Isolation of a phosphonate-degrading symbiotic bacterium from Prorocentrum donghaiense and its promoting effect on algal growth
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摘要: 海洋中的膦酸酯（C-P键有机磷）是可供浮游植物利用的一种潜在磷源。甲藻自身无法直接利用膦酸酯，但是其共生细菌可将膦酸酯降解为磷酸盐，从而促进藻细胞的生长。然而，目前尚未有针对特定菌株的相关研究。本研究在2-氨基乙基膦酸（2-AEP）作为唯一磷源条件下对东海原甲藻进行培养，对其中的共生细菌进行分离纯化，初步得到5种细菌。基因组测序结果表明，其中一株尹氏菌属细菌Yoonia sp. PD-AEP-1中存在两种C-P裂解酶途径。通过藻菌共培养实验对菌株功能进行验证，结果显示，将藻细胞处理至磷饥饿状态之后，同时加入2-AEP与PD-AEP-1悬液，与只加2-AEP或只加细菌悬液的条件相比，藻细胞生长速率和体系内磷酸盐浓度显著升高，同时碱性磷酸酶活性及非光化学淬灭值则明显降低，表明PD-AEP-1具备将2-AEP降解为磷酸盐的能力，进而缓解了东海原甲藻细胞的磷限制状态，有效促进了藻细胞的生长。该研究表明，东海原甲藻共生细菌在降解膦酸酯从而为藻细胞提供磷源方面扮演着一定角色，这一过程很可能有助于东海原甲藻赤潮的暴发，凸显了海洋生态系统中藻−菌相互作用的重要性。Abstract: Phosphonates in the ocean are a kind of potential phosphorus (P) source which could be utilized by phytoplankton. Although dinoflagellates cannot directly utilize phosphonates themselves, their symbiotic bacteria have the capability to degrade phosphonates into phosphate, thereby promoting the growth of algal cells. However, no studies focusing on a specific bacteria strain have been conducted thus far. In this study, Prorocentrum donghaiense was cultured under conditions with 2-Aminoethylphosphonic acid (2-AEP) as the sole P source. Isolation and purification of the symbiotic bacteria from the culture was conducted and five kinds of bacteria were obtained. Genome sequencing results revealed the presence of two types of C-P lyase pathways in the bacterial strain designated as Yoonia sp. PD-AEP-1. The function of the bacteira strain was verified through the co-culture of bacteria and algal cells. The results demonstrated that after the algal cells were treated to phosphorus-starved condition, when 2-AEP and the bacteria suspension were added together, as compared to conditions which only 2-AEP or the bacterial suspension of PD-AEP-1 was introduced, both the growth rate of algal cells and the phosphate concentration in the cultures showed a significant increase. Meanwhile, alkaline phosphatase activity and non-photochemical quenching of the algal cells decreased significantly, indicating that PD-AEP-1 has the ability to degrade 2-AEP into phosphate, thereby alleviating phosphorus limitation for P. donghaiense cells and effectively promoting the growth of algal cells. The study suggests that symbiotic bacteria of P. donghaiense might play a part in providing P sources to the algal cells through the degradation of phosphonates. This process could probably contribute to the outbreak of P. donghaiense bloom, highlighting the importance of algae-bacteira interactions in marine ecosystems.
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Key words:
- phosphonates /
- Prorocentrum donghaiens /
- symbiotic bacteria /
- algal-growth-promoting effect /
- red tide
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图 1 3种磷源条件下东海原甲藻细胞的生长曲线（a）及培养体系内磷酸盐浓度（b）
磷酸盐：f/2培养基，磷酸盐浓度为36 μmol/L；2-AEP：f/2-P培养基基础上添加36 μmol/L的2-AEP；无磷：f/2-P培养基，未添加任何磷源
Fig. 1 Growth curve of Prorocentrum donghaiense (a) and phosphate concentration in the culture (b) under three P conditions
Phosphate: f/2 medium, phosphate concentration was 36 μmol/L; 2-AEP: f/2-P medium, while 36 μmol/L 2-AEP was added; No phosphorus: f/2-P medium, no P source was added
图 2 基于16S rRNA基因序列构建的东海原甲藻共生细菌及其相近菌株Neighbour-Joining树
Fig. 2 Neighbour-Joining tree of Prorocentrum donghaiense symbiotic bacteria and their close strains constructed in the basis of the 16S rRNA gene sequences
图 3 PD-AEP-1基因组中归属于RAST不同子系统类别基因的分布情况
Fig. 3 Distribution of the genes from the genome of PD-AEP-1 which belong to the “Subsystem Category” of RAST
图 4 PD-APE-1基因组中两个C-P裂解酶途径基因簇的排布
“*”表示基因簇II中的基因；不同颜色分别代表编码膦酸酯转运蛋白（绿色）、调控蛋白（紫色）及C-P裂解酶亚基蛋白的基因，黑色为未知功能蛋白；atf: 膦酸酯利用相关乙酰转移酶基因, atu: 未知功能蛋白Atu0170编码基因
Fig. 4 The organization of two gene clusters of C-P lyase pathways in the genome of the PD-AEP-1
“*” indicates the genes of the second cluster. Genes encoding phosphonate transport (green) and regulation (purple), the C-P lyase subunits (yellow) and other proteins of unknown function (black) are shown in different colors. atf: phosphonate utilization associated acetyltransferase, atu: uncharacterized protein Atu0170
图 5 3种培养条件下东海原甲藻细胞的生长曲线（a）、磷酸盐浓度（b）、碱性磷酸酶活性（c）及第12 d的NPQ诱导曲线（d）
藻 + 菌：藻细胞培养体系中加入1%体积细菌悬液；藻 + 2-AEP：藻细胞培养体系中加入36 μmol/L 2-AEP；藻 + 菌 + 2-AEP：藻细胞培养体系中同时加入1%体积细菌悬液和36 μmol/L 2-AEP
Fig. 5 Growth curve and of Prorocentrum donghaiense, phosphate concentration measurement, alkaline phosphatase activity (APA) measurement and induction curve of NPQ in the 12th day under three culture conditions
Algae + bacteria: algal culture systems added with 1% volume of bacteria suspension; Algae + 2-AEP: algal culture systems added with 36 μmol/L 2-AEP; Algae + bacteria + 2-AEP: algal culture systems added with 1% volume of bacteria suspension and 36 μmol/L 2-AEP
表 1 PD-AEP-1基因组中与磷代谢相关的基因及其特征
Tab. 1 Genes and their characteristics related to P metabolism in the genome of PD-AEP-1
子系统 基因编号 功能 高亲和力磷酸盐转运蛋白和 Pho 调节子调控 peg.1464 磷酸盐转运系统调节蛋白PhoU peg.1463 磷酸盐调节子转录调节蛋白PhoB (SphR) peg.1832 磷酸盐调节子传感蛋白PhoR (SphS) (EC 2.7.13.3) 多聚磷酸盐 peg.2944 聚磷酸盐激酶 (EC 2.7.4.1) peg.2027 外切聚磷酸酶 (EC 3.6.1.11) 磷酸盐代谢 peg.1508 NAD(P) 转氢酶β亚基 (EC 1.6.1.2) peg.3897 碱性磷酸酶 (EC 3.1.3.1) peg.3045 磷酸盐饥饿诱导蛋白PhoH peg.1039 锰依赖型无机焦磷酸酶 (EC 3.6.1.1) 
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表 2 PD-AEP-1基因组中与膦酸酯利用相关的基因及其特征
Tab. 2 Genes related to phosphonate utilization in the genome of PD-AEP-1 and their characteristics
重叠群 基因编号 长度/bp 编码的酶/蛋白* NODE_9_length_69264_cov_65.868739 peg.3912 1146 Alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase PhnM2 (EC 3.6.1.63) peg.3913 675 Uncharacterized protein Atu0170, clustered with phosphonate utilization peg.3914 543 Ribose 1,5-bisphosphate phosphokinase PhnN (EC 2.7.4.23) peg.3915 684 Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnL (EC 2.7.8.37) peg.3916 771 Phosphonates utilization ATP-binding protein PhnK peg.3917 831 Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase PhnJ (EC 4.7.1.1) peg.3918 1083 Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI (EC 2.7.8.37) peg.3919 561 Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnH (EC 2.7.8.37) peg.3920 456 Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnG (EC 2.7.8.37) peg.3921 723 Transcriptional regulator PhnF peg.3922 1188 Metal-dependent hydrolase involved in phosphonate metabolism PhnM1 peg.3923 615 Phosphonate utilization associated acetyltransferase (ATF) peg.3924 1329 Phosphonate ABC transporter permease protein PhnE1 (TC 3.A.1.9.1) peg.3925 873 Phosphonate ABC transporter permease protein PhnE2 (TC 3.A.1.9.1) peg.3926 903 Phosphonate ABC transporter substrate-binding protein PhnD (TC 3.A.1.9.1) peg.3927 819 Phosphonate ABC transporter ATP-binding protein PhnC (TC 3.A.1.9.1) NODE_1_length_861959_cov_71.815100 peg.775 537 PhnH protein peg.776 1056 Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI (EC 2.7.8.37) peg.777 915 Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase PhnJ (EC 4.7.1.1) peg.778 798 Phosphonates utilization ATP-binding protein PhnK peg.779 720 Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnL (EC 2.7.8.37) peg.780 1194 Alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase PhnM (EC 3.6.1.63) peg.781 816 Phosphonate ABC transporter ATP-binding protein PhnC (TC 3.A.1.9.1) peg.782 915 Phosphonate ABC transporter substrate-binding protein PhnD (TC 3.A.1.9.1) peg.783 933 ABC transporter, permease protein PhnE1 peg.784 858 Phosphonate ABC transporter permease protein PhnE2(TC 3.A.1.9.1) peg.785 630 Phosphonate utilization associated acetyltransferase NODE_24_length_14478_cov_37.311755 peg.1318 576 PhnH protein peg.1319 1014 Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI (EC 2.7.8.37) peg.1320 846 Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase PhnJ (EC 4.7.1.1) peg.1321 768 Phosphonates utilization ATP-binding protein PhnK 注：因该列酶和蛋白的名称仍然未有公认的中文译名，因此采用英文名称。
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