類別:

龜山島淺海熱泉系統中烏龜怪方蟹共生體之環境互動與適應機制

Wed, 01 Jan 2025 00:00:00 GMT

標題: 龜山島淺海熱泉系統中烏龜怪方蟹共生體之環境互動與適應機制; Environmental Interactions and Adaptive Mechanisms of the Xenograpsus testudinatus Holobiont in Kueishan Island Shallow-Water Hydrothermal Vent System 作者: 邱翎; Ling Chiu 摘要: 近年來，淺水熱泉因其複雜的特性，受到越來越多的關注，這些特性受到多種表層海洋因素的影響，如日照、潮汐、水流和季節性變化，與深海熱泉有明顯的差異。台灣東北方宜蘭海域的龜山島，同時擁有淺水熱泉及珊瑚生態系統，相當適合作為研究熱泉環境相互作用的自然實驗室。通過監測水質及聲景特徵，我們觀察到熱泉區的間歇性熱液排放，硫化物 (HS-/S2-)、溶解無機碳 (dissolved inorganic carbon, DIC) 和pH值為區分龜山島周圍棲地的重要指標，尤其在活躍期展現了熱泉活動在淺海環境中時間與空間的動態變化。烏龜怪方蟹 (Xenograpsus testudinatus) 作為龜山島熱泉系統最優勢其中一種動物，已發展出能存活於熱泉極端環境中的生理機制來維持體內恆定。然而，其共生菌與環境變化之間的相互作用仍未完全了解。利用全長16S rRNA基因定序和Alpha多樣性分析，我們觀察到水中細菌群落與熱泉相關的水質參數有相關性。在綱 (class) 的階層下，Campylobacteria和Gammaproteobacteria的相對豐度有相反的變化趨勢，其中，一種硫還原菌Thioreductor是Campylobacteria中相對豐度最高的菌屬，而Gammaproteobacteria中最豐富的菌屬則是一種硫氧化菌Thiomicrorhabdus，說明環境變動與微生物的物質利用之間可能密切相關。而對怪方蟹X. testudinatus來說，鰓的菌群與水質化學變化的相關性高於殼表的細菌，儘管Campylobacteria中的Sulfurovum在鰓和殼表都是優勢菌屬，但殼表的菌群有更高的多樣性。螢光原位雜交 (fluorescence in situ hybridization, FISH) 支持鰓中Sulfurovum的優勢地位。功能預測分析顯示菌群主要進行硫氧化 (sulfur oxidation) 及脫硝作用 (denitrification)，相關反應可能由Sulfurovum主導。由於在海水中Sulfurovum並不是豐度較高的菌屬，怪方蟹的鰓可能為其及相關硫氧化菌 (sulfur-oxidizing bacteria, SOB) 提供了一個適合定殖 (colonization) 的微棲地 (microhabitat)，進而幫助宿主乃至共生體的硫解毒機制 (sulfide detoxification) 及有機物質的提供。熱泉的間歇性使得X. testudinatus反覆暴露於一般海水與極端環境之間。為了研究牠們的適應機制，我們將實驗室馴化的X. testudinatus回放到原熱泉棲地，採樣並透過定序技術分析鰓的細菌微生物群 (bacterial microbiota)、轉錄體 (transcriptome)，同時測定其氨基酸及脂肪酸組成。在回放轉移後的0, 1, 2, 4小時 (H) 期間，細菌多樣性在2H時觀察到的屬數量 (observed genus taxa number) 和Chao 1顯著下降，Sulfurovum在1H豐度最高，並伴隨著異營性功能 (heterotrophy) 的減少和氮代謝及硫化物代謝的增加，同時轉錄組顯示宿主組織中GTPase活性和肌動蛋白骨架重構 (actin cytoskeleton remodeling) 相關的路徑被上調，而幾丁質和外骨骼的形成 (chitin and cuticle formation) 受到抑制。在之後的2H和4H，硫化物代謝有逐漸增強的趨勢，與硫化物解毒相關的氨基酸牛磺酸 (taurine) 也顯著減少，而與氮代謝相關的組氨酸 (histidine)、精氨酸 (arginine) 和谷氨酰胺 (glutamine) 則在2H及4H時累積，同時與上述胺基酸相關的代謝酵素基因如谷氨酰胺酶 (glutaminase)、組氨酸氨基水解酶 (histidine ammonia-lyase) 及丙氨酸轉氨酶 (alanine transaminase) 也被上調。抗氧化防禦 (antioxidant defense) 則藉由穀胱甘肽過氧化酶 (glutathione peroxidase) 及麩胱甘肽轉移酶 (glutathione S- transferase) 的旁系同原體 (paralogs) 在回放過程中持續進行，說明抗氧化機制對烏龜怪方蟹適應熱泉環境的重要性。此外，脂肪酸含量雖然並沒有顯著變化，相關性和倍數差異 (fold change) 分析顯示不飽和脂肪酸可能比飽和脂肪酸對環境的反應更加明顯，脂肪酸的累積與消耗可能與細胞結構的維持及抗氧化物的調節相關。上述結果顯示X. testudinatus熱泉共生體棲息於一個比以往認知更為複雜的動態環境中，我們的研究透過多方面的分析，包含環境變量、細菌群時間性變化以及宿主生理代謝反應，探討不同層面之間的交互作用及相互依賴關係。研究熱泉共生體為我們提供了生命在挑戰性環境中所展現出韌性的相關見解，並且揭示了極端條件下跨域共演化 (inter-domain evolution) 的奧秘。; Shallow-water hydrothermal vents have garnered growing attention due to their complex characteristics, influenced by various epipelagic factors such as insolation, tides, currents, and seasonal changes, in contrast to their deep-sea analogues. Kueishan Island, which harbors both shallow-water hydrothermal and coral ecosystems, provides an exceptional natural laboratory for investigating hydrothermal environmental interactions. We captured sporadic fluid discharges at the vent site by monitoring water quality and soundscape features. Sulfide (HS-/S2-), dissolved inorganic carbon (DIC), and pH levels were identified as key indicators for habitats differentiation around Kueishan Island, especially during active venting periods, which highlights the profound spatial and temporal dynamics of hydrothermal activity in shallow water marine environments. The brachyuran vent crab Xenograpsus testudinatus, a dominant metazoan inhabiting Kueishan Island hydrothermal vent system, has developed robust physiological mechanisms to sustain homeostasis in this extreme environment. However, the interactions between its symbiotic bacteria and environmental fluctuations remain incompletely understood. Through the application of full-length 16S rRNA gene sequencing and alpha diversity analysis, we observed strong correlations between water bacterial community and hydrothermal-associated physicochemical parameters at the vent site. The relative abundances of Campylobacteria and Gammaproteobacteria exhibited inverse temporal patterns, where Thioreductor, a sulfur-reducing bacteria, was the most abundant genus within Campylobacteria, while the sulfur-oxidizing Thiomicrorhabdus predominated among Gammaproteobacteria, indicating a potential link between environmental dynamics and microbial resource availability. In X. testudinatus, gill-associated bacteria showed greater correlations with water quality compared to those present on the carapace surface. While Sulfurovum (Campylobacteria) was predominant in both the gills and carapace surface, the carapace surface demonstrated higher bacterial diversity. Furthermore, fluorescence in situ hybridization (FISH) and functional prediction analysis supported the branchial predominance of Sulfurovum, which performs sulfur oxidation and denitrification processes. Given that Sulfurovum is not abundant in the ambient seawater, the gills may serve as an enclave for sulfur-oxidizing bacteria (SOB) such as Sulfurovum, facilitating sulfide detoxification and organic production to the host. The intermittent nature of hydrothermal venting repeatedly exposes X. testudinatus to transitions between normal seawater and extreme environmental conditions. To investigate their adaptive responses, we reintroduced lab-acclimated X. testudinatus to their native habitat and analyzed their gill tissue for bacterial microbiota, transcriptome, amino acid compositions, and fatty acid profiles. During the period, 0, 1, 2, and 4 hours (H) post-reintroduction, bacterial diversity showed a significant reduction in observed taxa numbers and Chao 1 estimates at the genus level at 2H. Sulfurovum had the highest abundance at 1H, coinciding with elevated nitrogen and sulfide metabolism and reduced heterotrophy-associated functions. Meanwhile, transcriptomic analysis revealed upregulation of GTPase activity and actin cytoskeleton remodeling in the host tissue, while chitin and cuticle formation pathways were suppressed. At subsequent time points (2H or 4H), both sulfide metabolism and stress responses showed progressive enhancement. Taurine, crucial for sulfide detoxification, significantly depleted at 2 and 4H. Additionally, nitrogen metabolism-related amino acids, histidine, arginine, and glutamine, accumulated at the later time points, accompanied by upregulation of related enzyme genes, including glutaminase, histidine ammonia-lyase, and alanine transaminase. During the reintroduction, fatty acid levels did not show significant changes; however, correlation and fold change analyses revealed that unsaturated fatty acids had more pronounced responses to environmental transition compared to saturated fatty acids. These analyses demonstrate that X. testudinatus holobiont exists in a dynamic environment, more complicated than previously acknowledged. Our study provides a multi-faceted examination of environmental variables, bacteria community dynamics, and the crab host’s physiological responses, elucidating their intricate interactions and interdependencies. Exploring hydrothermal-endemic holobionts provides valuable insights into the remarkable resilience of life in a challenging environment, shedding light on the mechanisms of inter-kingdom coevolution under extreme conditions.

鼠尾鱈科魚類（鱈形目：鼠尾鱈科）聚焦於奈氏鱈屬之親緣關係及分類研究

Sun, 01 Jan 2023 00:00:00 GMT

標題: 鼠尾鱈科魚類（鱈形目：鼠尾鱈科）聚焦於奈氏鱈屬之親緣關係及分類研究; Phylogeny and taxonomy of Grenadiers (Gadiformes: Macrouridae) with a focus on Nezumia species 作者: 陳泓維; Hung-Wei Chen 摘要: 鼠尾鱈科是多樣性和豐富度很高的一科深海真骨魚（包括27個屬共計372種）。牠們主要分布在熱帶和亞熱帶海域，尤其是印度-西太平洋地區（包括23個屬共計126種）。而其中五個屬，奈氏鱈屬、庫隆長尾鱈屬、軟首鱈屬、凹腹鱈屬和梭鱈屬因爲其外觀的相似性，而被認為是源自於共同祖先。早期的分子親緣關係研究受限於涵蓋的種類及基因標記的數量，推斷出的親緣關係不夠完整或是不夠具有可信度，導致五個屬及其他屬之間的演化關係未得到解決。奈氏鱈屬是鼠尾鱈科中第三大的屬，包含 54 種物種且多樣性仍未完全被探知。其特徵為具有發達的眶下架和吻兩端的特化鱗片。目前總共有 25種奈氏鱈分布在印度-西太平洋地區。本研究第一部分使用了新構建的多基因資料集並利用之去測試了五個相似屬之間的演化關係。在研究結果發現，總共有10個鼠尾鱈科的屬為單系群。而縱使上述提及的五個屬形態上相似，分子結果顯示五個屬並不能形成一個單系群，並發現了梭鱈屬與其外觀差異極大的單長尾鱈屬互為姊妹群。此外，本研究發現奈氏鱈屬跟庫隆長尾鱈屬能形成一個單系群，證明了兩個屬的演化相關性，然而兩個屬皆不是單系群，因此建議不再將庫隆長尾鱈視為一個有效屬名。在第二部分裡，本研究使用綜合分類學的分析方法，探討了印度-西太平洋地區奈氏鱈屬種間層級的多樣性。利用粒線體細胞色素c氧化酶亞基1（COI）資料及進行物種界定並提出初步的物種假設，並使用了形態學、生物地理資訊等其他標準來驗證推斷的物種。在對16個形態種進行了98個樣本的檢查後，最終在確定了20個潛在物種，其中有10個型態種來自於印度-西太平洋地區，表明了奈氏鱈屬存在的隱藏多樣性。本研究在大鱗奈氏鱈種團和長棘奈氏鱈種團中發現了五個隱蔽種，並指出原始奈氏鱈與科氏奈氏鱈的同種性，建議將科氏奈氏鱈視為原始奈氏鱈的同種異名。總體來說，本研究有效地利用分子證據闡明了五個形態相似的屬的演化關係，並為奈氏鱈屬的分類學，尤其是分布在印度-西太平洋地區的物種提供了新的見解。; Macrouridae represents the most dominant teleost fish family in terms of species diversity and abundance in the world's deep oceans, especially from the tropical and subtropical regions. This family, commonly known as grenadiers, rattails, or whiptails, currently comprises 372 valid species in 27 genera. From the Indo-West Pacific (IWP) region, 126 species in 23 genera are found. Five particular genera within the family (Nezumia, Kuronezumia, Malacocephalus, Ventrifossa, and Lucigadus) share similar morphological features and were thought to descent from a common ancestor. The early molecular phylogenetic studies of the Macrouridae were mostly based on limited number of taxa and fewer gene markers. The inferred phylogeny was either incomprehensive or weakly or non-supported, leading to the evolutionary relationships among the five morphologically resembling genera and other genera unresolved. One of the genera, Nezumia, is the third largest genus of the family Macrouridae comprising 54 valid species but its taxonomy has never been throughout studied. The Nezumia species are featured by a well-developed suborbital ridge and tubercle-like scales in the snout. Twenty-five currently recognized Nezumia species are present in the IWP region. In this study, I firstly used a newly constructed multigene dataset to test the evolutionary affinity among the five morphologically resembling genera of the Macrouridae. The inferred phylogeny recovered ten sampled macrourid genera as monophyly. The results also show that these five genera together do not form a monophyletic group and reject thus the hypothesis regarding their closer relationship based on morphology. Instead, I uncover the sister group of Lucigadus is Haplomacrourus, a genus with a distinct feature in the appearance from Lucigadus and its resembling genera. All of the representative taxa from Nezumia and Kuronezumia together still form a monophyletic group, indicating their evolutionary affinity. However, neither of the genera appears to be monophyletic. Herein, I propose that the name “Kuronezumia” is no longer a valid genus name. Secondly, the species-level diversity of Nezumia occurring in the IWP region was explored using the integrated approach in taxonomy. Here, the species delimitation analyses based on the constructed mitochondrial cytochrome c oxidase subunit 1 (COI) gene dataset were conducted to suggest the primary species hypothesis. Other criteria such as the morphology and biogeographic information, were also used to validate the inferred species. A total of 20 species were finally inferred based on the examination of 98 samples in 16 morpho-species among which 10 morpho-species were from IWP region. This finding indicates a presence of hidden diversity of Nezumia species. The five potential new cryptic species were especially discovered in two IWP species groups, Nezumia propinqua group and the Nezumia spinosa group. My results also support the conspecificity of Nezumia coheni and Nezumia proxima, suggesting placing Nezumia coheni in the synonymy of Nezumia proxima. Overall, this study effectively utilized molecular evidence to elucidate the evolutionary relationships of the five morphologically similar genera and provide new insights into the taxonomy of the Nezumia, especially the species occurring in the IWP region.

黑皮旗魚在太平洋及東印度洋之族群遺傳結構和族群變動史

Fri, 01 Jan 2016 00:00:00 GMT

標題: 黑皮旗魚在太平洋及東印度洋之族群遺傳結構和族群變動史; Population genetic structure and demographic history of blue marlin, Makaira nigricans, in the Pacific and eastern Indian oceans 作者: Hui Chen; 陳卉摘要: 黑皮旗魚是一種棲息於熱帶、亞熱帶及溫帶水域的世界性魚種。儘管本種在漁業上有其重要的經濟價值，但此物種之族群結構在某些海域所知甚少，特別是在擁有最高漁獲量的太平洋及漁獲量逐年增加且面臨過漁的印度洋。在台灣本地市場可採集到粗或細鱗兩種形態特徵的黑皮旗魚。利用粒線體DNA序列長度為1140個鹼基對的細胞色素b和905個鹼基對的控制區域進行親緣關係分析(phylogenetic analysis)，發現兩種不同外型的黑皮旗魚係屬於同一物種。本研究共採集183個太平洋和印度洋樣本，其中包括三個太平洋採樣區，東太平洋54個標本，西北太平洋56個標本，南中國海40個標本;一個印度洋採樣區33個標本，以粒線體DNA之控制區域分析，發現這些黑皮旗魚皆為同一個演化支(clade)-遍在演化支(ubiquitous clade)。目前太平洋和印度洋的黑皮旗魚資源分別由兩個區域性漁業管理組織（中西太平洋漁業委員會WCPFC及印度洋鮪魚委員會IOTC）來管理。本研究利用粒線體DNA中的細胞色素b和控制區域分析太平洋和東印度洋黑皮旗魚的族群結構，結果發現固定指標(ΦST)、分子變異的階層分析(AMOVA)和分子變異的空間分析(SAMOVA)皆支持黑皮旗魚在東印度洋和太平洋間無族群分化的現象，故而應屬於單一系群。所有東印度洋和太平洋黑皮旗魚皆擁有高的基因型歧異度和低的核甘酸歧異度。中性測試、分佈落差(pairwise mismatch distribution)和貝氏天際線分析(Bayesian skyline analysis)皆顯示東印度洋和太平洋黑皮旗魚在0.3至0.74百萬年前遭遇快速族群擴張。本研究顯示太平洋和東印度洋的黑皮旗魚為單一系群，此項發現對往後該資源之評估研究提供非常重要的資訊，將有助於該黑皮旗魚資源之進一步保育管理與永續利用。; Blue marlin (Makaira nigricans) is a species that inhabits tropical, subtropical, and temperate waters worldwide. While blue marlin is economically important for fisheries, there are regions in this species’ distribution where little is known about its population structure. This is especially true in the Pacific Ocean, which yields the largest catch of blue marlin, and in the Indian Ocean, where catch has increased consistently over the years and the area is commonly overfished. Sampled Taiwan local market blue marlin shows two morphological characteristics of thick or thin scales. Phylogenetic analysis for taxonomy by mitochondrial DNA (mtDNA) cytochrome b (cyt b) (1140 bp) and control region (CR) (905 bp), these two morphological characteristics of the blue marlin belong to the same species. A total of 183 blue marlin was collected from three Pacific localities, eastern Pacific (EP) (n= 54), western North Pacific (WNP) (n= 56), and South China Sea (SCS) (n= 40) and one Indian Ocean locality (EI) (n= 33), analysis of mtDNA CR revealed that these are both of the ubiquitous clade. Currently blue marlin in the Pacific and Indian Oceans are managed as two distinct management units (the Western and Central Pacific Fisheries Commission [WCPFC] and the Indian Ocean Tuna Commission [IOTC]). This study investigated the genetic structure of blue marlin population inhabiting the Pacific and eastern Indian Oceans based on mtDNA cyt b and CR sequence variation. The results of pairwise ΦST, hierarchical analysis of molecular variance (AMOVA), and spatial analysis of molecular variance (SAMOVA) all support that there is no population differentiation among eastern Indian and Pacific blue marlin, thereby the population are comprised of a single stock. All eastern Indian and Pacific blue marlin possess high haplotype diversity (h) and low nucleotide diversity (π). Neutrality tests, pairwise mismatch distribution, and Bayesian skyline analysis all indicate that eastern Indian and Pacific blue marlin have undergone a rapid population expansion on the order of 0.30 to 0.74 million years ago. This study demonstrates that blue marlin in the Pacific and eastern Indian Oceans constitute a single genetic stock, which provides very important information for stock assessment purpose and for further conservation and sustainable utilization of this resource.

黑潮流經海底山所引發之紊流混合及其時空變異

Sat, 01 Jan 2022 00:00:00 GMT

標題: 黑潮流經海底山所引發之紊流混合及其時空變異; Spatial and temporal variations of turbulent mixing along the Kuroshio over a seamount 作者: YU-YU Yeh; 葉祐瑜摘要: 本研究分別使用了2020年10月及2021年9月分別在新海研1號及新海研2號上進行的現場觀測來探討臺灣東方海域黑潮與海底山的交互作用，並特別著重於海流流經陡峭地形所產生的小尺度物理過程。觀測資料顯示，當黑潮流過綠島西北方高度約200公尺的海底山時，海底山的下游處除了會形成背向波 (lee wave) 外，也可以透過聲納回波影像發現一長串由山峰向下游延伸數公里的凱文赫姆茲不穩定波 (Kelvin-Helmholtz billow)，而背向波所造成的流場、水文結構變形將會加速該不穩定波的成長。上述小尺度海水運動最終將會演變成紊流，使得海底山下游地區的紊流動消散率 (turbulent kinetic energy dissipation rate) 明顯較上游地區大2個數量級 (O ~ 10-5 W kg-1)，且其伴隨的紊流混合可能會改變當地的水文性質。此外，紊流動消散率在我們的實驗期間的變化和近岸潮位資料高度相關，因此推論黑潮流經陡峭海底山所衍生的紊流反應會受到潮汐調節，且理查遜數(Ri)的機率分布大致落於臨界值0.25附近，說明當地之流剪切力與紊流混合之間的平衡對於切變不穩定 (shear instability) 而言處於界穩定狀態 (marginally unstable state)，使得不穩定波及高紊流動能消散率 (O ~ 10^-5 W kg-1) 得以在實驗期間不斷地被觀測到。最後，我們將觀測結果所估計出的渦流擴散係數 (eddy diffusivity) 和前人研究中提出的經驗函數做比較，期望能對改善紊流混合的參數化有所幫助。; Two scientific cruises were conducted to investigate the flow-topography interactions along the Kuroshio over a seamount off the eastern coast of Taiwan and near Green Island. When the Kuroshio flowed over the 200-m-depth seamount, echo sounder captured the signals of lee waves and shear instability above the seamount and at the immediate lee of the seamount. These small-scale processes further induced vigorous turbulent mixing. Results of microstructure profiling revealed that turbulent kinetic energy dissipation rate (ϵ) varied in both space and time around the seamount. That is, ϵ was O(10^-5 W kg-1) downstream, which was 100 times larger than upstream of the seamount. Besides, ϵ was strongly modulated by the tide, i.e., strong and weak ϵ occurred at low and high tides, respectively. Using a simplified one-dimensional diffusion model, we demonstrated that turbulent mixing plays a role in shaping the downstream hydrographic structure. The lee wave is likely to create a circumstance favoring a higher growth rate of shear instability, which was examined using linear stability analysis. Mostly, the criterion for the occurrences of shear instability, Richardson number Ri < 0.25, was satisfied downstream. The distribution of Ri fluctuated around a central value near 0.25, which is a typical feature of the status of marginal instability, and this can be interpreted as a cyclic circumstance in a balance between shear forcing and turbulent mixing. Finally, we compared parameterizations of turbulent mixing based on the Ri between previous empirical relationships and our observations. This may help to improve the parameterization of turbulent mixing induced by flow encountering abrupt topography.