Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression.
Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression.
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DOI：
10.3389/fmicb.2015.00818
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发表时间：
2015
影响因子：
5.2
通讯作者：
Thompson JR
中科院分区：
文献类型：
--
作者：
Har JY;Helbig T;Lim JH;Fernando SC;Reitzel AM;Penn K;Thompson JR
我们对海葵微生物群的分子和基因组多样性进行了表征，海葵是比较发育和功能生物学的典范，是温带盐沼的常年居住者。16S rRNA基因克隆文库的分子系统发育分析显示，在多个地点和时间有四种核型与媒介新城疫相关。其中包括两种新的核型，分别与培养菌株有85%的同源性；两种ε-变形杆菌核型与内生单胞菌和油假单胞菌的16SRRNA同源性分别为99%和99%。这两种核型分别属于弯曲杆菌ε和螺旋藻γ。物种特异性聚合酶链式反应显示，这些种群持续存在于实验室条件下无性繁殖的媒介新月体中。结果表明，在马萨诸塞州西佩维塞特沼泽的海葵中，弯曲菌和内生单胞菌的16S rRNA均有表达。实验室培养的病原细菌以油假单胞菌和放射型根瘤菌为主。从现场采集的海葵分离出的菌株与利诺杆菌和葡萄球菌分离株有关联。对10株代表现场和实验室联合培养的细菌进行了基因组DNA测序，这些细菌分别是利姆诺杆菌属(Limnobacter spp.)、葡萄球菌属(Stappia spp.)、油假单胞菌属(P.oleovorans)和放射杆菌属(R.Radibacter)。基因组包含多个被鉴定为毒力(寄主联合)因子的基因，而星状链球菌和氧化硫乳杆菌基因组揭示了混合营养硫氧化途径。将实验室饲养的媒介乳杆菌的中间转录组与分离的基因组进行了比较，结果表明硫代氧化乳杆菌的ORF具有运动、清除营养物质(Fe和P)、合成碳源的聚羟基烷酸合成和选择性通透性(孔蛋白)等功能。我们推测，这种活动可能中介细菌在一个动态的沿海生境中的驯化和持久性，该细菌由化学物质和营养物质的内部和外部梯度定义。
We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing <85% identity with cultivated strains, and two γ-Proteobacterial ribotypes sharing >99% 16S rRNA identity with Endozoicomonas elysicola and Pseudomonas oleovorans, respectively. Species-specific PCR revealed that these populations persisted in N. vectensis asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and Endozoicomonas 16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised N. vectensis was dominated by isolates from P. oleovorans and Rhizobium radiobacter. Isolates from field-collected anemones revealed an association with Limnobacter and Stappia isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e., Limnobacter spp., Stappia spp., P. oleovorans and R. radiobacter. Genomes contained multiple genes identified as virulence (host-association) factors while S. stellulata and L. thiooxidans genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised N. vectensis was compared to the isolate genomes and indicated expression of ORFs from L. thiooxidans with predicted functions of motility, nutrient scavenging (Fe and P), polyhydroxyalkanoate synthesis for carbon storage, and selective permeability (porins). We hypothesize that such activities may mediate acclimation and persistence of bacteria in a N. vectensis holobiont defined by both internal and external gradients of chemicals and nutrients in a dynamic coastal habitat.