Marine Microbiomes Towards Standard Methods And Best Practices

A decade of technological advances and research on the human microbiome has re-defined our understanding of biological systems, and now offers diagnostic tools and new approaches to human health. Likewise, marine ecosystems are driven by their microbiome, the ensemble of microscopic organisms that inhabit the water column, sediments and aquatic organisms, and regulate most fluxes of energy and matter. While the human microbiome is composed principally of bacteria, the marine microbiome has a much broader ensemble of microscopic organisms with sizes spanning from viruses of a few tens of nanometres to metazoans of several centimetres. Advances in high throughput imaging and sequencing are emerging in aquatic science, providing important insights into ecosystem structure and functions, and contributing to develop new indicators of ecosystem health and potential hazards to living resources and humans. A number of research exploration and monitoring programs such as the Tara Oceans global expedition and the Marine Biological Observing Network (MBON), and the rising popularity of environmental DNA (eDNA) already led to a wealth of data. However, the wide range of methodologies used in this early exploration phase poses a challenge to integrative studies, prompting community responses such as the Genomic Standards Consortium. This Research Topic will foster cross-community exchange of standards and best practices. It is an opportunity for the different communities working on marine microbiomes to discuss the advantages and the limitations of their sampling and analysis methods. The collection of papers will constitute a knowledge base aimed at (1) addressing the integration of existing observations from heterogenous methods and data types, and (2) working towards cross-communities standards and best practices for future observations and experiments. This Research Topic will publish comprehensive methodological papers that review a sufficiently large body of field or experimental work. Supporting (meta)data, such as environmental context, sampling materials, sample treatments, extraction and imaging yields, must be provided and should preferably be uploaded to an online sample registry such as BioSamples. Protocols and analytical methods should preferably be uploaded to an online repository such as Protocols.io. We welcome contributions from communities working in different environments: · focus on marine systems, but also interested in estuarine and freshwater systems · coastal, open ocean and deep-sea regions · benthic, pelagic and aerosol environments We strongly encourage contributions from communities involved in: · networks of local observatories and long-term monitoring programs · regional & basin-scale surveys, and global expeditions · biodiscovery linked to economic sectors such as pharmaceutics and bioengineering · environmental and health assessments linked to economic sectors such as aquaculture, fisheries, seabed mining, wind-farms, and oil and gas

Plastic pollution is a growing environmental problem that is attracting increasing interest across society, from academics to the general public. A significant factor in the wide public interest in plastics is its visibility; present throughout urban and rural environments, washing up on beaches and even visible from space. However, 'invisible' microplastics and nanoplastics are also an issue. With growing plastic production and usage, plastic waste within the environment will continue to increase. This increased input along with its persistence leads to accumulation and increasing ecosystem exposure, with as-yet unknown consequences.This book brings together a collection of chapters written by world-leading experts in environmental plastic pollution inputs, fate, effects and solutions. It provides an accessible overview of the current scientific understanding, future implications and key considerations for the management and mitigation of plastic waste within the global ocean.Related Link(s)

This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.

The study of marine environments inevitably involves considering the problem of marine pollution, which includes questions that focus on the essential need to ensure the long-term health of these exceptional ecosystems and the lives and livelihoods they support. The open access textbook "Marine Pollution: monitoring, management and mitigation" approaches these questions in a practical and highly readable format. It gives newcomers to the field background and perspective through the first comprehensive, multidisciplinary exploration of the topic. The topic is indeed complex, requiring the integration of the natural sciences and chemistry with management, policymakers, industry and all of us who are users of the marine environment. The textbook was written by leading experts to especially prepare graduates for a career in marine pollution studies. At the same time, it is relevant for anyone invested in the marine environment with a will to reduce their impacts. The chapters can easily be used independently and are also connected through the cross-referencing of related content. The introductory chapter provides a historical account of marine pollution and explores the fundamental physicochemical conditions of seawater. Two full chapters cover the requisite resources for ensuring success in field and laboratory studies. Then, chapter by chapter the book dives into to the various types of marine pollutants. In closing, it discusses the challenges of understanding multiple stressors and presents mitigation and restoration practices, along with a global overview of marine pollution legislation. We envisioned this textbook as being open access for the very reason we created it: this topic calls for global contributions and champions, and financial restraints should not limit access to this knowledge.

Over the past several decades, new scientific tools and approaches for detecting microbial species have dramatically enhanced our appreciation of the diversity and abundance of the microbiota and its dynamic interactions with the environments within which these microorganisms reside. The first bacterial genome was sequenced in 1995 and took more than 13 months of work to complete. Today, a microorganism's entire genome can be sequenced in a few days. Much as our view of the cosmos was forever altered in the 17th century with the invention of the telescope, these genomic technologies, and the observations derived from them, have fundamentally transformed our appreciation of the microbial world around us. On June 12 and 13, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to discuss the scientific tools and approaches being used for detecting and characterizing microbial species, and the roles of microbial genomics and metagenomics to better understand the culturable and unculturable microbial world around us. Through invited presentations and discussions, participants examined the use of microbial genomics to explore the diversity, evolution, and adaptation of microorganisms in a wide variety of environments; the molecular mechanisms of disease emergence and epidemiology; and the ways that genomic technologies are being applied to disease outbreak trace back and microbial surveillance. Points that were emphasized by many participants included the need to develop robust standardized sampling protocols, the importance of having the appropriate metadata, data analysis and data management challenges, and information sharing in real time. The Science and Applications of Microbial Genomics summarizes this workshop.

The first comprehensive synthesis of genomic techniques in earth sciences The past 15 years have witnessed an explosion of DNA sequencing technologies that provide unprecedented insights into biology. Although this technological revolution has been driven by the biomedical sciences, it also offers extraordinary opportunities in the earth and environmental sciences. In particular, the application of "omics" methods (genomics, transcriptomics, proteomics) directly to environmental samples offers exciting new vistas of complex microbial communities and their roles in environmental and geochemical processes. This unique book fills the gap where there exists a lack of resources and infrastructure to educate and train geoscientists about the opportunities, approaches, and analytical methods available in the application of omic technologies to problems in the geosciences. Genomic Approaches in Earth and Environmental Sciences begins by covering the role of microorganisms in earth and environmental processes. It then goes on to discuss how omics approaches provide new windows into geobiological processes. It delves into the DNA sequencing revolution and the impact that genomics has made on the geosciences. The book then discusses the methods used in the field, beginning with an overview of current technologies. After that it offers in-depth coverage of single cell genomics, metagenomics, metatranscriptomics, metaproteomics, and functional approaches, before finishing up with an outlook on the future of the field. The very first synthesis of an important new family of techniques Shows strengths and limitations (both practical and theoretical) of the techniques Deals with both theoretical and laboratory basics Shows use of techniques in a variety of applications, including various aspects of environmental science, geobiology, and evolution Genomic Approaches in Earth and Environmental Sciences is a welcome addition to the library of all earth and environmental scientists and students working within a wide range of subdisciplines.