ALBERT

Description / Table of Contents: Petroleum hydrocarbons are both a product of, and rich substrate for, microorganisms from across all Domains of life. Rooted deeply in the history of microbiology, hydrocarbons have been studied as sources of carbon and energy for microorganisms for over a century. As global demand for petroleum and its refined products continues to rise, so do challenges associated with environmental pollution, oil well souring, infrastructure corrosion, oil recovery, transport, refining, and upgrading of heavy crude oils and bitumens. Advances in genomics, synthetic biology and metabolic engineering has invigorated interest in petroleum microbial biotechnology as interest grows in technologies for in situ methane production, biodesulfurization and biodenitrogenation, bio-upgrading of heavy crudes, microbial enhanced oil recovery, corrosion control, and biocatalysts for generating value-added products. Given the complexity of the global petroleum industry and the harsh conditions in which it operates, a deeper understanding of the ecophysiology of aerobic and anaerobic microbial communities that have associations with petroleum hydrocarbons is needed if robust technologies are to be deployed successfully. This research topic highlights recent advances in microbial enhanced oil recovery, methanogenic hydrocarbon metabolism and carbon dioxide sequestration, bioremediation, microbiologically influenced corrosion, biodesulfurization, and the application of metagenomics to better understand microbial communities associated with petroleum hydrocarbons.

Description / Table of Contents: It is well known that several climatic, environmental and socio-demographic changes that have occurred in the last years are some of the most important causes for the emergence/resurgence of vector-borne diseases worldwide. Global change can be defined as the impact of human activity on the fundamental mechanisms of biosphere functioning. Therefore, global change includes not only climate change, but also habitat transformation, water cycle modification, biodiversity loss, synanthropic incursion of alien species into new territories, or introduction of new chemicals in nature. On this respect, some of the effects of global change on vector-borne diseases can be currently evaluated. Globalization has enabled the movement of parasites, viruses and vectors among different countries, or even at intercontinental level. On this regard, it is important to note that the increase of imported malaria cases in different Southern European countries has led to the re-appearance of autochthonous cases of disease transmission. Moreover, the used tire trade, together with global warming, have facilitated the introduction, spread and establishment of potential Dengue tropical vectors, such as Aedes aegypti or Aedes albopictus in temperate areas. Consequently, recently the first Dengue indigenous cases in the last decades have been reported in different Southern areas of North America and Europe. Furthermore, habitat modification, mainly deforestation and transformation of aquatic environments, together with the changes in thermal and rainfall patterns, are two of the key factors to explain the increasing incidence of Leishmaniasis and several tick-borne diseases. The aim of this Research Topic is to cover all related fields with the binomial vector-borne diseases / global change, including basic and applied research, approaches to control measures, explanations of new theories, opinion articles, reviews, etc. To discuss these issues, a holistic and integrative point of view is necessary, which only would be achieved by the close and active participation of specialists on entomology, parasitology, virology and epidemiology. Our objective is to use a systems approach to the problem of global change and vector-borne diseases. To achieve this ambitious goal and to comply with a demand of first-rate scientific and medical interest, we are very keen on asking for the participation of multiple contributors.

Description / Table of Contents: Plant sciences research focuses predominantly on aboveground parameters. There is a scarcity of detailed information regarding the ecophysiology of root systems and the way root system functioning is affected by both internal and external factors. Furthermore, global climate change is expected to increase the intensity of climate extremes, such as severe drought, heat waves and periods of heavy rainfall; in addition other stresses such as salinization of soils are increasing world-wide. Recently an increasing awareness has developed that understanding plant traits will play a major role in breeding of future crop plants. For example, there is increasing evidence that the traits of root systems are defined by the properties of individual roots. However, further knowledge on the functional importance of root segments and the molecular/physiological mechanisms underlying root system functioning and persistence is needed, and would specifically allow modifying (crop) root system functionality and efficiency in the future. Another major gap in knowledge is localized at the root-soil interface and in regard to the potential adaptive plasticity of root-rhizosphere interactions under abiotic stress and/or competition. It is currently unknown whether adaptations in microbe communities occur, for example due to modified exudation rates, and what are the subsequent influences on nutrient mobilization and uptake. Furthermore, uncovering the mechanisms by which roots perceive neighboring roots may not only contribute to our understanding of plant developmental strategies, but also has important implications on the study of competitive interactions in natural communities, and in optimizing plant performance and resource use in agricultural and silvicultural systems. In this research topic, we aim to provide an on-line, open-access snapshot of the current state of the art of the field of root ecology and physiology, with special foci on the translation of root structure to function, and how root systems are influenced by interplay with internal and external factors such as abiotic stress, microbes and plant-plant interaction. We warmly welcome original research papers, but reviews of specific topics, articles formulating opinions or describing cutting-edge methods are also gladly accepted.

Description / Table of Contents: 1 Boden und Böden --- Einleitung --- 1.2 Der Umgang mit Böden --- Veränderungen von Böden durch menschliche Eingriffe --- Prähistorischer Umgang mit den Böden --- Die dunklen Erden Amazoniens --- Der Umgang mit Böden im vormodernen China --- Intensivierte Bodennutzung in der Neuzeit --- Der Umgang mit Böden im Ökologischen Landbau --- 1.3 Die Geschichte der Bodenkunde --- Die Wurzeln der Bodenkunde --- Die geobiowissenschaftliche/forstliche Tradition --- Die agrarwissenschaftliche Tradition --- Die chemische Tradition --- Die kulturtechnische Tradition --- 2 Böden als Naturkörper --- Einleitung --- Gliederung der Bodenlebewesen --- 2.1 Mineralkörper von Böden --- Silicate --- Gesteinsbildende Oxide --- Carbonate, Sulfate, Chloride, Phosphate --- Gesteine als Ausgangsmaterial der Bodenentwicklung --- Gesteinsgemische und Substratabfolgen --- Saprolite --- Anthropogene Gesteine --- Chemische Verwitterungsprozesse --- Tonminerale --- Carbonate, Gips und lösliche Salze --- Schwerminerale --- Tonminerale Methodik --- Pedogene Oxide --- Carbonate und Salze --- Textur der mineralischen Substanz --- 2.2 Humuskörper von Böden --- Humusformen und -typen --- Waldstreu --- Streu landwirtschaftlicher Nutzflächen --- Modellsysteme für Huminstoffe --- Alter der Humusstoffe --- Nährstoffgehalte und -nachlieferung --- 2.4 Bodenlebewesen --- Bodenfauna --- Biodenbiomasse --- Einfluss der Standort- und Bodeneigenschaften auf die Bodenfauna --- Einfluss des Bodenlebens auf Streuabbau und Aggregatbildung --- Bodenenzyme --- 2.5 Potenziale in Böden --- Bodenreaktion --- 2.6 Gefüge und Porengrößenverteilung --- Körnung und Konsistenz --- Mineralischer Feinboden --- Mineralischer Grobboden --- Organische Bodenpartikel --- Gefüge --- Morphologie --- Kräfte und Spannungen in Böden --- Wasserbindung und Porengrößenverteilung --- Wasserbewegung und Wasserleitfähigkeit des Bodens --- Thermisches Verhalten der Böden --- Bodenmechanik --- Makroskopische mechanische Verfahren --- Rheologie --- 2.7 Flüsse in Böden --- Makroporen und präferenzielle Sickerung --- Transportformen --- Wärmefluss und Wärmehaushalt --- Physikochemische Aspekte des Stofftransports in Böden --- Gastransport in Böden --- Transport gelöster Stoffe im Boden --- 3 Böden als Teile von Landschaften --- Einleitung --- 3.2 Klassifikation von Böden --- Geschichte und Prinzipien der Bodenklassifikation --- Systematik der Böden Deutschlands --- Die Österreichische Bodensystematik 2000 (OBS 2000) --- Bezugsgrundlage der Boden-Ressourcen der Erde (WRB) --- Bezugsgrundlage der Boden-Ressourcen der Erde (WRB), 2. Auflage 2006, 1. Update 2007 --- FAO/Unesco, Bodenkarte der Welt --- Systematik der bodenbildenden Substrate --- 3.3 Wichtige Bodeneinheiten --- Podsole --- Terrae calcis --- Reduktosole --- Watten und Strände – Salzwiesen und Mangrovenwälder --- Subhydrische Böden --- Moore --- 3.4 Böden als Landschaftssegmente --- Grundsätze der Bodenvergesellschaftung --- Bodentragende Landschaftsformen --- Klassifikation von Bodengesellschaften --- Watten und Marschen Nordwestdeutschlands --- Norddeutsche Jungmoränenlandschaften --- Norddeutsche Altmoränenlandschaften --- Nord- und mitteldeutsche Lössbörden und Sandlössgebiete --- Böden städtisch-industrieller Verdichtungsräume --- Bodenlandschaften kühlhumider Zonen (Boreale Wälder) --- Bodengeographie der Waldsteppen und Steppen --- Bodenlandschaften subtropischer mediterraner Zonen --- Bodengeografie der wechselfeuchten Tropen am Beispiel Indiens --- 3.5 Kartierungstechnik --- Kartierungstechnik --- 3.6 Bodenkundliche Kartenwerke --- Bodenkundliche Kartenwerke --- 4 Funktionen von Böden --- Einleitung --- 4.2 Standortfunktionen von Böden --- Böden als Waldstandorte --- Böden als Grünlandstandorte --- Deutsche Weinbaustandorte --- Böden als Obstbaustandorte --- Böden als Baugrund und Baustoff --- Die amtliche Bodenschätzung in Deutschland --- 4.4 Böden als Bestandteil des Landschaftshaushaltes --- Boden und Landschaftswasserhaushalt --- Landschaftsstoffhaushalt --- 4.5 Böden als landschafts- und kulturgeschichtliche Urkunden --- Böden als landschafts- und kulturgeschichtliche Urkunden --- Böden und Bodenmerkmale unterschiedlichen Alters --- Datierungsmethoden --- Norddeutsches Vereisungsgebiet --- Süddeutsches Vereisungsgebiet --- Lößgebiete Süddeutschlands --- Paläoböden in periglazialen Lagen der Mittelgebirge --- 5 Bodenkultivierung, Bodenmelioration --- Einleitung --- 5.1 Grundlagen der Bodenkultivierung und Bodenmelioration --- Grundlagen der Bodenkultivierung und Bodenmelioration --- 5.2 Meliorationsverfahren --- Meliorationsverfahren --- 5.3 Kultivierungsverfahren --- Marschkultur --- Einleitung --- Moorkulturen --- Plaggen --- Tiefenbearbeitung --- Bewässerung --- 6 Anthropogene Bodenveränderungen und -belastungen --- Einleitung --- 6.1 Bodenüberformung und -versiegelung --- Bodenüberformung und -versiegelung --- 6.2 Anthropogene Gefügeänderung --- Bewirtschaftungssysteme und ihre Auswirkungen auf das Bodengefüge --- Anthropogene Gefügeänderungen --- Forstliche Bodenbewirtschaftung --- Melioration von tiefreichend schadverdichteten Neu- und Altlandstandorten --- 6.3 Abtrag von Böden --- Physikalische Ursachen der Wassererosion --- Erosionsformen --- Winderosion --- Abtrag von Böden --- Feststofftransport in Fließgewässern --- Quantifizierung des Bodenabtrags anhand von Modellen --- 6.4 Düngung von Böden --- Düngung von Böden --- 6.5 Kontamination von Böden --- Organische Pflanzenschutzmittel --- Antibiotika --- Radionuklide 7 Bodenschutz --- Einleitung --- 7.1 Gesetzliche Grundlagen --- Bundes-Bodenschutzgesetz (Wortlaut) --- Bundes-Bodenschutz- und Altlastenverordnung (Wortlaut) --- Bodenschutzrecht --- 7.2 Bodenschutz in der Landwirtschaft --- Einleitung --- Gesetzliche Instrumente --- Ökonomische Instrumente --- 7.3 Bodenschutzrelevante Planungen --- Planung und Umsetzung im urbanindustriellen und suburbanen Raum --- 7.4 Schutz vor mechanischer Belastung --- Schutz vor mechanischer Belastung --- 7.5 Schutz vor Abtrag und Überflutung --- Schutz vor Abtrag und Überflutung --- 7.6 Schutz vor stofflichen Belastungen --- Schutz landwirtschaftlicher Böden vor Überdüngung --- Schutz vor Säuren --- Schutz vor Salzen und Alkalinität --- Schutz vor Belastung mit Pflanzenschutzmitteln --- Schutz vor Organika --- Schutz vor Kontamination durch Deponien --- Schutz vor Kontamination bei Reststoffverwertung --- 7.7 Erziehung zum Bodenschutz --- Erziehung zum Bodenschutz --- 8 Bodensicherung, -sanierung und -restaurierung --- Einleitung --- 8.1 Rechtsgrundlagen der Bodensanierung --- Rechtsgrundlagen der Bodensanierung --- 8.3 Rekultivierung unterschiedlicher Böden und Substrate --- Rekultivierung unterschiedlicher Böden und Substrate --- 8.4 Rekultivierung fremdgenutzter Standorte --- Rekultivierung aufgegebener Industrie-, Gewerbe und Verkehrsflächen --- 8.5 Rekultivierung und Renaturierung von Abgrabungsflächen --- Rekultivierung und Renaturierung von Abgrabungsflächen --- 8.6 Sanierungsbedürftigkeit und Schutzwürdigkeit von Böden --- Sanierungsbedürftigkeit und Schutzwürdigkeit von Böden

Description / Table of Contents: Igneous oceanic crust is one of the largest potential habitats for life on earth, and microbial activity supported by rock-water-microbe reactions in this environment can impact global biogeochemical cycles. However, our understanding of the microbiology of this system, especially the subsurface “deep biosphere” component of it, has traditionally been limited by sample availability and quality. Over the past decade, several major international programs (such as the Center for Dark Energy Biosphere Investigations, the current International Ocean Discovery Program and its predecessor Integrated Ocean Drilling Program, and the Deep Carbon Observatory) have focused on advancing our understanding of life in this cryptic, yet globally relevant, biosphere. Additionally, many field and laboratory research programs are examining hydrothermal vent systems –a seafloor expression of seawater that has been thermally and chemically altered in subseafloor crust – and the microbial communities supported by these mineral-rich fluids. The Frontiers in Microbiology 3 September 2017 | Recent Advances in Geomicrobiology of the Ocean Crust papers in this special issue bring together recent discoveries of microbial presence, diversity and activity in these dynamic ocean environments. Cumulatively, the articles in this special issue serve as a tribute to the late Dr. Katrina J. Edwards, who was a pioneer and profound champion of studying microbes that “rust the crust”. This special issue volume serves as a foundation for the continued exploration of the subsurface ocean crust deep biosphere.

Description / Table of Contents: There is observational evidence that global mean sea levels are rising and there is concern that the rate of rise will accelerate throughout the 21st century, significantly threatening growing coastal communities. Modern society is vulnerable to even small changes in sea level. More than 600 million people currently live within 10 m of present-day sea level, in an area that generates 10% of the world’s total GDP. An assessment of 136 of the world’s largest port cities estimated that, by the 2070s, the population exposed to flooding risk may grow by more than a factor of three in these cities due to the combined effects of sea level rise, land subsidence, population growth and urbanization, with asset exposure increasing to more than ten times current levels. Therefore, understanding future sea level rise and variability is of utmost importance. In June 2015 we are holding a workshop in Majorca, Spain with a focus on sea level variability and change (see https://slrmallorca.wordpress.com for more details). Over 100 sea level experts from around the world will attend this workshop, from a range of different disciplines. We would like to propose a Research Topic, based on the papers presented at this workshop. The main aims of the workshop are to: 1.) Evaluate the current state-of-knowledge of sea level science; 2.) Identify gaps and unresolved questions in any aspect of sea level science; and 3.) Design future research to address these issue. The workshop will provide a forum for the discussion and the exchange of ideas on key sea level issues, and foster collaboration across the wide range of disciplines involved in sea level research. All aspects of sea level changes will be covered, from global to regional, observations and modelling, processes driving mean sea level changes and extremes, from the geological scale to the instrumental era and future projections and including impacts on the coastal zones.

Description / Table of Contents: Deep subsurface microbiology is a highly active and rapidly advancing research field at the interface of microbiology and the geosciences; it focuses on the detection, identification, quantification, cultivation and activity measurements of bacteria, archaea and eukaryotes that permeate the subsurface biosphere of deep marine sediments and the basaltic ocean and continental crust. The deep subsurface biosphere abounds with uncultured, only recently discovered and – at best - incompletely understood microbial populations. In spatial extent and volume, Earth’s subsurface biosphere is only rivaled by the deep sea water column. So far, no deep subsurface sediment has been found that is entirely devoid of microbial life; microbial cells and DNA remain detectable at sediment depths of more than 1 km; microbial life permeates deeply buried hydrocarbon reservoirs, and is also found several kilometers down in continental crust aquifers. Severe energy limitation, either as electron acceptor or donor shortage, and scarcity of microbially degradable organic carbon sources are among the evolutionary pressures that have shaped the genomic and physiological repertoire of the deep subsurface biosphere. Its biogeochemical role as long-term organic carbon repository, inorganic electron and energy source, and subduction recycling engine continues to be explored by current research at the interface of microbiology, geochemistry and biosphere/geosphere evolution. This Research Topic addresses some of the central research questions about deep subsurface microbiology and biogeochemistry: phylogenetic and physiological microbial diversity in the deep subsurface; microbial activity and survival strategies in severely energy-limited subsurface habitats; microbial activity as reflected in process rates and gene expression patterns; biogeographic isolation and connectivity in deep subsurface microbial communities; the ecological standing of subsurface biospheres in comparison to the surface biosphere – an independently flourishing biosphere, or mere survivors that tolerate burial (along with organic carbon compounds), or a combination of both? Advancing these questions on Earth’s deep subsurface biosphere redefines the habitat range, environmental tolerance, activity and diversity of microbial life.

Description / Table of Contents: In the last three decades, research has extensively focused on the role of Fe and other mineral nutrients in regulating biological processes, ranging from the surface to the deep ocean. This has produced major breakthroughs in our understanding of the fundamental role of those bioactive elements on the carbon, nitrogen and sulfur cycles and ecosystem function. However, biological processes cannot be entirely sustained by that small set of chemical elements, and new scientific evidence suggests that trace metals other than Fe (e.g., Co, Mo and Ni) as well as essential organic growth factors (e.g., vitamins) may also be crucial in most aquatic systems.

Description / Table of Contents: Hydrothermally influenced microbial habitats and communities represent a much wider spectrum of geological setting, chemical in-situ regimes, and biotic community than the classical examples from basalt-hosted black smoker chimneys at active mid-ocean spreading centers. Hydrothermal vent ecosystems now include hydrothermally heated and chemically altered sediments, microbiota fueled by serpentinization reactions, and low-temperature vents with unusual menus of electron donors. Novel marine provinces and hydrothermal areas are being charted and explored, such as new hydrothermal vent systems in the Arctic, around Antarctica, in the Western Pacific and in the Indian Ocean. Novel environmental gradients and niches provide habitats for unusual or unprecedented microorganisms and microbial ecosystems. The discovery of novel extremophiles such as Aciduliprofundum and the Nanoarchaeota underscores that hydrothermal vent microbial communities can no longer be characterized as assemblages of only “typical” sulfur oxidizers, methanogens and heterotrophs. Different stages of hydrothermal activity, from early onset to peak activity, gradual decline, and persistence of cold and fossil vent sites, correspond to different colonization waves by microorganisms as well as megafauna. This research topic will continue to stretch the limits of hydrothermal vent microbiology, and also provide a forum for the chemical and microbial linkages of hydrothermal vents to the ocean water column and the ocean crust or sedimentary subsurface.

Description / Table of Contents: Advances in next generation sequencing technologies, omics, and bioinformatics are revealing a tremendous and unsuspected diversity of microbes, both at a compositional and functional level. Moreover, the expansion of ecological concepts into microbial ecology has greatly advanced our comprehension of the role microbes play in the functioning of ecosystems across a wide range of biomes. Super-imposed on this new information about microbes, their functions and how they are organized, environmental gradients are changing rapidly, largely driven by direct and indirect human activities. In the context of global change, understanding the mechanisms that shape microbial communities is pivotal to predict microbial responses to novel selective forces and their implications at the local as well as global scale. One of the main features of microbial communities is their ability to react to changes in the environment. Thus, many studies have reported changes in the performance and composition of communities along environmental gradients. However, the mechanisms underlying these responses remain unclear. It is assumed that the response of microbes to changes in the environment is mediated by a complex combination of shifts in the physiological properties, single-cell activities, or composition of communities: it may occur by means of physiological adjustments of the taxa present in a community or selecting towards more tolerant/better adapted phylotypes. Knowing whether certain factors trigger one, many, or all mechanisms would greatly increase confidence in predictions of future microbial composition and processes. This Research Topic brings together studies that applied the latest molecular techniques for studying microbial composition and functioning and integrated ecological, biogeochemical and/or modeling approaches to provide a comprehensive and mechanistic perspective of the responses of micro-organisms to environmental changes. This Research Topic presents new findings on environmental parameters influencing microbial communities, the type and magnitude of response and differences in the response among microbial groups, and which collectively deepen our current understanding and knowledge of the underlying mechanisms of microbial structural and functional responses to environmental changes and gradients in both aquatic and terrestrial ecosystems. The body of work has, furthermore, identified many challenges and questions that yet remain to be addressed and new perspectives to follow up on.