Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions

16 páginas.-- 8 figuras.-- 2 tablas.-- 66 referencias.-- Material suplementario http://dx.doi.org/10.3389/fmicb.2015.01342Volcanic caves are filled with colorful microbial mats on the walls and ceilings. These volcanic caves are found worldwide, and studies are finding vast bacteria diversity within these caves. One group of bacteria that can be abundant in volcanic caves, as well as other caves, is Actinobacteria. As Actinobacteria are valued for their ability to produce a variety of secondary metabolites, rare and novel Actinobacteria are being sought in underexplored environments. The abundance of novel Actinobacteria in volcanic caves makes this environment an excellent location to study these bacteria. Scanning electron microscopy (SEM) from several volcanic caves worldwide revealed diversity in the morphologies present. Spores, coccoid, and filamentous cells, many with hair-like or knobby extensions, were some of the microbial structures observed within the microbial mat samples. In addition, the SEM study pointed out that these features figure prominently in both constructive and destructive mineral processes. To further investigate this diversity, we conducted both Sanger sequencing and 454 pyrosequencing of the Actinobacteria in volcanic caves from four locations, two islands in the Azores, Portugal, and Hawai'i and New Mexico, USA. This comparison represents one of the largest sequencing efforts of Actinobacteria in volcanic caves to date. The diversity was shown to be dominated by Actinomycetales, but also included several newly described orders, such as Euzebyales, and Gaiellales. Sixty-two percent of the clones from the four locations shared less than 97% similarity to known sequences, and nearly 71% of the clones were singletons, supporting the commonly held belief that volcanic caves are an untapped resource for novel and rare Actinobacteria. The amplicon libraries depicted a wider view of the microbial diversity in Azorean volcanic caves revealing three additional orders, Rubrobacterales, Solirubrobacterales, and Coriobacteriales. Studies of microbial ecology in volcanic caves are still very limited. To rectify this deficiency, the results from our study help fill in the gaps in our knowledge of actinobacterial diversity and their potential roles in the volcanic cave ecosystems.The authors acknowledge the Spanish Ministry of Economy and Competitiveness (project CGL2013-41674-P) and FEDER Funds for financial support. AM acknowledges the support from the Marie Curie Intra-European Fellowship of the European Commission's 7th Framework Programme (PIEF-GA-2012-328689). CR was funded by the Regional Fund for Science and Technology and Pro-Emprego program of the Regional Government of the Azores, Portugal [M3.1.7/F/013/2011, M3.1.7/F/030/2011]. Her work was partly supported by National funds from the Foundation for Science and Technology of the Portuguese Government, [Understanding Underground Biodiversity: Studies in Azorean Lava Tubes (reference PTDC/AMB/70801/2006]. The authors would like to thank the TRU Innovation in Research Grant, TRU UREAP Fund, Western Economic Diversification Canada Fund, Kent Watson (assisted with the Helmcken Falls Cave sample collection), Derrick Horne (UBC BioImaging Facility for the SEM work). We acknowledged the Canadian Ministry of Forests, Lands, and Natural Resource Operations for Park Use Permit#102172. This work was also supported by the Cave Conservancy of the Virginias, the Graduate Research Allocation Committee at UNM Biology, UNM Biology Grove Scholarship, the Student Research Allocation Committee at UNM, the National Speleological Society, the New Mexico Space Grant Consortium, the New Mexico Alliance for Minority Participation Program, the New Mexico Geological Society, and Kenneth Ingham Consulting. We acknowledge support from the UNM Molecular Biology Facility, which is supported by NIH grant number P20GM103452. The authors also wish to thank Fernando Pereira, Ana Rita Varela, Pedro Correia, Berta Borges, and Guida Pires for help during field and lab work in the Azores. The authors gratefully acknowledge the photographic contributions of Kenneth Ingham and Pedro Cardoso and Michael Spilde (SEM images). The authors would like to thank Dr. Steven Van Wagoner (TRU) and Drs. Julian Davies and Vivian Miao (UBC) for their invaluable comments in manuscript preparation. We gratefully acknowledge the help and collecting permits granted by the staff of El Malpais National Monument and Hawai'i Volcanoes National Park (USA).Peer reviewe

Islands Within Islands: Bacterial Phylogenetic Structure and Consortia in Hawaiian Lava Caves and Fumaroles

Lava caves, tubes, and fumaroles in Hawai‘i present a range of volcanic, oligotrophic environments from different lava flows and host unexpectedly high levels of bacterial diversity. These features provide an opportunity to study the ecological drivers that structure bacterial community diversity and assemblies in volcanic ecosystems and compare the older, more stable environments of lava tubes, to the more variable and extreme conditions of younger, geothermally active caves and fumaroles. Using 16S rRNA amplicon-based sequencing methods, we investigated the phylogenetic distinctness and diversity and identified microbial interactions and consortia through co-occurrence networks in 70 samples from lava tubes, geothermal lava caves, and fumaroles on the island of Hawai‘i. Our data illustrate that lava caves and geothermal sites harbor unique microbial communities, with very little overlap between caves or sites. We also found that older lava tubes (500–800 yrs old) hosted greater phylogenetic diversity (Faith's PD) than sites that were either geothermally active or younger (<400 yrs old). Geothermally active sites had a greater number of interactions and complexity than lava tubes. Average phylogenetic distinctness, a measure of the phylogenetic relatedness of a community, was higher than would be expected if communities were structured at random. This suggests that bacterial communities of Hawaiian volcanic environments are phylogenetically over-dispersed and that competitive exclusion is the main driver in structuring these communities. This was supported by network analyses that found that taxa (Class level) co-occurred with more distantly related organisms than close relatives, particularly in geothermal sites. Network “hubs” (taxa of potentially higher ecological importance) were not the most abundant taxa in either geothermal sites or lava tubes and were identified as unknown families or genera of the phyla, Chloroflexi and Acidobacteria. These results highlight the need for further study on the ecological role of microbes in caves through targeted culturing methods, metagenomics, and long-read sequence technologies

Fundamental research questions in subterranean biology

Five decades ago, a landmark paper inSciencetitledThe Cave Environmentheralded caves as ideal natural experimental laboratories in which to develop and address general questions in geology, ecology, biogeography, and evolutionary biology. Although the 'caves as laboratory' paradigm has since been advocated by subterranean biologists, there are few examples of studies that successfully translated their results into general principles. The contemporary era of big data, modelling tools, and revolutionary advances in genetics and (meta)genomics provides an opportunity to revisit unresolved questions and challenges, as well as examine promising new avenues of research in subterranean biology. Accordingly, we have developed a roadmap to guide future research endeavours in subterranean biology by adapting a well-established methodology of 'horizon scanning' to identify the highest priority research questions across six subject areas. Based on the expert opinion of 30 scientists from around the globe with complementary expertise and of different academic ages, we assembled an initial list of 258 fundamental questions concentrating on macroecology and microbial ecology, adaptation, evolution, and conservation. Subsequently, through online surveys, 130 subterranean biologists with various backgrounds assisted us in reducing our list to 50 top-priority questions. These research questions are broad in scope and ready to be addressed in the next decade. We believe this exercise will stimulate research towards a deeper understanding of subterranean biology and foster hypothesis-driven studies likely to resonate broadly from the traditional boundaries of this field.Peer reviewe

Humanizing the Business of Medicine: The Use of Simulated Patients to Train Medical Students

The Primary Care Curriculum of the University of New Mexico utilizes simulated patients to develop medical students’ ability to create a good doctor-patient relationship. Simulated patients are laypersons who are trained to simulate the physical signs, verbal responses, and emotional reactions of patients with particular medical conditions. These simulators provide immediate verbal feedback to students concerning their affective skills. Additionally, student skill in conducting a patient interview, performing a physical exam, problem-solving, and making management recommendations is evaluated using simulated patients. Details of the development and implementation of the simulated patient program are discussed

GEOMICROBIOLOGY IN CAVE ENVIRONMENTS: PAST, CURRENT AND FUTURE PERSPECTIVES

The Karst Waters Institute Breakthroughs in Karst Geomicrobiology and Redox Geochemistry conference in 1994 was a watershed event in the history of cave geomicrobiology studies within the US. Since that time, studies of cave geomicrobiology have accelerated in number, complexity of techniques used, and depth of the results obtained. The field has moved from being sparse and largely descriptive in nature, to rich in experimental studies yielding fresh insights into the nature of microbe-mineral interactions in caves. To provide insight into the changing nature of cave geomicrobiology we have divided our review into research occurring before and after the Breakthroughs conference, and concentrated on secondary cave deposits: sulfur (sulfidic systems), iron and manganese (ferromanganese, a.k.a. corrosion residue deposits), nitrate (a.k.a. saltpeter), and carbonate compounds (speleothems and moonmilk deposits). The debate concerning the origin of saltpeter remains unresolved; progress has been made on identifying the roles of bacteria in sulfur cave ecosystems, including cavern enlargement through biogenic sulfuric acid; new evidence provides a model for the action of bacteria in forming some moonmilk deposits; combined geochemical and molecular phylogenetic studies suggest that some ferromanganese deposits are biogenic, the result of redox reactions; and evidence is accumulating that points to an active role for microorganisms in carbonate precipitation in speleothems

GEOMICROBIOLOGY IN CAVE ENVIRONMENTS: PAST, CURRENT AND FUTURE PERSPECTIVES

The Karst Waters Institute Breakthroughs in Karst Geomicrobiology and Redox Geochemistry conference in 1994 was a watershed event in the history of cave geomicrobiology studies within the US. Since that time, studies of cave geomicrobiology have accelerated in number, complexity of techniques used, and depth of the results obtained. The field has moved from being sparse and largely descriptive in nature, to rich in experimental studies yielding fresh insights into the nature of microbe-mineral interactions in caves. To provide insight into the changing nature of cave geomicrobiology we have divided our review into research occurring before and after the Breakthroughs conference, and concentrated on secondary cave deposits: sulfur (sulfidic systems), iron and manganese (ferromanganese, a.k.a. corrosion residue deposits), nitrate (a.k.a. saltpeter), and carbonate compounds (speleothems and moonmilk deposits). The debate concerning the origin of saltpeter remains unresolved; progress has been made on identifying the roles of bacteria in sulfur cave ecosystems, including cavern enlargement through biogenic sulfuric acid; new evidence provides a model for the action of bacteria in forming some moonmilk deposits; combined geochemical and molecular phylogenetic studies suggest that some ferromanganese deposits are biogenic, the result of redox reactions; and evidence is accumulating that points to an active role for microorganisms in carbonate precipitation in speleothems

GEOMICROBIOLOGY IN CAVE ENVIRONMENTS: PAST, CURRENT AND FUTURE PERSPECTIVES

The Karst Waters Institute Breakthroughs in Karst Geomicrobiology and Redox Geochemistry conference in 1994 was a watershed event in the history of cave geomicrobiology studies within the US. Since that time, studies of cave geomicrobiology have accelerated in number, complexity of techniques used, and depth of the results obtained. The field has moved from being sparse and largely descriptive in nature, to rich in experimental studies yielding fresh insights into the nature of microbe-mineral interactions in caves. To provide insight into the changing nature of cave geomicrobiology we have divided our review into research occurring before and after the Breakthroughs conference, and concentrated on secondary cave deposits: sulfur (sulfidic systems), iron and manganese (ferromanganese, a.k.a. corrosion residue deposits), nitrate (a.k.a. saltpeter), and carbonate compounds (speleothems and moonmilk deposits). The debate concerning the origin of saltpeter remains unresolved; progress has been made on identifying the roles of bacteria in sulfur cave ecosystems, including cavern enlargement through biogenic sulfuric acid; new evidence provides a model for the action of bacteria in forming some moonmilk deposits; combined geochemical and molecular phylogenetic studies suggest that some ferromanganese deposits are biogenic, the result of redox reactions; and evidence is accumulating that points to an active role for microorganisms in carbonate precipitation in speleothems

GEOMICROBIOLOGY IN CAVE ENVIRONMENTS: PAST, CURRENT AND FUTURE PERSPECTIVES

The Karst Waters Institute Breakthroughs in Karst Geomicrobiology and Redox Geochemistry conference in 1994 was a watershed event in the history of cave geomicrobiology studies within the US. Since that time, studies of cave geomicrobiology have accelerated in number, complexity of techniques used, and depth of the results obtained. The field has moved from being sparse and largely descriptive in nature, to rich in experimental studies yielding fresh insights into the nature of microbe-mineral interactions in caves. To provide insight into the changing nature of cave geomicrobiology we have divided our review into research occurring before and after the Breakthroughs conference, and concentrated on secondary cave deposits: sulfur (sulfidic systems), iron and manganese (ferromanganese, a.k.a. corrosion residue deposits), nitrate (a.k.a. saltpeter), and carbonate compounds (speleothems and moonmilk deposits). The debate concerning the origin of saltpeter remains unresolved; progress has been made on identifying the roles of bacteria in sulfur cave ecosystems, including cavern enlargement through biogenic sulfuric acid; new evidence provides a model for the action of bacteria in forming some moonmilk deposits; combined geochemical and molecular phylogenetic studies suggest that some ferromanganese deposits are biogenic, the result of redox reactions; and evidence is accumulating that points to an active role for microorganisms in carbonate precipitation in speleothems

Bioenergetics of camel crickets (Ceuthophilus carlsbadensis, C. longipes and C. Conicaudus) from carlsbad caverns national park, new mexico

1. 1. Camel crickets in Carlsbad Caverns National Park exhibit linear long-term weight loss patterns for combined sexes of 1.05 mg/hr for Ceuthophilus carlsbadensis, 0.261 mg/hr for C. conicaudus, and 0.321 mg/hr for C. longipes.2. 2. From these patterns, maximal foraging intervals for females and males, respectively, of 5.1 and 4.4 days for C. carlsbadensis, 4.6 and 5.7 days for C. longipes, and 5.0 and 4.2 days for C. conicaudus were predicted.3. 3. Calculated metabolic rates (cal/hr) of 1.04 for C. carlsbadensis and 0.52 for C. longipes were half that predicted for epigean species of similar size.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30490/1/0000118.pd