Whole Genome Sequencing and Metabolomic Study of Cave Streptomyces Isolates ICC1 and ICC4

The terrestrial subsurface microbiome has gained considerable amount of interests in the recent years because of its rich potential resource for biomining novel genes coding for metabolites possessing antimicrobial activities. In our previous study, we identified two Streptomyces isolates, designated as ICC1 and ICC4, from the Iron Curtain Cave, Chilliwack, Canada that exhibited antagonistic activities against the multidrug resistant strains of Escherichia coli. In this study, the genomes of these two isolates were sequenced by Illumina MiSeq, assembled and annotated. The genes associated with secondary metabolite production were identified and annotated using the bioinformatics platforms antiSMASH and BAGEL. ICC1 and ICC4 were then cultivated and ICC1 metabolome characterized by UHPLC-ESI-HRMS. The Global Natural Products Social Molecular Networking was used to identify metabolites based on the MS/MS spectral data. ICC1 and ICC4 showed a high level of sequence identity with the terrestrial bacteria Streptomyces lavendulae; however, they possess a greater secondary metabolite potential as estimated by the total number of identified biosynthetic gene clusters (BGCs). In particular, ICC1 and ICC4 had a greater number of polyketide and non-ribosomal peptide BGCs. The most frequently detected BGCs were those predicted to generate terpenes, small and low complexity dipeptides and lipids. Spectral analysis clearly identified a number of diketopiperazine products through matched reference spectra for cyclo (Leu-Pro), cyclo (Pro-Val) and cyclo [(4-hydroxyPro)-Leu]. One of the terpenes gene clusters predicted by antiSMASH possesses a seven-gene pathway consistent with diazepinomicin biosynthesis. This molecule contains a very rare core structure and its BGC, to date, has only been identified from a single bacterial genome. The tetrapeptide siderophore coelichelin BGC was unambiguously identified in the genome, however, the metabolite could not be identified from the culture extracts. Two type III polyketides, 2′, 5′ – dimethoxyflavone and nordentatin, were identified from the UHPLC-HRMS data of the aqueous and n-butanolic fractions of Streptomyces sp. ICC1, respectively. A BGC likely encoding these metabolites was predicted in both genomes. The predicted similarities in molecule production and genome shared by these two strains could be an indicative of a cooperative mode of living in extreme habitats instead of a competitive one. This secondary metabolite potential may contribute to the fitness of ICC1 and ICC4 in the Iron Curtain Cave

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

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

A conservation roadmap for the subterranean biome

The 15th UN Convention on Biological Diversity (CBD) (COP15) will be held in Kunming, China in October 2021. Historically, CBDs and other multilateral treaties have either alluded to or entirely overlooked the subterranean biome. A multilateral effort to robustly examine, monitor, and incorporate the subterranean biome into future conservation targets will enable the CBD to further improve the ecological effectiveness of protected areas by including groundwater resources, subterranean ecosystem services, and the profoundly endemic subsurface biodiversity. To this end, we proffer a conservation roadmap that embodies five conceptual areas: (1) science gaps and data management needs; (2) anthropogenic stressors; (3) socioeconomic analysis and conflict resolution; (4) environmental education; and (5) national policies and multilateral agreements.Peer reviewe

The effects of UV light on the antimicrobial activities of cave actinomycetes

The goal of this study was to determine whether actinomycetes isolated from a volcanic cave in western Canada could produce novel antimicrobial compounds against six multidrugresistant pathogens when exposed to UV light. One hundred and seventy-six actinomycete strains isolated from Helmcken Falls Cave, Wells Gray Provincial Park, BC, were screened against six pathogens using the “plug assay” in UV light and no light conditions. Of the 176 strains tested, 100 or 57% of the cave actinomycete strains had antimicrobial activities against the pathogens in 124 different instances: 35 instances when exposed to UV and no light, 30 when exposed to UV light, and 59 instances when exposed to no light. The metabolites of six actinomycete strains also lost their antimicrobial activities when exposed to UV light. While the metabolites produced by these strains have yet to be determined, exposure to lighted environments may either deactivate or enhance the antimicrobial activities of cave actinomycete strains. This study represents a confirmation that cave actinomycetes are potential sources of novel antimicrobial compounds and also is the first report of the enhancement of antimicrobial activities of some cave bacteria by exposure to UV light. Further investigation of the role of UV light with respect to activation/deactivation of antimicrobial activities of cave actinomycetes is required

Intellectual property management and awareness at the university level in the biotechnology era: a Thai perspective

Developing countries Thai universities Intellectual property protection Intellectual property management Biotechnology patents Intellectual property awareness Traditional medicines Intellectual property department

Chapter 12. New Sources of Antibiotics: Caves

Caves are regarded as extreme habitats because their conditions are unique and harsh for microbial life. Though demanding, these irreplaceable habitats have been demonstrated to support a great diversity of microbial communities that are believed to hold great promise as new sources of antibiotics and industrially relevant compounds. This chapter highlights recent findings that convincingly solidify the concept that caves are potentially homes to novel and rare microorganisms and tomorrow’s antibiotics.Our thanks go to Dr Ken Wagner of Thompson Rivers University for his time and assistance in proofreading this manuscript and to Dr Hazel Barton of the University of Akron for her insights and for sharing her latest and yet-to-be published work with us. NC was supported by TRU Research Innovation Funds. CSJ was supported by CSIC project 201230E125.Peer Reviewe