Hewson Ian, Poretsky Rachel S, Beinart Roxanne A, White Angelicque E, Shi Tuo, Bench Shellie R, Moisander Pia H, Paerl Ryan W, Tripp H James, Montoya Joseph P, Moran Mary Ann, Zehr Jonathan P
Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.
ISME J. 2009 May;3(5):618-31. doi: 10.1038/ismej.2009.8. Epub 2009 Feb 19.
The diazotrophic cyanobacterium Crocosphaera watsonii supplies fixed nitrogen (N) to N-depleted surface waters of the tropical oceans, but the factors that determine its distribution and contribution to global N(2) fixation are not well constrained for natural populations. Despite the heterogeneity of the marine environment, the genome of C. watsonii is highly conserved in nucleotide sequence in contrast to sympatric planktonic cyanobacteria. We applied a whole assemblage shotgun transcript sequencing approach to samples collected from a bloom of C. watsonii observed in the South Pacific to understand the genomic mechanisms that may lead to high population densities. We obtained 999 C. watsonii transcript reads from two metatranscriptomes prepared from mixed assemblage RNA collected in the day and at night. The C. watsonii population had unexpectedly high transcription of hypothetical protein genes (31% of protein-encoding genes) and transposases (12%). Furthermore, genes were expressed that are necessary for living in the oligotrophic ocean, including the nitrogenase cluster and the iron-stress-induced protein A (isiA) that functions to protect photosystem I from high-light-induced damage. C. watsonii transcripts retrieved from metatranscriptomes at other locations in the southwest Pacific Ocean, station ALOHA and the equatorial Atlantic Ocean were similar in composition to those recovered in the enriched population. Quantitative PCR and quantitative reverse transcriptase PCR were used to confirm the high expression of these genes within the bloom, but transcription patterns varied at shallower and deeper horizons. These data represent the first transcript study of a rare individual microorganism in situ and provide insight into the mechanisms of genome diversification and the ecophysiology of natural populations of keystone organisms that are important in global nitrogen cycling.
固氮蓝细菌沃氏聚球藻（Crocosphaera watsonii）为热带海洋中氮匮乏的表层水体提供固定氮，但对于自然种群而言，决定其分布及对全球氮固定贡献的因素尚不明确。尽管海洋环境存在异质性，但与同域浮游蓝细菌相比，沃氏聚球藻的基因组在核苷酸序列上高度保守。我们采用全群落鸟枪法转录组测序方法，对从南太平洋观测到的沃氏聚球藻水华采集的样本进行分析，以了解可能导致其高种群密度的基因组机制。我们从白天和夜晚采集的混合群落RNA制备的两个宏转录组中获得了999条沃氏聚球藻转录本读数。沃氏聚球藻种群中假定蛋白基因（占蛋白编码基因的31%）和转座酶（12%）的转录出乎意料地高。此外，还表达了在贫营养海洋中生存所必需的基因，包括固氮酶簇和铁应激诱导蛋白A（isiA），后者的功能是保护光系统I免受高光诱导的损伤。从西南太平洋其他地点、Aloha站和赤道大西洋的宏转录组中检索到的沃氏聚球藻转录本在组成上与在富集种群中回收的转录本相似。定量PCR和定量逆转录PCR用于确认这些基因在水华中的高表达，但转录模式在较浅和较深水层有所不同。这些数据代表了对一种罕见个体微生物的首次原位转录研究，并为基因组多样化机制以及在全球氮循环中起重要作用的关键生物自然种群的生态生理学提供了见解。
