\\n\\n
Dr. Pletser’s experience includes 30 years of working with the European Space Agency as a Senior Physicist/Engineer and coordinating their parabolic flight campaigns, and he is the Guinness World Record holder for the most number of aircraft flown (12) in parabolas, personally logging more than 7,300 parabolas.
\\n\\nSeeing the 5,000th book published makes us at the same time proud, happy, humble, and grateful. This is a great opportunity to stop and celebrate what we have done so far, but is also an opportunity to engage even more, grow, and succeed. It wouldn't be possible to get here without the synergy of team members’ hard work and authors and editors who devote time and their expertise into Open Access book publishing with us.
\\n\\nOver these years, we have gone from pioneering the scientific Open Access book publishing field to being the world’s largest Open Access book publisher. Nonetheless, our vision has remained the same: to meet the challenges of making relevant knowledge available to the worldwide community under the Open Access model.
\\n\\nWe are excited about the present, and we look forward to sharing many more successes in the future.
\\n\\nThank you all for being part of the journey. 5,000 times thank you!
\\n\\nNow with 5,000 titles available Open Access, which one will you read next?
\\n\\nRead, share and download for free: https://www.intechopen.com/books
\\n\\n\\n\\n
\\n"}]',published:!0,mainMedia:null},components:[{type:"htmlEditorComponent",content:'
Preparation of Space Experiments edited by international leading expert Dr. Vladimir Pletser, Director of Space Training Operations at Blue Abyss is the 5,000th Open Access book published by IntechOpen and our milestone publication!
\n\n"This book presents some of the current trends in space microgravity research. The eleven chapters introduce various facets of space research in physical sciences, human physiology and technology developed using the microgravity environment not only to improve our fundamental understanding in these domains but also to adapt this new knowledge for application on earth." says the editor. Listen what else Dr. Pletser has to say...
\n\n\n\nDr. Pletser’s experience includes 30 years of working with the European Space Agency as a Senior Physicist/Engineer and coordinating their parabolic flight campaigns, and he is the Guinness World Record holder for the most number of aircraft flown (12) in parabolas, personally logging more than 7,300 parabolas.
\n\nSeeing the 5,000th book published makes us at the same time proud, happy, humble, and grateful. This is a great opportunity to stop and celebrate what we have done so far, but is also an opportunity to engage even more, grow, and succeed. It wouldn't be possible to get here without the synergy of team members’ hard work and authors and editors who devote time and their expertise into Open Access book publishing with us.
\n\nOver these years, we have gone from pioneering the scientific Open Access book publishing field to being the world’s largest Open Access book publisher. Nonetheless, our vision has remained the same: to meet the challenges of making relevant knowledge available to the worldwide community under the Open Access model.
\n\nWe are excited about the present, and we look forward to sharing many more successes in the future.
\n\nThank you all for being part of the journey. 5,000 times thank you!
\n\nNow with 5,000 titles available Open Access, which one will you read next?
\n\nRead, share and download for free: https://www.intechopen.com/books
\n\n\n\n
\n'}],latestNews:[{slug:"stanford-university-identifies-top-2-scientists-over-1-000-are-intechopen-authors-and-editors-20210122",title:"Stanford University Identifies Top 2% Scientists, Over 1,000 are IntechOpen Authors and Editors"},{slug:"intechopen-authors-included-in-the-highly-cited-researchers-list-for-2020-20210121",title:"IntechOpen Authors Included in the Highly Cited Researchers List for 2020"},{slug:"intechopen-maintains-position-as-the-world-s-largest-oa-book-publisher-20201218",title:"IntechOpen Maintains Position as the World’s Largest OA Book Publisher"},{slug:"all-intechopen-books-available-on-perlego-20201215",title:"All IntechOpen Books Available on Perlego"},{slug:"oiv-awards-recognizes-intechopen-s-editors-20201127",title:"OIV Awards Recognizes IntechOpen's Editors"},{slug:"intechopen-joins-crossref-s-initiative-for-open-abstracts-i4oa-to-boost-the-discovery-of-research-20201005",title:"IntechOpen joins Crossref's Initiative for Open Abstracts (I4OA) to Boost the Discovery of Research"},{slug:"intechopen-hits-milestone-5-000-open-access-books-published-20200908",title:"IntechOpen hits milestone: 5,000 Open Access books published!"},{slug:"intechopen-books-hosted-on-the-mathworks-book-program-20200819",title:"IntechOpen Books Hosted on the MathWorks Book Program"}]},book:{item:{type:"book",id:"6276",leadTitle:null,fullTitle:"Residual Stress Analysis on Welded Joints by Means of Numerical Simulation and Experiments",title:"Residual Stress Analysis on Welded Joints by Means of Numerical Simulation and Experiments",subtitle:null,reviewType:"peer-reviewed",abstract:"The ability to quantify residual stresses induced by welding processes through experimentation or numerical simulation has become, today more than ever, of strategic importance in the context of their application to advanced design. This is an ongoing challenge that commenced many years ago. Recent design criteria endeavour to quantify the effect of residual stresses on fatigue strength of welded joints to allow a more efficient use of materials and a greater reliability of welded structures. The aim of the present book is contributing to these aspects of design through a collection of case-studies that illustrate both standard and advanced experimental and numerical methodologies used to assess the residual stress field in welded joints. The work is intended to be of assistance to designers, industrial engineers and academics who want to deepen their knowledge of this challenging topic.",isbn:"978-1-78923-107-6",printIsbn:"978-1-78923-106-9",pdfIsbn:"978-1-83881-373-4",doi:"10.5772/intechopen.69093",price:119,priceEur:129,priceUsd:155,slug:"residual-stress-analysis-on-welded-joints-by-means-of-numerical-simulation-and-experiments",numberOfPages:162,isOpenForSubmission:!1,isInWos:1,hash:"df9c0c97df0bed4d93eed96c30903b2b",bookSignature:"Paolo Ferro and Filippo Berto",publishedDate:"May 16th 2018",coverURL:"https://cdn.intechopen.com/books/images_new/6276.jpg",numberOfDownloads:4745,numberOfWosCitations:3,numberOfCrossrefCitations:0,numberOfDimensionsCitations:4,hasAltmetrics:0,numberOfTotalCitations:7,isAvailableForWebshopOrdering:!0,dateEndFirstStepPublish:"May 11th 2017",dateEndSecondStepPublish:"June 1st 2017",dateEndThirdStepPublish:"September 24th 2017",dateEndFourthStepPublish:"November 26th 2017",dateEndFifthStepPublish:"January 25th 2018",currentStepOfPublishingProcess:5,indexedIn:"1,2,3,4,5,6,7",editedByType:"Edited by",kuFlag:!1,editors:[{id:"43915",title:"Dr.",name:"Paolo",middleName:null,surname:"Ferro",slug:"paolo-ferro",fullName:"Paolo Ferro",profilePictureURL:"https://mts.intechopen.com/storage/users/43915/images/5365_n.jpg",biography:"Paolo Ferro is actually Associate Professor of Metallurgy and Materials Selection at the University of Padua (Italy). After the degree in Materials Engineering (with first-class honours) he received the Ph.D. degree from University of Padua in Metallurgical Engineering. From 2006 to April 2015 he served as Assistant Professor in the Department of Engineering and Management of the same University. He was scientific director of the research program \\'Numerical and Experimental Determination of Residual Stresses in Welded Joints and their Influence on Fatigue Strength\\' (Young Researchers Project, 2003-2004). He won the prize for young researchers ‘Aldo Daccò’ 2002. He is a member of CMBM (Centre for Mechanics of Biological Materials). His research is mainly focused on the analytical and numerical modelling of welding and heat treatment processes. He is interested in the local criteria based on the Notch Stress Intensity Factor (NSIF) and the Strain Energy Density (SED) averaged over a control volume for the evaluation of fatigue strength of welded joints. He works also on the modelling of intermetallic phases evolution during heat treatments of Duplex and Superduplex Stainless Steels and mechanical and metallurgical characterisation of Cast Irons. He has published more than 100 papers in international peer-reviewed journals, conference proceedings and contributed book chapters. In addition to his editorial role with Advances in Materials Science and Engineering he frequently serves as reviewer for many other professional journals and national as well as international funding agencies.",institutionString:null,position:null,outsideEditionCount:0,totalCites:0,totalAuthoredChapters:"1",totalChapterViews:"0",totalEditedBooks:"1",institution:{name:"University of Padua",institutionURL:null,country:{name:"Italy"}}}],equalEditorOne:null,equalEditorTwo:null,equalEditorThree:null,coeditorOne:{id:"199954",title:"Dr.",name:"Filippo",middleName:null,surname:"Berto",slug:"filippo-berto",fullName:"Filippo Berto",profilePictureURL:"https://mts.intechopen.com/storage/users/199954/images/5366_n.jpg",biography:"Filippo Berto got his degree summa cum laude in \\'Management Engineering\\' in 2003 at the University of Padua (Italy). After attending the PhD course on \\'Design Machine\\' at the University of Florence, he worked as researcher in \\'Machine Design\\' at the University of Padua. From October 2014 to September 2016 he was Associate Professor of Mechanics. Since 1 January 2016 he has been appointed with the most prestigious available position at NTNU as international outstanding renowned Chair of Mechanics of Materials (top research program for international researchers recognized internationally for the quality of their academic achievements and having an impressive track record of publications and research projects, historically regius professorship). He is the co-founder of the new fatigue lab at IPM together with Prof. A. Vinogradov. His area of expertise is oriented to the brittle failure of different materials, notch effect, the application of the finite element method to the structural analysis, the mechanical behaviour of metallic materials, the fatigue performance of notched components as well as the reliability of welded, bolted and bonded joints.",institutionString:null,position:null,outsideEditionCount:0,totalCites:0,totalAuthoredChapters:"0",totalChapterViews:"0",totalEditedBooks:"0",institution:null},coeditorTwo:null,coeditorThree:null,coeditorFour:null,coeditorFive:null,topics:[{id:"816",title:"Manufacturing Engineering",slug:"mechanical-engineering-manufacturing-engineering"}],chapters:[{id:"57583",title:"Experimental Techniques to Investigate Residual Stress in Joints",doi:"10.5772/intechopen.71564",slug:"experimental-techniques-to-investigate-residual-stress-in-joints",totalDownloads:828,totalCrossrefCites:0,totalDimensionsCites:3,signatures:"Roberto Montanari, Alessandra Fava and Giuseppe 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This chapter provides a review of the principles underpinning open scientific data and the policies mandating open access to scientific data. It has a specific focus on the policies of research funders and journal publishers.
\nThe chapter consists of five parts, as follows:
\n1. Main international developments
\n2. Key policies of research funders
\n3. Selected policies of publishers
\n4. Issues covered in the open data policies
\n5. Open scientific data in emerging and developing countries
Increased data sharing among scientists and with non-scientists can generate vast benefits to society and to the economy. Yet creating conditions conducive to data sharing remains a challenge. Inspired by the positive experience with open publications, similar policies have been introduced in recent years with a view to facilitating greater sharing of research data.
\nThis chapter surveys open data policies, paying particular attention to the scope of the open data mandates. It starts with an overview of major international developments and declarations that have inspired governments and research funders to introduce open data policies. This is followed by an analysis of the policies of research funders and publishers in several jurisdictions. Next is identification of the components of ideal data sharing policies. The final section surveys the open data landscape in emerging and developing countries.
\nSome of the world’s leading research organisations are based in the United States. Many of them were also among the first in the world to recognise the potential of open science. The first policy statement for open access to research data consists of the Bromley Principles issued by the United States Global Change Research Program in 1991 [169]. Five years later the Bermuda Principles—developed as part of the Human Genome Project—established an international practice in the sharing of genomic data prior to publication of research findings in scientific journals [170]. These principles of free release and data sharing have been one of the major outputs of the Human Genome Project and have established the practice of genomic data sharing globally.
\nThe Access to Databases Principles first published by the International Council for Science/Committee on Data for Science and Technology (ICSU/CODATA) in 2002 provided a further impetus for promoting open access to scientific data among policymakers [171]. The principles were developed to facilitate the evaluation of legislative proposals that may affect the use of scientific databases.
\nThe Human Genome Project was declared complete in 2003. In the same year, open access to scientific data was first codified internationally, in the Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities. The declaration emerged from a conference hosted by the Max Planck Institute in Munich and represents a landmark statement on open access to scientific contributions1 including:
… original scientific research results, raw data and metadata, source materials, digital representations of pictorial and graphical materials and scholarly multimedia material [63].
Such scientific contributions need to satisfy two conditions to quality as ‘open’:
\nFirst, the author(s) and right holder(s) of such contributions grant(s) to all users a free, irrevocable, worldwide, right of access to, and a licence to copy, use, distribute, transmit and display the work publicly and to make and distribute derivative works, in any digital medium for any responsible purpose, subject to proper attribution of authorship … as well as the right to make small numbers of printed copies for their personal use.
\nSecond, a complete version of the work and all supplemental materials, including a copy of the permission as stated above, in an appropriate standard electronic format is deposited (and thus published) in at least one online repository using suitable technical standards (such as the Open Archive definitions) that is supported and maintained by an academic institution, scholarly society, government agency, or other well-established organisation that seeks to enable open access, unrestricted distribution, interoperability and long-term archiving.2
\nOrganisations committed to implementing these objectives and the two key principles can sign the declaration. As of October 2007, there were over 240 signatories, mostly research organisations. As of early June 2018, the number of signatories had reached 620 [172].
\nThe United Nations Educational, Scientific and Cultural Organization (UNESCO) is the only UN agency with a specific mandate for science. One of its main functions, articulated in the UNESCO constitution, is to:
… maintain, increase and diffuse knowledge: by assuring the conservation and protection of the world’s inheritance of books, works of art and monuments of history and science, and recommending to the nations concerned the necessary international conventions.3
At the same time, facilitating the sharing of scientific outcomes is only one of the many responsibilities assigned to UNESCO. Perhaps for this reason the organisation has not played a pivotal role in recommending any international conventions for open science in recent years. Many provisions of the UNESCO Declaration on Science and the Use of Scientific Knowledge—adopted in 1999—are now outdated due to rapid technological developments and changing methods of science production and dissemination.4
\nHaving said that, one of the key objectives articulated in the Strategy on UNESCO Contribution to the Promotion of Open Access to Scientific Information and Research is to convene an international congress on scholarly communication to examine the feasibility of developing a UNESCO convention on open access for scientific information and research ([29], p. 13).
\nMore recently, UNESCO endorsed several open science initiatives, including the Open Science for the 21st Century Declaration by All European Academies,5 which encourage scientists and their organisations, particularly publicly funded organisations, to apply open-sharing principles to the data underpinning research publications, including negative results. The Declaration also calls for measures to ensure data quality and preservation to enable future reuse.6
\nIn addition, UNESCO supports several public education projects aimed at raising awareness of open access, including in developing countries. In 2012, UNESCO issued Policy Guidelines for the Development and Promotion of Open Access written by Swan [27]. The report notes that:
Research data are increasingly covered by policies and often these policies are being implemented by smaller, niche players as well as large research funders. These policies are not usually, however, the same (Open Access) policies that cover the text-based literature. Data are exceptional because policies must take into account issues of privacy and special cases where data cannot be released for other reasons. Developing and wording Open Data policies is therefore a specialised issue that is not as straightforward as developing polices for Open Access to the literature. Where there is Open Access policy development now, Open Data policy development will follow.7
In recent years, UNESCO has taken a more active role in developing open scientific repositories. One recent example is the World Library of Science [173], an online repository of short e-books and articles, developed in partnership with the publishers Nature Education and the pharmaceutical company Roche. This currently contains resources in the field of genetics intended for university undergraduate faculties and students. The platform enables science teachers and students from all parts of the world to exchange views, information and knowledge.
\nIn January 2004, the ministers of science and technology from OECD countries and from China, Israel, Russia and South Africa adopted a Declaration on Access to Research Data from Public Funding. They also called on the OECD to develop a set of guidelines based on commonly agreed principles to facilitate optimal cost-effective access to digital research data [174]. The OECD responded with such a set of principles, published in late 2006, which highlighted the importance of open access to publicly funded research data.8 The principles held that open access has a vast potential to improve the scientific and social return on public investment [175]. The OECD noted, however, that the level of public research funding varies significantly across countries, as do data access policies and practices at the national, disciplinary and institutional levels. The OECD Principles, summarised below, were developed with a view to providing broad policy recommendations to governments, research organisations and funding bodies:
\nPrinciple A. Openness—access on equal terms and at the lowest possible cost. Open access to research data should be easy, timely, user-friendly and preferably Internet-based.
\nPrinciple B. Flexibility—recognising the rapid and often unpredictable changes in information technologies, the characteristics of each research field and the diversity of research systems, legal systems and cultures of each member country.
\nPrinciple C. Transparency—information on research data and data-producing organisations and the conditions attached to the use of the data should be available in a transparent way, ideally through the Internet.
\nPrinciple D. Legal conformity—data access arrangements should respect the legal rights and legitimate interests of all stakeholders in a public research enterprise. Subscribing to professional codes of conduct may facilitate meeting legal requirements.
\nPrinciple E. Protection of intellectual property—data access arrangements should consider the applicability of copyright and other intellectual property laws that may be relevant to research databases. At the same time, the fact that there is private sector involvement in the data collection or that the data may be protected by intellectual property laws should not be used as a reason to restrict access to the data.
\nPrinciple F. Formal responsibility—formal institutional practices should be promoted. These include rules and regulations regarding the responsibilities of the various parties involved in data-related activities. The issues to be covered include authorship, producer credits, ownership, dissemination, usage restrictions, financial arrangements, ethical rules, licencing terms, liability and sustainable archiving.
\nPrinciple G. Professionalism—institutional arrangements for the management of research data should be based on relevant professional standards and values embodied in the codes of conduct of the scientific communities involved.
\nPrinciple H. Interoperability—technological and semantic interoperability is the key consideration in enabling and promoting international and interdisciplinary access to, and use of, research data. Member countries and research institutions should cooperate with international organisations in developing data documentation standards.
\nPrinciple I. Quality—data managers and data collection organisations should pay particular attention to ensuring compliance with explicit data quality standards.
\nPrinciple J. Security—supporting the use of techniques and instruments to guarantee the integrity and security of research data. Data integrity means completeness of the data and absence of errors. Security means that the data, along with relevant metadata and descriptions, should be protected against intentional or unintentional loss, destruction, modification and unauthorised access.
\nPrinciple K. Efficiency—improve the overall efficiency of publicly funded scientific research by avoiding unnecessary duplication of data collection efforts.
\nPrinciple L. Accountability—data access arrangements should be subject to periodic evaluation by user groups, responsible institutions and research funding agencies.
\nPrinciple M. Sustainability—research funders and research institutions should consider long-term preservation of data at the outset of each new project and determine appropriate archiving mechanisms for the data.
\nThese core OECD Principles were the early guidelines for policymakers to promote open data, including open research data. These principles have been widely adopted. However, the definition of research data in this source is very narrow, referring to research data as:
… factual records used in primary sources … that are commonly accepted in the scientific community as necessary to validate research findings.
Later documents have adopted a far broader approach to research data. These more recent policies are discussed in the following sections.
\nIn May 2012 [176], at the University of North Texas, a group of technologists and librarians, scholars, researchers and university administrators gathered to discuss best practices and emerging trends in research data management. Resulting from this discussion was a vision for openness in research data titled ‘The Denton Declaration: An Open Data Manifesto’. The declaration includes 6 declarations, 13 principles and 7 intentions.
\nThe principles set out general guidelines for open data in science:
\n1. Open access to research data benefits society and facilitates decision-making for public policy.
\n2. Publicly available research data helps promote a more cost-effective and efficient research environment by reducing redundancy of efforts.
\n3. Access to research data ensures transparency in the deployment of public funds for research and helps safeguard public goodwill towards research.
\n4. Open access to research data facilitates validation of research results, allows data to be improved by identifying errors and enables the reuse and analysis of legacy data using new techniques developed through advances and changing perceptions.
\n5. Funding entities should support reliable long-term access to research data as a component of research grants due to the benefits that accrue from the availability of research data.
\n6. Data preservation should involve sufficient identifying characteristics and descriptive information so that others besides the data producer can use and analyse the data.
\n7. Data should be made available in a timely manner: neither too soon to ensure that researchers benefit from their labour nor too late to allow for verification of the results.
\n8. A reasonable plan for the disposition of research data should be established as part of data management planning, rather than arbitrarily claiming the need for preservation in perpetuity.
\n9. Open access to research data should be a central goal of the lifecycle approach to data management, with consideration given at each stage of the data lifecycle to what metadata, data architecture, and infrastructure will be necessary to support data discoverability, accessibility and long-term stewardship.
\n10. The costs of cyberinfrastructure should be distributed among the stakeholders—including researchers, agencies and institutions—in a way that supports a long-term strategy for research data acquisition, collection, preservation and access.
\n11. The academy should adapt existing frameworks for tenure and promotion and merit-based incentives to account for alternative forms of publication and research output including data papers, public datasets and digital products. Value inheres in data as a stand-alone research output.
\n12. The principles of open access should not be in conflict with the intellectual property rights of researchers, and a culture of citation and acknowledgement should be cultivated rigorously and conscientiously among all practitioners.
\n13. Open access should not compromise the confidentiality of research subjects and will comply with principles of data security, HIPAA, FERPA [177, 178], and other privacy guidelines.
\nThe intentions articulated the issues of most importance to librarians at the time. They include developing a culture of openness in research, building the infrastructure that is extensible and sustainable for archiving and making the data discoverable, developing metadata standards and recognising and supporting the intellectual property rights of researchers.
\nThe principles are widely known among librarians in the United States and in other countries.
\nSeveral statements and policies have emerged promoting the dissemination of scientific data in online spaces following adoption of the Berlin Declaration and the OECD Open Access Principles. In 2009 the Toronto Statement reaffirmed earlier principles relating to the prepublication release of genomic data and recommended these principles be extended to other types of large biological datasets [179]. The Rome Agenda called for scientific data to be released immediately after the publication of journal articles [180]. The Panton Principle for Open Data in Science—developed in 2010—provides guidelines on licencing of open scientific data [181]. In early 2015, the Research Data Alliance released draft principles on the legal interoperability of research data [182]. These initiatives have facilitated broadening the scope and coverage of open access to research data to include prepublished, published and unpublished data—particularly data generated from publicly funded research.
\nMany attempts to define the principles of open scientific data also incorporate the challenges associated with implementation, thus restraining the scope for data sharing. These include legal, ethical and commercial limitations on data release; early availability and long-term preservation of research data; the management and curation of the data, metadata and software; sharing the costs of developing research data infrastructures; developing incentives and reward structures; facilitating searchability of the data; and respecting the privacy of research subjects. The challenges are clearly articulated in more recent and more comprehensive sets of principles for open scientific data, summarised below and canvassed in Chapters 4–7.
\nFor several years now, leading funders of research have required grant recipients to share their data with other investigators. However, originally they had no policies on how this should be accomplished. The game has changed completely in recent years, with many funders requiring the recipients of grants to enable open access to research data and, often, requiring the submission of research data management plans at the grant proposal stage. Such policies ensure that data resulting from publicly funded research is retained and can be reused over time—usually 3–10 years.
\nResearch organisations and universities are largely dependent on grant funding. Suddenly, these institutions realised that to enable researchers to successfully compete for grants, they had to provide support in the formulation of data management plans. Libraries, too, have taken up this approach, and researchers are changing their research data management practices as a result. Within the past decade, the policies introduced by research funders appear to have built a momentum for significant organisational and behavioural changes, and these changes are driving the retention and sharing of research data globally.
\nThe funders of research in the United States are the leaders when it comes to open research data. The National Institutes of Health (NIH) were among the first to introduce open access deposit of peer-reviewed journal articles in PubMed Central as a condition of receipt of grant funds.9 The NIH also:
… expects a data sharing plan for all proposals over $500,000 per year in direct costs. Some research communities have developed their own policies [183] in which sharing is expected—and executed—for all grants, not just those over the $500,000 threshold [184].
Awareness of the need to develop data management infrastructure took a leap forward in 2010 when the National Science Foundation (NSF) announced that it, too, would begin requiring data management plans with applications. Proposals submitted to NSF on or after 18 January 2011:
… must include a supplementary document of no more than two pages labelled ‘Data Management Plan’. This supplementary document should describe how the proposal will conform to NSF policy on the dissemination and sharing of research results [185].
Importantly, the data management plan is to be included with every application for NSF funding, even if the plan is a statement that ‘no detailed plan is needed’. According to the NSF policy:
Investigators are expected to share with other researchers, at no more than incremental cost and within a reasonable time, the primary data, samples, physical collections and other supporting materials created or gathered in the course of work under NSF grants. Grantees are expected to encourage and facilitate such sharing. Investigators and grantees are encouraged to share software and inventions created under the grant or otherwise make them or their products widely available and usable.10
The US government has taken significant steps to enable the dissemination of scientific outcomes arising from public research. On 22 February 2013, the Office of Science and Technology Policy at the White House issued the memo ‘Increasing Access to the Results of Federally Funded Scientific Research’. It directed each federal agency with over US$100 million in annual research and development expenditure to develop plans to make ‘the results of unclassified research arising from public funding publicly accessible to search, retrieve and analyse and to store such results for long-term preservation’.11 The research results include peer-reviewed publications, publication metadata and digitally formatted scientific data. The major shortcoming is that the memo does not mention metadata associated with research data. This omission is unfortunate because, in many cases, scientific data without metadata is unlikely to be reusable.
\nThe memo also directed agencies to ensure that intramural researchers and all extramural researchers receiving federal grants and contracts for scientific research have data management plans in place along with mechanisms to ensure compliance with the plans. To support the implementation of data management plans, grant proposals may include appropriate costs for data management and access. Further, agencies are to promote the deposit of data in publicly accessible repositories and develop approaches for identifying and providing appropriate attribution to scientific datasets.
\nThe memo builds on the NIH and NSF open data mandates and covers all larger federally funded organisations. Prior to the memorandum, only six federal funders of research had in place policies requiring the retention and sharing of research data—NIH, NSF, the National Aeronautics and Space Administration, the National Oceanic and Atmospheric Organisation, and the National Endowment for the Humanities, Office of Digital Humanities [186].
\nThe European Commission was one of the first major research funders to recognise open access to research data. The Commission considers that facilitating broader access to scientific publication and data can improve the quality of research results, foster collaboration, avoid duplication of research effort and improve the transparency of scientific enquiry—including through increased involvement by citizens [187]. Increasing access to the outcomes of publicly funded research lies at the core of the European policies. Underlying this vision is realisation that research outcomes originating from public sources should not require payment with each access or use. Instead, the outcomes should be preserved and made freely available for the benefit of all.
\nOpen access to science falls broadly under three flagship initiatives of the Commission—namely the Digital Agenda for Europe [188], the Innovation Union Policy [189], and the European Research Area Partnership [190]. The Recommendation on Access to and Preservation of Scientific Information [191], published in July 2012, encourages European Union member states to develop policies for open access to scientific results, including research data and information. The Commission further stated that such policies should include concrete objectives and indicators of progress, implementation plans and appropriate funding mechanisms.12 The Communication of the Commission regarding open access is not binding on European Union member states, and they are free to adopt any policy that best suits the needs of their own scientific communities. Some countries—Germany, Spain and the Netherlands—have legislated open access to scientific publications and data [192].
\nThe European Commission was among the first large funders to test funding arrangements that encourage open access to publicly funded research. In 2008, the Commission launched the Open Access Pilot as part of its Framework Program 7 (later replaced by the Horizon 2020 Pilot) for data underlying publications, including curated data and raw data [21]. The Rules of Participation [193] represent the legal basis for open access to research data funded by the European Commission under Horizon 2020:
With regard to the dissemination of research data, the grant agreement may, in the context of the open access to and the preservation of research data, lay down terms and conditions under which open access to such results shall be provided, in particular in ERC (European Research Council) frontier research and FET (Future and Emerging Technologies) research or in other appropriate areas, and taking into consideration the legitimate interests of the participants and any constraints pertaining to data protection rules, security rules or intellectual property rights. In such cases, the work programme or work plan shall indicate if the dissemination of research data through open access is required.13
These principles are translated into specific requirements in the Model Grant Agreement14 under the Horizon 2020 Work Programme. The Commission has also developed a user guide that explains the provisions of the Model Grant Agreement to applicants and beneficiaries, including guidance for open scientific data, as follows:
\nRegarding the digital research data generated in the action, the beneficiaries [participating in the open research data pilot] must:
Deposit in a research data repository and take measures to make it possible for third parties to access, mine, exploit, reproduce and disseminate—free of charge for any user—the following:
The data, including associated metadata, needed to validate the results presented in scientific publications as soon as possible
Other data, including associated metadata, as specified and within the deadlines laid down in the ‘data management plan’
Provide information—via the repository—about tools and instruments at the disposal of the beneficiaries and necessary for validating the results (and, where possible, provide the tools and instruments themselves).15
The guidelines also define exceptions to data sharing. These include the obligation to protect research results with intellectual property, confidentiality and security obligations and the need to protect personal data and specific cases in which open access might jeopardise the project. If any of these exceptions is applied, then the data research management plan must state the reasons for not giving or restricting access.
\nThe European Research Council (ERC) is a leading funder of research in the sciences and humanities. The ERC regards open access as the most effective way for ensuring that the fruits of the research it funds can be accessed, read and used in further research. On that basis, the ERC:
… considers it essential that primary data, as well as data-related products such as computer codes, is deposited in the relevant databases as soon as possible, preferably immediately after publication and in any case not later than 6 months after the date of publication [194].
The guidelines also list discipline-specific repositories. The recommended repository for life sciences is the Europe PubMed Central [195] (formerly known as UK PubMed Central), and for physical sciences and engineering, the recommendation is to use ArXiv [196].
\nThe peak body for research councils in the United Kingdom, Research Councils UK (RCUK, now transitioned into UK Research and Innovation),16 instituted policies on open access in 2005 and their Common Principles for Open Data [198] that took account of the evolving global policy landscape. These Principles encouraged the practice of making research data openly available, with as few restrictions as possible, in a timely and responsible manner.17 The Principles further addressed a number of important issues.
\nFirstly, data management policies and plans should be in accordance with community best practice and relevant standards set by research institutions themselves.18 The onus for ensuring that legal, ethical and commercial issues are considered lies with research institutions, and these issues should be considered at all stages in the research process.19
\nSecondly, published results should always include information on how to access the supporting data. Metadata should be recorded and made openly available.20
\nThirdly, the principles allow for the delay in data release to enable the original data collectors to publish the results of their research.21
\nFinally, public funds can be used to support the management and sharing of publicly funded research data.22 At the same time, research organisations are responsible for ensuring there are enough resources allocated to research data management—for example, from research grants. RCUK clarified in 2013 that all costs associated with research data management are eligible expenditure of research grant funds, but the expenditure must be incurred before the end date of the grant [199].
\nOpen data is thus defined as an integral part of doing research, and the costs are front-loaded into that research. This can initially make the conduct of research more expensive, but significant savings are realised down the track through the recycling of research data and improved quality of research outcomes. These principles are important as they address the concerns raised by several organisations and scientists who pointed out that open scientific data should not be an unfunded mandate [200].
\nSince the release of RCUK Common Principles on Data Policy in 2011, many member funding organisations have mandated the requirement for a data management plan with each new application. Most research funders in the United Kingdom have issued data policies; however, the extent and coverage of these vary greatly [201].
\nThe RCUK policy on open access states:
\nPeer-reviewed research papers which result from research that is wholly or partially funded by the research councils:
\n1. Must be published in journals which are compliant with Research Council policy on Open Access
\n2. Must include details of the funding that supported the research and a statement on how the underlying research materials—such as data, samples, or models—can be accessed [202]
\nUnlike the United States, where institutional approaches to research data management are developing, most research councils in the United Kingdom ‘place the responsibility on individual researchers to provide evidence that data management and sharing issues have been considered’ [203].
\nHowever, one research council—the Engineering and Physical Sciences Research Council (EPSRC)—took a different approach. The EPSRC encouraged research organisations to develop their specific approaches to data management, appropriate to their own structures and cultures. At the same time, these approaches were required to align with the EPSRC’s expectations. To that end, EPSRC requested that applicant institutions develop road maps for open data management. These requirements appear to have acted as a catalyst for developing data management policies and support systems in many UK research organisations.
\nIn 2015, RCUK provided publicly funded research institutions and investigators with explanatory text on each of the seven ‘common principles’ first developed in 2005. This guidance was intended to inform the RCUK consultation on a draft Concordat on Open Research Data23—a broader network of stakeholders and interested parties in open data. The Concordat committed to the seven ‘common principles’ adopted by the RCUK.
\nThe Australian Government was among the first to invest in the development of research data infrastructure. The Australian National Data Service (ANDS) was established in 2008 to develop an Australian Research Data Commons platform [204]—an Internet-based discovery service designed to provide rich connections between data, projects, researchers and institutions. Funding was also allocated for the development of metadata tools through the ‘Seeding the Commons’ initiative.
\nOpen research data is a priority area for the Data to Decisions Cooperative Research Centre established in July 2014. The centre brings together researchers and industry to contribute to the development of Australia’s big data capability.
\nThe Australian data management framework, which has emerged over time, is based on four principles:
\n1. The institutional data management framework is in accordance with the Australian Code for the Responsible Conduct of Research and other external legal and regulatory frameworks.
\n2. The research institution will support all aspects of the data lifecycle, through creation and collection, storage, manipulation, sharing and collaboration, publishing, archiving and reuse.
\n3. Data management is an essential part of doing good research and supporting the research community of which each researcher is a part.
\n4. Effective data management is best achieved through teamwork and collaboration between researchers, research offices, information specialists and technical support staff.
\nWhile the principles were originally drafted to outline how responsibilities between research institutions and researchers should be divided, it is now clear that increasing the availability of open scientific data is a collective endeavour. At the same time, accountability for the preparation and curation of such data must be clearly assigned. It is for this reason that research funders, providers and researchers themselves are likely to remain the key stakeholders in this process. The Australian Code for the Responsible Conduct of Research (revised in 2007) remains the principal document guiding Australian research organisations and researchers in data management. The code states:
Each institution must have a policy on the retention of materials and research data. It is important that institutions acknowledge their continuing role in the management of research material and data [205].
The Australian Research Council (ARC) and National Health and Medical Research Council (NHMRC)—two principal funders of national research—mandated open access to peer-reviewed publications in 2012. Starting from 2014, the ARC requires data publication for selected grants. The ARC Centre of Excellence funding agreement:
… strongly encourages … the depositing of data and any publications arising from a Project in an appropriate subject and/or institutional repository [206].
The NHMRC mandate did not extend to open data until early 2018. These very recent developments are covered in Chapter 8, Section 8.2.
\nThe principal funders of research in Canada—the Canadian Institutes of Health Research (CIHR), the Natural Sciences and Engineering Research Council and the Social Sciences and Humanities Research Council—all adhere to open access practices in research. Following a long consultation process, the final version of their Tri-Agency Open Access Policy was released in March 2015. With regard to open data, several submissions suggested that all three agencies should practice long-term preservation and digital release. Yet only the CIHR has committed to a policy on open research data at this stage:
\nRecipients of CIHR funding are required to adhere with the following responsibilities:
\n1. Deposit bioinformatics and atomic and molecular coordinate data into the appropriate public database (e.g. gene sequences deposited in GenBank) immediately upon publication of research results.
\n2. Retain original datasets for a minimum of 5 years after the end of the grant (or longer if other policies apply). This applies to all data, whether published or not. The grant recipient’s institution and research ethics board may have additional policies and practices regarding the preservation, retention and protection of research data that must be respected.24
\nThis policy applies to all CIHR grants awarded from 1 January 2008 and onwards. An important aspect that the data deposit is required (not just encouraged) for all CIHR grants.
\nMeanwhile, publishers are also having a profound influence, with changes to how they provide scholarly communications. Journal publication is the primary mode of disseminating scientific research. However, recent years have seen the emergence of data journals and of open access data repositories for holding the data associated with journal articles.
\nThe best-known example of the latter is perhaps the Dryad Digital Repository [208], governed by a consortium of scientific members who collaboratively promote data archiving, free access, reusability and citation. Membership of Dryad is open to any stakeholder organisation—including journals, scientific societies, publishers, research institutions and libraries. Dryad initially covered biosciences and ecology studies and, in recent years, has expanded to other disciplines. Many libraries and research organisations now refer to Dryad as a generic data repository and recommend it for deposit in all instances where discipline-specific online repositories do not exist.
\nAs a result of these practices, Dryad is increasingly becoming an interdisciplinary resource covering data from a variety of scientific fields and international sources. Data repositories such as Dryad can provide quicker access to findings in advance of results published in paper journals or e-journals.
\nThe growing significance of data publications has prompted established journals to expand their offerings. In early 2014 the Nature Publishing Group announced a new peer-reviewed open data publication, Scientific Data. The journal introduces data descriptors—a combination of traditional content and structured data and information to be curated in-house. Such descriptors may include articles and data from multiple journals. The actual datasets will not be stored in-house but in a recognised discipline data repository25 or, in the absence of such repository, in a more generic data repository such as Dryad. The initial focus of Scientific Data is on biomedical, life and environmental sciences—subject matter that appears to overlap with the initial collecting priorities at Dryad. It will be interesting to see how Dryad and Scientific Data differentiate themselves and develop into the future.
\nAnother important driver of open research data is the changing policy among traditional journal publishers who increasingly require that underlying data be made available to both peer reviewers and readers. In many cases, the publishers also specify the requirements for sufficient data description so as to facilitate reuse and validation of the research findings. For instance, the policy of Journal of the Royal Society Interface states:
To allow others to verify and build on the work published in Royal Society journals it is a condition of publication that authors make available the data and research materials supporting the results in the article. Datasets should be deposited in an appropriate, recognised repository and the associated accession number, link, or digital object identifier (DOI) to the datasets must be included in the methods section of the article. Reference(s) to datasets should also be included in the reference list of the article with DOIs (where available). Where no discipline-specific data repository exists authors should deposit their datasets in a general repository such as Dryad [210].
Similarly, the journal Nature has a policy on the availability of data and materials that implies that the data should be described sufficiently to allow for validation and reuse:
An inherent principle of publication is that others should be able to replicate and build upon the authors’ published claims. Therefore, a condition of publication in a Nature journal is that authors are required to make materials, data and associated protocols promptly available to readers without undue qualifications.26
Importantly, Nature reserves the right to refuse publication to authors who fail to comply with the journal’s requirements on data availability.
\nThis open data policy is far more specific and stringent than similar policies introduced by other publishers. An authoritative study by Vasilevsky et al. published in 2017 evaluated the open data policies of 318 biomedical journals [211]. That investigation found that only 12% of these journals required data sharing as a condition of publication—a policy similar to that of Nature.27 Out of the journals surveyed, 23% explicitly encouraged or addressed data sharing, but did not require it as a condition of publication, while 9% required data sharing but made no explicit statement regarding the effect on publication. Additionally, 15% only addressed data sharing for specific subsets of genomic data. Sadly, 32% of all journals did not mention anything about data sharing.28 The study confirmed earlier findings by the same authors that fewer than 50% of journals require data sharing [212].
\nHowever, in 2017-18 many publishers introduced changes to their editorial policies that provide for greater transparency and openness, including statements on expectations for data sharing. Publishers typically choose one of the following approaches for implementing data transparency.
\nOption 1: Duty to disclose. Published articles must state whether the data upon which they are based is available and must provide information on how to access it. The wording of publisher policies typically includes ‘sharing upon reasonable request’, or ‘expects data sharing’.
Option 2: Mandate to deposit. Authors of articles must include in a trusted repository the underlying data for sharing. If any portion of such data cannot be shared, this must be clearly identified while the authors must provide as much of the remaining data as can be reasonably shared. This type of policy typically focuses on creating ‘open data’ or even ‘open FAIR data’.
Option 3: Verification of reproducibility. Open data must be verified by a third party to establish whether the data enables the replication of findings as represented in the article. This type of data is typically referred to as ‘peer-reviewed data’.
The introduction of 2017-18 policies by leading publishers such as Springer Nature, Elsevier, Taylor and Francis, and Wiley has appeared to have increased the expectations not only for the digital availability of research data, but also for the credibility and veracity of that data.
\nReflecting on the above analysis of the emergent principles and policies in this chapter, it becomes clear that open scientific data extends open access to scientific publications. Several issues need consideration when developing policies for open research data, specifically:
\n1. The ‘data’ that should be covered by the policy
\n2. The timeframe for releasing research data into the public domain and who is responsible for the data deposit
\n3. The period for storing the data in digital archives
\n4. Whether research data management policies should be required and, if so, whether they should be submitted at the grant proposal stage or later
\n5. How open access to research data should be provided and under what conditions
\n6. Whether to recommend specific data repositories or whether to leave the decision with the project participants
\n7. When data sharing may not be required and whether the reasons for not sharing should be known to the broader research community
\n8. Whether and how data deposits should be embedded in the rewards and recognition frameworks for researchers and their organisations
\n9. Whether compliance with the policies should be monitored and, if so, whether penalties should apply
\n10. How to foster an environment that enables researchers and the public to maximise the value of research data
\n11. How to encourage the sharing of the best practices and experiences with research data management, including data transparency, code transparency, design and citation standards, and replication policies.
\nWhile the above points represent an ideal open data policy, the current policies of research funders and journal publishers are highly fragmented, covering only selected aspects of the data preservation, sharing and reuse process. This gap leaves those aiming to implement open data in a position of experimentation. The gap also makes any comparative analyses difficult. Nevertheless, it is apparent that the open data mandates have created a momentum driving the release of research data in many parts of the world.
\nAt the same time, the policies are more like high-level statements of principles and expectations rather than detailed guidelines for researchers. One particular concern is the unclear meaning of research data in the policies. At best, the list of possible research data outputs included in the policies is incomplete and lacks a level of detail. At worst, the definitions of ‘data’ provided do not appear to match the notions of data commonly used by the key stakeholders across different scientific disciplines. The inability to clearly acknowledge and articulate the heterogenous nature of research data is a major shortcoming of the open data mandates.
\nThe above overview of policy statements supporting access to scientific data shows that all major players in the system have shown a commitment to open data. The policies also illustrate, however, that concerns about implementing open scientific data remain and require further attention. And while policies may state clearly what challenges exist, the solutions and best practices are only just starting to emerge.
\nNevertheless, open scientific content is increasingly becoming readily available, largely due to policies recently introduced by research funders and publishers.
\nElsewhere in Europe and Asia, open scientific data practice is already in place, and it is emerging in many Latin American countries. Yet these policies are not readily available in English and therefore are not analysed in this chapter. The awareness of open access has increased rapidly in recent years, with countries including China introducing open access mandates.
\nChinese research output has increased rapidly—from 48,000 articles in 2003, or 5.6% of the global total, to more than 186,000 articles in 2012, or 13.9% [213]. Of those, more than 100,000, or 55.2% of the global share, involved some funding from the National Natural Science Foundation (NNSF) of China, one of the country’s major basic science funding agencies. This administered the equivalent of US$3.1 billion in its 2014 budget.29 The research output from the Chinese Academy of Sciences (CAS)—which funds and conducts research at more than 100 institutions—is also impressive. CAS scientists published more than 18,000 Science Citation Index30 articles in 2012 and more than 12,000 articles in Chinese journals [214].
\nOn 15 May 2014, these two principal funders of research in China announced an open access policy for publications. Researchers supported by NNSF or CAS should deposit their papers into online repositories and make them publicly accessible within 12 months of publication. The policies are modelled around those introduced by the NIH in the United States and came into effect the same day they were announced.31 At this point the open access mandate does not appear to extend to scientific data.
\nBoth CAS and NNSF plan to release more detailed guidelines on implementation. In particular, the NSFC will establish a repository into which researchers can upload papers. This repository is likely to be modelled on PubMed Central developed by the NIH.32 CAS started developing a network of repositories for its institutes 5 years ago and has a central website [215] for searching them. As of December 2013, more than 400,000 articles had been deposited and had generated 14 million downloads.33
\nMany countries in Central and Eastern Europe have well-developed digital infrastructures, and several countries have increased their R&D expenditure in recent years. Estonia and Slovenia now spend more on R&D than the European Union average. The Czech Republic has reached a level that is close to the average, while Hungary, Lithuania, Latvia, Slovakia, and Romania spend significantly less than the average.34 While these countries do not appear at this stage to have formulated open access policies, the digital agenda promoted by the European Union and the conditions already embedded in European grants are likely to drive the digital sharing of research outcomes originating from these countries in the near future.
\nIn large parts of Africa, scientific education remains underdeveloped, and funding for science is lacking. At the same time, many African countries have, in recent years, adopted important open access and open government projects and also have committed significant resources to develop relevant infrastructures. The vision for the open access movement in Africa is to spur development and promote the transfer of technologies to the continent.
\nKenya recently announced the establishment of a pilot regional data-sharing centre at the Jomo Kenyatta University. The centre aims to accelerate the generation, analysis, management, and archiving of scientific data emanating from Africa. Other significant open data programmes are implemented in Kenya [218], Morocco [219], Tunisia [220], Tanzania [221], Sierra Leone [222], Nigeria [223, 224], and Ghana [225]. In addition, the African Development Bank sponsors the Open Data for Africa Initiative [226] that aims to enhance the statistical capacity of African countries as well as provide the tools necessary to monitor developments, such as progress with implementing the Millennium Development Goals.
\nIt will be interesting to see how open scientific data will be used in innovative ways to promote development across Africa.
\nThe early stages of implementing data stewardship in open science are promising. Key players in the system—research funders, governments, and leading publishers—have made a clear commitment to open scientific data and have developed policies governing it. Such policies are now in place in the developed world and Latin America and are starting to emerge in other countries.
\nThese policies have created a momentum for data curation and are driving the release and sharing of research data globally. Data journals and discipline-specific data repositories have emerged and are becoming more popular. Scientists are increasingly aware of the need to share data and are more readily prepared to work with librarians to develop and implement research data management policies.
\nYet challenges remain. The policies for open scientific data explicitly list limitations to data release. This appears to have sent mixed messages to research organisations. Instead of focusing their efforts on finding opportunities for data sharing, many have diverted their resources to ensuring compliance with existing limitations.
\nIn the long term, this stage can be necessary to identify best practices for responsible research data management. In the short term, however, this stage may have delayed data release for other purposes, with major concerns surrounding research data management, particularly the interface between intellectual property and open knowledge, and the sharing of data involving personal information of subjects involved in data collection.
\nA major shortcoming of the open data policies is the high-level statements of objectives and expectations. They provide little guidance to researchers regarding the preparation of data management plans, the curating, and the sharing of data. One particular concern is the unclear meaning of research data, which leaves many researchers guessing what ‘data’ they need to make available.
\nThese concerns are examined further in the next chapter, which discusses the meaning of open scientific data.
\nExtremophile organisms capable of growing in extreme conditions draw considerable attention since they show that life is robust and adaptable and help us understand its limits. In addition, they show a high biotechnological potential [1, 2]. Most of the best-characterized extreme environments on Earth are geophysical constraints (temperature, pressure, ionic strength, radiation, etc.) in which opportunistic microorganisms have developed various adaptation strategies. Deep-sea environments, hot springs and geysers, extreme acid waters, hypersaline environments, deserts, and permafrost or ice are some or the most recurrent examples of extreme environments [3]. However, the atmosphere is rarely thought of as an extreme habitat. In the atmosphere, the dynamics of chemical and biological interactions are very complex, and the organisms that survive in this environment must tolerate high levels of UV radiation, desiccation (wind drying), temperature (extremely low and high temperatures), and atmospheric chemistry (humidity, oxygen radicals, etc.) [4]. These factors turn the atmosphere (especially its higher layers) into one of the most extreme environments described to date and the airborne microorganisms into extremophiles or, at least, multiresistant ones [5].
\nIt is known that airborne cells can maintain viability during their atmospheric residence and can exist in the air as spores or as vegetative cells thanks to diverse molecular mechanisms of resistance and adaptation [2, 6]. The big question is whether some of them can be metabolically active and divide. Bacterial residence times can be several days, which facilitate transport over long distances. This fact, together with the extreme conditions of the atmosphere, has led researchers to think for years that they do not remain active during their dispersion. However, recent studies strongly suggest that atmospheric microbes are metabolically active and were aerosolized organic matter and water in clouds would provide the right environment for metabolic activity to take place. Thus, the role played by microorganisms in the air would not only be passive but could also influence the chemistry of the atmosphere. In any case, only a certain fraction of bacteria in the atmosphere would be metabolically active [2, 7].
\nDespite recognizing its ecological importance, the diversity of airborne microorganisms remains largely unknown as well as the factors influencing diversity levels. Recent studies on airborne microbial biodiversity have reported a diverse assemblage of bacteria and fungi [4, 8, 9, 10, 11, 12], including taxa also commonly found on leaf surfaces [13, 14] and in soil habitats [15]. The abundance and composition of airborne microbial communities are variable across time and space [11, 16, 17, 18, 19]. However, the atmospheric conditions responsible for driving the observed changes in microbial abundances have not been thoroughly established. One reason for these limitations in the knowledge of aerobiology is that until recently, microbiological methods based on culture have been the standard, and it is known that such methods capture only a small portion of the total microbial diversity [20]. In addition, because pure cultures of microorganisms contain a unique type of microbes, culture-based approaches miss the opportunity to study the interactions between different microbes and their environment.
\nAnother limitation for the study of aerial microbial ecology at higher altitudes or in open ocean areas is the difficulty of repeated and dedicated use of airborne platforms (i.e., aircraft or balloons) to sample the air. Most studies to date on the atmospheric microbiome are restricted to samples collected near the Earth’s surface (e.g., top of mountains or buildings). Aircraft, unmanned aerial systems (UASs), balloons or even rockets, and satellites could represent the future in aerobiology knowledge [5, 21, 22]. These platforms could open the door to conducting microbial studies in the stratosphere and troposphere at high altitudes and in open-air masses, where long-range atmospheric transport is more efficient, something that is still poorly characterized today. The main challenge in conducting these kinds of studies stems from the fact that microbial collection systems are not sufficiently developed. There is a need for improvement and implementation of suitable sampling systems for platforms capable of sampling large volumes of air for subsequent analyses using multiple techniques, as this would provide a wide range of applications in the atmospheric, environmental, and health sciences.
\nIn aerobiology, dust storms deserve special mention. Most of them originate in the world’s deserts and semideserts and play an integral role in the Earth system [23, 24]. They are the result of turbulent winds, including convective haboobs [25]. This dust reaches concentrations in excess of 6000 μg m−3 in severe events [26]. Dust and dust-associated bacteria, fungal spores, and pollen can be transported thousands of kilometers in the presence of dust [9].
\nIn this chapter, we approach the atmosphere as an extreme environment and make use of some advanced data from an example of an in situ study of the atmosphere: the analysis of bacterial diversity of the low troposphere of the Iberian Peninsula during an intrusion of Saharan dust using a C-212 aircraft adequately improved for aerobiological sampling.
\nIt is well known that there is a biota in the atmospheric air. The first study dates back to the nineteenth century, which speak about the presence and dispersion of microorganisms and spores in the atmosphere [27, 28]. Although the atmosphere represents a large part of the biosphere, the density of airborne microorganisms is very low. Estimates suggest that from the ground surface up to about 18 km above sea level (troposphere), there is less than a billionth of the number of cells found in the oceans, soils, and subsurface. Between approximately 18 and 50 km above sea level (stratosphere), temperature, oxygen, and humidity decrease and with them the number of cells. Above the ozone layer (between 18 and 35 km into stratosphere), ultraviolet (UV) and cosmic radiation become lethal factors. Once in the mesosphere (above 50 km), life is difficult to imagine; however microorganisms of terrestrial origin could arrive to the stratosphere from lower layers via different phenomena (human activity, thunderstorms, dust storms, or volcanic activity), and bacteria have been found isolated up to 41 km or in dust samples from the International Space Station (\nFigure 1\n) [6, 29]. Therefore, airborne microbes are always present in the atmosphere [11, 30, 31], and their permanence is dynamic, resulting in an environment with enormous variability. Estimates calculate that over 1021 cells are lifted into the atmosphere every year, leading to considerable transport and dispersal around the atmosphere, with a large portion of these cells returning to the surface due to different atmospheric events as part of a feedback cycle. Undoubtedly, airborne microbes play an important role in meteorological processes. They have been linked to the nucleation phenomena that lead to the formation of clouds, rain, and snow and to the alteration of precipitation events [32, 33, 34]. Their presence is essential to understand long-range dispersal of plant and potential pathogens [7, 35, 36] and maintain diversity in ground systems and could interfere with the productivity of natural ecosystems [17, 18]. On the other hand, airborne bacteria can have important effects on human health, being responsible for different phenomena such as seasonal allergies and respiratory diseases. Based on data from terrestrial environments, the global abundance of airborne bacteria has been estimated to range between 104 and 106 m−3 [37]. However, more recent studies incorporating direct counting by microscopy or quantitative PCR have provided more accurate estimates of the number of airborne microbes, which apparently point to a higher number of cells present in the atmosphere [38, 39, 40, 41].
\nDiagram displaying atmosphere layers, temperature and airborne emission sources. Yellow line marks atmospheric temperature. Bottom of the figures shows the common sources of aerosolized bacteria, with special attention to dust storms.
There is a great variety of airborne microorganism sampling systems, allowing us to select the most suitable one depending on our objectives [42]. On the other hand, no standardized protocols exist, which is a major pitfall when developing our objectives. This fact has led some authors to propose the creation of consortiums of interested parties for establishing standardized protocol reproducibility [20], as well as the need to establish global networks of aerobiological studies [11]. Two approaches are proposed: particles or cells can be collected passively or directly from the atmosphere. Passive media usually involves decanting [43] and collecting particles over snow [44] or through the collection of atmospheric water [45]. On the other hand, active methodologies entail three major approaches: filtration, impaction, and liquid impingement. All three approaches are very efficient when developing culture-dependent techniques. In contrast, culture-independent approaches produce some serious problems that make the work difficult: the high variability of the system and the low biomass mean that sampling campaigns are, in many cases, extremely inefficient [20]. Lastly, the use of airborne platforms is not very extended, but they represent a good opportunity to conduct a more direct study of the atmosphere [5, 19, 31].
\nFiltration is a simple and cheap method that is often efficient. It involves pumping air through a filter where the mineral and biological particles are trapped. Filters of different materials and porosity are available made of cellulose, nylon, polycarbonate or fiberglass, or quartz. Sizes used range from 0.2 to 8 μm, depending on the size of the particles to be captured and the capacity of the pump. In many cases, a PM10 filter can give better results when collecting smaller bacteria, as it allows greater airflow. Airflow filtration rates generally range between 300 and 1000 L/minute [4, 46]. Microorganisms trapped in the filter can be cultured, or the filters can be directly used for DNA extraction. In addition, filters are a very suitable support for microscopy, and countless holders for filters are available (an example is shown in \nFigure 2A\n).
\nThree different samplers of airborne microorganisms. (A) Filter holder and a filter (PALL Corporation). (B) Impinger sampling of bioaerosols (BioSampler, SKC, Inc.). (C) Six-stages Andersen Cascade Impactor (Thermo Fisher Scientific).
In impingement, particles are collected in a liquid matrix [20]. Normally a buffer is used such as phosphate buffer saline (PBS) that helps maintain the viability of the cells. One of the more widely used liquid impingers is BioSampler SKC (\nFigure 2B\n). In this case, the tangential movement of the particles inside the flow impinger retains the particles in the collecting liquid. The suspension obtained could be used for culturing or for molecular ecology assays [20]. One of the advantages of impingement collection is that it facilitates quantitative techniques such as flow cytometry or in situ hybridization [47].
\nIn this system, the particles generally impact into a petri dish with an enrichment medium. It is, possibly, the most efficient and most used method to conduct studies based on culture. Airflow impacting onto the plates is controlled by slots that allow the homogeneous distribution of the air. The system can be single stage or several stages in cascade, causing the particles to be distributed by size in the different petri dishes [20]. Some variants replace petri dishes with agarose filters or Vaseline strips, in order to carry out independent culture methodologies, but efficiency is very low. The original and more popular impactor is the Andersen cascade impactor (\nFigure 2C\n) [48].
\nSeveral studies explain and compare sampling methodologies in aerobiology, but most of them focus on the surface of the Earth (e.g., on top of mountains or buildings) or indoors [42, 49, 50, 51, 52, 53, 54]. However, small studies have been conducted at higher altitudes or in open sea areas. The use of airborne platforms (balloons, aircraft, rockets, etc.) for aerobiology sampling would allow conducting a direct study of the microbial ecology of the atmosphere. Another advantage of airborne platforms is the possibility of studying the vertical distribution of airborne microbial communities. In addition, some aircraft allow us to develop studies in the upper troposphere or in the stratosphere. Unfortunately, atmospheric microbial collection instruments have not been developed enough for airborne platforms.
\nAmong the different airborne platforms, aircraft, due to their versatility and access, are particularly interesting. Some studies have been conducted, but not enough samples have been developed yet, and efficiency is still very low. As already mentioned, the efficiency of samplers in soil-level aerobiology faces a series of problems (low biomass, high variability of populations, lack of standardized protocols). In the case of airplanes, in addition to these intrinsic problems associated with atmospheric microbial ecology, other additional ones exist: (1) the high velocity of the aircraft in relation to the relative quiescent air mass. This makes it difficult to obtain an isokinetic sampler and, therefore, one that is sufficiently efficient that would allow us to obtain a correct quantification of the incoming air [55]; (2) the sampler must be in a location on the airplane that avoids chemical contamination from the operation of the device. Previous studies have used wing-mounted air samplers or the roof of the aircraft to reduce the possibility of in-flight contamination [21, 22, 56, 57, 58]. Similarly, it should allow the aseptic collection of samples, avoiding microbiological contamination during the process. This operation, which can be very simple in the laboratory or at ground level, becomes tremendously complicated on an airplane, since air intakes that are part of the fuselage of the aircraft are often difficult to sterilize. It is therefore necessary to develop robust sterilization protocols. The spectacular work of DeLeon-Rodríguez of 2013 has been criticized in this aspect [40, 59]; (3) sampling time. A possible solution to the low biomass of the atmosphere is to increase sampling time, but in the case of flights, we are limited to the flight autonomy of the aircraft. Although scarce, some studies from airplanes have been conducted. The first studies that were conducted in airplanes were carried out by impaction on a petri plate with enrichment means, which allowed isolating microorganisms from the upper troposphere and even from the stratosphere [21, 57, 60]. However, advances in molecular ecology have caused the most recent studies to favor filtration [40, 58].
\nThe European Facility for Airborne Research (EUFAR) program brings together infrastructure operators of both instrumented research aircraft and remote sensing instruments with the scientific user community. However, it lacked aircraft prepared for microbiological sampling. The National Institute for Aerospace Technology (INTA) belonging to the Spanish Ministry of Defence has two CASA C-212-200 aircraft that were suitably modified to be used as flying research platforms. Now, these two aircraft are a unique tool for the study of atmospheric microbial diversity and the different environments of the EUFAR program. Our research group has a CASA-212 aircraft with an air intake located on the roof of the aircraft. A metal tube fits the entrance and is fitted inside the aircraft to a filter holder, a flowmeter, and a pump (\nFigure 3\n). This simple system is easy to sterilize, and both the metal tube and the filter holder can be replaced in flight by other sterile ones if we want to take different samples. Using PM10 fiberglass filters, we can obtain isokinetic conditions and pass 1800 L of air per hour through the filter, as indicated by the flowmeter.
\nAirborne microorganisms sampler installed in INTA’s CASA C-212-200 aircraft.
In a series of recent experiments, we tried to install a multi-sampler system in our aircraft, where we had five systems in parallel and connected to the same intake of the plane: one filter holder, two impingement systems, and two impactors (\nFigure 4\n). The results clearly showed that in the case of our aircraft, filtration was more efficient (data not shown).
\nMulti-sampler system tested in INTA’s CASA C-212-200 aircraft. (A) Impinger sampler, design and manufacture own. (B) Impactor sampler (Impaktor FH6, Markus Klotz GmbH). (C) Coriolis μ (Bertin Technologies SAS) a impinger biological air sampler. (D) Filter holder (PALL Corporation). (E) Six-stages Andersen Cascade Impactor (Thermo Fisher Scientific).
Aerobiology studies have traditionally focused on the collection of bacterial cells and the analysis of samples by total counting and culture-based techniques. It is known that such methods capture only a small portion of the total microbial diversity [61]. The almost exclusive use, for years, of these methodologies is one of the reasons for these limitations in the knowledge of aerobiology. In addition, culture-dependent methods do not allow us to study the interactions between different species of microorganisms. Culture-independent methods have been used to assess microbial diversity, increasing the specificity of microbial identification and the sensitivity of environmental studies, especially in extreme environments. These methods have recently been applied to various areas of airborne microbiology [62, 63, 64, 65] revealing a greater diversity of airborne microorganisms when compared to culture-dependent methods. Some good studies approach the challenges and opportunities of using molecular methodologies to address airborne microbiology [20, 66]. Although molecular ecology methods allow the rapid characterization of the diversity of complex ecosystems, the isolation of the different components is essential for the study of their phenotypic properties in order to evaluate their role in the system and their biotechnological potential. A combination of culture-dependent and culture-independent methods is ideal to address the complete study of the system.
\nModern culture-independent approaches to community analysis, for example, metagenomics and individual cell genomics, have the potential to provide a much deeper understanding of the atmospheric microbiome. However, molecular ecology techniques face several particular challenges in the case of the atmospheric microbiome: (1) very low biomass [20]; (2) inefficient sampling methods [20]; (3) lack of standard protocols [9, 20]; (4) the composition of airborne microbes continuously changes due to meteorological, spatial, and temporal patterns [7, 62, 67, 68, 69, 70]; and (5) avoidance of the presence of foreign DNA in the system [59]. Because these issues are not yet resolved, most of the non-culturing approaches focus on microbial diversity, where they are highly efficient.
\nThe most recurrent techniques are those based on DNA extraction, gene amplification of 16S/18S rRNA, and next-generation sequencing (NGS) technologies. Often, this approach is more efficient due to the greater efficiency and sensitivity of this process, as opposed to gene cloning and Sanger sequencing; thus some authors are inclined toward metagenomics instead of amplification. This provides more information and avoids an intermediate step, but bioinformatic processing is tedious and often only provides data in relation to diversity, making the annotation of the rest of the information very complicated [20]. These approaches can be complemented with quantitative methods such as qPCR, flow cytometry, or fluorescence in situ hybridization (FISH) [41, 47, 66, 71]. FISH is surely the best and most specific cell quantification methodology that exists. However, in the case of aerobiology, it cannot always be used. A minimum number of cells must exist so that we can observe and count them under a fluorescence microscope. Due to the variability of microbial populations in the air, this is not always achieved. In our research group, we have obtained very good results in this regard, optimizing cell concentration. \nFigure 5\n shows epifluorescence micrographs of bacteria from an air sample. On this occasion, sampling was performed using a biological air sampler (Coriolis μ, Bertin Technologies SAS), where biological particles are collected and concentrated in a liquid (PBS). Sampling was conducted for 2 hours at ground level, pumping a total of 36,000 L of air. After this time, the sample was paraformaldehyde fixed and filtered through a 0.2 μm pore size, hydrophilic polycarbonate membrane, 13 mm diameter (GTTP, Millipore). A half sample was hybridized with the universal Bacteria domain probe, EUB338I-III [72], following a conventional protocol [73]. The second half was hybridized with the probe NON338 [74] as negative control. In this case, an average of 140 cells per liter of air was counted. Occasionally, FISH also allows to observe bacteria attached to mineral particles (\nFigure 5C\n–\nD\n).
\nEpifluorescence micrographs of bacteria from an air sample. (A and C) DAPI-stained cells; (B and D) same fields a A, and C, respectively, showing cells hybridized with probes EUB338I-III (Cy3 labeled), specific for Bacteria domain. All micrographs correspond to the same hybridization process, performed with a sample obtained after 4 hours sampling at ground. C and D show microorganisms attaches to a mineral particles (arrow sign). Bars, 5 μm.
DNA gives us much information about the diversity of the system, but if we wish to obtain information about the metabolic activity that is taking place in the ecosystem, metabolomic and metatranscriptomic approaches are needed [50, 66]. In the case of the atmosphere, this is crucial, since we are not fully certain if the cells present are active. Some studies indicate that a part of the microorganisms in the atmosphere are developing an activity [6], but until we conduct RNA-based and metabolite-based studies, we will not have the certainty that this is the case. The big problem is that it is very difficult to carry out these studies using the current microbial capture systems.
\nScanning electron microscopy (SEM) also provides much information of the aerobiology [7]. Specifically, it allows the characterization of eukaryotic cells (e.g., diatoms) and, above all, pollens and fungal spores, from which we can obtain great information with good images alone. \nFigure 6A\n shows pine tree pollen observed via SEM in a sample obtained after a 30 minutes flight of the C-212 aircraft.
\nSEM images of different airborne samples. (A) Pinus pollen. Ground sample after 2 hours sampling. (B) Air sample collected from C-212-200 aircraft during a Saharan dust intrusion (February 24, 2017). Filter appear completely cover of mineral particles. (B and C) Biological particles sampled using C-212-200 aircraft. (E) Diatomea sampled by C-212-200 aircraft in a fligth along the northern coast of Spain (9 March 2017). (F) Cell attached to mineral particles and organic matter.
As mentioned above, factors, such as the shortage of nutrients and substrates, high UV radiation, drying, changes in temperature and pH, or the presence of reactive oxygen species, make the atmosphere an extreme environment. However, it is possible that the high variability of its conditions is the one characteristic that makes this environment more extreme [1, 20]. Among the cells present in the atmosphere, a considerable portion appears in the resistance forms capable of withstanding low-temperature and high-radiation conditions. This is what probably happens with fungi and gram-positive bacteria. Bacillus strains recurrently isolated from the atmosphere have characteristics and a capacity to sporulate very similar to strains isolated from the soil. Undoubtedly, another part of the cells will be in the form of latency and may even suffer modifications of the cell wall and slow down or stop their metabolic activity [75, 76]. These transformations can improve resistance to physical stresses, such as UV radiation [58]. On the other hand, some of the bacteria present in the atmosphere, such as Geodermatophilus, show pigmentation that undoubtedly protects it from excessive radiation. The microorganisms that are usually detected in the atmosphere originate mainly from the soil, which means they will share similar mechanisms of resistance. In some strains, metabolic adaptations have been observed to lack nutrients such as cytochrome bd biosynthesis to survive iron deprivation [77]. Deinococcus is also a recurrent genus in the atmosphere, which, like those in soil, has multiresistance mechanisms based on high DNA-repair efficiency. Bacteria that do not form spores and certain archaea, in contrast, often have genomes rich in G + C, which may increase tolerance to UV rays and overall survival [78].
\nAnother strategy of resistance could be cell clustering and adhesion to particles. Several studies have confirmed the loss of viability and shielding or the reflective properties of the mineral particles as an important role for the protection of UV radiation [19, 31]. In that sense, it is very possible that many cells have mechanisms that promote aggregation. In our samples, we often find the cells adhered to each other or to minerals, which undoubtedly makes them more resistant (\nFigure 6\n).
\nGlobal and regional models have been used to explain bioaerosol emission, transport, and atmospheric impact [17, 18, 79, 80, 81, 82, 83, 84]. Even so, it is not an easy phenomenon to explain, since it depends on a large number of factors. On the one hand, there are numerous sources of tropospheric aerosols, which include sea salt, volcanic dust, cosmic dust, industrial pollutants, and desert and semidesert areas [6, 85]. We must also consider the factors that make the transfer of particles possible, for example, meteorological phenomena, solar radiation, temperature, tides, erosion, etc. [85]. On the other hand, anthropogenic activities can also affect dust emissions indirectly, by changing the climate and the hydrological cycle. In these aerosols, microorganisms will be included in a greater or lesser number. The degree of richness in cells of tropospheric aerosols will depend largely on the source of emission. Thus, the large wooded masses or fields of crops provide the atmosphere with a good number of microorganisms due to the effect of air or the aerosols produced by rain. Similarly, anthropogenic activity contributes large amounts of bacteria to the environment, treatment plants, and composting areas being sources of airborne microorganisms [85].
\nDesert dust storms play a major role in particle emissions and with them that of microorganisms. In this way, most of the material reaching the atmosphere from the surface comes from desert and semidesert areas, which is known as desert dust. The Sahara-Sahel desert, the Middle East, central and eastern Asia, and Australia are the major sources of desert dust, although all the arid zones of the world are emission sources [9, 86]. Dust storms are atmospheric events typically associated with dry lands due to the preponderance of dried and unconsolidated substrates with little vegetation cover. The strong and turbulent winds that blow on these surfaces raise fine-grained material, a large part of which consists of particles the size of silt (4–62.5 μm) and clay (<4 μm), reducing visibility to less than 1 km. The atmospheric concentrations of PM10 dust exceed 15,000 μg/m3 in severe events [87], although the concentrations naturally decrease with the distance from the areas of origin, extending hundreds of kilometers. The dust particles and cells associated with them are transported in this manner and will be deposited finally, by the effect of rain, snow, or other meteorological phenomena. Therefore, there is a continuous transfer of mineral and biological matter through the atmosphere that moves from the air to the terrestrial environment and changes its geographical area [7, 24].
\nThe Sahara-Sahel desert located in northwestern Africa is one of the major sources of windblown dust in the world [9]. This phenomenon has an impact on the Mediterranean coastline, but Saharan dust has been transported toward the north of Europe and has been found on numerous occasions in the Alps [88, 89] or blown toward the Atlantic and Caribbean [8, 90]. It has been estimated that 80–120 tons of dust are transported annually through the Mediterranean toward Europe [23, 91, 92]. In particular, dust transported by the winds can reach an elevation of up to 8 km in the atmosphere over the Mediterranean basin [93]. Because of its geographic position, the Iberian Peninsula is often affected by these dust events. Specifically, the Sahara-Bodele depression, located at the southern edge of the Sahara desert, has been described as the richest dust source reaching the Iberian Peninsula. Southern Spain is the main area affected, but dust can reach the Pyrenees and even France [43]. Different researchers have studied the mineralogical and chemical composition of Saharan dust, which has been observed to contain calcite, dolomite, quartz, different clay minerals, and feldspars as the main mineral components [94]. The intrusion of big amounts of these components is an important influence on nutrient dynamics and biogeochemical cycling in the atmosphere of the Iberian Peninsula.
\nDespite the large number of studies on dispersion, geochemistry, and mineralogy of African dust, few are focused on microbiology. All these studies conclude that there are microbes associated with dust because there are higher concentrations of aerosolized microorganisms during dust events [43, 90, 93, 94, 95, 96]. However, the magnitude of the concentrations and the specific microbes associated with dust events remain the subject of debate. On the other hand, the viability of these microorganisms is another big question. The United States Geological Survey (USGS) develops the Global Dust Program to investigate the viability of microorganisms transported in dust masses. USGS authors using DNA sequencing of the ribosomal gene were able to isolate and identify more than 200 viable bacteria and fungi in St. John’s samples in the USA [8, 36, 90]. Fungi and bacteria associated with atmospheric dust can be recovered and cultivated, but they must be gram-positive bacteria and many spore formers, which makes them resistant to the extreme conditions of the atmosphere.
\nTherefore, fungi and bacteria associated with dust may have been isolated from dust intrusions, but a percentage of the viable ones already remains an unanswered question. Another big question is the activity of these cells in the atmosphere. It is clear that they are resistant to extremophile conditions, but the question is whether they are developing their life cycle in this particular environment. This question could be answered by molecular ecology methodologies based on the isolation and sequencing of mRNA, but low atmospheric biomass and high variability are, once again, the great problem when developing this type of RNA-based methodologies. On the other hand, clinical records point to many of the viable microorganisms identified in the Saharan dust as the cause of respiratory diseases (asthma and lung infections or allergic reactions), cardiovascular diseases, and skin infections [7, 90, 97, 98]. It is known that other microbes associated with dust in the air are pathogenic to humans, including those that cause anthrax and tuberculosis, or to livestock (such as foot and mouth disease) or plants [7, 90, 97, 98]. Characterization, quantification, and feasibility studies are vital to address these problems.
\nIt is common to find fungal spores belonging to the genus Aspergillus, Nigrospora, Arthrinium, and Curvularia associated with Saharan dust. Bacterial taxa comprised a wide range of phyla, including Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. Generators of genus spores such as Clostridium and Bacillus are very common, along with other gram-positive ones such as Geodermatophilus or Streptococcus. Also, Alphaproteobacteria, a very common bacterium class in soils (e.g., the family Sphingomonadaceae), are associated with dust [4, 9]. As regards Archaea, there are few studies of the atmosphere, in general, and of dust, in particular, that focus on this domain. Surely, reduced cases of pathogenic archaea have been studied to a lesser extent. Aeropyrum is the most detected genus of airborne archaea, but it is related to marine aerosols [11]. On the other hand, studies of pollen associated with dust are widespread. An interesting study investigated pollen transported from North Africa to Spain through Saharan dust and found that pollen from five non-native plant species was detected exclusively during dust events [99]. Lastly, viruses and virus-like particles have a great interest in the emission of dust. One study mentions virus-like particles associated with a transoceanic dust event. This report is based on epifluorescent microscopy of filters stained with a specific nucleic acid stain. An increase in the order of magnitude of virus-like particles was observed, from 104 to 2105 m−3 between the baseline condition and dust conditions in the Caribbean [41]. It is speculated that free airborne viruses show worse resistance to high ultraviolet radiation and dry air associated with long-distance transport in dust events resist worse than others [9].
\nFour aerobiology sampling flights took place during February and March 2017 using the CASA C-212-200 aircraft from INTA. The study focused on microbial diversity in the atmosphere of the Iberian Peninsula during and after a Saharan dust intrusion. Flights took place under four different conditions: (1) during a strong Sahara dust storm that reached the north of the Iberian Peninsula, from February 22 to 24, 2017 (February 23, 2017) (\nFigure 7\n); (2) following precipitation (February 28, 2017); (3) following a dry period (March 8, 2017); and (4) along the northern coast of Spain (March 9, 2017). In each flight, samples were collected at different altitudes, and air samples were obtained simultaneously at ground level. A total of 20 samples were collected and are being analyzed. Cell presence was observed by scanning electron microscopy (SEM), and bacterial diversity is being studied by DNA extraction, 16S rRNA gene amplification, and Illumina MiSeq sequencing. Results are being analyzed via bioinformatics and biostatistical software (MOTHUR, SPSS, STAMP, CANOCO, and PAST) which will allow us to compare the results between the different flows and scenarios.
\nSaharan dust intrusion. Dust pours off the northweat Afrincan coast and blankets the Iberian Peninsula, 23 February, 2016. NASA satelital imagen via MODIS.
Although this study is not yet finished, some data can be advanced in this chapter. \nFigure 6\n shows SEM microphotographs obtained from samples in different scenarios. In general, the samples obtained during the days of dust intrusion (flight of February 23) appear completely covered with mineral particles. In these cases, more biological cells were detected than in the rest of the days. In the particular case of samples from the marine coast flight, more diatoms were observed (\nFigure 6E\n).
\nThe analysis of diversity using the Shannon index showed that, in all cases, diversity was greater on days of Saharan dust intrusion, both in the samples taken from the ground and those taken at higher altitudes with the aircraft. This indicates that Saharan dust contributes microorganisms that are not present in the atmosphere on a daily basis. Diversity analysis showed phylum characteristics of soils, being Alpha- and Betaproteobacteria the most abundant classes. All of the analyses performed showed that bacterial diversity detected at ground level and in-flight samples during the dust intrusion event were similar among one another. The genus taxonomic levels of Sphingomonas, Geodermatophilus, Methylobacter, Rhizobiales, Bacillus, or Clostridium were present in every sample, but their sequences were more abundant in the case of ground samples and dust intrusion samples collected during the day flight. However, sequences of the genus Flavobacterium, Streptococcus, or Cupriavidus were most abundant in the case of samples collected during flight.
\nPreliminary conclusions show that bacterial diversity of airborne bacteria during days of dust intrusion is higher and similar to bacterial diversity commonly detected in soil samples. Further analyses are being conducted with these samples to obtain a complete description of the evolution of bacterial diversity during those days.
\nIntense UV radiation, low pressure, lack of water and nutrients, and freezing temperatures turn the atmosphere into an extreme environment, especially its upper layers. However, it is widely known that airborne bacteria, fungal spores, pollen, and other bioparticles exist. Numerous bacteria and fungi have been isolated and can survive even at stratospheric altitudes. Microbial survival in the atmosphere requires extremophilic characteristics, and therefore airborne microbiota is potentially useful for biotechnological applications. The role of airborne microbial communities is vital in the Earth, including interactions among the atmosphere, biosphere, climate, and public health. Airborne microorganisms are involved in meteorological processes and can serve as nuclei for cloud drops and ice crystals that precede precipitation, which influences the hydrological cycle and climate. Furthermore, their knowledge is essential in understanding the reproduction and propagation of organisms through various ecosystems. Furthermore, they can cause or improve human, animal, and plant diseases.
\nAirborne platforms that allow conducting a direct study of microorganisms in the atmosphere and molecular methodologies (e.g., “omics”) could represent a major opportunity for approaching this question. Nevertheless, some challenges must yet be solved, such as low biomass, efficiency of sampling methods, the absence of standard protocols, or the high variability of the atmospheric environment.
\nDeserts and arid lands are one of the most important sources of aerosol emissions. Clouds of dust generated by storms mobilize tons of mineral particles, and it is known that microorganisms remain attached to the particles being transported over long distances. The large number of mineral particles and microorganisms thus placed into the atmosphere has global implications for climate, biochemical cycling, and health. North African soils, primarily the Sahara Desert, are one of the major sources of airborne dust on Earth. Saharan dust is often transported to southern Europe and could even reach high altitudes over the Atlantic Ocean and the European continent. Again, airborne platforms could be a perfect opportunity for conducting a direct study of the microbiology of this kind of events.
\nThis work has been supported by grants from the Spanish government (
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