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Site effects on wildlife enteric bacterial diversity: You are where you eat?

机译：对野生生物肠道细菌多样性的现场影响：您在哪里吃饭？

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摘要

The study of microbial biogeography has made vast strides in recent years due, in part, to advances in the technological capacity to document microscopic biodiversity at the community, population and genomic levels. In this dissertation, we apply a combination of molecular and cultivation approaches to the study of enteric microbial diversity in a unique system of sister iguanid species, the Galapagos land and marine iguanas (Conolophus spp. and Amblyrhynchus subcristatus, respectively). We explored the spatial diversity of enteric bacteria in these two species at multiple levels, from communities to genetic traits. The unique host population history and geography of this island chain informed hypotheses about expected biogeographical patterns and the underlying processes that shape microbial diversity in this system.;In Chapter 1, we reviewed current understanding of microbial biogeography and explored how incorporation of such ecological theory might benefit understanding of enteric microbial community structure and function across space and time.;Chapter 2 explored the spatial community diversity of marine and land iguana enteric communities using a molecular approach based on 454 pyrosequencing. Firstly, we demonstrated that while host species was the strongest force shaping these communities, within a host species, geographical proximity also determined overlap in community composition at the genus level. In addition, we found that the degree of contact among host species can produce distinct local effects in community richness and composition, especially when host species have amplified opportunities for microbial exchange such as higher population densities or limited habitat area.;Next in Chapter 3, we explored taxonomically finer-scale diversity patterns among marine iguana populations for the rich enteric genus Clostridium . In contrast to the expectation that each host population should have relatively distinct Clostridium communities, we found a surprising amount of phylogenetic conservation across all sites, despite also demonstrating evidence suggesting on-going taxonomic turnover---forces which might otherwise lead to rapid divergence of enteric communities in allopatric host populations.;We then applied a more traditional cultivation and molecular genetic approach in Chapter 4 in order to document Salmonella enterica strain diversity among sites. We serotyped and genotyped Salmonella enterica isolates carried by land and marine iguanas across a geographical gradient and found nearly complete isolation among strain pools. However, we also found suggestions of geographically-dependent genomic similarity among sites, possibly due to long-distance transport of genetic elements by oceanic currents.;Finally, in Chapter 5 we explored genetic trait biogeography in this system by documenting phenotypic and genetic patterns of antibiotic resistance. We found that sites farther from high densities of humans (i.e. major port towns) harbored fewer resistant bacteria. We also noted that these antibiotic resistance traits may not be retained within the broader endemic bacterial community of Galapagos wildlife for any appreciable length of time, as Salmonella enteric isolates did not share resistance traits found in Escherichia coli within the same site or even within the same individual fecal sample.;Through this work as a whole we demonstrated that, within the context of a single study system, biogeographical patterns and mechanisms can vary widely across bacterial taxonomic levels, with both ecological and evolutionary forces acting in concert on enteric biodiversity. Increased understanding of the interplay among these forces for shaping microbial community form and function across taxonomic scales has potential to improve not only theoretical understanding of microbial ecology but also to advance management of pressing issues such as novel disease emergence or antibiotic resistance dissemination.
机译：近年来，微生物生物地理学的研究取得了长足的进步，部分原因是在社区，人口和基因组水平上记录微观生物多样性的技术能力的提高。在本文中，我们将分子和栽培方法相结合，用于研究独特的姊妹类鬣蜥，加拉帕戈斯群岛陆生鬣蜥（分别为Conolophus spp。和Amblyrhynchus subcristatus）的肠道微生物多样性。我们探索了这两个物种中肠道细菌在空间上的多样性，从群落到遗传性状都处于多个层次。该岛链独特的宿主种群历史和地理学为有关预期的生物地理模式和形成该系统中微生物多样性的潜在过程提供了假设。；在第1章中，我们回顾了对微生物生物地理学的当前理解，并探讨了如何将这种生态学理论纳入其中第二章利用基于454焦磷酸测序的分子方法探讨了海洋和陆地鬣蜥肠道菌群的空间群落多样性。首先，我们证明了寄主物种是塑造这些群落的最强力量，但在寄主物种内，地理邻近度也决定了属水平上群落组成的重叠。此外，我们发现宿主物种之间的接触程度可以对社区的丰富程度和组成产生明显的局部影响，尤其是当宿主物种具有扩大的微生物交换机会（例如更高的种群密度或有限的栖息地）时;第三章，我们探索了富含肠溶梭菌属的海鬣蜥种群中分类学上更精细的多样性模式。与预期每个寄主种群应该具有相对不同的梭菌群落相反，我们发现所有地点的系统发育保护量都令人惊讶，尽管也有证据表明正在进行的分类学周转-否则可能导致生物分类的快速分化异源寄主群体中的肠道菌群。然后在第4章中应用了更传统的栽培和分子遗传学方法，以记录地点之间肠沙门氏菌菌株的多样性。我们对由陆地和海洋鬣蜥携带的肠炎沙门氏菌进行了分型和基因分型，跨越了地理梯度，发现菌株库之间几乎完全隔离。然而，我们也发现了位点之间的地理相关基因组相似性的建议，这可能是由于洋流对遗传要素的长距离运输所致。最后，在第五章中，我们通过记录了表型和遗传模式探讨了该系统的遗传特征生物地理学。抗生素耐药性。我们发现，远离人类高密度地区（即主要港口城市）的地方所携带的抗性细菌较少。我们还注意到，这些抗生素抗性特征可能不会在加拉帕戈斯野生动物的更广泛的地方性细菌群落中保留任何明显的时间长度，因为沙门氏菌肠分离株在同一部位甚至同一部位都没有在大肠杆菌中发现的抗性特征。通过整个工作，我们证明了，在一个研究系统的背景下，生物地理模式和机制在细菌分类学水平上可以有很大差异，生态和进化力共同作用于肠道生物多样性。越来越多地了解这些力在整个分类学尺度上塑造微生物群落形式和功能的相互作用，不仅有可能增进对微生物生态学的理论理解，而且有可能促进对诸如新疾病的出现或抗生素耐药性传播等紧迫问题的处理。

著录项

  • 作者

    Lankau, Emily Ruth Wheeler.;

  • 作者单位

    University of Illinois at Urbana-Champaign.;

  • 授予单位 University of Illinois at Urbana-Champaign.;
  • 学科 Biology Ecology.;Biology Microbiology.;Agriculture Animal Culture and Nutrition.
  • 学位 Ph.D.
  • 年度 2011
  • 页码 167 p.
  • 总页数 167
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

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