Shaping the gut microbiota of decapod crustaceans: host phylogeny vs. habitat

Decapoda represents one of the most diverse invertebrate groups on this planet. With a global distribution in almost all kinds of aquatic habitats and in some terrestrial habitats, decapods play essential roles in various ecosystems. Besides, many decapod species are of economic importance in fisheries and aquaculture, particularly in many developing countries. Increasing studies are conducted to understand the evolution, biology, ecology and nutrition for a variety of decapod species due to their values to human society and nature. However, little is known regarding the associated microbiota of decapods compared with numerous investigations in other animal groups, including vertebrates (mammals, birds and fish) and other invertebrates, especially the insects. Thus, this thesis research was conducted to explore the gut microbiota of decapods and the factors that shape their microbial communities.In the first part of the thesis research, I investigated whether host phylogeny has an impact on the gut microbiota assemblages in decapod shrimps. Twenty shrimp species from three families (Atyidae, Pandalidae and Penaeidae) inhabiting different environments were included in the study. The gut microbiota of shrimp was analyzed using metabarcoding sequencing of the V1-V3 hypervariable region of the 16S rRNA gene. The functional profiles of shrimp gut microbiota were predicted based on 16S reads using PICRUSt2. The congruences between host phylogeny tree and gut microbial dendrogram, as well as between host phylogeny tree and the dendrogram of predicted functional pathways were evaluated. Gut microbial communities varied within each shrimp family but were generally dominated by Proteobacteria. A prevalent phylosymbiotic pattern in shrimps was documented for the first time through the observations of (1) the distinguishability of microbial communities among species within each group, (2) a significantly lower intraspecific than interspecific gut microbial beta diversity across shrimp families, (3) topological congruence between host phylogenetic trees and gut microbiota dendrograms, and (4) a correlation between host genetic distances and microbial dissimilarities. Besides, a weak phylogenetic signal was detected in the predicted functions of the penaeid gut microbiota. However, the functional diversities of the two caridean families were not significantly related to host phylogeny. A parallelism in the taxonomy of the gut microbiota with host phylogeny for the three shrimp families examined and in the predicted functions for the penaeid shrimp indicate a tight host-microbial relationship during evolution.The second part of the thesis research aims to understand the relationship of gut microbiota with habitat and a higher level of host taxonomy. A total of 126 samples representing seven decapod major lineages (infraorders), namely Astacidea, Brachyura, Caridea, Gebiidea, Anomura, Achelata, Stenopodidea, were collected from freshwater, marine and terrestrial habitats. By adding some data from the first part, totally 197 samples from 37 species representing seven infraorders and the suborder Dendronbranchiata were analyzed. The results show distinct gut microbiota in terrestrial decapods compared to those in the aquatic habitats. Variation partitioning analysis suggests that host phylogeny explains more variation of the gut microbiota than habitat, indicating a stronger effect of host than habitat on the assembly of gut microbial communities. The discriminative bacterial taxa in Mollicutes found in terrestrial decapods identified by LEfSe analysis are common gut members found in isopods and are considered important for the isopod adaptation to the leaf litter diet during their invasion to land. This may indicate the crucial role of Mollicutes in terrestrial adaptation of decapods. Moreover, the phylosymbiotic pattern can be detected at the species, family and infraordinal/subordinal levels of decapods with significant congruence observed between the host phylogenetic tree and microbial dendrogram, as well as correlation between host cophenetic phylogenetic distances and microbial dissimilarities, indicating the important role of host in the assembly of gut microbial community during evolution.To further detangle the influences of host and environmental factors on decapod gut microbial communities, two euryhaline decapod species, the prawn Macrobrachium rosenbergii and the crab Scylla paramanosain were acclimated to different salinities. Analyses of gut microbiota of the two decapods after salinity acclimation indicate that their gut microbial communities significantly varied with salinity. The core gut microbiota identified from the two species suggest host specific microbiota in decapods.By summarizing findings from the three parts of the study, I conclude that both habitat and host phylogeny are driving forces in the assembly of decapod gut microbiota, with the host phylogeny contributing more than habitat. The gut microbes are of vital importance for decapod hosts to cope with environmental changes.十足目是地球上最龐大的無脊椎動物群之一。由於其廣汎分佈於全球的各種水生環境中，十足目動物在多種生態系統中扮演著重要的角色。此外，很多十足目動物是發展中國家主要的漁業和水產養殖的重要物種。因其在自然界和人類發展中的重要地位，越來越多的研究致力於解開十足目相關的進化，生理，生態和營養問題。然而，相對其他動物種群而言，如脊椎動物(哺乳類，鳥類和魚類)和其他無脊椎動物, 我們對十足目動物的腸道微生物知之甚少。因此，本研究對十足目動物的腸道微生物以及影響腸道微生物群建立的因素進行研究。本文的第一部分進行了十足目宿主系統發育對腸道微生物影響的研究。來自十足目下三個科(淡水Atyidae, 海水Penaeidae 和 深海Pandalidae)的二十種蝦被用作研究對象。通過對細菌16s rRNA 的V1-V3 高變區進行高通量測序，對蝦的腸道微生物群落進行分析。此後，用PICRUSt2 對蝦腸道微生物的功能進行預測。對宿主的系統發育樹與腸道微生物系統樹圖及腸道微生物預測功能系統樹圖之間一致性進行了評估。結果顯示，不同科的蝦的腸道微生物種群均含有屬於來自變形菌門的優勢種。基於所觀察到的現象：1. 可通過腸道微生物對宿主進行區分；2.腸道微生物的種内相似性顯著高於種閒相似性；3. 宿主系統發育樹與腸道微生物系統樹圖之間的顯著一致性；以及4. 宿主的遺傳距離與微生物的差異性顯著相關，本研究首次證實了在蝦中存在Phylosymbiosis。此外，在對蝦（Penaeidae）腸道微生物的預測功能中檢測到了微弱的系統發育信號。然而，在兩個來自於真蝦下目的科（Atyidae 和 Pandalidae）中，並沒有發現微生物預測功能的多樣性與宿主系統發育有顯著相關。我們的關於宿主系統發育和腸道微生物的顯著關聯表明宿主在進化過程中與其腸道微生物之間的緊密關聯。本文的第二部分旨在瞭解栖息地及宿主在不同分類水平下對腸道微生物的影響。在本章中， 對總共來自十足目7 個主要系譜分支，即Astacidea,Brachyura, Caridea, Gebiidea, Anomura, Achelata, Stenopodide，的 24 個物種進行了樣品采集。這些物種分別來自於淡水，海洋以及陸地等不同的栖息地。此外，加入了來自於第一部分的13 個物種。因此，有37 個物種，共197 個樣本，代表了7 個十足目下目，以及一個亞目（Dendronbranchiata）被用於比較分析。結果表明，陸生十足目與水生十足目的腸道微生物存在顯著差異。相比栖息地而言，宿主系統發育能夠解釋更多腸道微生物的變化，表明腸道微生物的構建更多受到宿主的影響。在陸生十足目動物腸道中，柔膜菌綱（Mollicutes）的細菌豐度顯著高於來自其他栖息地的十足目動物。這可能是因爲柔膜菌綱（Mollicutes）的細菌對十足目適應陸生環境有重要的作用。此外，在宿主不同的分類水平上，都能觀察到phylosymbiosis，再一次印證了宿主對腸道微生物的重要影響。爲了進一步探究環境對十足目腸道微生物的影響，我們對兩個廣鹽性物種，Macrobrachium rosenbergii 和Scylla paramanosain，進行了鹽度適應性實驗。對不同鹽度處理的動物的腸道微生物分析發現，腸道微生物群落受到鹽度的顯著性影響。對每個物種的核心腸道微生物的識別發現，這兩個物種都含有各自特殊的微生物群落。總結以上三個部分的發現，得出以下結論：1.宿主系統發育和栖息地是十足目腸道微生物建立的主要驅動力；2. 腸道微生物在宿主對抗環境變化過程中有重要作用。Tang, Yuanyuan.Ph.D. Chinese University of Hong Kong 2021.Includes bibliographical references (leaves ).Abstracts also in Chinese.Title from PDF title page (viewed on …)