Vadose Zone Journal Research Articles

Spatio‐temporal scaling of Vegetation Growth and Soil Formation from Percolation Theory

Spatio‐temporal scaling of Vegetation Growth and Soil Formation from Percolation Theory

New Vadose Zone Journal Initiatives for 2016

![Figure][1] Harry Vereecken In 2016, Vadose Zone Journal (VZJ) will roll out two new features: Focus Topics and a new type of manuscript called Updates. The ideas for these two new features were proposed at the VZJ editorial board meeting in Minneapolis, in 2015, and the concepts were

Preface to the Special Issue of Vadose Zone Journal on Soil as Complex Systems

This special issue of the Vadose Zone Journal entitled “Soil as Complex Systems” is a product of the first Complex Soil Systems Conference, “A Path to Improved Understanding of Complex Soil Systems,” ( , accessed 22 Jan. 2016)

Vadose Zone Journal to Feature ‘Update’ Articles, Focus Topics in 2016

<i>Vadose Zone Journal</i> to Feature ‘Update’ Articles, Focus Topics in 2016

Reproducible Research in the Vadose Zone Sciences

The scientific method is the foundation upon which we seek answers to questions and the pathway we use to build on previous knowledge. The notion that experimental results should be reproducible has been part of this method for centuries, since the days of Kepler and Galileo. Reproducibility reduces experimental biases and circumstances that influence results. A lack of it can hamper our ability to generalize and extend physical processes outside of the limited conditions of the experiment. In today's world, and relevant to vadose zone sciences, we rely on computational approaches, advanced mathematical and statistical models, and simulation software, to process and analyze complex datasets. Much like yesterday's physical experimentalists, modern-day computational scientists also must insure that algorithms and analytical approaches can be replicated by the scientific community. Opportunities for scientific progress are greatly diminished if reproducing and building on published research is difficult or impossible due to the complexity or opacity of computational systems. The need for transparency in these approaches has been recognized by scientific journals (e.g., Science and Nature) and funding agencies (e.g., National Institutes of Health). These days, transparency also influences public discourse and acceptance of research results. As described in a recent article by Skaggs et al. (see https://doi.org/10.2136/vzj2015.06.0088), Vadose Zone Journal (VZJ) is launching a new Reproducible Research (RR) program, in which the code and data (less than 10 MB in size) accompanying a research article will be hosted by the Alliance of Crop, Soil, and Environmental Science Societies (ACSESS). Author participation in RR is voluntary, but benefits are many. For example, availability of supporting information will enable readers to analyze data in a manner similar to that presented in the article, more efficiently building on results in future research and applications. It's expected that by year's end, RR policies and procedures will be in place and tested on articles selected by VZJ editors. Policies will cover author and reviewer guidelines, including allowable file types and copyright issues. Where applicable, all code and datasets will have a Creative Commons license that credits authors and permits non-commercial use of the material. Vadose Zone Journal does not expect source code in commercial software packages to be released, but the software version should be stated so that readers can replicate experimental conditions. The article's authors also discuss the challenges of providing RR supplemental material, including the need for authors to “clean” and document their code more than they would otherwise, a possible loss of competitive advantage to other colleagues, to name just two examples. So, there is some effort to archiving this extra material, but the effort could substantially widen how the research is used by the community. To make the process easier, VZJ will add associate editors who understand RR concepts and can manage both the technical review and RR archive review. The latter will focus on readability, understandability, and technical soundness of the code so that key results can be reproduced from the publication. Vadose Zone Journal is developing this program due to the strong computational and analytical nature of many articles, and because the public and funding agencies accept and support research more readily when its underpinnings are available for review and use. The authors of this article and editors of VZJ believe this level of transparency is necessary for healthy discussions and advances in our sciences, and will ultimately be used in many earth sciences journals.

Reproducible Research in Vadose Zone Sciences

A significant portion of present-day soil and Earth science research is computational, involving complex data analysis pipelines, advanced mathematical and statistical models, and sophisticated computer codes. Opportunities for scientific progress are greatly diminished if reproducing and building on published research is difficult or impossible due to the complexity of these computational systems. Vadose Zone Journal (VZJ) is launching a Reproducible Research (RR) program in which code and data underlying a research article will be published alongside the article, thereby enabling readers to analyze data in a manner similar to that presented in the article and build on results in future research and applications. In this article, we discuss reproducible research, its background and use across other disciplines, its value to the scientific community, and its implementation in VZJ.

Critical Zone Services: Expanding Context, Constraints, and Currency beyond Ecosystem Services

CSA NewsVolume 60, Issue 2 p. 10-10 ScienceOpen Access Critical Zone Services: Expanding Context, Constraints, and Currency beyond Ecosystem Services First published: 03 February 2015 https://doi.org/10.2134/csa2015-60-2-2 Adapted from Field, J.P., D.D. Breshears, D.J. Law, J.C. Villegas, L. López-Hoffman, P.D. Brooks, J. Chorover et al. 2015. Critical zone services: expanding context, constraints, and currency beyond ecosystem services. Vadose Z. J. 14(1). View the full article online at https://doi.org/10.2136/vzj2014.10.0142 AboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Humans derive many ecological, economical, water, and nutritional benefits from the critical zone (CZ), which is defined by the National Research Council (2001) as the area extending from the top of the vegetation canopy to the vertical depth of the freely moving groundwater. It is very important to note that soil in the CZ takes hundreds of thousands of year to form, whereas erosion or human disturbance can wash it away or otherwise reduce the productive nature of this important feature of the biosphere. The January 2015 issue of Vadose Zone Journal includes an article introducing a vision of ecosystem services and its connection to CZ processes. The authors propose a new perspective that incorporates CZ processes to expand the traditional focus within the four categories of ecosystem services: (a) provisioning—outputs of food, water and energy; (b) regulating—water quality, floods, and disease; (c) supporting—helping animals and plants maintain genetic diversity; and (d) cultural—recreational, educational, and aesthetic services. This work helps to expand the role of these services and the constraints thereon by explicitly considering CZ processes under the categories of context, constraints, and currency. Context describes the millions of years and the interaction of the physical, chemical, and biological processes that helped in the formation of the CZ. The time scale for CZ processes, such as formation of the soil, hydrologic partitioning, and landscape evolution is much longer than the conventional ecosystem services paradigm. Constraints describe physical processes that limit the delivery of goods and services. Examples include the rate of groundwater recharge and soil formation, both of which take place over centuries and millions of years, respectively. Currency is the valuation of the ecosystem service of the CZ for the ecological processes/services that are the output of the system. This could be the energy available to do work in the physical, chemical, and biological contexts. The authors suggest incorporating CZ processes into the conventional definition of ecosystem services by considering the physical nature of the soil, processes that result in the formation of the soil that are on much longer time scales, and the interconnectedness of the physical, chemical, and biological processes. Incorporating CZ processes into the valuation of ecosystem services, which is receiving substantial attention by national and international bodies, provides a more thorough and effective framework by which policy makers can assess impacts from climate change and associated disturbances. Critical zone services provide context, constraints, and currency that enable more effective management and valuation of ecosystem services (adapted from MEA, 2005). Reference National Research Council (NRC). 2001. Basic research opportunities in the earth sciences. National Academies Press, Washington, DC. Volume60, Issue2February 2015Pages 10-10 ReferencesRelatedInformation

Vadose Zone Journal: The First Ten Years

We proudly present a special section inspired by the 10-year anniversary of Vadose Zone Journal. From the outset, the journal was intended to be different than traditional “soils” journals, with the goal of publishing contributions, reviews, and opinion papers across a broader range of disciplines concerned with the vadose zone, including scientific and societal issues related to the role of vadose zone processes in climate change, biofuels, sustainability, and nanotechnology. Since its inception, Vadose Zone Journal has grown tremendously as a scholarly publication with a strong reputation for high quality and diverse science. Accessible and timely reviews, in addition to technical notes and articles, have secured the journal’s reputation as a definitive and valuable resource for soil scientists, hydrologists, ecologists, hydrogeophysicists, and other earth scientists. The growth of the journal is impressive and is partly reflected by the 2012 impact factor (IF) of 2.20 (5-yr IF of 2.67), ranking eighth in the soil science category, and 16th in the field of water resources. When the article influence score is used as the primary metric, then Vadose Zone Journal ranks fourth in soil science. The success of the journal is also reflected in the editorial board, which is composed of many leading vadose zone scientists from the United States and internationally. The high proportion of scholarly submissions from international scien tists outside of the United States (approximately two-thirds of the manuscripts published) reflects on the status of the Vadose Zone Journal as a multi-disciplinary and multi-national scholarly outlet—an important goal from the outset.

Vadose Zone Journal: A Decade of Multidisciplinary Research

Ten years ago we welcomed you to the first issue of Vadose Zone Journal (VZJ). As the first two editors of VZJ, we very much remember the enormous excitement about finally having a dedicated outlet designed to bring much-needed direction to vadose zone research ([van Genuchten, 2002][1]; [Hopmans et

VZJ Launches New Paper Type: “Priority Communications”

Vadose Zone Journal (VZJ) is rolling out a new type of manuscript called “Priority Communications.” This idea was suggested by one of the associate editors and was accepted by the co-editors of the journal in June 2013. These new manuscripts are intended to highlight time-sensitive research

Vadose Zone Journal – 2012 Summary Editorial Reports

This report on the 2012 status of Vadose Zone Journal was prepared for the 2012 VZJ Editorial Board Meetings, and was presented on behalf of the Vadose Zone Journal Editorial Board leadership, comprising Dani Or, VZJ Editor; Susan Hubbard, Harry Vereecken and Michael Young, Co‐Editors; Rien van Genuchten and Jan Hopmans, Consulting Editors; Ty Ferre, Invited Reviews Coordinator; and Ed Perfect – Book Reviews Editor. The report also includes the Managing Editor and Director of Publication reports.

Interweaving Monitoring Activities and Model Development towards Enhancing Knowledge of the Soil-Plant-Atmosphere Continuum

The study of water pathways from the soil to the atmosphere through plants—the so-called soil–plant–atmosphere conƟ nuum (SPAC)—has always been central to agronomy, hydrology, plant physiology, and other disciplines, using a wide range of approaches and tools. In recent years, we have been witnessing a rapid expansion of interweaving monitoring acƟ viƟ es and model development related to SPAC in climaƟ c, ecological, and applicaƟ ons other than the tradiƟ onal agrohydrological, and it is therefore Ɵ mely to review the current status of this topic and outline future direcƟ ons of research. The iniƟ aƟ ve for the special secƟ on of Vadose Zone Journal on SPAC emanated from several sessions we recently organized in internaƟ onal conferences and meeƟ ngs. With a view to the specifi c research quesƟ ons covered in this special secƟ on, this arƟ cle introduces and reviews SPAC underlying issues and then provides a brief overview of the invited contribuƟ ons. We have grouped together the 15 contribuƟ ons under three main secƟ ons related to the local, fi eld, and landscape spaƟ al scales of interests. Within these secƟ ons, the papers present their innovaƟ ve results using diff erent measuring techniques (from classic tensiometers and TDR sensors to more advanced and sophisƟ cated equipment based on tomography and geophysics) and different modeling tools (from mechanisƟ c models based on the Richards equaƟ on to more parametrically parsimonious hydrologic balance models). They provide a snapshot of the current state of the art while emphasizing the signifi cant progress aƩ ained in this fi eld of research. New technological developments and applicaƟ ons are also highlighted. AbbreviaƟ ons: SPAC, soil–plant–atmosphere conƟ nuum Soil is a key component of the earth’s biosphere linking surface water and groundwater and the atmosphere. Most soil hydrological processes take place over vegetated land areas, and therefore the plant rooting system becomes the most active zone for transfer of water (and dissolved nutrients) between soil and atmosphere through the plants.

Vadose Zone Journal – 2011 Summary Editorial Reports

Vadose Zone JournalVolume 11, Issue 2 vzj2011.001rep Other Items Vadose Zone Journal – 2011 Summary Editorial Reports First published: 01 May 2012 https://doi.org/10.2136/vzj2011.001rep All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Abstract This report on the 2011 status of Vadose Zone Journal was prepared by Dani Or, October 2011, for the 2011 VZJ Editorial Board Meetings, and was presented on behalf of the Vadose Zone Journal Editorial Board leadership, comprising Dani Or, VZJ Editor; Susan Hubbard, Harry Vereecken and Michael Young, Co-Editors; Rien van Genuchten and Jan Hopmans, Consulting Editors; Ty Ferre, Invited Reviews Coordinator; and Ed Perfect – Book Reviews Editor. The report also includes the Managing Editor's report. Volume11, Issue2May 2012vzj2011.001rep RelatedInformation

Soil Architecture and Physicochemical Functions: An Introduction

Soils function as Earth's life support system, a thin layer full of life covering most of the terrestrial surfaces. Soils form the foundation of society. Norman Borlaug stated in his Nobel laureate lecture that “the first essential component of social justice is adequate food for all mankind.” If we are to provide this component while sustaining environmental quality in the midst of a growing population and rapidly diminishing resources, it is imperative to study and obtain a deeper level of understanding of soil functions using state‐of‐the‐art technologies as well as provide the next generation of environmentalists, soil scientists, and environmental engineers with the best education possible. The 16 papers in this special section on soil architecture and physicochemical functions in the Vadose Zone Journal contribute to these goals by improving and linking measurement, visualization, and modeling of soil structure (architecture) and physical, chemical, and biological processes in different porous media systems and at different scales. Several studies in this special section also outline and discuss emerging and exciting interdisciplinary challenges for the rapidly growing vadose zone research community, including the need for enhanced public awareness of the soil's essential life‐support functions, putting value on soil ecosystem services (“capital of soil”), and design of optimal soil‐based growth media for long‐term missions in space.

Introduction to Production, Transport, and Emission of Trace Gases from the Vadose Zone to the Atmosphere

Rising concerns about global warming as a consequence of increased anthropogenic greenhouse gas emissions have markedly strengthened scientific, political, and even public interest in issues surrounding human-induced climate change. This has resulted in fundamental economic and ecologic debates

Patterns in Soil–Vegetation–Atmosphere Systems: Monitoring, Modeling, and Data Assimilation

In this special issue, we present recent scientific work that analyzes the role of patterns in soil–vegetation–atmosphere (SVA) systems over a wide range of scales ranging from the pore scale up to mesoscale catchments. Specific attention is given to the development of novel data assimilation methods, noninvasive measurement techniques that allow mapping spatial patterns of state variables and fluxes, and two‐way coupling of models in a scale‐consistent way. “Patterns in Soil–Vegetation–Atmosphere Systems” is also the research topic of a collaborative research center (TR32) between the universities of Aachen, Bonn, and Cologne and the Forschungszentrum Jülich. In this center, which is funded by the Deutsche Forschungsgemeinschaft, on the basis of an international evaluation, scientists covering a broad range of earth science disciplines are working together. During June 11–12, 2010 the center organized its first international workshop in Aachen. The contributions presented in this special issue of Vadose Zone Journal include contributions from the collaborative research center and external contributions, both from Germany and worldwide.

Applicability of Time Domain Reflectometry Water Content Measurements in Municipal Solid Waste

Vadose Zone Journal 9:160–171 (February 2010) The original Table 1 showed inconsistent values for the initial gravimetric water content, volumetric water content, and porosity. The values should be understood as percent kg kg−1 and percent L L−1 as shown in Table 1 here: In addition, the labels of Fig. 5 and Fig. 6 should be “Ta (ns)” and not “T (ns)”, as both graphs show the apparent travel time and not the absolute travel time, coated time-domain reflectometry probes being used.

The Influence of Biofilm Spatial Distribution Scenarios on Hydraulic Conductivity of Unsaturated Soils

The development of biofilms in unsaturated soils is likely to influence the hydraulic conductivity function. Despite its importance, this effect has received little attention. Mostafa and Van Geel (2007, Vadose Zone Journal, 6:175–185) proposed several hydraulic conductivity models that acount for the effect of bacteria in unsaturated soils. We have expanded these models by considering the change in biofilm pore‐size distribution and its effect on the entire hydraulic conductivity function. Three scenarios were considered: (i) the biofilm fills the smallest pores first; (ii) a biofilm of uniform thickness coats all pore walls; and (iii) the biofilm coats the soil with a constant volume fraction of each pore. The results show that the pore‐scale distribution of the biofilm has a significant effect on the hydraulic properties of the soil and therefore has to be accounted for when modeling flow and transport in biofilm‐affected soils.

Randomnicity: Rules and Randomness in the Realm of the Infinite

After seeing an announcement of the publication of Randomnicity , and reading its description in January 2009, I immediately requested that our library purchase a copy. Then I was pleased to receive, and eager to accept, the invitation to review it for Vadose Zone Journal . The experience reminded

UZIG USGS Research: Advances through Interdisciplinary Interaction

Because vadose zone research relates to diverse disciplines, applications, and modes of research, collaboration across traditional operational and topical divisions is especially likely to yield major advances in understanding. The Unsaturated Zone Interest Group (UZIG) is an informal organization sponsored by the USGS to encourage and support interdisciplinary collaboration in vadose or unsaturated zone hydrologic research across organizational boundaries. It includes both USGS and non‐USGS scientists. Formed in 1987, the UZIG operates to promote communication, especially through periodic meetings with presentations, discussions, and field trips. The 10th meeting of the UZIG at Los Alamos, NM, in August 2007 was jointly sponsored by the USGS and Los Alamos National Laboratory. Presentations at this meeting served as the initial basis for selecting papers for this special section of Vadose Zone Journal, the purpose of which is to present noteworthy cutting‐edge unsaturated zone research promoted by, facilitated by, or presented in connection with the UZIG.