PAMC 26628 Reveals the Presence of Polysaccharide-Degrading Ability Based on Habitat. Curr Microbiol 2020; 77:2940-2952. [PMID: 32681312 DOI: 10.1007/s00284-020-02120-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/07/2020] [Indexed: 12/20/2022]
Abstract
The genus Hymenobacter is classified in the family Hymenobacteraceae under the phylum Bacteroidetes. They have been isolated from diverse environments, such as air, soil, and lichen, along with extreme polar environments, including the Arctic and Antarctic regions. The polar regions have attracted intense research interest for the discovery of novel microorganisms and their functions. Analysis of the polysaccharide utilization-related carbohydrate-active enzyme among the two lichen-associated polar organisms Hymenobacter sp. PAMC 26554 and Hymenobacter sp. PAMC 26628 was performed, along with its comparison with the complete genome of the same genus available in the NCBI database. The study was conducted relying on the AZCL screening data for the two polar lichen-associated species. While comparing with eight other complete genomes, differences in polysaccharide preferences based on the isolation environment and biosample source were discovered. All the species showed almost similar percentage of cellulose synthesis and degradation genes. However, the polar lichen-associated microorganism was found to have a high percentage of hemicellulose degradation genes, and less starch and laminarin degradation. The Hymenobacter species with higher number of hemicellulose degradation genes was found to have a lower number of starch and laminarin degradation genes and vice versa, highlighting the differences in polysaccharide utilization among the species.
Collapse
|
33
|
Cheng W, Yan X, Xiao J, Chen Y, Chen M, Jin J, Bai Y, Wang Q, Liao Z, Chen Q. Isolation, identification, and whole genome sequence analysis of the alginate-degrading bacterium Cobetia sp. cqz5-12. Sci Rep 2020; 10:10920. [PMID: 32616809 PMCID: PMC7331586 DOI: 10.1038/s41598-020-67921-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 06/16/2020] [Indexed: 01/09/2023] Open
Abstract
Alginate-degrading bacteria or alginate lyases can be used to oligomerize alginate. In this study, an alginate-degrading bacterium with high alginolytic activity was successfully screened by using Sargassum fusiforme sludge. When the strain was grown on a plate containing sodium alginate, the transparent ring diameter (D) was 2.2 cm and the ratio (D/d) of transparent ring diameter to colony diameter (d) was 8.8. After 36 h in culture at a temperature of 28 °C shaken at 150 r/min, the enzymatic activity of the fermentation supernatant reached 160 U/mL, and the enzymatic activity of the bacterial precipitate harvested was 2,645 U/mL. The strain was named Cobetia sp. cqz5-12. Its genome is circular in shape, 4,209,007 bp in size, with a 62.36% GC content. It contains 3,498 predicted coding genes, 72 tRNA genes, and 21 rRNA genes. The functional annotations for the coding genes demonstrated that there were 181 coding genes in the genome related to carbohydrate transport and metabolism and 699 coding genes with unknown functions. Three putative coding genes, alg2107, alg2108 and alg2112, related to alginate degradation were identified by analyzing the carbohydrate active enzyme (CAZy) database. Moreover, proteins Alg2107 and Alg2112 were successfully expressed and exhibited alginate lyase activity.
Collapse
Affiliation(s)
- Wenwen Cheng
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Xuanyu Yan
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Jiali Xiao
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Yunyun Chen
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Minghui Chen
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Jiayi Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Yu Bai
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Qi Wang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Zhiyong Liao
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China.
| | - Qiongzhen Chen
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China.
| |
Collapse
|
34
|
Xing J, Jiang X, Kong D, Zhou Y, Li M, Han X, Ma Q, Tan H, Ruan Z. Streptomyces soli sp. nov., isolated from birch forest soil. Arch Microbiol 2020; 202:1687-1692. [PMID: 32285167 DOI: 10.1007/s00203-020-01878-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 03/22/2020] [Accepted: 04/01/2020] [Indexed: 11/27/2022]
Abstract
A Gram-staining positive, aerobic, non-motile, rod-shaped bacterium, designated strain LAM7114T, was isolated from soil sample collected from a birch forest in Xinjiang Uygur Autonomous Region, China. The optimal temperature and pH for the growth of strain LAM7114T were 30 °C and 7.0, respectively. Strain LAM7114T could grow in the presence of NaCl up to 10% (w/v). Comparative analysis of the 16S rRNA gene sequences revealed that LAM7114T was closely related to the members of the family genus Streptomyces, with the highest similarity to Streptomyces urticae NEAU-PCY-1T (98.3%) and Streptomyces fildesensis GW25-5T (98.2%). The genomic G + C content was 70.0 mol%. The DNA-DNA hybridization values between strain LAM7114T and S. urticae CCTCC AA 2017015T, S. fildesensis CGMCC 4.5735T were 32.5 ± 1.8% and 27.5 ± 2.6%, respectively. The cell wall contained LL-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan. The whole-cell hydrolysates included glucose and mannose. The major fatty acids were anteiso-C15:0, iso-C15:0 and iso-C16:0. The predominant menaquinones were MK-9(H6), MK-9(H4) and MK-9(H8). The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, three unidentified aminophospholipids, three unidentified phospholipids, and an unidentified aminolipid. Based on the phenotypic characteristics and genotypic analyses, we propose that strain LAM7114T represents a novel species in the genus Streptomyces, for which the name Streptomyces soli sp. nov. is proposed. The type strain is LAM7114T (= CGMCC 4.7581T = JCM 32822T).
Collapse
Affiliation(s)
- Jialing Xing
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China
| | - Xu Jiang
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China
| | - Delong Kong
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China
| | - Yiqing Zhou
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China
| | - Miaomiao Li
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China.,College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Xiaoyan Han
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China.,College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Qingyun Ma
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China
| | - Hao Tan
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China
| | - Zhiyong Ruan
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, China.
| |
Collapse
|
35
|
Zhou LY, Meng X, Zhong YL, Li GY, Du ZJ, Mu DS. Dokdonia sinensis sp. nov., a flavobacterium isolated from surface seawater. Int J Syst Evol Microbiol 2020; 70:1617-1622. [PMID: 32228747 DOI: 10.1099/ijsem.0.003949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was carried out on strain SH27T, which was isolated from seawater collected around Xiaoshi Island, PR China. Cells of strain SH27T were Gram-stain-negative, non-motile, rod-shaped, orange-pigmented and grew at 15-37 °C (optimum, 28 °C), at pH 6.0-8.0 (pH 7.0) and in 1.0-7.0 % (w/v) NaCl (2.0-3.0 %). The isolate was positive for catalase, but negative for nitrate reduction, oxidase, indole production and urease. Carotenoid pigment was produced. Phylogenetic analysis based on the 16S rRNA gene placed strain SH27T in the genus Dokdonia with the closest relative being Dokdonia donghaensis KCTC 12391T, exhibiting 96.7 % 16S rRNA gene pairwise similarity. The results of genomic comparisons, including average nucleotide identity and digital DNA-DNA hybridization, showed 72.9 and 19.2 % identity to D. donghaensis KCTC 12391T, respectively. The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine and two unidentified lipids. Menaquinone-6 was the only respiratory quinone. The G+C content of the genomic DNA was 32.9 mol%. On the basis of the phenotypic and phylogenetic data, strain SH27T represents a novel species of the genus Dokdonia, for which the name Dokdonia sinensis sp. nov. is proposed, with the type strain SH27T (MCCC 1H00358T=CCTCC AB 2018323T=KCTC 62962T).
Collapse
Affiliation(s)
- Liu-Yan Zhou
- Marine College, Shandong University, Weihai 264209, PR China
| | - Xue Meng
- Marine College, Shandong University, Weihai 264209, PR China
| | - Yan-Lin Zhong
- Marine College, Shandong University, Weihai 264209, PR China
| | - Guang-Yu Li
- Third Institute of Oceanography, Ministry of Natural Resources, XiaMen 361000, PR China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.,Marine College, Shandong University, Weihai 264209, PR China
| | - Da-Shuai Mu
- Marine College, Shandong University, Weihai 264209, PR China.,State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| |
Collapse
|
36
|
Liu J, Cai SD, Wang YJ, Wang Q, Zhang DC. Algibacter pacificus sp. nov., isolated from a deep-sea seamount. Int J Syst Evol Microbiol 2020; 70:2907-2911. [DOI: 10.1099/ijsem.0.004119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Gram-stain-negative, rod-shaped, yellow-pigmented and facultative anaerobic bacterial strain, designated H164T, was isolated from seawater collected from the Caroline Seamounts in the Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain H164T was related to the genus
Algibacter
and had highest 16S rRNA gene sequence similarity to
Algibacter wandonensis
WS-MY22T (97.4 %). The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1 G, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH. The predominant menaquinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, one unidentified aminolipid and two unidentified lipids. The genomic DNA G+C content of strain H164T was 33.2 mol%. The values of in silico DNA–DNA hybridization (isDDH) and average nucleotide identity (ANI) between strain H164T and
A. wandonensis
KCTC 32381T were 26.10 and 81.88 %. The isDDH and ANI values between strain H164T and
Algibacter lectus
DSM 15365T were 25.40 and 81.79 %. Combined data from phenotypic, phylogenetic, isDDH and ANI analyses demonstrated that strain H164T represents a novel species of the genus
Algibacter
, for which we propose the name Algibacter pacificus sp. nov. (type strain H164T=KCTC 72432T=CGMCC 1.17117T).
Collapse
Affiliation(s)
- Jie Liu
- Department of Bioengineering, College of Marine Sciences and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Sheng-Dong Cai
- Department of Bioengineering, College of Marine Sciences and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Yu-Jing Wang
- Department of Bioengineering, College of Marine Sciences and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Qian Wang
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - De-Chao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China
| |
Collapse
|
37
|
Hameed A, Lai WA, Shahina M, Stothard P, Young LS, Lin SY, Sridhar KR, Young CC. Differential visible spectral influence on carbon metabolism in heterotrophic marine flavobacteria. FEMS Microbiol Ecol 2020; 96:5710931. [PMID: 31960903 DOI: 10.1093/femsec/fiaa011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 01/20/2020] [Indexed: 12/26/2022] Open
Abstract
The visible spectrum of solar radiation is known to stimulate photoheterotrophic bacterial carbon metabolism. However, its impact on 'strictly' heterotrophic bacteria remains less explored. Here, we show that heterotrophic flavobacteria exhibit enhanced uptake and mineralization of dissolved organic carbon with increasing wavelengths of visible light, without employing any 'known' light-harvesting mechanisms. RNA sequencing identified blue light as a major constraint in the extracellular enzymatic hydrolysis of polymeric carbohydrates and acquisition of sugars, despite acting as a stimulus for inorganic carbon sequestration. In contrast, green-red and continuous full-spectrum lights activated diverse hydrolytic enzymes and sugar transporters, but obstructed inorganic carbon fixation. This 'metabolic switching' was apparent through limited nutrient uptake, suppressed light-sensitivity, oxidative stress response and promotion of inorganic carbon sequestration pathways under blue light. The visible light impact on metabolism may be of significant ecological relevance as it appears to promote cell-mediated mineralization of organic carbon in 'green-colored' chlorophyll-rich copiotrophic coastal seawater and inorganic carbon sequestration in 'blue-colored' oligotrophic open ocean. Thus, a novel regulatory role played by light on heterotrophic metabolism and a hidden potential of flavobacteria to sense and respond differentially to monochromatic lights influencing marine carbon cycling were unraveled.
Collapse
Affiliation(s)
- Asif Hameed
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Road, Taichung 40227, Taiwan
| | - Wei-An Lai
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Road, Taichung 40227, Taiwan
| | - Mariyam Shahina
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Road, Taichung 40227, Taiwan
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 1427 College Plaza, Edmonton, Alberta, Canada
| | - Li-Sen Young
- Tetanti AgriBiotech Inc. No. 1, Gongyequ 10th Rd., Xitun Dist., Taichung 40755, Taiwan
| | - Shih-Yao Lin
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Road, Taichung 40227, Taiwan
| | | | - Chiu-Chung Young
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Road, Taichung 40227, Taiwan.,Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, 145, XingDa Road, Taichung 40227, Taiwan
| |
Collapse
|
38
|
Li Y, Lei L, Zheng L, Xiao X, Tang H, Luo C. Genome sequencing of gut symbiotic Bacillus velezensis LC1 for bioethanol production from bamboo shoots. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:34. [PMID: 32140179 PMCID: PMC7048129 DOI: 10.1186/s13068-020-1671-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Bamboo, a lignocellulosic feedstock, is considered as a potentially excellent raw material and evaluated for lignocellulose degradation and bioethanol production, with a focus on using physical and chemical pre-treatment. However, studies reporting the biodegradation of bamboo lignocellulose using microbes such as bacteria and fungi are scarce. RESULTS In the present study, Bacillus velezensis LC1 was isolated from Cyrtotrachelus buqueti, in which the symbiotic bacteria exhibited lignocellulose degradation ability and cellulase activities. We performed genome sequencing of B. velezensis LC1, which has a 3929,782-bp ring chromosome and 46.5% GC content. The total gene length was 3,502,596 bp using gene prediction, and the GC contents were 47.29% and 40.04% in the gene and intergene regions, respectively. The genome contains 4018 coding DNA sequences, and all have been assigned predicted functions. Carbohydrate-active enzyme annotation identified 136 genes annotated to CAZy families, including GH, GTs, CEs, PLs, AAs and CBMs. Genes involved in lignocellulose degradation were identified. After a 6-day treatment, the bamboo shoot cellulose degradation efficiency reached 39.32%, and the hydrolysate was subjected to ethanol fermentation with Saccharomyces cerevisiae and Escherichia coli KO11, yielding 7.2 g/L of ethanol at 96 h. CONCLUSIONS These findings provide an insight for B. velezensis strains in converting lignocellulose into ethanol. B. velezensis LC1, a symbiotic bacteria, can potentially degrade bamboo lignocellulose components and further transformation to ethanol, and expand the bamboo lignocellulosic bioethanol production.
Collapse
Affiliation(s)
- Yuanqiu Li
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Binhe Road, Central District, Leshan, 614000 China
| | - Lu Lei
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Binhe Road, Central District, Leshan, 614000 China
| | - Li Zheng
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Binhe Road, Central District, Leshan, 614000 China
| | - Ximeng Xiao
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Binhe Road, Central District, Leshan, 614000 China
| | - Hao Tang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Binhe Road, Central District, Leshan, 614000 China
| | - Chaobing Luo
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Binhe Road, Central District, Leshan, 614000 China
| |
Collapse
|
39
|
Li M, Song J, Ma Q, Kong D, Zhou Y, Jiang X, Parales R, Ruan Z, Zhang Q. Insight into the Characteristics and New Mechanism of Nicosulfuron Biodegradation by a Pseudomonas sp. LAM1902. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:826-837. [PMID: 31895558 DOI: 10.1021/acs.jafc.9b06897] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A total of five strains of nicosulfuron-degrading bacteria were isolated from a continuously cultivated microbial consortium using culturomics. Among them, a novel Pseudomonas strain, LAM1902, with the highest degradation efficiency was investigated in detail. The characteristics of nicosulfuron-degradation by LAM1902 were investigated and optimized by response surface analysis. Furthermore, non-targeted metabolomic analysis of extracellular and intracellular biodegradation of nicosulfuron by LAM1902 was carried out by liquid chromatography/mass spectroscopy (LC-MS) and gas chromatography-time-of-flight/mass spectroscopy (GC-TOF/MS). It was found that nicosulfuron was degraded by LAM1902 mainly via breaking the sulfonylurea bridge, and this degradation might be attributed to oxalate accumulation. The results of GC-TOF/MS also showed that the intracellular degradation of nicosulfuron did not occur. However, nicosulfuron exerted a significant influence on the metabolism of inositol phosphate, pyrimidine, arginine/proline, glyoxylate, and dicarboxylate metabolism and streptomycin biosynthesis. The changes of myo-inositol, trehalose, and 3-aminoisobutanoic acid were proposed as a mechanism of self-protection against nicosulfuron stress.
Collapse
Affiliation(s)
- Miaomiao Li
- College of Bioscience and Engineering , Jiangxi Agricultural University , Nanchang 330045 , PR China
| | - Jinlong Song
- Chinese Academy of Fishery Sciences , Beijing 100141 , China
| | - Qingyun Ma
- Institute of Agricultural Resources and Regional Planning , Chinese Academy of Agricultural Sciences , Beijing 100081 , China
| | - Delong Kong
- Institute of Agricultural Resources and Regional Planning , Chinese Academy of Agricultural Sciences , Beijing 100081 , China
| | - Yiqing Zhou
- Institute of Agricultural Resources and Regional Planning , Chinese Academy of Agricultural Sciences , Beijing 100081 , China
| | - Xu Jiang
- Institute of Agricultural Resources and Regional Planning , Chinese Academy of Agricultural Sciences , Beijing 100081 , China
| | - Rebecca Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences , University of California, Davis , Davis 95616 , California , United States
| | - Zhiyong Ruan
- Institute of Agricultural Resources and Regional Planning , Chinese Academy of Agricultural Sciences , Beijing 100081 , China
| | - Qinghua Zhang
- College of Bioscience and Engineering , Jiangxi Agricultural University , Nanchang 330045 , PR China
| |
Collapse
|
40
|
Li J, Wang T, Yu S, Bai J, Qin S. Community characteristics and ecological roles of bacterial biofilms associated with various algal settlements on coastal reefs. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 250:109459. [PMID: 31479939 DOI: 10.1016/j.jenvman.2019.109459] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/20/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
Bacterial biofilms, which are a group of bacteria attaching to and ultimately forming communities on reefs, perform essential ecological functions in coastal ecosystems. Particularly, they may attract or repulse the settling down of opportunistic algae. However, this phenomenon and the interaction mechanism are not fully understood. This study investigated reefs from the Changdao coastal zone to determine the structures and functions of bacterial biofilms symbiosing with various algae using high-throughput sequencing analysis. The Shannon diversity index of microbiota with algal symbiosis reached 5.34, which was higher than that of microbiota wherein algae were absent (4.80). The beta diversity results for 11 samples revealed that there existed a separation between bacterial communities on reefs with and without attached algae, while communities with similar algae clustered together. The taxa mostly associated with algae-symbiotic microbiota are the Actinobacteria phylum, and the Flavobacteriia and Gammaproteobacteria classes. The Cyanobacteria phylum was not associated with algae-symbiotic microbiota. As revealed by functional analysis, the bacteria mostly involved in the metabolism of sulfur were represented by brown and red algae in the biofilm symbiosis. Bacteria related to the metabolism of certain trace elements were observed only in specific groups. Moreover, phototrophy-related bacteria were less abundant in samples coexisting with algae. This study established the link between bacterial biofilms and algal settlements on costal reefs, and revealed the possible holobiont relationship between them. This may provide new technical directions toward realizing algal cultivation and management during the construction of artificial reef ecosystems.
Collapse
Affiliation(s)
- Jialin Li
- Key Lab of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264000, Shandong, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Ting Wang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China; Key Lab of Marine Environmental Science and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Shuxian Yu
- Key Lab of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264000, Shandong, China
| | - Jie Bai
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China; Key Lab of Marine Environmental Science and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China.
| | - Song Qin
- Key Lab of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264000, Shandong, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| |
Collapse
|
41
|
Li M, Kong D, Wang Y, Ma Q, Han X, Zhou Y, Jiang X, Zhang Y, Ruan Z, Zhang Q. Photobacterium salinisoli sp. nov., isolated from a sulfonylurea herbicide-degrading consortium enriched with saline soil. Int J Syst Evol Microbiol 2019; 69:3910-3916. [PMID: 31693472 DOI: 10.1099/ijsem.0.003705] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, designated strain LAM9072T, was isolated from a sample of a sulfonylurea herbicide-degrading consortium enriched with saline soil. The optimal temperature and pH for the growth of strain LAM9072T were 35 °C and 7.0, respectively. Strain LAM9072T could grow in the presence of NaCl up to 9 % (w/v). Comparative analysis of the 16S rRNA gene sequences revealed that strain LAM9072T was closely related to members of the family Vibrionaceae, with the highest similarities to Photobacterium halotolerans MACL01T (97.7 %) and Photobacterium galatheae S2753T (97.7 %). Strain LAM9072T formed a distinct phylogenetic subclade within the genus Photobacterium in the 16S rRNA gene phylogenetic trees. The results of multi-locus sequence analysis revealed a distinct lineage with P. halotolerans MACL01T as its closest relative. The genomic G+C content was 50.2 mol%. The DNA-DNA hybridization values between strain LAM9072T and P. halotolerans LMG 22194T and P. galatheae LMG 28894T were 41.6 and 22.2 %, respectively. The average nucleotide identity values were 90.9 and 78.8 %, respectively, by comparing the draft genome sequences of strain LAM9072T and P. halotolerans LMG 22194T and P. galatheae LMG 28894T. The major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). Ubiquinone 8 was detected as the predominant respiratory quinone. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and four unidentified lipids. Based on its phenotypic characteristics and the results of genotypic analyses, we propose that strain LAM9072T represents a novel species, for which the name Photobacteriumsalinisoli sp. nov. is proposed. The type strain is LAM9072T (=ACCC 19961T=JCM 30852T).
Collapse
Affiliation(s)
- Miaomiao Li
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Delong Kong
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Yani Wang
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Qingyun Ma
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Xiaoyan Han
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Yiqing Zhou
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Xu Jiang
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Yuqin Zhang
- Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Medicinal Biotechnology, Beijing 100050, PR China
| | - Zhiyong Ruan
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Qinghua Zhang
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| |
Collapse
|
42
|
Schneider YKH, Ø. Hansen K, Isaksson J, Ullsten S, H. Hansen E, Hammer Andersen J. Anti-Bacterial Effect and Cytotoxicity Assessment of Lipid 430 Isolated from Algibacter sp. Molecules 2019; 24:molecules24213991. [PMID: 31694159 PMCID: PMC6864645 DOI: 10.3390/molecules24213991] [Citation(s) in RCA: 10] [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: 10/02/2019] [Revised: 10/30/2019] [Accepted: 11/04/2019] [Indexed: 12/14/2022] Open
Abstract
Two bacterial isolates from the Barents Sea, both belonging to the genus Algibacter, were found to yield extracts with anti-bacterial bioactivity. Mass spectrometry guided dereplication and purification of the active extracts lead to the isolation of the same active principle in both extracts. The structure of the bioactive compound was identified via mass spectrometry and nuclear resonance spectroscopy and it turned out to be the known lipopeptide Lipid 430. We discovered and determined its previously unknown anti-bacterial activity against Streptococcus agalactiae and revealed a cytotoxic effect against the A2058 human melanoma cell line at significantly lower concentrations compared to its anti-bacterial concentration. Flow cytometry and microscopy investigations of the cytotoxicity against the melanoma cell line indicated that Lipid 430 did not cause immediate cell lysis. The experiments with melanoma cells suggest that the compound functions trough more complex pathways than acting as a simple detergent.
Collapse
Affiliation(s)
- Yannik K.-H. Schneider
- Marbio, Faculty for Fisheries, Biosciences and Economy, UiT—The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway (S.U.); (E.H.H.); (J.H.A.)
- Correspondence: ; Tel.: +47-77649267
| | - Kine Ø. Hansen
- Marbio, Faculty for Fisheries, Biosciences and Economy, UiT—The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway (S.U.); (E.H.H.); (J.H.A.)
| | - Johan Isaksson
- Department of Chemistry, Faculty of Natural Sciences, UiT—The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway;
| | - Sara Ullsten
- Marbio, Faculty for Fisheries, Biosciences and Economy, UiT—The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway (S.U.); (E.H.H.); (J.H.A.)
| | - Espen H. Hansen
- Marbio, Faculty for Fisheries, Biosciences and Economy, UiT—The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway (S.U.); (E.H.H.); (J.H.A.)
| | - Jeanette Hammer Andersen
- Marbio, Faculty for Fisheries, Biosciences and Economy, UiT—The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway (S.U.); (E.H.H.); (J.H.A.)
| |
Collapse
|
43
|
Liu J, Xue CX, Sun H, Zheng Y, Meng Z, Zhang XH. Carbohydrate catabolic capability of a Flavobacteriia bacterium isolated from hadal water. Syst Appl Microbiol 2019; 42:263-274. [DOI: 10.1016/j.syapm.2019.01.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 12/17/2018] [Accepted: 01/15/2019] [Indexed: 11/26/2022]
|
44
|
Murphy AE, Kolkmeyer R, Song B, Anderson IC, Bowen J. Bioreactivity and Microbiome of Biodeposits from Filter-Feeding Bivalves. MICROBIAL ECOLOGY 2019; 77:343-357. [PMID: 30612185 DOI: 10.1007/s00248-018-01312-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/20/2018] [Indexed: 06/09/2023]
Abstract
Bivalves serve an important ecosystem function in delivering organic matter from pelagic to benthic zones and are important in mediating eutrophication. However, the fate of this organic matter (i.e., biodeposits) is an important consideration when assessing the ecological roles of these organisms in coastal ecosystems. In addition to environmental conditions, the processing of biodeposits is dependent on its composition and the metabolic capacity of the associated microbial community. The objectives of this study were to compare the biological reactivity, potential denitrification rates, and microbial communities of biodeposits sourced from different bivalve species: hard clam (Mercenaria mercenaria), eastern oyster (Crassostrea virginica), and ribbed mussel (Geukensia demissa). To our knowledge, this is the first study to investigate and compare the microbiome of bivalve biodeposits using high-throughput sequencing and provide important insight into the mechanisms by which bivalves may alter sediment microbial communities and benthic biogeochemical cycles. We show that clam biodeposits had significantly higher bioreactivity compared to mussel and oyster biodeposits, as reflected in higher dissolved inorganic carbon and ammonium production rates in controlled incubations. Potential denitrification rates were also significantly higher for clam biodeposits compared to oyster and mussel biodeposits. The microbial communities associated with the biodeposits were significantly different across bivalve species, with significantly greater abundances of Alteromonadales, Chitinophagales, Rhodobacterales, and Thiotrichales associated with the clam biodeposits. These bioreactivity and microbial differences across bivalve species are likely due to differences in bivalve physiology and feeding behavior and should be considered when evaluating the effects of bivalves on water quality and ecosystem function.
Collapse
Affiliation(s)
- Anna E Murphy
- Marine Science Center, Northeastern University, Nahant, MA, 01908, USA.
- College of William & Mary, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA.
| | | | - Bongkuen Song
- College of William & Mary, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA
| | - Iris C Anderson
- College of William & Mary, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA
| | - Jennifer Bowen
- Marine Science Center, Northeastern University, Nahant, MA, 01908, USA
| |
Collapse
|
45
|
Sun C, Xamxidin M, Wu YH, Cheng H, Wang CS, Xu XW. Alteromonas alba sp. nov., a marine bacterium isolated from seawater of the West Pacific Ocean. Int J Syst Evol Microbiol 2019; 69:278-284. [DOI: 10.1099/ijsem.0.003151] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Cong Sun
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Maripat Xamxidin
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, 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
| | - Chun-Sheng Wang
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| |
Collapse
|
46
|
Hooper R, Brealey JC, van der Valk T, Alberdi A, Durban JW, Fearnbach H, Robertson KM, Baird RW, Bradley Hanson M, Wade P, Gilbert MTP, Morin PA, Wolf JBW, Foote AD, Guschanski K. Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin. Mol Ecol 2019; 28:484-502. [PMID: 30187987 PMCID: PMC6487819 DOI: 10.1111/mec.14860] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/15/2018] [Accepted: 08/27/2018] [Indexed: 12/20/2022]
Abstract
Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.
Collapse
Affiliation(s)
- Rebecca Hooper
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Jaelle C. Brealey
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Tom van der Valk
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Antton Alberdi
- Centre for GeoGeneticsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagen KDenmark
| | - John W. Durban
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCalifornia
| | - Holly Fearnbach
- SR3, SeaLife Response, Rehabilitation, and ResearchSeattleWashington
| | - Kelly M. Robertson
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCalifornia
| | | | - M. Bradley Hanson
- Northwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWashington
| | - Paul Wade
- National Marine Mammal LaboratoryAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWashington
| | - M. Thomas P. Gilbert
- Centre for GeoGeneticsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagen KDenmark
- NTNU University MuseumTrondheimNorway
| | - Phillip A. Morin
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCalifornia
| | - Jochen B. W. Wolf
- Science of Life Laboratories and Department of Evolutionary BiologyEvolutionary Biology CentreUppsala UniversityUppsalaSweden
- Section of Evolutionary BiologyFaculty of BiologyLMU MunichMunichGermany
| | - Andrew D. Foote
- Molecular Ecology and Fisheries Genetics LaboratorySchool of Biological SciencesBangor UniversityBangorGwyneddUK
| | - Katerina Guschanski
- Animal EcologyDepartment of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| |
Collapse
|
47
|
Complete genome sequence of Bordetella sp. HZ20 sheds light on the ecological role of bacterium without algal-polysaccharides degrading abilities in the brown seaweed-abundant environment. Mar Genomics 2018. [DOI: 10.1016/j.margen.2018.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
48
|
Li Y, Guo XH, Dang YR, Sun LL, Zhang XY, Chen XL, Qin QL, Wang P. Complete genome sequence of Arcticibacterium luteifluviistationis SM1504 T, a cytophagaceae bacterium isolated from Arctic surface seawater. Stand Genomic Sci 2018; 13:33. [PMID: 30505389 PMCID: PMC6258284 DOI: 10.1186/s40793-018-0335-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/10/2018] [Indexed: 11/10/2022] Open
Abstract
Arcticibacterium luteifluviistationis SM1504T was isolated from Arctic surface seawater and classified as a novel genus of the phylum Bacteroides. To date, no Arcticibacterium genomes have been reported, their genomic compositions and metabolic features are still unknown. Here, we reported the complete genome sequence of A. luteifluviistationis SM1504T, which comprises 5,379,839 bp with an average GC content of 37.20%. Genes related to various stress (such as radiation, osmosis and antibiotics) resistance and gene clusters coding for carotenoid and flexirubin biosynthesis were detected in the genome. Moreover, the genome contained a 245-kb genomic island and a 15-kb incomplete prophage region. A great percentage of proteins belonging to carbohydrate metabolism especially in regard to polysaccharides utilization were found. These related genes and metabolic characteristics revealed genetic basis for adapting to the diverse extreme Arctic environments. The genome sequence of A. luteifluviistationis SM1504T also implied that the genus Arcticibacterium may act as a vital organic carbon matter decomposer in the Arctic seawater ecosystem.
Collapse
Affiliation(s)
- Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
| | - Xiao-Han Guo
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
| | - Yan-Ru Dang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
| | - Lin-Lin Sun
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, No.1, Wenhai Rd, Qingdao, 266237 China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, No.1, Wenhai Rd, Qingdao, 266237 China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, No.1, Wenhai Rd, Qingdao, 266237 China
| | - Peng Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, No.72, Binhai Rd, Qingdao, 266237 China
| |
Collapse
|
49
|
Sun C, Xu L, Yu XY, Zhao Z, Wu YH, Oren A, Wang CS, Xu XW. Minwuia thermotolerans gen. nov., sp. nov., a marine bacterium forming a deep branch in the Alphaproteobacteria, and proposal of Minwuiaceae fam. nov. and Minwuiales ord. nov. Int J Syst Evol Microbiol 2018; 68:3856-3862. [PMID: 30325296 DOI: 10.1099/ijsem.0.003073] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, strictly aerobic, non-motile, non-spore-forming, rod-shaped bacteria, designated as SY3-15Tand SY3-13, were isolated from a seawater sample of the South China Sea. Colonies were 0.5-1.0 mm in diameter, smooth, circular, convex and translucent after growth on marine agar at 37 °C for 3 days. The strains were found to grow at 20-50 °C (optimum, 42 °C), pH 6.0-8.5 (optimum, pH 6.5-7.5) and with 0.5-6.0 % (w/v) NaCl (optimum, 1.5-2.0 %). Chemotaxonomic analysis showed the sole respiratory quinone to be ubiquinone-10, the major fatty acids (>10 %) were C16 : 0 3-OH, C19 : 0cyclo ω9c, C18 : 1 3-OH and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), and the polar lipids were phosphatidylglycerol, two unidentified aminolipids and three unidentified lipids. The DNA G+C content was 67.2-67.4 mol% calculated by genome. The 16S rRNA gene sequences of strains SY3-15T and SY3-13 were identical and related to the genus Lutibaculum with a similarity of 92.1 %. The 16S rRNA gene phylogenetic trees reconstructed with neighbour-joining, maximum-parsimony and minimum-evolution methods showed that the strains constituted a deep and separated branch from other families of Alphaproteobacteria, and the phylogenetic trees based on concatenated 163 protein sequences from genome sequences showed that the clade in which strains SY3-15T and SY3-13 located was separated from the clade of the other orders of Alphaproteobacteria, indicating it may represent a novel family of a novel order. Based on their phenotypic properties and their phylogenetic distinctiveness, we propose strains SY3-15T (=MCCC 1K03467T=KCTC 62335T) and SY3-13 (=MCCC 1K03466=KCTC 62329) to represent a novel species of a novel genus with the name Minwuia thermotolerans gen. nov., sp. nov., and we propose Minwuiaceae fam. nov. and Minwuiales ord. nov. with Minwuia as the type genus.
Collapse
Affiliation(s)
- Cong Sun
- 1College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, PR China.,2Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Lin Xu
- 1College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Xiao-Yun Yu
- 3College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Zhe Zhao
- 3College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yue-Hong Wu
- 2Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Aharon Oren
- 4The Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Chun-Sheng Wang
- 2Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Xue-Wei Xu
- 2Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| |
Collapse
|
50
|
Zhao Z, Shen X, Chen W, Yu XY, Fu GY, Sun C, Wu M. Emcibacter congregatus sp. nov., isolated from sediment cultured in situ. Int J Syst Evol Microbiol 2018; 68:2846-2850. [PMID: 30016229 DOI: 10.1099/ijsem.0.002906] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic, motile, rod-shaped, pale-yellow bacterial strain, designated as ZYLT, isolated from a cultured in situ sediment sample collected from the East China Sea coast, was studied using a polyphasic taxonomic approach. Strain ZYLT grew at 4-30 °C (optimum, 25 °C), at pH 6.0-8.5 (pH 7.0) and with 0-7.0 % (w/v) NaCl (2.0 %). Results of phylogenetic analysis based on 16S rRNA gene sequences clearly showed that strain ZYLT and Emcibacter nanhaiensis HTCJW17T, which was most closely related to strain ZYLT with 93.6 % sequence similarity, clustered together. The genomic DNA G+C content was 51.5 % (genome sequence). The quinone system was composed only of ubiquinone-10. Strain ZYLT possessed C18 : 1ω7c and/or C18 : 1ω6c (summed feature 8), iso-C15 : 0 2-OH and/or C16 : 1ω7c (summed feature 3), C14 : 0 2-OH and C14 : 0 as the major fatty acids. The content of summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) in strain ZYLT was far greater than that in E. nanhaiensis. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminophospholipids, three unidentified phospholipids, one unidentified aminolipid and four unidentified lipids. One unidentified aminophospholipid and two unidentified lipids present in strain ZYLT were not found in E. nanhaiensis in this research. On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain ZYLT (=KCTC 62328T=JCM 32378T=MCCC 1K03526T) represents a novel species of the genus Emcibacter for which the name Emcibacter congregatus sp. nov. is proposed.
Collapse
Affiliation(s)
- Zhe Zhao
- 1College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xia Shen
- 1College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Wu Chen
- 2Zhejiang University of Water Resources and Electric Power, Hangzhou 310058, PR China
| | - Xiao-Yun Yu
- 1College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Ge-Yi Fu
- 3Ocean College, Zhejiang University, Hangzhou 310058, PR China
| | - Cong Sun
- 4College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Min Wu
- 1College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| |
Collapse
|