Functional adaptation of diatoms to environmental conditions in sea ice of the Southern Ocean

硅藻对南大洋海冰环境条件的功能适应

• 批准号: NE/I001751/1
• 负责人: Thomas Mock
• 金额: $ 4.9万
• 依托单位: University of East Anglia
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2010
• 资助国家: 英国
• 起止时间: 2010 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FI001751%2F1
• 关键词: Functional; adaptation; diatoms; environmental; conditions

In winter sea ice covers an area of up to 7% of the earth surface, which clearly as such is one of the largest biomes on earth. Sea ice can be thought of as a thin blanket covering the ocean surface, which controls, but is also controlled by fluxes of heat and moisture. The life cycles of many marine organisms ranging from bacteria, algae, small animals, whales and even humans are influenced by large-scale cycles of sea ice formation. Thus, sea ice is recognized as a fundamental component of the system earth, which is key for our predictions of future climate conditions as has become increasingly apparent in the last decade due to rapid global warming. The possible implications of a gradual loss of sea ice due to higher global temperatures are not fully understood yet but pictures of shrinking Arctic sea ice in summer has become the focus of media and increasing attention from the general public. Focus of this grant application are microalgae that live inside the porous matrix of sea ice. Most of them belong to the group of diatoms, which in general play a key role on earth because they are responsible for 25% of primary fixation of carbon dioxide, which is as much as all tropical rain forests combined. Why especially diatoms dominate sea ice algal communities is not fully understood yet but we know that they are virtually the sole source of fixed carbon for higher trophical levels in ice-covered waters. In fact, the short food chain diatom-krill-whale is depend on ice algae because they provide food for young krill when other sources of food in winter are lacking. This food chain might be severely influenced by a reduction of sea ice due to global warming. Despite the significance of polar sea ice algae virtually nothing is know about their fundamental biology. This is why the US Department of Energy (DOE) has selected one of the most important sea ice diatom species (Fragilariopsis cylindrus) to sequence its genome under the guidance of the applicant. The genome sequence is now available and has brought exciting new insights into life at and below the freezing point of sea water. For instance, the genome encodes a previously unknown family of antifreeze proteins. It also encodes genes that were not anticipated to be present in this genome such as a gene that encodes a protein from bacteria for harvesting light to generate ATP. It was not anticipated because F. cylindrus has chloroplasts in which photosynthesis like in higher plants generates ATP. Thus, the function of this gene is not known yet as for many other genes in the genome as well. One first step to shed light on the function of genes is to study their expression under different environmental conditions, which is one main goal of this proposal. We propose to conduct experiments where we treat the cells under conditions that are present in sea ice (e.g. freezing temperatures, nutrient limitation) and which are predicted outcomes of global warming in polar regions (e.g. elevated temperatures and carbon dioxide concentrations). We will then sequence the transcriptome with high-throughput sequencing technology to identify genes that are differentially expressed under our experimental conditions. Selected genes will be confirmed by quantitative qPCR. This study will help to identify the short term acclimation of F. cylindrus to sea ice as it forms every autumn. Adaptation to sea ice will be studied by comparative genome analysis between F. cylindrus and the close relative F. kerguelensis, which lives also in cold polar sea water but doesn't thrive in sea ice. This comparison will not only shed light on specific adaptation necessary for thriving in sea ice but also the predicted outcomes of global warming in polar oceans because ice free waters will more and more dominate these habitats. High-throughput sequencing will be used to sequence the genome of F. kerguelensis and large and small scale genome analysis will reveal the differences.

在冬季，海冰覆盖了高达7％的地球表面的区域，这显然是地球上最大的生物群落之一。可以将海冰视为覆盖海面的薄毯子，可以控制，但也由热和水分的通量控制。许多海洋生物的生命周期，包括细菌，藻类，小动物，鲸鱼甚至人类的生命周期受海冰形成的大规模周期的影响。因此，海冰被认为是地球系统的基本组成部分，这对于我们对未来气候条件的预测至关重要，因为由于全球迅速的变暖，在过去十年中变得越来越明显。由于全球温度较高而导致海冰逐渐丧失的可能含义尚未完全了解，但是夏季北极海冰萎缩的图片已成为媒体的焦点，并越来越受到公众的关注。该赠款应用的重点是生活在海冰多孔基质内的微藻。它们中的大多数属于硅藻群，这通常在地球上起着关键作用，因为它们是二氧化碳主要固定的25％，这与所有热带雨林的总和一样多。为什么尚不完全了解为什么硅冰藻类社区占主导地位的原因，但我们知道它们实际上是固定碳的唯一来源，用于冰覆盖的水域中较高的营养水平。实际上，短食链硅藻 - 克里尔白鲸取决于冰藻，因为当缺少其他食物来源时，它们为年轻的磷虾提供食物。由于全球变暖，这种食物链可能受到海冰减少的严重影响。尽管极地海冰藻类的重要性实际上对它们的基本生物学一无所知。这就是为什么美国能源部（DOE）选择了最重要的海冰硅藻物种（fragilariopsis cylindrus）来在申请人的指导下对其基因组进行测序的原因。基因组序列现已上市，并在海水冰点的生活和之下带来了令人兴奋的新见解。例如，基因组编码先前未知的抗冻蛋白家族。它还编码预计不会存在于该基因组中的基因，例如一个基因，该基因编码从细菌中的蛋白质收集光生成ATP的基因。这是没有预见的，因为cylindrus具有叶绿体，其中像高等植物一样的光合作用会产生ATP。因此，对于基因组中的许多其他基因，该基因的功能尚不称为。阐明基因功能的第一步是在不同的环境条件下研究其表达，这是该提案的主要目标。我们建议进行实验，以便在海冰中存在的条件下对细胞进行处理（例如冻结温度，营养限制），并预测了极性区域全球变暖的预期（例如温度升高和二氧化碳浓度）。然后，我们将使用高通量测序技术对转录组进行对，以识别在我们的实验条件下差异表达的基因。选定的基因将通过定量QPCR确认。这项研究将有助于确定每年秋天形成的cylindrus对海冰的短期适应。通过F. cylindrus和近亲F. kerguelensis之间的比较基因组分析，将研究对海冰的适应，它们也生活在冷极海水中，但不会在海冰中壮成长。这种比较不仅会阐明在海冰中繁荣发展所需的特定适应性，而且还可以预测在极地海洋中全球变暖的预测结果，因为无冰的水将越来越多地主导这些栖息地。高通量测序将用于测序F. kerguelensis的基因组，大小规模的基因组分析将揭示差异。

项目成果

Global discovery and characterization of small non-coding RNAs in marine microalgae.

海洋微藻中小非编码 RNA 的全球发现和表征。

• DOI: 10.1186/1471-2164-15-697
• 发表时间: 2014-08-20
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Lopez-Gomollon S;Beckers M;Rathjen T;Moxon S;Maumus F;Mohorianu I;Moulton V;Dalmay T;Mock T
• 通讯作者: Mock T

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

• DOI: 10.1038/nature20803
• 发表时间: 2017-01-26
• 期刊: NATURE
• 影响因子: 64.8
• 作者: Mock, Thomas;Otillar, Robert P.;Grigoriev, Igor V.
• 通讯作者: Grigoriev, Igor V.

Polar Microalgae: New Approaches towards Understanding Adaptations to an Extreme and Changing Environment.

• DOI: 10.3390/biology3010056
• 发表时间: 2014-01-28
• 期刊: Biology
• 影响因子: 4.2
• 作者: Lyon BR;Mock T
• 通讯作者: Mock T

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing.

• DOI: 10.1371/journal.pbio.1001889
• 发表时间: 2014-06
• 期刊: PLoS biology
• 影响因子: 9.8
• 作者: Keeling PJ;Burki F;Wilcox HM;Allam B;Allen EE;Amaral-Zettler LA;Armbrust EV;Archibald JM;Bharti AK;Bell CJ;Beszteri B;Bidle KD;Cameron CT;Campbell L;Caron DA;Cattolico RA;Collier JL;Coyne K;Davy SK;Deschamps P;Dyhrman ST;Edvardsen B;Gates RD;Gobler CJ;Greenwood SJ;Guida SM;Jacobi JL;Jakobsen KS;James ER;Jenkins B;John U;Johnson MD;Juhl AR;Kamp A;Katz LA;Kiene R;Kudryavtsev A;Leander BS;Lin S;Lovejoy C;Lynn D;Marchetti A;McManus G;Nedelcu AM;Menden-Deuer S;Miceli C;Mock T;Montresor M;Moran MA;Murray S;Nadathur G;Nagai S;Ngam PB;Palenik B;Pawlowski J;Petroni G;Piganeau G;Posewitz MC;Rengefors K;Romano G;Rumpho ME;Rynearson T;Schilling KB;Schroeder DC;Simpson AG;Slamovits CH;Smith DR;Smith GJ;Smith SR;Sosik HM;Stief P;Theriot E;Twary SN;Umale PE;Vaulot D;Wawrik B;Wheeler GL;Wilson WH;Xu Y;Zingone A;Worden AZ
• 通讯作者: Worden AZ