Dataset Information

Adaptive Molecular Evolution of PHYE in Primulina, a Karst Cave Plant.

ABSTRACT: Limestone Karst areas possess high levels of biodiversity and endemism. Primulina is a typical component of Karst endemic floras. The high species richness and wide distribution in various Karst microenvironments make the genus an idea model for studying speciation and local adaptation. In this study, we obtained 10 full-length sequences of the phytochrome PHYE from available transcriptome resources of Primulina and amplified partial sequences of PHYE from the genomic DNA of 74 Primulina species. Then, we used maximum-likelihood approaches to explore molecular evolution of PHYE in this Karst cave plant. The results showed that PHYE was dominated by purifying selection in both data sets, and two sites were identified as potentially under positive selection. Furthermore, the ? ratio varies greatly among different functional domains of PHYE and among different species lineages. These results suggest that potential positive selection in PHYE might have played an important role in the adaption of Primulina to heterogeneous light environments in Karst regions, and different species lineages might have been subjected to different selective pressures.

SUBMITTER: Tao J

PROVIDER: S-EPMC4452542 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Adaptive Molecular Evolution of PHYE in Primulina, a Karst Cave Plant.

Tao Junjie J Qi Qingwen Q Kang Ming M Huang Hongwen H

PloS one 20150601 6

Limestone Karst areas possess high levels of biodiversity and endemism. Primulina is a typical component of Karst endemic floras. The high species richness and wide distribution in various Karst microenvironments make the genus an idea model for studying speciation and local adaptation. In this study, we obtained 10 full-length sequences of the phytochrome PHYE from available transcriptome resources of Primulina and amplified partial sequences of PHYE from the genomic DNA of 74 Primulina species ...[more]

PMID: 26030408

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Project description:BACKGROUND:Karst caves are considered as extreme environments with nutrition deficiency, darkness, and oxygen deprivation, and they are also the sources of biodiversity and metabolic pathways. Microorganisms are usually involved in the formation and maintenance of the cave system through various metabolic activities, and are indicators of changes environment influenced by human. Zhijin cave is a typical Karst cave and attracts tourists in China. However, the bacterial diversity and composition of the Karst cave are still unclear. The present study aims to reveal the bacterial diversity and composition in the cave and the potential impact of tourism activities, and better understand the roles and co-occurrence pattern of the bacterial community in the extreme cave habitats. RESULTS:The bacterial community consisted of the major Proteobacteria, Actinobacteria, and Firmicutes, with Proteobacteria being the predominant phylum in the rock, soil, and stalactite samples. Compositions and specialized bacterial phyla of the bacterial communities were different among different sample types. The highest diversity index was found in the rock samples with a Shannon index of 4.71. Overall, Zhijin cave has relatively lower diversity than that in natural caves. The prediction of function showed that various enzymes, including ribulose-bisphosphate carboxylase, 4-hydroxybutyryl-CoA dehydratase, nitrogenase NifH, and Nitrite reductase, involved in carbon and nitrogen cycles were detected in Zhijin cave. Additionally, the modularity indices of all co-occurrence network were greater than 0.40 and the species interactions were complex across different sample types. Co-occurring positive interactions in the bacteria groups in different phyla were also observed. CONCLUSION:These results uncovered that the oligotrophic Zhijin cave maintains the bacterial communities with the diverse metabolic pathways, interdependent and cooperative co-existence patterns. Moreover, as a hotspot for tourism, the composition and diversity of bacterial community are influenced by tourism activities. These afford new insights for further exploring the adaptation of bacteria to extreme environments and the conservation of cave ecosystem.

Project description:The geological role of microorganisms has been widely studied in the karst cave ecosystem. However, microbial interactions and ecological functions in such a dark, humid, and oligotrophic habitat have received far less attention, which is crucial to understanding cave biogeochemistry. Herein, microorganisms from weathered rock and sediment along the Heshang Cave depth were analyzed by random matrix theory-based network and Tax4Fun functional prediction. The results showed that although the cave microbial communities have spatial heterogeneity, differential habitats drove the community structure and diversity. Actinobacteria were predominant in weathered rock, whereas Proteobacteria dominated the sediment. The sediment communities presented significantly higher alpha diversities due to the relatively abundant nutrition from the outside by the intermittent stream. Consistently, microbial interactions in sediment were more complex, as visualized by more nodes and links. The abundant taxa presented more positive correlations with other community members in both of the two networks, indicating that they relied on promotion effects to adapt to the extreme environment. The keystones in weathered rock were mainly involved in the biodegradation of organic compounds, whereas the keystone Nitrospira in sediment contributed to carbon/nitrogen fixation. Collectively, these findings suggest that microbial interactions may lead to distinct taxonomic and functional communities in weathered rock and sediment in the subsurface Heshang Cave. IMPORTANCE In general, the constant physicochemical conditions and limited nutrient sources over long periods in the subsurface support a stable ecosystem in karst cave. Previous studies on cave microbial ecology were mostly focused on community composition, diversity, and the relationship with local environmental factors. There are still many unknowns about the microbial interactions and functions in such a dark environment with little human interference. Two representative habitats, including weathered rock and sediment in Heshang Cave, were selected to give an integrated insight into microbial interactions and potential functions. The cooccurrence network, especially the subnetwork, was used to characterize the cave microbial interactions in detail. We demonstrated that abundant taxa primarily relied on promotion effects rather than inhibition effects to survive in Heshang Cave. Keystone species may play important metabolic roles in sustaining ecological functions. Our study provides improved understanding of microbial interaction patterns and community ecological functions in the karst cave ecosystem.

Project description:Karst caves are usually considered as natural laboratories to study pristine microbiomes in subsurface biosphere. However, effects of the increasingly detected nitrate in underground karst ecosystem due to the acid rain impact on microbiota and their functions in subsurface karst caves have remained largely unknown. In this study, samples of weathered rocks and sediments were collected from the Chang Cave, Hubei province and subjected to high-throughput sequencing of 16S rRNA genes. The results showed that nitrate significantly impacted bacterial compositions, interactions, and functions in different habitats. Bacterial communities clustered according to their habitats with distinguished indicator groups identified for each individual habitat. Nitrate shaped the overall bacterial communities across two habitats with a contribution of 27.2%, whereas the pH and TOC, respectively, structured bacterial communities in weathered rocks and sediments. Alpha and beta diversities of bacterial communities increased with nitrate concentration in both habitats, with nitrate directly affecting alpha diversity in sediments, but indirectly on weathered rocks by lowering pH. Nitrate impacted more on bacterial communities in weathered rocks at the genus level than in sediments because more genera significantly correlated with nitrate concentration in weathered rocks. Diverse keystone taxa involved in nitrogen cycling were identified in the co-occurrence networks such as nitrate reducers, ammonium-oxidizers, and N2-fixers. Tax4Fun2 analysis further confirmed the dominance of genes involved in nitrogen cycling. Genes of methane metabolism and carbon fixation were also dominant. The dominance of dissimilatory and assimilatory nitrate reduction in nitrogen cycling substantiated nitrate impact on bacterial functions. Our results for the first time revealed the impact of nitrate on subsurface karst ecosystem in terms of bacterial compositions, interactions, and functions, providing an important reference for further deciphering the disturbance of human activities on the subsurface biosphere.

Dataset Information

Adaptive Molecular Evolution of PHYE in Primulina, a Karst Cave Plant.

Publications

Adaptive Molecular Evolution of PHYE in Primulina, a Karst Cave Plant.

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