Technical development of PubMed Interact: an improved interface for MEDLINE/PubMed searches

PubMed Central

Muin, Michael; Fontelo, Paul

2006-01-01

Background The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results. Results PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience. Conclusion PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications. PMID:17083729

NOBLAST and JAMBLAST: New Options for BLAST and a Java Application Manager for BLAST results.

PubMed

Lagnel, Jacques; Tsigenopoulos, Costas S; Iliopoulos, Ioannis

2009-03-15

NOBLAST (New Options for BLAST) is an open source program that provides a new user-friendly tabular output format for various NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn, Tblastx, Mega BLAST and Psi BLAST) without any use of a parser and provides E-value correction in case of use of segmented BLAST database. JAMBLAST using the NOBLAST output allows the user to manage, view and filter the BLAST hits using a number of selection criteria. A distribution package of NOBLAST and JAMBLAST including detailed installation procedure is freely available from http://sourceforge.net/projects/JAMBLAST/ and http://sourceforge.net/projects/NOBLAST. Supplementary data are available at Bioinformatics online.

Syntactic dependency parsers for biomedical-NLP.

PubMed

Cohen, Raphael; Elhadad, Michael

2012-01-01

Syntactic parsers have made a leap in accuracy and speed in recent years. The high order structural information provided by dependency parsers is useful for a variety of NLP applications. We present a biomedical model for the EasyFirst parser, a fast and accurate parser for creating Stanford Dependencies. We evaluate the models trained in the biomedical domains of EasyFirst and Clear-Parser in a number of task oriented metrics. Both parsers provide stat of the art speed and accuracy in the Genia of over 89%. We show that Clear-Parser excels at tasks relating to negation identification while EasyFirst excels at tasks relating to Named Entities and is more robust to changes in domain.

Semantic Role Labeling of Clinical Text: Comparing Syntactic Parsers and Features

PubMed Central

Zhang, Yaoyun; Jiang, Min; Wang, Jingqi; Xu, Hua

2016-01-01

Semantic role labeling (SRL), which extracts shallow semantic relation representation from different surface textual forms of free text sentences, is important for understanding clinical narratives. Since semantic roles are formed by syntactic constituents in the sentence, an effective parser, as well as an effective syntactic feature set are essential to build a practical SRL system. Our study initiates a formal evaluation and comparison of SRL performance on a clinical text corpus MiPACQ, using three state-of-the-art parsers, the Stanford parser, the Berkeley parser, and the Charniak parser. First, the original parsers trained on the open domain syntactic corpus Penn Treebank were employed. Next, those parsers were retrained on the clinical Treebank of MiPACQ for further comparison. Additionally, state-of-the-art syntactic features from open domain SRL were also examined for clinical text. Experimental results showed that retraining the parsers on clinical Treebank improved the performance significantly, with an optimal F1 measure of 71.41% achieved by the Berkeley parser. PMID:28269926

The effects of natural language processing on cross-institutional portability of influenza case detection for disease surveillance.

PubMed

Ferraro, Jeffrey P; Ye, Ye; Gesteland, Per H; Haug, Peter J; Tsui, Fuchiang Rich; Cooper, Gregory F; Van Bree, Rudy; Ginter, Thomas; Nowalk, Andrew J; Wagner, Michael

2017-05-31

This study evaluates the accuracy and portability of a natural language processing (NLP) tool for extracting clinical findings of influenza from clinical notes across two large healthcare systems. Effectiveness is evaluated on how well NLP supports downstream influenza case-detection for disease surveillance. We independently developed two NLP parsers, one at Intermountain Healthcare (IH) in Utah and the other at University of Pittsburgh Medical Center (UPMC) using local clinical notes from emergency department (ED) encounters of influenza. We measured NLP parser performance for the presence and absence of 70 clinical findings indicative of influenza. We then developed Bayesian network models from NLP processed reports and tested their ability to discriminate among cases of (1) influenza, (2) non-influenza influenza-like illness (NI-ILI), and (3) 'other' diagnosis. On Intermountain Healthcare reports, recall and precision of the IH NLP parser were 0.71 and 0.75, respectively, and UPMC NLP parser, 0.67 and 0.79. On University of Pittsburgh Medical Center reports, recall and precision of the UPMC NLP parser were 0.73 and 0.80, respectively, and IH NLP parser, 0.53 and 0.80. Bayesian case-detection performance measured by AUROC for influenza versus non-influenza on Intermountain Healthcare cases was 0.93 (using IH NLP parser) and 0.93 (using UPMC NLP parser). Case-detection on University of Pittsburgh Medical Center cases was 0.95 (using UPMC NLP parser) and 0.83 (using IH NLP parser). For influenza versus NI-ILI on Intermountain Healthcare cases performance was 0.70 (using IH NLP parser) and 0.76 (using UPMC NLP parser). On University of Pisstburgh Medical Center cases, 0.76 (using UPMC NLP parser) and 0.65 (using IH NLP parser). In all but one instance (influenza versus NI-ILI using IH cases), local parsers were more effective at supporting case-detection although performances of non-local parsers were reasonable.

Parsing clinical text: how good are the state-of-the-art parsers?

PubMed

Jiang, Min; Huang, Yang; Fan, Jung-wei; Tang, Buzhou; Denny, Josh; Xu, Hua

2015-01-01

Parsing, which generates a syntactic structure of a sentence (a parse tree), is a critical component of natural language processing (NLP) research in any domain including medicine. Although parsers developed in the general English domain, such as the Stanford parser, have been applied to clinical text, there are no formal evaluations and comparisons of their performance in the medical domain. In this study, we investigated the performance of three state-of-the-art parsers: the Stanford parser, the Bikel parser, and the Charniak parser, using following two datasets: (1) A Treebank containing 1,100 sentences that were randomly selected from progress notes used in the 2010 i2b2 NLP challenge and manually annotated according to a Penn Treebank based guideline; and (2) the MiPACQ Treebank, which is developed based on pathology notes and clinical notes, containing 13,091 sentences. We conducted three experiments on both datasets. First, we measured the performance of the three state-of-the-art parsers on the clinical Treebanks with their default settings. Then we re-trained the parsers using the clinical Treebanks and evaluated their performance using the 10-fold cross validation method. Finally we re-trained the parsers by combining the clinical Treebanks with the Penn Treebank. Our results showed that the original parsers achieved lower performance in clinical text (Bracketing F-measure in the range of 66.6%-70.3%) compared to general English text. After retraining on the clinical Treebank, all parsers achieved better performance, with the best performance from the Stanford parser that reached the highest Bracketing F-measure of 73.68% on progress notes and 83.72% on the MiPACQ corpus using 10-fold cross validation. When the combined clinical Treebanks and Penn Treebank was used, of the three parsers, the Charniak parser achieved the highest Bracketing F-measure of 73.53% on progress notes and the Stanford parser reached the highest F-measure of 84.15% on the MiPACQ corpus. Our study demonstrates that re-training using clinical Treebanks is critical for improving general English parsers' performance on clinical text, and combining clinical and open domain corpora might achieve optimal performance for parsing clinical text.

Parsing clinical text: how good are the state-of-the-art parsers?

PubMed Central

2015-01-01

Background Parsing, which generates a syntactic structure of a sentence (a parse tree), is a critical component of natural language processing (NLP) research in any domain including medicine. Although parsers developed in the general English domain, such as the Stanford parser, have been applied to clinical text, there are no formal evaluations and comparisons of their performance in the medical domain. Methods In this study, we investigated the performance of three state-of-the-art parsers: the Stanford parser, the Bikel parser, and the Charniak parser, using following two datasets: (1) A Treebank containing 1,100 sentences that were randomly selected from progress notes used in the 2010 i2b2 NLP challenge and manually annotated according to a Penn Treebank based guideline; and (2) the MiPACQ Treebank, which is developed based on pathology notes and clinical notes, containing 13,091 sentences. We conducted three experiments on both datasets. First, we measured the performance of the three state-of-the-art parsers on the clinical Treebanks with their default settings. Then we re-trained the parsers using the clinical Treebanks and evaluated their performance using the 10-fold cross validation method. Finally we re-trained the parsers by combining the clinical Treebanks with the Penn Treebank. Results Our results showed that the original parsers achieved lower performance in clinical text (Bracketing F-measure in the range of 66.6%-70.3%) compared to general English text. After retraining on the clinical Treebank, all parsers achieved better performance, with the best performance from the Stanford parser that reached the highest Bracketing F-measure of 73.68% on progress notes and 83.72% on the MiPACQ corpus using 10-fold cross validation. When the combined clinical Treebanks and Penn Treebank was used, of the three parsers, the Charniak parser achieved the highest Bracketing F-measure of 73.53% on progress notes and the Stanford parser reached the highest F-measure of 84.15% on the MiPACQ corpus. Conclusions Our study demonstrates that re-training using clinical Treebanks is critical for improving general English parsers' performance on clinical text, and combining clinical and open domain corpora might achieve optimal performance for parsing clinical text. PMID:26045009

COD::CIF::Parser: an error-correcting CIF parser for the Perl language.

PubMed

Merkys, Andrius; Vaitkus, Antanas; Butkus, Justas; Okulič-Kazarinas, Mykolas; Kairys, Visvaldas; Gražulis, Saulius

2016-02-01

A syntax-correcting CIF parser, COD::CIF::Parser , is presented that can parse CIF 1.1 files and accurately report the position and the nature of the discovered syntactic problems. In addition, the parser is able to automatically fix the most common and the most obvious syntactic deficiencies of the input files. Bindings for Perl, C and Python programming environments are available. Based on COD::CIF::Parser , the cod-tools package for manipulating the CIFs in the Crystallography Open Database (COD) has been developed. The cod-tools package has been successfully used for continuous updates of the data in the automated COD data deposition pipeline, and to check the validity of COD data against the IUCr data validation guidelines. The performance, capabilities and applications of different parsers are compared.

Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks.

PubMed

Balaur, Irina; Mazein, Alexander; Saqi, Mansoor; Lysenko, Artem; Rawlings, Christopher J; Auffray, Charles

2017-04-01

The goal of this work is to offer a computational framework for exploring data from the Recon2 human metabolic reconstruction model. Advanced user access features have been developed using the Neo4j graph database technology and this paper describes key features such as efficient management of the network data, examples of the network querying for addressing particular tasks, and how query results are converted back to the Systems Biology Markup Language (SBML) standard format. The Neo4j-based metabolic framework facilitates exploration of highly connected and comprehensive human metabolic data and identification of metabolic subnetworks of interest. A Java-based parser component has been developed to convert query results (available in the JSON format) into SBML and SIF formats in order to facilitate further results exploration, enhancement or network sharing. The Neo4j-based metabolic framework is freely available from: https://diseaseknowledgebase.etriks.org/metabolic/browser/ . The java code files developed for this work are available from the following url: https://github.com/ibalaur/MetabolicFramework . ibalaur@eisbm.org. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks

PubMed Central

Mazein, Alexander; Saqi, Mansoor; Lysenko, Artem; Rawlings, Christopher J.; Auffray, Charles

2017-01-01

Abstract Summary: The goal of this work is to offer a computational framework for exploring data from the Recon2 human metabolic reconstruction model. Advanced user access features have been developed using the Neo4j graph database technology and this paper describes key features such as efficient management of the network data, examples of the network querying for addressing particular tasks, and how query results are converted back to the Systems Biology Markup Language (SBML) standard format. The Neo4j-based metabolic framework facilitates exploration of highly connected and comprehensive human metabolic data and identification of metabolic subnetworks of interest. A Java-based parser component has been developed to convert query results (available in the JSON format) into SBML and SIF formats in order to facilitate further results exploration, enhancement or network sharing. Availability and Implementation: The Neo4j-based metabolic framework is freely available from: https://diseaseknowledgebase.etriks.org/metabolic/browser/. The java code files developed for this work are available from the following url: https://github.com/ibalaur/MetabolicFramework. Contact: ibalaur@eisbm.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27993779

XML schemas for common bioinformatic data types and their application in workflow systems

PubMed Central

Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

2006-01-01

Background Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data – therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Results Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at , the BioDOM library can be obtained at . Conclusion The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios. PMID:17087823

PubMed Interact: an Interactive Search Application for MEDLINE/PubMed

PubMed Central

Muin, Michael; Fontelo, Paul; Ackerman, Michael

2006-01-01

Online search and retrieval systems are important resources for medical literature research. Progressive Web 2.0 technologies provide opportunities to improve search strategies and user experience. Using PHP, Document Object Model (DOM) manipulation and Asynchronous JavaScript and XML (Ajax), PubMed Interact allows greater functionality so users can refine search parameters with ease and interact with the search results to retrieve and display relevant information and related articles. PMID:17238658

Storing files in a parallel computing system based on user-specified parser function

DOEpatents

Faibish, Sorin; Bent, John M; Tzelnic, Percy; Grider, Gary; Manzanares, Adam; Torres, Aaron

2014-10-21

Techniques are provided for storing files in a parallel computing system based on a user-specified parser function. A plurality of files generated by a distributed application in a parallel computing system are stored by obtaining a parser from the distributed application for processing the plurality of files prior to storage; and storing one or more of the plurality of files in one or more storage nodes of the parallel computing system based on the processing by the parser. The plurality of files comprise one or more of a plurality of complete files and a plurality of sub-files. The parser can optionally store only those files that satisfy one or more semantic requirements of the parser. The parser can also extract metadata from one or more of the files and the extracted metadata can be stored with one or more of the plurality of files and used for searching for files.

XML schemas for common bioinformatic data types and their application in workflow systems.

PubMed

Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

2006-11-06

Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data--therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at http://bioschemas.sourceforge.net, the BioDOM library can be obtained at http://biodom.sourceforge.net. The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios.

MetaJC++: A flexible and automatic program transformation technique using meta framework

NASA Astrophysics Data System (ADS)

Beevi, Nadera S.; Reghu, M.; Chitraprasad, D.; Vinodchandra, S. S.

2014-09-01

Compiler is a tool to translate abstract code containing natural language terms to machine code. Meta compilers are available to compile more than one languages. We have developed a meta framework intends to combine two dissimilar programming languages, namely C++ and Java to provide a flexible object oriented programming platform for the user. Suitable constructs from both the languages have been combined, thereby forming a new and stronger Meta-Language. The framework is developed using the compiler writing tools, Flex and Yacc to design the front end of the compiler. The lexer and parser have been developed to accommodate the complete keyword set and syntax set of both the languages. Two intermediate representations have been used in between the translation of the source program to machine code. Abstract Syntax Tree has been used as a high level intermediate representation that preserves the hierarchical properties of the source program. A new machine-independent stack-based byte-code has also been devised to act as a low level intermediate representation. The byte-code is essentially organised into an output class file that can be used to produce an interpreted output. The results especially in the spheres of providing C++ concepts in Java have given an insight regarding the potential strong features of the resultant meta-language.

Benchmarking natural-language parsers for biological applications using dependency graphs.

PubMed

Clegg, Andrew B; Shepherd, Adrian J

2007-01-25

Interest is growing in the application of syntactic parsers to natural language processing problems in biology, but assessing their performance is difficult because differences in linguistic convention can falsely appear to be errors. We present a method for evaluating their accuracy using an intermediate representation based on dependency graphs, in which the semantic relationships important in most information extraction tasks are closer to the surface. We also demonstrate how this method can be easily tailored to various application-driven criteria. Using the GENIA corpus as a gold standard, we tested four open-source parsers which have been used in bioinformatics projects. We first present overall performance measures, and test the two leading tools, the Charniak-Lease and Bikel parsers, on subtasks tailored to reflect the requirements of a system for extracting gene expression relationships. These two tools clearly outperform the other parsers in the evaluation, and achieve accuracy levels comparable to or exceeding native dependency parsers on similar tasks in previous biological evaluations. Evaluating using dependency graphs allows parsers to be tested easily on criteria chosen according to the semantics of particular biological applications, drawing attention to important mistakes and soaking up many insignificant differences that would otherwise be reported as errors. Generating high-accuracy dependency graphs from the output of phrase-structure parsers also provides access to the more detailed syntax trees that are used in several natural-language processing techniques.

Benchmarking natural-language parsers for biological applications using dependency graphs

PubMed Central

Clegg, Andrew B; Shepherd, Adrian J

2007-01-01

Background Interest is growing in the application of syntactic parsers to natural language processing problems in biology, but assessing their performance is difficult because differences in linguistic convention can falsely appear to be errors. We present a method for evaluating their accuracy using an intermediate representation based on dependency graphs, in which the semantic relationships important in most information extraction tasks are closer to the surface. We also demonstrate how this method can be easily tailored to various application-driven criteria. Results Using the GENIA corpus as a gold standard, we tested four open-source parsers which have been used in bioinformatics projects. We first present overall performance measures, and test the two leading tools, the Charniak-Lease and Bikel parsers, on subtasks tailored to reflect the requirements of a system for extracting gene expression relationships. These two tools clearly outperform the other parsers in the evaluation, and achieve accuracy levels comparable to or exceeding native dependency parsers on similar tasks in previous biological evaluations. Conclusion Evaluating using dependency graphs allows parsers to be tested easily on criteria chosen according to the semantics of particular biological applications, drawing attention to important mistakes and soaking up many insignificant differences that would otherwise be reported as errors. Generating high-accuracy dependency graphs from the output of phrase-structure parsers also provides access to the more detailed syntax trees that are used in several natural-language processing techniques. PMID:17254351

Assembling proteomics data as a prerequisite for the analysis of large scale experiments

PubMed Central

Schmidt, Frank; Schmid, Monika; Thiede, Bernd; Pleißner, Klaus-Peter; Böhme, Martina; Jungblut, Peter R

2009-01-01

Background Despite the complete determination of the genome sequence of a huge number of bacteria, their proteomes remain relatively poorly defined. Beside new methods to increase the number of identified proteins new database applications are necessary to store and present results of large- scale proteomics experiments. Results In the present study, a database concept has been developed to address these issues and to offer complete information via a web interface. In our concept, the Oracle based data repository system SQL-LIMS plays the central role in the proteomics workflow and was applied to the proteomes of Mycobacterium tuberculosis, Helicobacter pylori, Salmonella typhimurium and protein complexes such as 20S proteasome. Technical operations of our proteomics labs were used as the standard for SQL-LIMS template creation. By means of a Java based data parser, post-processed data of different approaches, such as LC/ESI-MS, MALDI-MS and 2-D gel electrophoresis (2-DE), were stored in SQL-LIMS. A minimum set of the proteomics data were transferred in our public 2D-PAGE database using a Java based interface (Data Transfer Tool) with the requirements of the PEDRo standardization. Furthermore, the stored proteomics data were extractable out of SQL-LIMS via XML. Conclusion The Oracle based data repository system SQL-LIMS played the central role in the proteomics workflow concept. Technical operations of our proteomics labs were used as standards for SQL-LIMS templates. Using a Java based parser, post-processed data of different approaches such as LC/ESI-MS, MALDI-MS and 1-DE and 2-DE were stored in SQL-LIMS. Thus, unique data formats of different instruments were unified and stored in SQL-LIMS tables. Moreover, a unique submission identifier allowed fast access to all experimental data. This was the main advantage compared to multi software solutions, especially if personnel fluctuations are high. Moreover, large scale and high-throughput experiments must be managed in a comprehensive repository system such as SQL-LIMS, to query results in a systematic manner. On the other hand, these database systems are expensive and require at least one full time administrator and specialized lab manager. Moreover, the high technical dynamics in proteomics may cause problems to adjust new data formats. To summarize, SQL-LIMS met the requirements of proteomics data handling especially in skilled processes such as gel-electrophoresis or mass spectrometry and fulfilled the PSI standardization criteria. The data transfer into a public domain via DTT facilitated validation of proteomics data. Additionally, evaluation of mass spectra by post-processing using MS-Screener improved the reliability of mass analysis and prevented storage of data junk. PMID:19166578

Extracting noun phrases for all of MEDLINE.

PubMed Central

Bennett, N. A.; He, Q.; Powell, K.; Schatz, B. R.

1999-01-01

A natural language parser that could extract noun phrases for all medical texts would be of great utility in analyzing content for information retrieval. We discuss the extraction of noun phrases from MEDLINE, using a general parser not tuned specifically for any medical domain. The noun phrase extractor is made up of three modules: tokenization; part-of-speech tagging; noun phrase identification. Using our program, we extracted noun phrases from the entire MEDLINE collection, encompassing 9.3 million abstracts. Over 270 million noun phrases were generated, of which 45 million were unique. The quality of these phrases was evaluated by examining all phrases from a sample collection of abstracts. The precision and recall of the phrases from our general parser compared favorably with those from three other parsers we had previously evaluated. We are continuing to improve our parser and evaluate our claim that a generic parser can effectively extract all the different phrases across the entire medical literature. PMID:10566444

A Protocol for Annotating Parser Differences. Research Report. ETS RR-16-02

ERIC Educational Resources Information Center

Bruno, James V.; Cahill, Aoife; Gyawali, Binod

2016-01-01

We present an annotation scheme for classifying differences in the outputs of syntactic constituency parsers when a gold standard is unavailable or undesired, as in the case of texts written by nonnative speakers of English. We discuss its automated implementation and the results of a case study that uses the scheme to choose a parser best suited…

Processing of ICARTT Data Files Using Fuzzy Matching and Parser Combinators

NASA Technical Reports Server (NTRS)

Rutherford, Matthew T.; Typanski, Nathan D.; Wang, Dali; Chen, Gao

2014-01-01

In this paper, the task of parsing and matching inconsistent, poorly formed text data through the use of parser combinators and fuzzy matching is discussed. An object-oriented implementation of the parser combinator technique is used to allow for a relatively simple interface for adapting base parsers. For matching tasks, a fuzzy matching algorithm with Levenshtein distance calculations is implemented to match string pair, which are otherwise difficult to match due to the aforementioned irregularities and errors in one or both pair members. Used in concert, the two techniques allow parsing and matching operations to be performed which had previously only been done manually.

The parser generator as a general purpose tool

NASA Technical Reports Server (NTRS)

Noonan, R. E.; Collins, W. R.

1985-01-01

The parser generator has proven to be an extremely useful, general purpose tool. It can be used effectively by programmers having only a knowledge of grammars and no training at all in the theory of formal parsing. Some of the application areas for which a table-driven parser can be used include interactive, query languages, menu systems, translators, and programming support tools. Each of these is illustrated by an example grammar.

Domain Adaption of Parsing for Operative Notes

PubMed Central

Wang, Yan; Pakhomov, Serguei; Ryan, James O.; Melton, Genevieve B.

2016-01-01

Background Full syntactic parsing of clinical text as a part of clinical natural language processing (NLP) is critical for a wide range of applications, such as identification of adverse drug reactions, patient cohort identification, and gene interaction extraction. Several robust syntactic parsers are publicly available to produce linguistic representations for sentences. However, these existing parsers are mostly trained on general English text and often require adaptation for optimal performance on clinical text. Our objective was to adapt an existing general English parser for the clinical text of operative reports via lexicon augmentation, statistics adjusting, and grammar rules modification based on a set of biomedical text. Method The Stanford unlexicalized probabilistic context-free grammar (PCFG) parser lexicon was expanded with SPECIALIST lexicon along with statistics collected from a limited set of operative notes tagged with a two of POS taggers (GENIA tagger and MedPost). The most frequently occurring verb entries of the SPECIALIST lexicon were adjusted based on manual review of verb usage in operative notes. Stanford parser grammar production rules were also modified based on linguistic features of operative reports. An analogous approach was then applied to the GENIA corpus to test the generalizability of this approach to biomedical text. Results The new unlexicalized PCFG parser extended with the extra lexicon from SPECIALIST along with accurate statistics collected from an operative note corpus tagged with GENIA POS tagger improved the parser performance by 2.26% from 87.64% to 89.90%. There was a progressive improvement with the addition of multiple approaches. Most of the improvement occurred with lexicon augmentation combined with statistics from the operative notes corpus. Application of this approach on the GENIA corpus showed that parsing performance was boosted by 3.81% with a simple new grammar and the addition of the GENIA corpus lexicon. Conclusion Using statistics collected from clinical text tagged with POS taggers along with proper modification of grammars and lexicons of an unlexicalized PCFG parser can improve parsing performance. PMID:25661593

PDB file parser and structure class implemented in Python.

PubMed

Hamelryck, Thomas; Manderick, Bernard

2003-11-22

The biopython project provides a set of bioinformatics tools implemented in Python. Recently, biopython was extended with a set of modules that deal with macromolecular structure. Biopython now contains a parser for PDB files that makes the atomic information available in an easy-to-use but powerful data structure. The parser and data structure deal with features that are often left out or handled inadequately by other packages, e.g. atom and residue disorder (if point mutants are present in the crystal), anisotropic B factors, multiple models and insertion codes. In addition, the parser performs some sanity checking to detect obvious errors. The Biopython distribution (including source code and documentation) is freely available (under the Biopython license) from http://www.biopython.org

KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats.

PubMed

Wrzodek, Clemens; Dräger, Andreas; Zell, Andreas

2011-08-15

The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms. We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. KEGGtranslator is freely available as a Java(™) Web Start application and for download at http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/. KGML files can be downloaded from within the application. clemens.wrzodek@uni-tuebingen.de Supplementary data are available at Bioinformatics online.

GazeParser: an open-source and multiplatform library for low-cost eye tracking and analysis.

PubMed

Sogo, Hiroyuki

2013-09-01

Eye movement analysis is an effective method for research on visual perception and cognition. However, recordings of eye movements present practical difficulties related to the cost of the recording devices and the programming of device controls for use in experiments. GazeParser is an open-source library for low-cost eye tracking and data analysis; it consists of a video-based eyetracker and libraries for data recording and analysis. The libraries are written in Python and can be used in conjunction with PsychoPy and VisionEgg experimental control libraries. Three eye movement experiments are reported on performance tests of GazeParser. These showed that the means and standard deviations for errors in sampling intervals were less than 1 ms. Spatial accuracy ranged from 0.7° to 1.2°, depending on participant. In gap/overlap tasks and antisaccade tasks, the latency and amplitude of the saccades detected by GazeParser agreed with those detected by a commercial eyetracker. These results showed that the GazeParser demonstrates adequate performance for use in psychological experiments.

Is human sentence parsing serial or parallel? Evidence from event-related brain potentials.

PubMed

Hopf, Jens-Max; Bader, Markus; Meng, Michael; Bayer, Josef

2003-01-01

In this ERP study we investigate the processes that occur in syntactically ambiguous German sentences at the point of disambiguation. Whereas most psycholinguistic theories agree on the view that processing difficulties arise when parsing preferences are disconfirmed (so-called garden-path effects), important differences exist with respect to theoretical assumptions about the parser's recovery from a misparse. A key distinction can be made between parsers that compute all alternative syntactic structures in parallel (parallel parsers) and parsers that compute only a single preferred analysis (serial parsers). To distinguish empirically between parallel and serial parsing models, we compare ERP responses to garden-path sentences with ERP responses to truly ungrammatical sentences. Garden-path sentences contain a temporary and ultimately curable ungrammaticality, whereas truly ungrammatical sentences remain so permanently--a difference which gives rise to different predictions in the two classes of parsing architectures. At the disambiguating word, ERPs in both sentence types show negative shifts of similar onset latency, amplitude, and scalp distribution in an initial time window between 300 and 500 ms. In a following time window (500-700 ms), the negative shift to garden-path sentences disappears at right central parietal sites, while it continues in permanently ungrammatical sentences. These data are taken as evidence for a strictly serial parser. The absence of a difference in the early time window indicates that temporary and permanent ungrammaticalities trigger the same kind of parsing responses. Later differences can be related to successful reanalysis in garden-path but not in ungrammatical sentences. Copyright 2003 Elsevier Science B.V.

Investigating AI with BASIC and Logo: Helping the Computer to Understand INPUTS.

ERIC Educational Resources Information Center

Mandell, Alan; Lucking, Robert

1988-01-01

Investigates using the microcomputer to develop a sentence parser to simulate intelligent conversation used in artificial intelligence applications. Compares the ability of LOGO and BASIC for this use. Lists and critiques several LOGO and BASIC parser programs. (MVL)

Progress in The Semantic Analysis of Scientific Code

NASA Technical Reports Server (NTRS)

Stewart, Mark

2000-01-01

This paper concerns a procedure that analyzes aspects of the meaning or semantics of scientific and engineering code. This procedure involves taking a user's existing code, adding semantic declarations for some primitive variables, and parsing this annotated code using multiple, independent expert parsers. These semantic parsers encode domain knowledge and recognize formulae in different disciplines including physics, numerical methods, mathematics, and geometry. The parsers will automatically recognize and document some static, semantic concepts and help locate some program semantic errors. These techniques may apply to a wider range of scientific codes. If so, the techniques could reduce the time, risk, and effort required to develop and modify scientific codes.

Construction of a robust, large-scale, collaborative database for raw data in computational chemistry: the Collaborative Chemistry Database Tool (CCDBT).

PubMed

Chen, Mingyang; Stott, Amanda C; Li, Shenggang; Dixon, David A

2012-04-01

A robust metadata database called the Collaborative Chemistry Database Tool (CCDBT) for massive amounts of computational chemistry raw data has been designed and implemented. It performs data synchronization and simultaneously extracts the metadata. Computational chemistry data in various formats from different computing sources, software packages, and users can be parsed into uniform metadata for storage in a MySQL database. Parsing is performed by a parsing pyramid, including parsers written for different levels of data types and sets created by the parser loader after loading parser engines and configurations. Copyright © 2011 Elsevier Inc. All rights reserved.

Memory Retrieval in Parsing and Interpretation

ERIC Educational Resources Information Center

Schlueter, Ananda Lila Zoe

2017-01-01

This dissertation explores the relationship between the parser and the grammar in error-driven retrieval by examining the mechanism underlying the illusory licensing of subject-verb agreement violations ("agreement attraction"). Previous work motivates a two-stage model of agreement attraction in which the parser predicts the verb's…

Looking forwards and backwards: The real-time processing of Strong and Weak Crossover

PubMed Central

Lidz, Jeffrey; Phillips, Colin

2017-01-01

We investigated the processing of pronouns in Strong and Weak Crossover constructions as a means of probing the extent to which the incremental parser can use syntactic information to guide antecedent retrieval. In Experiment 1 we show that the parser accesses a displaced wh-phrase as an antecedent for a pronoun when no grammatical constraints prohibit binding, but the parser ignores the same wh-phrase when it stands in a Strong Crossover relation to the pronoun. These results are consistent with two possibilities. First, the parser could apply Principle C at antecedent retrieval to exclude the wh-phrase on the basis of the c-command relation between its gap and the pronoun. Alternatively, retrieval might ignore any phrases that do not occupy an Argument position. Experiment 2 distinguished between these two possibilities by testing antecedent retrieval under Weak Crossover. In Weak Crossover binding of the pronoun is ruled out by the argument condition, but not Principle C. The results of Experiment 2 indicate that antecedent retrieval accesses matching wh-phrases in Weak Crossover configurations. On the basis of these findings we conclude that the parser can make rapid use of Principle C and c-command information to constrain retrieval. We discuss how our results support a view of antecedent retrieval that integrates inferences made over unseen syntactic structure into constraints on backward-looking processes like memory retrieval. PMID:28936483

Towards automated processing of clinical Finnish: sublanguage analysis and a rule-based parser.

PubMed

Laippala, Veronika; Ginter, Filip; Pyysalo, Sampo; Salakoski, Tapio

2009-12-01

In this paper, we present steps taken towards more efficient automated processing of clinical Finnish, focusing on daily nursing notes in a Finnish Intensive Care Unit (ICU). First, we analyze ICU Finnish as a sublanguage, identifying its specific features facilitating, for example, the development of a specialized syntactic analyser. The identified features include frequent omission of finite verbs, limitations in allowed syntactic structures, and domain-specific vocabulary. Second, we develop a formal grammar and a parser for ICU Finnish, thus providing better tools for the development of further applications in the clinical domain. The grammar is implemented in the LKB system in a typed feature structure formalism. The lexicon is automatically generated based on the output of the FinTWOL morphological analyzer adapted to the clinical domain. As an additional experiment, we study the effect of using Finnish constraint grammar to reduce the size of the lexicon. The parser construction thus makes efficient use of existing resources for Finnish. The grammar currently covers 76.6% of ICU Finnish sentences, producing highly accurate best-parse analyzes with F-score of 91.1%. We find that building a parser for the highly specialized domain sublanguage is not only feasible, but also surprisingly efficient, given an existing morphological analyzer with broad vocabulary coverage. The resulting parser enables a deeper analysis of the text than was previously possible.

Linking Parser Development to Acquisition of Syntactic Knowledge

ERIC Educational Resources Information Center

Omaki, Akira; Lidz, Jeffrey

2015-01-01

Traditionally, acquisition of syntactic knowledge and the development of sentence comprehension behaviors have been treated as separate disciplines. This article reviews a growing body of work on the development of incremental sentence comprehension mechanisms and discusses how a better understanding of the developing parser can shed light on two…

The value of parsing as feature generation for gene mention recognition

PubMed Central

Smith, Larry H; Wilbur, W John

2009-01-01

We measured the extent to which information surrounding a base noun phrase reflects the presence of a gene name, and evaluated seven different parsers in their ability to provide information for that purpose. Using the GENETAG corpus as a gold standard, we performed machine learning to recognize from its context when a base noun phrase contained a gene name. Starting with the best lexical features, we assessed the gain of adding dependency or dependency-like relations from a full sentence parse. Features derived from parsers improved performance in this partial gene mention recognition task by a small but statistically significant amount. There were virtually no differences between parsers in these experiments. PMID:19345281

A python tool for the implementation of domain-specific languages

NASA Astrophysics Data System (ADS)

Dejanović, Igor; Vaderna, Renata; Milosavljević, Gordana; Simić, Miloš; Vuković, Željko

2017-07-01

In this paper we describe textX, a meta-language and a tool for building Domain-Specific Languages. It is implemented in Python using Arpeggio PEG (Parsing Expression Grammar) parser library. From a single language description (grammar) textX will build a parser and a meta-model (a.k.a. abstract syntax) of the language. The parser is used to parse textual representations of models conforming to the meta-model. As a result of parsing, a Python object graph will be automatically created. The structure of the object graph will conform to the meta-model defined by the grammar. This approach frees a developer from the need to manually analyse a parse tree and transform it to other suitable representation. The textX library is independent of any integrated development environment and can be easily integrated in any Python project. The textX tool works as a grammar interpreter. The parser is configured at run-time using the grammar. The textX tool is a free and open-source project available at GitHub.

Structure before Meaning: Sentence Processing, Plausibility, and Subcategorization

PubMed Central

Kizach, Johannes; Nyvad, Anne Mette; Christensen, Ken Ramshøj

2013-01-01

Natural language processing is a fast and automatized process. A crucial part of this process is parsing, the online incremental construction of a syntactic structure. The aim of this study was to test whether a wh-filler extracted from an embedded clause is initially attached as the object of the matrix verb with subsequent reanalysis, and if so, whether the plausibility of such an attachment has an effect on reaction time. Finally, we wanted to examine whether subcategorization plays a role. We used a method called G-Maze to measure response time in a self-paced reading design. The experiments confirmed that there is early attachment of fillers to the matrix verb. When this attachment is implausible, the off-line acceptability of the whole sentence is significantly reduced. The on-line results showed that G-Maze was highly suited for this type of experiment. In accordance with our predictions, the results suggest that the parser ignores (or has no access to information about) implausibility and attaches fillers as soon as possible to the matrix verb. However, the results also show that the parser uses the subcategorization frame of the matrix verb. In short, the parser ignores semantic information and allows implausible attachments but adheres to information about which type of object a verb can take, ensuring that the parser does not make impossible attachments. We argue that the evidence supports a syntactic parser informed by syntactic cues, rather than one guided by semantic cues or one that is blind, or completely autonomous. PMID:24116101

Structure before meaning: sentence processing, plausibility, and subcategorization.

PubMed

Kizach, Johannes; Nyvad, Anne Mette; Christensen, Ken Ramshøj

2013-01-01

Natural language processing is a fast and automatized process. A crucial part of this process is parsing, the online incremental construction of a syntactic structure. The aim of this study was to test whether a wh-filler extracted from an embedded clause is initially attached as the object of the matrix verb with subsequent reanalysis, and if so, whether the plausibility of such an attachment has an effect on reaction time. Finally, we wanted to examine whether subcategorization plays a role. We used a method called G-Maze to measure response time in a self-paced reading design. The experiments confirmed that there is early attachment of fillers to the matrix verb. When this attachment is implausible, the off-line acceptability of the whole sentence is significantly reduced. The on-line results showed that G-Maze was highly suited for this type of experiment. In accordance with our predictions, the results suggest that the parser ignores (or has no access to information about) implausibility and attaches fillers as soon as possible to the matrix verb. However, the results also show that the parser uses the subcategorization frame of the matrix verb. In short, the parser ignores semantic information and allows implausible attachments but adheres to information about which type of object a verb can take, ensuring that the parser does not make impossible attachments. We argue that the evidence supports a syntactic parser informed by syntactic cues, rather than one guided by semantic cues or one that is blind, or completely autonomous.

Touch Interaction with 3D Geographical Visualization on Web: Selected Technological and User Issues

NASA Astrophysics Data System (ADS)

Herman, L.; Stachoň, Z.; Stuchlík, R.; Hladík, J.; Kubíček, P.

2016-10-01

The use of both 3D visualization and devices with touch displays is increasing. In this paper, we focused on the Web technologies for 3D visualization of spatial data and its interaction via touch screen gestures. At the first stage, we compared the support of touch interaction in selected JavaScript libraries on different hardware (desktop PCs with touch screens, tablets, and smartphones) and software platforms. Afterward, we realized simple empiric test (within-subject design, 6 participants, 2 simple tasks, LCD touch monitor Acer and digital terrain models as stimuli) focusing on the ability of users to solve simple spatial tasks via touch screens. An in-house testing web tool was developed and used based on JavaScript, PHP, and X3DOM languages and Hammer.js libraries. The correctness of answers, speed of users' performances, used gestures, and a simple gesture metric was recorded and analysed. Preliminary results revealed that the pan gesture is most frequently used by test participants and it is also supported by the majority of 3D libraries. Possible gesture metrics and future developments including the interpersonal differences are discussed in the conclusion.

A study of the transferability of influenza case detection systems between two large healthcare systems

PubMed Central

Wagner, Michael M.; Cooper, Gregory F.; Ferraro, Jeffrey P.; Su, Howard; Gesteland, Per H.; Haug, Peter J.; Millett, Nicholas E.; Aronis, John M.; Nowalk, Andrew J.; Ruiz, Victor M.; López Pineda, Arturo; Shi, Lingyun; Van Bree, Rudy; Ginter, Thomas; Tsui, Fuchiang

2017-01-01

Objectives This study evaluates the accuracy and transferability of Bayesian case detection systems (BCD) that use clinical notes from emergency department (ED) to detect influenza cases. Methods A BCD uses natural language processing (NLP) to infer the presence or absence of clinical findings from ED notes, which are fed into a Bayesain network classifier (BN) to infer patients’ diagnoses. We developed BCDs at the University of Pittsburgh Medical Center (BCDUPMC) and Intermountain Healthcare in Utah (BCDIH). At each site, we manually built a rule-based NLP and trained a Bayesain network classifier from over 40,000 ED encounters between Jan. 2008 and May. 2010 using feature selection, machine learning, and expert debiasing approach. Transferability of a BCD in this study may be impacted by seven factors: development (source) institution, development parser, application (target) institution, application parser, NLP transfer, BN transfer, and classification task. We employed an ANOVA analysis to study their impacts on BCD performance. Results Both BCDs discriminated well between influenza and non-influenza on local test cases (AUCs > 0.92). When tested for transferability using the other institution’s cases, BCDUPMC discriminations declined minimally (AUC decreased from 0.95 to 0.94, p<0.01), and BCDIH discriminations declined more (from 0.93 to 0.87, p<0.0001). We attributed the BCDIH decline to the lower recall of the IH parser on UPMC notes. The ANOVA analysis showed five significant factors: development parser, application institution, application parser, BN transfer, and classification task. Conclusion We demonstrated high influenza case detection performance in two large healthcare systems in two geographically separated regions, providing evidentiary support for the use of automated case detection from routinely collected electronic clinical notes in national influenza surveillance. The transferability could be improved by training Bayesian network classifier locally and increasing the accuracy of the NLP parser. PMID:28380048

A study of the transferability of influenza case detection systems between two large healthcare systems.

PubMed

Ye, Ye; Wagner, Michael M; Cooper, Gregory F; Ferraro, Jeffrey P; Su, Howard; Gesteland, Per H; Haug, Peter J; Millett, Nicholas E; Aronis, John M; Nowalk, Andrew J; Ruiz, Victor M; López Pineda, Arturo; Shi, Lingyun; Van Bree, Rudy; Ginter, Thomas; Tsui, Fuchiang

2017-01-01

This study evaluates the accuracy and transferability of Bayesian case detection systems (BCD) that use clinical notes from emergency department (ED) to detect influenza cases. A BCD uses natural language processing (NLP) to infer the presence or absence of clinical findings from ED notes, which are fed into a Bayesain network classifier (BN) to infer patients' diagnoses. We developed BCDs at the University of Pittsburgh Medical Center (BCDUPMC) and Intermountain Healthcare in Utah (BCDIH). At each site, we manually built a rule-based NLP and trained a Bayesain network classifier from over 40,000 ED encounters between Jan. 2008 and May. 2010 using feature selection, machine learning, and expert debiasing approach. Transferability of a BCD in this study may be impacted by seven factors: development (source) institution, development parser, application (target) institution, application parser, NLP transfer, BN transfer, and classification task. We employed an ANOVA analysis to study their impacts on BCD performance. Both BCDs discriminated well between influenza and non-influenza on local test cases (AUCs > 0.92). When tested for transferability using the other institution's cases, BCDUPMC discriminations declined minimally (AUC decreased from 0.95 to 0.94, p<0.01), and BCDIH discriminations declined more (from 0.93 to 0.87, p<0.0001). We attributed the BCDIH decline to the lower recall of the IH parser on UPMC notes. The ANOVA analysis showed five significant factors: development parser, application institution, application parser, BN transfer, and classification task. We demonstrated high influenza case detection performance in two large healthcare systems in two geographically separated regions, providing evidentiary support for the use of automated case detection from routinely collected electronic clinical notes in national influenza surveillance. The transferability could be improved by training Bayesian network classifier locally and increasing the accuracy of the NLP parser.

An Experiment in Scientific Code Semantic Analysis

NASA Technical Reports Server (NTRS)

Stewart, Mark E. M.

1998-01-01

This paper concerns a procedure that analyzes aspects of the meaning or semantics of scientific and engineering code. This procedure involves taking a user's existing code, adding semantic declarations for some primitive variables, and parsing this annotated code using multiple, distributed expert parsers. These semantic parser are designed to recognize formulae in different disciplines including physical and mathematical formulae and geometrical position in a numerical scheme. The parsers will automatically recognize and document some static, semantic concepts and locate some program semantic errors. Results are shown for a subroutine test case and a collection of combustion code routines. This ability to locate some semantic errors and document semantic concepts in scientific and engineering code should reduce the time, risk, and effort of developing and using these codes.

ImageParser: a tool for finite element generation from three-dimensional medical images

PubMed Central

Yin, HM; Sun, LZ; Wang, G; Yamada, T; Wang, J; Vannier, MW

2004-01-01

Background The finite element method (FEM) is a powerful mathematical tool to simulate and visualize the mechanical deformation of tissues and organs during medical examinations or interventions. It is yet a challenge to build up an FEM mesh directly from a volumetric image partially because the regions (or structures) of interest (ROIs) may be irregular and fuzzy. Methods A software package, ImageParser, is developed to generate an FEM mesh from 3-D tomographic medical images. This software uses a semi-automatic method to detect ROIs from the context of image including neighboring tissues and organs, completes segmentation of different tissues, and meshes the organ into elements. Results The ImageParser is shown to build up an FEM model for simulating the mechanical responses of the breast based on 3-D CT images. The breast is compressed by two plate paddles under an overall displacement as large as 20% of the initial distance between the paddles. The strain and tangential Young's modulus distributions are specified for the biomechanical analysis of breast tissues. Conclusion The ImageParser can successfully exact the geometry of ROIs from a complex medical image and generate the FEM mesh with customer-defined segmentation information. PMID:15461787

An Experiment in Scientific Program Understanding

NASA Technical Reports Server (NTRS)

Stewart, Mark E. M.; Owen, Karl (Technical Monitor)

2000-01-01

This paper concerns a procedure that analyzes aspects of the meaning or semantics of scientific and engineering code. This procedure involves taking a user's existing code, adding semantic declarations for some primitive variables, and parsing this annotated code using multiple, independent expert parsers. These semantic parsers encode domain knowledge and recognize formulae in different disciplines including physics, numerical methods, mathematics, and geometry. The parsers will automatically recognize and document some static, semantic concepts and help locate some program semantic errors. Results are shown for three intensively studied codes and seven blind test cases; all test cases are state of the art scientific codes. These techniques may apply to a wider range of scientific codes. If so, the techniques could reduce the time, risk, and effort required to develop and modify scientific codes.

Syntactic analysis in sentence comprehension: effects of dependency types and grammatical constraints.

PubMed

De Vincenzi, M

1996-01-01

This paper presents three experiments on the parsing of Italian wh-questions that manipulate the wh-type (who vs. which-N) and the wh extraction site (main clause, dependent clause with or without complementizer). The aim of these manipulations is to see whether the parser is sensitive to the type of dependencies being processed and whether the processing effects can be explained by a unique processing principle, the minimal chain principle (MCP; De Vincenzi, 1991). The results show that the parser, following the MCP, prefers structures with fewer and less complex chains. In particular: (1) There is a processing advantage for the wh-subject extractions, the structures with less complex chains; (2) there is a processing dissociation between the who and which questions; (3) the parser respects the principle that governs the well-formedness of the empty categories (ECP).

Morphosyntactic annotation of CHILDES transcripts*

PubMed Central

SAGAE, KENJI; DAVIS, ERIC; LAVIE, ALON; MACWHINNEY, BRIAN; WINTNER, SHULY

2014-01-01

Corpora of child language are essential for research in child language acquisition and psycholinguistics. Linguistic annotation of the corpora provides researchers with better means for exploring the development of grammatical constructions and their usage. We describe a project whose goal is to annotate the English section of the CHILDES database with grammatical relations in the form of labeled dependency structures. We have produced a corpus of over 18,800 utterances (approximately 65,000 words) with manually curated gold-standard grammatical relation annotations. Using this corpus, we have developed a highly accurate data-driven parser for the English CHILDES data, which we used to automatically annotate the remainder of the English section of CHILDES. We have also extended the parser to Spanish, and are currently working on supporting more languages. The parser and the manually and automatically annotated data are freely available for research purposes. PMID:20334720

Designing a Constraint Based Parser for Sanskrit

NASA Astrophysics Data System (ADS)

Kulkarni, Amba; Pokar, Sheetal; Shukl, Devanand

Verbal understanding (śā bdabodha) of any utterance requires the knowledge of how words in that utterance are related to each other. Such knowledge is usually available in the form of cognition of grammatical relations. Generative grammars describe how a language codes these relations. Thus the knowledge of what information various grammatical relations convey is available from the generation point of view and not the analysis point of view. In order to develop a parser based on any grammar one should then know precisely the semantic content of the grammatical relations expressed in a language string, the clues for extracting these relations and finally whether these relations are expressed explicitly or implicitly. Based on the design principles that emerge from this knowledge, we model the parser as finding a directed Tree, given a graph with nodes representing the words and edges representing the possible relations between them. Further, we also use the Mīmā ṃsā constraint of ākā ṅkṣā (expectancy) to rule out non-solutions and sannidhi (proximity) to prioritize the solutions. We have implemented a parser based on these principles and its performance was found to be satisfactory giving us a confidence to extend its functionality to handle the complex sentences.

Incorporating intelligence into structured radiology reports

NASA Astrophysics Data System (ADS)

Kahn, Charles E.

2014-03-01

The new standard for radiology reporting templates being developed through the Integrating the Healthcare Enterprise (IHE) and DICOM organizations defines the storage and exchange of reporting templates as Hypertext Markup Language version 5 (HTML5) documents. The use of HTML5 enables the incorporation of "dynamic HTML," in which documents can be altered in response to their content. HTML5 documents can employ JavaScript, the HTML Document Object Model (DOM), and external web services to create intelligent reporting templates. Several reporting templates were created to demonstrate the use of scripts to perform in-template calculations and decision support. For example, a template for adrenal CT was created to compute contrast washout percentage from input values of precontrast, dynamic postcontrast, and delayed adrenal nodule attenuation values; the washout value can used to classify an adrenal nodule as a benign cortical adenoma. Dynamic templates were developed to compute volumes and apply diagnostic criteria, such as those for determination of internal carotid artery stenosis. Although reporting systems need not use a web browser to render the templates or their contents, the use of JavaScript creates innumerable opportunities to construct highly sophisticated HTML5 reporting templates. This report demonstrates the ability to incorporate dynamic content to enhance the use of radiology reporting templates.

An Improved Tarpit for Network Deception

DTIC Science & Technology

2016-03-25

World” program was, to one who is ready to join the cyber security workforce. Thirdly, I thank my mom and dad for their constant love , support, and...arrow in a part-whole relationship . In the diagram GreaseMonkey contains the three packet handler classes. The numbers next to the PriorityQueue and...arrow from Greasy to the config_parser module represents a usage relationship , where Greasy uses functions from config_parser to parse the configuration

Extracting BI-RADS Features from Portuguese Clinical Texts.

PubMed

Nassif, Houssam; Cunha, Filipe; Moreira, Inês C; Cruz-Correia, Ricardo; Sousa, Eliana; Page, David; Burnside, Elizabeth; Dutra, Inês

2012-01-01

In this work we build the first BI-RADS parser for Portuguese free texts, modeled after existing approaches to extract BI-RADS features from English medical records. Our concept finder uses a semantic grammar based on the BIRADS lexicon and on iterative transferred expert knowledge. We compare the performance of our algorithm to manual annotation by a specialist in mammography. Our results show that our parser's performance is comparable to the manual method.

A Semantic Analysis Method for Scientific and Engineering Code

NASA Technical Reports Server (NTRS)

Stewart, Mark E. M.

1998-01-01

This paper develops a procedure to statically analyze aspects of the meaning or semantics of scientific and engineering code. The analysis involves adding semantic declarations to a user's code and parsing this semantic knowledge with the original code using multiple expert parsers. These semantic parsers are designed to recognize formulae in different disciplines including physical and mathematical formulae and geometrical position in a numerical scheme. In practice, a user would submit code with semantic declarations of primitive variables to the analysis procedure, and its semantic parsers would automatically recognize and document some static, semantic concepts and locate some program semantic errors. A prototype implementation of this analysis procedure is demonstrated. Further, the relationship between the fundamental algebraic manipulations of equations and the parsing of expressions is explained. This ability to locate some semantic errors and document semantic concepts in scientific and engineering code should reduce the time, risk, and effort of developing and using these codes.

Policy-Based Management Natural Language Parser

NASA Technical Reports Server (NTRS)

James, Mark

2009-01-01

The Policy-Based Management Natural Language Parser (PBEM) is a rules-based approach to enterprise management that can be used to automate certain management tasks. This parser simplifies the management of a given endeavor by establishing policies to deal with situations that are likely to occur. Policies are operating rules that can be referred to as a means of maintaining order, security, consistency, or other ways of successfully furthering a goal or mission. PBEM provides a way of managing configuration of network elements, applications, and processes via a set of high-level rules or business policies rather than managing individual elements, thus switching the control to a higher level. This software allows unique management rules (or commands) to be specified and applied to a cross-section of the Global Information Grid (GIG). This software embodies a parser that is capable of recognizing and understanding conversational English. Because all possible dialect variants cannot be anticipated, a unique capability was developed that parses passed on conversation intent rather than the exact way the words are used. This software can increase productivity by enabling a user to converse with the system in conversational English to define network policies. PBEM can be used in both manned and unmanned science-gathering programs. Because policy statements can be domain-independent, this software can be applied equally to a wide variety of applications.

Adding a Medical Lexicon to an English Parser

PubMed Central

Szolovits, Peter

2003-01-01

We present a heuristic method to map lexical (syntactic) information from one lexicon to another, and apply the technique to augment the lexicon of the Link Grammar Parser with an enormous medical vocabulary drawn from the Specialist lexicon developed by the National Library of Medicine. This paper presents and justifies the mapping method and addresses technical problems that have to be overcome. It illustrates the utility of the method with respect to a large corpus of emergency department notes. PMID:14728251

Semantic based man-machine interface for real-time communication

NASA Technical Reports Server (NTRS)

Ali, M.; Ai, C.-S.

1988-01-01

A flight expert system (FLES) was developed to assist pilots in monitoring, diagnosing and recovering from in-flight faults. To provide a communications interface between the flight crew and FLES, a natural language interface (NALI) was implemented. Input to NALI is processed by three processors: (1) the semantics parser; (2) the knowledge retriever; and (3) the response generator. First the semantic parser extracts meaningful words and phrases to generate an internal representation of the query. At this point, the semantic parser has the ability to map different input forms related to the same concept into the same internal representation. Then the knowledge retriever analyzes and stores the context of the query to aid in resolving ellipses and pronoun references. At the end of this process, a sequence of retrievel functions is created as a first step in generating the proper response. Finally, the response generator generates the natural language response to the query. The architecture of NALI was designed to process both temporal and nontemporal queries. The architecture and implementation of NALI are described.

Software Development Of XML Parser Based On Algebraic Tools

NASA Astrophysics Data System (ADS)

Georgiev, Bozhidar; Georgieva, Adriana

2011-12-01

In this paper, is presented one software development and implementation of an algebraic method for XML data processing, which accelerates XML parsing process. Therefore, the proposed in this article nontraditional approach for fast XML navigation with algebraic tools contributes to advanced efforts in the making of an easier user-friendly API for XML transformations. Here the proposed software for XML documents processing (parser) is easy to use and can manage files with strictly defined data structure. The purpose of the presented algorithm is to offer a new approach for search and restructuring hierarchical XML data. This approach permits fast XML documents processing, using algebraic model developed in details in previous works of the same authors. So proposed parsing mechanism is easy accessible to the web consumer who is able to control XML file processing, to search different elements (tags) in it, to delete and to add a new XML content as well. The presented various tests show higher rapidity and low consumption of resources in comparison with some existing commercial parsers.

Overview of the ArbiTER edge plasma eigenvalue code

NASA Astrophysics Data System (ADS)

Baver, Derek; Myra, James; Umansky, Maxim

2011-10-01

The Arbitrary Topology Equation Reader, or ArbiTER, is a flexible eigenvalue solver that is currently under development for plasma physics applications. The ArbiTER code builds on the equation parser framework of the existing 2DX code, extending it to include a topology parser. This will give the code the capability to model problems with complicated geometries (such as multiple X-points and scrape-off layers) or model equations with arbitrary numbers of dimensions (e.g. for kinetic analysis). In the equation parser framework, model equations are not included in the program's source code. Instead, an input file contains instructions for building a matrix from profile functions and elementary differential operators. The program then executes these instructions in a sequential manner. These instructions may also be translated into analytic form, thus giving the code transparency as well as flexibility. We will present an overview of how the ArbiTER code is to work, as well as preliminary results from early versions of this code. Work supported by the U.S. DOE.

Archetype Model-Driven Development Framework for EHR Web System.

PubMed

Kobayashi, Shinji; Kimura, Eizen; Ishihara, Ken

2013-12-01

This article describes the Web application framework for Electronic Health Records (EHRs) we have developed to reduce construction costs for EHR sytems. The openEHR project has developed clinical model driven architecture for future-proof interoperable EHR systems. This project provides the specifications to standardize clinical domain model implementations, upon which the ISO/CEN 13606 standards are based. The reference implementation has been formally described in Eiffel. Moreover C# and Java implementations have been developed as reference. While scripting languages had been more popular because of their higher efficiency and faster development in recent years, they had not been involved in the openEHR implementations. From 2007, we have used the Ruby language and Ruby on Rails (RoR) as an agile development platform to implement EHR systems, which is in conformity with the openEHR specifications. We implemented almost all of the specifications, the Archetype Definition Language parser, and RoR scaffold generator from archetype. Although some problems have emerged, most of them have been resolved. We have provided an agile EHR Web framework, which can build up Web systems from archetype models using RoR. The feasibility of the archetype model to provide semantic interoperability of EHRs has been demonstrated and we have verified that that it is suitable for the construction of EHR systems.

Detecting modification of biomedical events using a deep parsing approach.

PubMed

Mackinlay, Andrew; Martinez, David; Baldwin, Timothy

2012-04-30

This work describes a system for identifying event mentions in bio-molecular research abstracts that are either speculative (e.g. analysis of IkappaBalpha phosphorylation, where it is not specified whether phosphorylation did or did not occur) or negated (e.g. inhibition of IkappaBalpha phosphorylation, where phosphorylation did not occur). The data comes from a standard dataset created for the BioNLP 2009 Shared Task. The system uses a machine-learning approach, where the features used for classification are a combination of shallow features derived from the words of the sentences and more complex features based on the semantic outputs produced by a deep parser. To detect event modification, we use a Maximum Entropy learner with features extracted from the data relative to the trigger words of the events. The shallow features are bag-of-words features based on a small sliding context window of 3-4 tokens on either side of the trigger word. The deep parser features are derived from parses produced by the English Resource Grammar and the RASP parser. The outputs of these parsers are converted into the Minimal Recursion Semantics formalism, and from this, we extract features motivated by linguistics and the data itself. All of these features are combined to create training or test data for the machine learning algorithm. Over the test data, our methods produce approximately a 4% absolute increase in F-score for detection of event modification compared to a baseline based only on the shallow bag-of-words features. Our results indicate that grammar-based techniques can enhance the accuracy of methods for detecting event modification.

The Unification Space implemented as a localist neural net: predictions and error-tolerance in a constraint-based parser.

PubMed

Vosse, Theo; Kempen, Gerard

2009-12-01

We introduce a novel computer implementation of the Unification-Space parser (Vosse and Kempen in Cognition 75:105-143, 2000) in the form of a localist neural network whose dynamics is based on interactive activation and inhibition. The wiring of the network is determined by Performance Grammar (Kempen and Harbusch in Verb constructions in German and Dutch. Benjamins, Amsterdam, 2003), a lexicalist formalism with feature unification as binding operation. While the network is processing input word strings incrementally, the evolving shape of parse trees is represented in the form of changing patterns of activation in nodes that code for syntactic properties of words and phrases, and for the grammatical functions they fulfill. The system is capable, at least qualitatively and rudimentarily, of simulating several important dynamic aspects of human syntactic parsing, including garden-path phenomena and reanalysis, effects of complexity (various types of clause embeddings), fault-tolerance in case of unification failures and unknown words, and predictive parsing (expectation-based analysis, surprisal effects). English is the target language of the parser described.

[The role of animacy in European Portuguese relative clause attachment: evidence from production and comprehension tasks].

PubMed

Soares, Ana Paula; Fraga, Isabel; Comesaña, Montserrat; Piñeiro, Ana

2010-11-01

This work presents an analysis of the role of animacy in attachment preferences of relative clauses to complex noun phrases in European Portuguese (EP). The study of how the human parser solves this kind of syntactic ambiguities has been focus of extensive research. However, what is known about EP is both limited and puzzling. Additionally, as recent studies have stressed the importance of extra-syntactic variables in this process, two experiments were carried out to assess EP attachment preferences considering four animacy conditions: Study 1 used a sentence-completion-task, and Study 2 a self-paced reading task. Both studies indicate a significant preference for high attachment in EP. Furthermore, they showed that this preference was modulated by the animacy of the host NP: if the first host was inanimate and the second one was animate, the parser's preference changed to low attachment preference. These findings shed light on previous results regarding EP and strengthen the idea that, even in early stages of processing, the parser seems to be sensitive to extra-syntactic information.

SAGA: A project to automate the management of software production systems

NASA Technical Reports Server (NTRS)

Campbell, R. H.

1983-01-01

The current work in progress for the SAGA project are described. The highlights of this research are: a parser independent SAGA editor, design for the screen editing facilities of the editor, delivery to NASA of release 1 of Olorin, the SAGA parser generator, personal workstation environment research, release 1 of the SAGA symbol table manager, delta generation in SAGA, requirements for a proof management system, documentation for and testing of the cyber pascal make prototype, a prototype cyber-based slicing facility, a June 1984 demonstration plan, SAGA utility programs, summary of UNIX software engineering support, and theorem prover review.

Detecting modification of biomedical events using a deep parsing approach

PubMed Central

2012-01-01

Background This work describes a system for identifying event mentions in bio-molecular research abstracts that are either speculative (e.g. analysis of IkappaBalpha phosphorylation, where it is not specified whether phosphorylation did or did not occur) or negated (e.g. inhibition of IkappaBalpha phosphorylation, where phosphorylation did not occur). The data comes from a standard dataset created for the BioNLP 2009 Shared Task. The system uses a machine-learning approach, where the features used for classification are a combination of shallow features derived from the words of the sentences and more complex features based on the semantic outputs produced by a deep parser. Method To detect event modification, we use a Maximum Entropy learner with features extracted from the data relative to the trigger words of the events. The shallow features are bag-of-words features based on a small sliding context window of 3-4 tokens on either side of the trigger word. The deep parser features are derived from parses produced by the English Resource Grammar and the RASP parser. The outputs of these parsers are converted into the Minimal Recursion Semantics formalism, and from this, we extract features motivated by linguistics and the data itself. All of these features are combined to create training or test data for the machine learning algorithm. Results Over the test data, our methods produce approximately a 4% absolute increase in F-score for detection of event modification compared to a baseline based only on the shallow bag-of-words features. Conclusions Our results indicate that grammar-based techniques can enhance the accuracy of methods for detecting event modification. PMID:22595089

Improved identification of noun phrases in clinical radiology reports using a high-performance statistical natural language parser augmented with the UMLS specialist lexicon.

PubMed

Huang, Yang; Lowe, Henry J; Klein, Dan; Cucina, Russell J

2005-01-01

The aim of this study was to develop and evaluate a method of extracting noun phrases with full phrase structures from a set of clinical radiology reports using natural language processing (NLP) and to investigate the effects of using the UMLS(R) Specialist Lexicon to improve noun phrase identification within clinical radiology documents. The noun phrase identification (NPI) module is composed of a sentence boundary detector, a statistical natural language parser trained on a nonmedical domain, and a noun phrase (NP) tagger. The NPI module processed a set of 100 XML-represented clinical radiology reports in Health Level 7 (HL7)(R) Clinical Document Architecture (CDA)-compatible format. Computed output was compared with manual markups made by four physicians and one author for maximal (longest) NP and those made by one author for base (simple) NP, respectively. An extended lexicon of biomedical terms was created from the UMLS Specialist Lexicon and used to improve NPI performance. The test set was 50 randomly selected reports. The sentence boundary detector achieved 99.0% precision and 98.6% recall. The overall maximal NPI precision and recall were 78.9% and 81.5% before using the UMLS Specialist Lexicon and 82.1% and 84.6% after. The overall base NPI precision and recall were 88.2% and 86.8% before using the UMLS Specialist Lexicon and 93.1% and 92.6% after, reducing false-positives by 31.1% and false-negatives by 34.3%. The sentence boundary detector performs excellently. After the adaptation using the UMLS Specialist Lexicon, the statistical parser's NPI performance on radiology reports increased to levels comparable to the parser's native performance in its newswire training domain and to that reported by other researchers in the general nonmedical domain.

Archetype Model-Driven Development Framework for EHR Web System

PubMed Central

Kimura, Eizen; Ishihara, Ken

2013-01-01

Objectives This article describes the Web application framework for Electronic Health Records (EHRs) we have developed to reduce construction costs for EHR sytems. Methods The openEHR project has developed clinical model driven architecture for future-proof interoperable EHR systems. This project provides the specifications to standardize clinical domain model implementations, upon which the ISO/CEN 13606 standards are based. The reference implementation has been formally described in Eiffel. Moreover C# and Java implementations have been developed as reference. While scripting languages had been more popular because of their higher efficiency and faster development in recent years, they had not been involved in the openEHR implementations. From 2007, we have used the Ruby language and Ruby on Rails (RoR) as an agile development platform to implement EHR systems, which is in conformity with the openEHR specifications. Results We implemented almost all of the specifications, the Archetype Definition Language parser, and RoR scaffold generator from archetype. Although some problems have emerged, most of them have been resolved. Conclusions We have provided an agile EHR Web framework, which can build up Web systems from archetype models using RoR. The feasibility of the archetype model to provide semantic interoperability of EHRs has been demonstrated and we have verified that that it is suitable for the construction of EHR systems. PMID:24523991

ANTLR Tree Grammar Generator and Extensions

NASA Technical Reports Server (NTRS)

Craymer, Loring

2005-01-01

A computer program implements two extensions of ANTLR (Another Tool for Language Recognition), which is a set of software tools for translating source codes between different computing languages. ANTLR supports predicated- LL(k) lexer and parser grammars, a notation for annotating parser grammars to direct tree construction, and predicated tree grammars. [ LL(k) signifies left-right, leftmost derivation with k tokens of look-ahead, referring to certain characteristics of a grammar.] One of the extensions is a syntax for tree transformations. The other extension is the generation of tree grammars from annotated parser or input tree grammars. These extensions can simplify the process of generating source-to-source language translators and they make possible an approach, called "polyphase parsing," to translation between computing languages. The typical approach to translator development is to identify high-level semantic constructs such as "expressions," "declarations," and "definitions" as fundamental building blocks in the grammar specification used for language recognition. The polyphase approach is to lump ambiguous syntactic constructs during parsing and then disambiguate the alternatives in subsequent tree transformation passes. Polyphase parsing is believed to be useful for generating efficient recognizers for C++ and other languages that, like C++, have significant ambiguities.

The parser doesn't ignore intransitivity, after all

PubMed Central

Staub, Adrian

2015-01-01

Several previous studies (Adams, Clifton, & Mitchell, 1998; Mitchell, 1987; van Gompel & Pickering, 2001) have explored the question of whether the parser initially analyzes a noun phrase that follows an intransitive verb as the verb's direct object. Three eyetracking experiments examined this issue in more detail. Experiment 1 strongly replicated the finding (van Gompel & Pickering, 2001) that readers experience difficulty on this noun phrase in normal reading, and found that this difficulty occurs even with a class of intransitive verbs for which a direct object is categorically prohibited. Experiment 2, however, demonstrated that this effect is not due to syntactic misanalysis, but is instead due to disruption that occurs when a comma is absent at a subordinate clause/main clause boundary. Exploring a different construction, Experiment 3 replicated the finding (Pickering & Traxler, 2003; Traxler & Pickering, 1996) that when a noun phrase “filler” is an implausible direct object for an optionally transitive relative clause verb, processing difficulty results; however, there was no evidence for such difficulty when the relative clause verb was strictly intransitive. Taken together, the three experiments undermine the support for the claim that the parser initially ignores a verb's subcategorization restrictions. PMID:17470005

Applying Semantic-based Probabilistic Context-Free Grammar to Medical Language Processing – A Preliminary Study on Parsing Medication Sentences

PubMed Central

Xu, Hua; AbdelRahman, Samir; Lu, Yanxin; Denny, Joshua C.; Doan, Son

2011-01-01

Semantic-based sublanguage grammars have been shown to be an efficient method for medical language processing. However, given the complexity of the medical domain, parsers using such grammars inevitably encounter ambiguous sentences, which could be interpreted by different groups of production rules and consequently result in two or more parse trees. One possible solution, which has not been extensively explored previously, is to augment productions in medical sublanguage grammars with probabilities to resolve the ambiguity. In this study, we associated probabilities with production rules in a semantic-based grammar for medication findings and evaluated its performance on reducing parsing ambiguity. Using the existing data set from 2009 i2b2 NLP (Natural Language Processing) challenge for medication extraction, we developed a semantic-based CFG (Context Free Grammar) for parsing medication sentences and manually created a Treebank of 4,564 medication sentences from discharge summaries. Using the Treebank, we derived a semantic-based PCFG (probabilistic Context Free Grammar) for parsing medication sentences. Our evaluation using a 10-fold cross validation showed that the PCFG parser dramatically improved parsing performance when compared to the CFG parser. PMID:21856440

Behavioral characterization of 2-O-desmethyl and 5-O-desmethyl metabolites of the phenylethylamine hallucinogen DOM.

PubMed

Eckler, J R; Chang-Fong, J; Rabin, R A; Smith, C; Teitler, M; Glennon, R A; Winter, J C

2003-07-01

The present investigation was undertaken to test the hypothesis that known metabolites of the phenylethylamine hallucinogen 1-(2,5-dimethoxy-4-methylphenyl)-2-aminopropane (DOM) are pharmacologically active. This hypothesis was tested by evaluating the ability of racemic DOM metabolites 2-O-desmethyl DOM (2-DM-DOM) and 5-O-desmethyl DOM (5-DM-DOM) to substitute for the stimulus properties of (+)lysergic acid diethylamide (LSD). The data indicate that both metabolites are active in LSD-trained subjects and are significantly inhibited by the selective 5-HT(2A) receptor antagonist M100907. Full generalization of LSD to both 2-DM-DOM and 5-DM-DOM occurred, and 5-DM-DOM was slightly more potent than 2-DM-DOM. Similarly, 5-DM-DOM had a slightly higher affinity than 2-DM-DOM for both 5-HT(2A) and 5-HT(2C) receptors. Additionally, it was of interest to determine if the formation of active metabolite(s) resulted in a temporal delay associated with maximal stimulus effects of DOM. We postulated that if metabolite formation resulted in the aforementioned delay, direct administration of the metabolites might result in maximally stable stimulus effects at an earlier pretreatment time. This hypothesis was tested by evaluating (1) the time point at which DOM produces the greatest degree of LSD-appropriate responding, (2) the involvement of 5-HT(2A) receptor in the stimulus effects of DOM at various pretreatment times by administration of M100907 and (3) the ability of 2-DM-DOM and 5-DM-DOM to substitute for the stimulus properties of LSD using either 15- or 75-min pretreatment time. The data indicate that (a) the DOM stimulus produces the greatest degree of LSD-appropriate responding at the 75-min time point in comparison with earlier pretreatment times and (b) the stimulus effects of DOM are differentially antagonized by M100907 and this effect is a function of DOM pretreatment time prior to testing. Both 2-DM-DOM and 5-DM-DOM were found to be most active, at all doses tested, using a 75-min versus a 15-min pretreatment time. The present data do not permit unequivocal acceptance or rejection of the hypothesis that active metabolites of (-)-DOM provide a full explanation of the observed discrepancy between brain levels of (-)-DOM and maximal stimulus effects.

Enhancing SAMOS Data Access in DOMS via a Neo4j Property Graph Database.

NASA Astrophysics Data System (ADS)

Stallard, A. P.; Smith, S. R.; Elya, J. L.

2016-12-01

The Shipboard Automated Meteorological and Oceanographic System (SAMOS) initiative provides routine access to high-quality marine meteorological and near-surface oceanographic observations from research vessels. The Distributed Oceanographic Match-Up Service (DOMS) under development is a centralized service that allows researchers to easily match in situ and satellite oceanographic data from distributed sources to facilitate satellite calibration, validation, and retrieval algorithm development. The service currently uses Apache Solr as a backend search engine on each node in the distributed network. While Solr is a high-performance solution that facilitates creation and maintenance of indexed data, it is limited in the sense that its schema is fixed. The property graph model escapes this limitation by creating relationships between data objects. The authors will present the development of the SAMOS Neo4j property graph database including new search possibilities that take advantage of the property graph model, performance comparisons with Apache Solr, and a vision for graph databases as a storage tool for oceanographic data. The integration of the SAMOS Neo4j graph into DOMS will also be described. Currently, Neo4j contains spatial and temporal records from SAMOS which are modeled into a time tree and r-tree using Graph Aware and Spatial plugin tools for Neo4j. These extensions provide callable Java procedures within CYPHER (Neo4j's query language) that generate in-graph structures. Once generated, these structures can be queried using procedures from these libraries, or directly via CYPHER statements. Neo4j excels at performing relationship and path-based queries, which challenge relational-SQL databases because they require memory intensive joins due to the limitation of their design. Consider a user who wants to find records over several years, but only for specific months. If a traditional database only stores timestamps, this type of query would be complex and likely prohibitively slow. Using the time tree model, one can specify a path from the root to the data which restricts resolutions to certain timeframes (e.g., months). This query can be executed without joins, unions, or other compute-intensive operations, putting Neo4j at a computational advantage to the SQL database alternative.

Singlet oxygen in the coupled photochemical and biochemical oxidation of dissolved organic matter.

PubMed

Cory, Rose M; McNeill, Kristopher; Cotner, James P; Amado, Andre; Purcell, Jeremiah M; Marshall, Alan G

2010-05-15

Dissolved organic matter (DOM) is a significant (>700 Pg) global C pool. Transport of terrestrial DOM to the inland waters and coastal zones represents the largest flux of reduced C from land to water (215 Tg yr(-1)) (Meybeck, M. Am. J. Sci. 1983, 282, 401-450). Oxidation of DOM by interdependent photochemical and biochemical processes largely controls the fate of DOM entering surface waters. Reactive oxygen species (ROS) have been hypothesized to play a significant role in the photooxidation of DOM, because they may oxidize the fraction of DOM that is inaccessible to direct photochemical degradation by sunlight. We followed the effects of photochemically produced singlet oxygen ((1)O(2)) on DOM by mass spectrometry with (18)O-labeled oxygen, to understand how (1)O(2)-mediated transformations of DOM may lead to altered DOM bioavailability. The photochemical oxygen uptake by DOM attributed to (1)O(2) increased with DOM concentration, yet it remained a minority contributor to photochemical oxygen uptake even at very high DOM concentrations. When DOM samples were exposed to (1)O(2)-generating conditions (Rose Bengal and visible light), increases were observed in DOM constituents with higher oxygen content and release of H(2)O(2) was detected. Differential effects of H(2)O(2) and (1)O(2)-treated DOM showed that (1)O(2)-treated DOM led to slower bacterial growth rates relative to unmodified DOM. Results of this study suggested that the net effect of the reactions between singlet oxygen and DOM may be production of partially oxidized substrates with correspondingly lower potential biological energy yield.

Effect of dissolved organic matter source and character on microbial Hg methylation in Hg–S–DOM solutions

USGS Publications Warehouse

Graham, Andrew M.; Aiken, George R.; Gilmour, Cynthia

2013-01-01

Dissolved organic matter (DOM) is a key component of fate and transport models for most metals, including mercury (Hg). Utilizing a suite of diverse DOM isolates, we demonstrated that DOM character, in addition to concentration, influences inorganic Hg (Hg(II)i) bioavailability to Hg-methylating bacteria. Using a model Hg-methylating bacterium, Desulfovibrio desulfuricansND132, we evaluated Hg-DOM-sulfide bioavailability in washed-cell assays at environmentally relevant Hg/DOM ratios (∼1–8 ng Hg/mg C) and sulfide concentrations (1–1000 μM). All tested DOM isolates significantly enhanced Hg methylation above DOM-free controls (from ∼2 to >20-fold for 20 mg C/L DOM solutions), but high molecular weight/highly aromatic DOM isolates and/or those with high sulfur content were particularly effective at enhancing Hg methylation. Because these experiments were conducted under conditions of predicted supersaturation with respect to metacinnabar (β-HgS(s)), we attribute the DOM-dependent enhancement of Hg(II)i bioavailability to steric and specific chemical (e.g., DOM thiols) inhibition of β-HgS(s) growth and aggregation by DOM. Experiments examining the role of DOM across a wide sulfide gradient revealed that DOM only enhances Hg methylation under fairly low sulfide conditions (≲30 μM), conditions that favor HgS nanoparticle/cluster formation relative to dissolved HgS species.

Bacterial production and their role in the removal of dissolved organic matter from tributaries of drinking water reservoirs.

PubMed

Kamjunke, Norbert; Oosterwoud, Marieke R; Herzsprung, Peter; Tittel, Jörg

2016-04-01

Enhanced concentrations of dissolved organic matter (DOM) in freshwaters are an increasing problem in drinking water reservoirs. In this study we investigated bacterial DOM degradation rates in the tributaries of the reservoirs and tested the hypotheses that (1) DOM degradation is high enough to decrease DOM loads to reservoirs considerably, (2) DOM degradation is affected by stream hydrology, and (3) phosphorus addition may stimulate bacterial DOM degradation. Bacterial biomass production, which was used as a measure of DOM degradation, was highest in summer, and was usually lower at upstream than at downstream sites. An important proportion of bacterial production was realized in epilithic biofilms. Production of planktonic and biofilm bacteria was related to water temperature. Planktonic production weakly correlated to DOM quality and to total phosphorus concentration. Addition of soluble reactive phosphorus did not stimulate bacterial DOM degradation. Overall, DOM was considerably degraded in summer at low discharge levels, whereas degradation was negligible during flood events (when DOM load in reservoirs was high). The ratio of DOM degradation to total DOM release was negatively related to discharge. On annual average, only 0.6-12% of total DOM released by the catchments was degraded within the tributaries. Copyright © 2016 Elsevier B.V. All rights reserved.

EOS ODL Metadata On-line Viewer

NASA Astrophysics Data System (ADS)

Yang, J.; Rabi, M.; Bane, B.; Ullman, R.

2002-12-01

We have recently developed and deployed an EOS ODL metadata on-line viewer. The EOS ODL metadata viewer is a web server that takes: 1) an EOS metadata file in Object Description Language (ODL), 2) parameters, such as which metadata to view and what style of display to use, and returns an HTML or XML document displaying the requested metadata in the requested style. This tool is developed to address widespread complaints by science community that the EOS Data and Information System (EOSDIS) metadata files in ODL are difficult to read by allowing users to upload and view an ODL metadata file in different styles using a web browser. Users have the selection to view all the metadata or part of the metadata, such as Collection metadata, Granule metadata, or Unsupported Metadata. Choices of display styles include 1) Web: a mouseable display with tabs and turn-down menus, 2) Outline: Formatted and colored text, suitable for printing, 3) Generic: Simple indented text, a direct representation of the underlying ODL metadata, and 4) None: No stylesheet is applied and the XML generated by the converter is returned directly. Not all display styles are implemented for all the metadata choices. For example, Web style is only implemented for Collection and Granule metadata groups with known attribute fields, but not for Unsupported, Other, and All metadata. The overall strategy of the ODL viewer is to transform an ODL metadata file to a viewable HTML in two steps. The first step is to convert the ODL metadata file to an XML using a Java-based parser/translator called ODL2XML. The second step is to transform the XML to an HTML using stylesheets. Both operations are done on the server side. This allows a lot of flexibility in the final result, and is very portable cross-platform. Perl CGI behind the Apache web server is used to run the Java ODL2XML, and then run the results through an XSLT processor. The EOS ODL viewer can be accessed from either a PC or a Mac using Internet Explorer 5.0+ or Netscape 4.7+.

Influence of dissolved organic matter on sorption and desorption of MCPA in ferralsol.

PubMed

Wu, Dongming; Yun, Yonghuan; Jiang, Lei; Wu, Chunyuan

2018-03-01

MCPA (4-chloro-2-methylphenoxyacetic acid) is an acidic herbicide, widely used in paddy fields. The presence of dissolved organic matter (DOM) modifies the sorption-desorption of herbicides in soils. In this study, effects of DOM on sorption- desorption of MCPA were tested using three typical ferralsol soil types from China: rhodic ferralsol, haplic ferralsol and paddy soil. DOM preparations were extracted from the paddy soil (DOM P ), from a compost mixture of cassava stems with chicken manure (DOM C ), and from rice straw (DOM R ). Sorption-desorption of MCPA in the tested soil types was shown to follow pseudo first-order kinetics, and the calculated isotherm data fitted well with a Freundlich equilibrium model in the range of the studied concentrations. MCPA was weakly sorbed by the soils, producing low Freundlich coefficient values (K f ) (0.854 to 4.237). The presence of DOM reduced the K f whereby DOM C had the strongest and DOM R the weakest effect. Presence of DOM also promoted MCPA desorption from the soils, again with DOM C having the strongest effect and DOM R the weakest. DOM coating changed the soil particle surface, as demonstrated by electron microscopy, and DOM also directly interacted with MCPA, as shown by Fourier-transform infrared spectroscopy. The experimental data were interpreted to suggest a competing sorption of DOM to ferralsol and an increased solubility of MCPA in the presence of DOM. The results indicate that the environmental risk of MCPA leaching to groundwater and surface flow is increased by presence of DOM, for instance as a result of organic fertilizer use. Copyright © 2017. Published by Elsevier B.V.

Relating the Chemical Composition of Dissolved Organic Matter Draining Permafrost Soils to its Photochemical Degradation in Arctic Surface Waters.

NASA Astrophysics Data System (ADS)

Ward, C.; Cory, R. M.

2015-12-01

Thawing permafrost soils are expected to shift the chemical composition of DOM exported to and degraded in arctic surface waters. While DOM photo-degradation is an important component of the freshwater C cycle in the Arctic, the molecular controls on DOM photo-degradation remain poorly understood, making it difficult to predict how shifting chemical composition may alter DOM photo-degradation in arctic surface waters. To address this knowledge gap, we quantified the susceptibility of DOM draining the shallow organic mat and the deeper permafrost layer to complete photo-oxidation to CO₂ and partial photo-oxidation to compounds that remain in the DOM pool, and investigated changes in DOM chemical composition following sunlight exposure. DOM leached from the organic mat contained higher molecular weight, more oxidized and unsaturated aromatic species compared to permafrost DOM. Despite significant differences in initial chemical composition, permafrost and organic mat DOM had similar susceptibilities to complete photo-oxidation to CO₂. Concurrent losses of carboxyl moieties and shifts in chemical composition during photo-degradation indicated that carboxyl-rich tannin-like compounds in both DOM sources were likely photo-decarboxylated to CO₂. Permafrost DOM had a higher susceptibility to partial photo-oxidation compared to organic mat DOM, potentially due to a lower abundance of phenolic compounds that act as "antioxidants" and slow the oxidation of DOM. These results demonstrated how chemical composition controls the photo-degradation of DOM in arctic surface waters, and that DOM photo-degradation will likely remain an important component of the freshwater C budget in the Arctic with increased export of permafrost DOM to surface waters.

The Mystro system: A comprehensive translator toolkit

NASA Technical Reports Server (NTRS)

Collins, W. R.; Noonan, R. E.

1985-01-01

Mystro is a system that facilities the construction of compilers, assemblers, code generators, query interpretors, and similar programs. It provides features to encourage the use of iterative enhancement. Mystro was developed in response to the needs of NASA Langley Research Center (LaRC) and enjoys a number of advantages over similar systems. There are other programs available that can be used in building translators. These typically build parser tables, usually supply the source of a parser and parts of a lexical analyzer, but provide little or no aid for code generation. In general, only the front end of the compiler is addressed. Mystro, on the other hand, emphasizes tools for both ends of a compiler.

Building pathway graphs from BioPAX data in R.

PubMed

Benis, Nirupama; Schokker, Dirkjan; Kramer, Frank; Smits, Mari A; Suarez-Diez, Maria

2016-01-01

Biological pathways are increasingly available in the BioPAX format which uses an RDF model for data storage. One can retrieve the information in this data model in the scripting language R using the package rBiopaxParser , which converts the BioPAX format to one readable in R. It also has a function to build a regulatory network from the pathway information. Here we describe an extension of this function. The new function allows the user to build graphs of entire pathways, including regulated as well as non-regulated elements, and therefore provides a maximum of information. This function is available as part of the rBiopaxParser distribution from Bioconductor.

Parsley: a Command-Line Parser for Astronomical Applications

NASA Astrophysics Data System (ADS)

Deich, William

Parsley is a sophisticated keyword + value parser, packaged as a library of routines that offers an easy method for providing command-line arguments to programs. It makes it easy for the user to enter values, and it makes it easy for the programmer to collect and validate the user's entries. Parsley is tuned for astronomical applications: for example, dates entered in Julian, Modified Julian, calendar, or several other formats are all recognized without special effort by the user or by the programmer; angles can be entered using decimal degrees or dd:mm:ss; time-like intervals as decimal hours, hh:mm:ss, or a variety of other units. Vectors of data are accepted as readily as scalars.

Solving LR Conflicts Through Context Aware Scanning

NASA Astrophysics Data System (ADS)

Leon, C. Rodriguez; Forte, L. Garcia

2011-09-01

This paper presents a new algorithm to compute the exact list of tokens expected by any LR syntax analyzer at any point of the scanning process. The lexer can, at any time, compute the exact list of valid tokens to return only tokens in this set. In the case than more than one matching token is in the valid set, the lexer can resort to a nested LR parser to disambiguate. Allowing nested LR parsing requires some slight modifications when building the LR parsing tables. We also show how LR parsers can parse conflictive and inherently ambiguous languages using a combination of nested parsing and context aware scanning. These expanded lexical analyzers can be generated from high level specifications.

Differences in dissolved organic matter between reclaimed water source and drinking water source.

PubMed

Hu, Hong-Ying; Du, Ye; Wu, Qian-Yuan; Zhao, Xin; Tang, Xin; Chen, Zhuo

2016-05-01

Dissolved organic matter (DOM) significantly affects the quality of reclaimed water and drinking water. Reclaimed water potable reuse is an effective way to augment drinking water source and de facto reuse exists worldwide. Hence, when reclaimed water source (namely secondary effluent) is blended with drinking water source, understanding the difference in DOM between drinking water source (dDOM) and reclaimed water source (rDOM) is essential. In this study, composition, transformation, and potential risk of dDOM from drinking water source and rDOM from secondary effluent were compared. Generally, the DOC concentration of rDOM and dissolved organic nitrogen (DON) content in reclaimed water source were higher but rDOM exhibited a lower aromaticity. Besides, rDOM comprises a higher proportion of hydrophilic fractions and more low-molecular weight compounds, which are difficult to be removed during coagulation. Although dDOM exhibited higher specific disinfection byproducts formation potential (SDBPFP), rDOM formed more total disinfection byproducts (DBPs) during chlorination including halomethanes (THMs) and haloacetic acids (HAAs) due to high DOC concentration. Likewise, in consideration of DOC basis, rDOM contained more absolute assimilable organic carbon (AOC) despite showing a lower specific AOC (normalized AOC per unit of DOC). Besides, rDOM exhibited higher biotoxicity including genotoxicity and endocrine disruption. Therefore, rDOM presents a greater potential risk than dDOM does. Reclaimed water source needs to be treated carefully when it is blended with drinking water source. Copyright © 2015. Published by Elsevier B.V.

Uncoupling of Bacterial and Terrigenous Dissolved Organic Matter Dynamics in Decomposition Experiments

PubMed Central

Herlemann, Daniel P. R.; Manecki, Marcus; Meeske, Christian; Pollehne, Falk; Labrenz, Matthias; Schulz-Bull, Detlef; Dittmar, Thorsten; Jürgens, Klaus

2014-01-01

The biodegradability of terrigenous dissolved organic matter (tDOM) exported to the sea has a major impact on the global carbon cycle, but our understanding of tDOM bioavailability is fragmentary. In this study, the effects of preparative tDOM isolation on microbial decomposition were investigated in incubation experiments consisting of mesocosms containing mesohaline water from the Baltic Sea. Dissolved organic carbon (DOC) consumption, molecular DOM composition, bacterial activities, and shifts in bacterial community structure were compared between mesocosms supplemented with riverine tDOM, either as filtered, particle-free river water or as a concentrate obtained by lyophilization/tangential ultrafiltration, and those containing only Baltic Sea water or river water. As shown using ultra-high-resolution mass spectrometry (15 Tesla Fourier-transform ion cyclotron resonance mass spectrometry, FT-ICR-MS) covering approximately 4600 different DOM compounds, the three DOM preparation protocols resulted in distinct patterns of molecular DOM composition. However, despite DOC losses of 4–16% and considerable bacterial production, there was no significant change in DOM composition during the 28-day experiment. Moreover, tDOM addition affected neither DOC degradation nor bacterial dynamics significantly, regardless of the tDOM preparation. This result suggested that the introduced tDOM was largely not bioavailable, at least on the temporal scale of our experiment, and that the observed bacterial activity and DOC decomposition mainly reflected the degradation of unknown, labile, colloidal and low-molecular weight DOM, both of which escape the analytical window of FT-ICR-MS. In contrast to the different tDOM preparations, the initial bacterial inoculum and batch culture conditions determined bacterial community succession and superseded the effects of tDOM addition. The uncoupling of tDOM and bacterial dynamics suggests that mesohaline bacterial communities cannot efficiently utilize tDOM and that in subarctic estuaries other factors are responsible for the removal of imported tDOM. PMID:24718626

Adsorptive fractionation of dissolved organic matter (DOM) by carbon nanotubes.

PubMed

Engel, Maya; Chefetz, Benny

2015-02-01

Dissolved organic matter (DOM) and carbon nanotubes are introduced into aquatic environments. Thus, it is important to elucidate whether their interaction affects DOM amount and composition. In this study, the composition of DOM, before and after interactions with single-walled carbon nanotubes (SWCNTs), was measured and the adsorption affinity of the individual structural fractions of DOM to SWCNTs was investigated. Adsorption of DOM to SWCNTs was dominated by the hydrophobic acid fraction, resulting in relative enhancement of the hydrophilic character of non-adsorbed DOM. The preferential adsorption of the HoA fraction was concentration-dependent, increasing with increasing concentration. Adsorption affinities of bulk DOM calculated as the normalized sum of affinities of the individual structural fractions were similar to the measured affinities, suggesting that the structural fractions of DOM act as independent adsorbates. The altered DOM composition may affect the nature and reactivity of DOM in aquatic environments polluted with carbon nanotubes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Removal of dissolved organic matter by anion exchange: Effect of dissolved organic matter properties

USGS Publications Warehouse

Boyer, T.H.; Singer, P.C.; Aiken, G.R.

2008-01-01

Ten isolates of aquatic dissolved organic matter (DOM) were evaluated to determine the effect that chemical properties of the DOM, such as charge density, aromaticity, and molecular weight, have on DOM removal by anion exchange. The DOM isolates were characterized asterrestrial, microbial, or intermediate humic substances or transphilic acids. All anion exchange experiments were conducted using a magnetic ion exchange (MIEX) resin. The charge density of the DOM isolates, determined by direct potentiometric titration, was fundamental to quantifying the stoichiometry of the anion exchange mechanism. The results clearly show that all DOM isolates were removed by anion exchange; however, differences among the DOM isolates did influence their removal by MIEX resin. In particular, MIEX resin had the greatest affinity for DOM with high charge density and the least affinity for DOM with low charge density and low aromaticity. This work illustrates that the chemical characteristics of DOM and solution conditions must be considered when evaluating anion exchange treatment for the removal of DOM. ?? 2008 American Chemical Society.

Hydrology controls dissolved organic matter export and composition in an Alpine stream and its hyporheic zone.

PubMed

Fasching, Christina; Ulseth, Amber J; Schelker, Jakob; Steniczka, Gertraud; Battin, Tom J

2016-03-01

Streams and rivers transport dissolved organic matter (DOM) from the terrestrial environment to downstream ecosystems. In light of climate and global change it is crucial to understand the temporal dynamics of DOM concentration and composition, and its export fluxes from headwaters to larger downstream ecosystems. We monitored DOM concentration and composition based on a diurnal sampling design for 3 years in an Alpine headwater stream. We found hydrologic variability to control DOM composition and the coupling of DOM dynamics in the streamwater and the hyporheic zone. High-flow events increased DOM inputs from terrestrial sources (as indicated by the contributions of humic- and fulvic-like fluorescence), while summer baseflow enhanced the autochthonous imprint of DOM. Diurnal and seasonal patterns of DOM composition were likely induced by biological processes linked to temperature and photosynthetic active radiation (PAR). Floods frequently interrupted diurnal and seasonal patterns of DOM, which led to a decoupling of streamwater and hyporheic water DOM composition and delivery of aromatic and humic-like DOM to the streamwater. Accordingly, DOM export fluxes were largely of terrigenous origin as indicated by optical properties. Our study highlights the relevance of hydrologic and seasonal dynamics for the origin, composition and fluxes of DOM in an Alpine headwater stream.

Improved Identification of Noun Phrases in Clinical Radiology Reports Using a High-Performance Statistical Natural Language Parser Augmented with the UMLS Specialist Lexicon

PubMed Central

Huang, Yang; Lowe, Henry J.; Klein, Dan; Cucina, Russell J.

2005-01-01

Objective: The aim of this study was to develop and evaluate a method of extracting noun phrases with full phrase structures from a set of clinical radiology reports using natural language processing (NLP) and to investigate the effects of using the UMLS® Specialist Lexicon to improve noun phrase identification within clinical radiology documents. Design: The noun phrase identification (NPI) module is composed of a sentence boundary detector, a statistical natural language parser trained on a nonmedical domain, and a noun phrase (NP) tagger. The NPI module processed a set of 100 XML-represented clinical radiology reports in Health Level 7 (HL7)® Clinical Document Architecture (CDA)–compatible format. Computed output was compared with manual markups made by four physicians and one author for maximal (longest) NP and those made by one author for base (simple) NP, respectively. An extended lexicon of biomedical terms was created from the UMLS Specialist Lexicon and used to improve NPI performance. Results: The test set was 50 randomly selected reports. The sentence boundary detector achieved 99.0% precision and 98.6% recall. The overall maximal NPI precision and recall were 78.9% and 81.5% before using the UMLS Specialist Lexicon and 82.1% and 84.6% after. The overall base NPI precision and recall were 88.2% and 86.8% before using the UMLS Specialist Lexicon and 93.1% and 92.6% after, reducing false-positives by 31.1% and false-negatives by 34.3%. Conclusion: The sentence boundary detector performs excellently. After the adaptation using the UMLS Specialist Lexicon, the statistical parser's NPI performance on radiology reports increased to levels comparable to the parser's native performance in its newswire training domain and to that reported by other researchers in the general nonmedical domain. PMID:15684131

Dissolved organic matter and estrogen interactions regulate estrogen removal in the aqueous environment: A review.

PubMed

Ma, Li; Yates, Scott R

2018-06-03

This review summarizes the characterization and quantification of interactions between dissolved organic matter (DOM) and estrogens as well as the effects of DOM on aquatic estrogen removal. DOM interacts with estrogens via binding or sorption mechanisms like π-π interaction and hydrogen bonding. The binding affinity is evaluated in terms of organic-carbon-normalized sorption coefficient (Log K OC ) which varies with types and composition of DOM. DOM has been suggested to be a more efficient sorbent compared with other matrices, such as suspended particulate matter, sediment and soil; likely associated with its large surface area and concentrated carbon content. As a photosensitizer, DOM enhanced estrogen photodegradation when the concentration of DOM was below a threshold value, and when above, the acceleration effect was not observed. DOM played a dual role in affecting biodegradation of estrogens depending on the recalcitrance of the DOM and the nutrition status of the degraders. DOM also acted as an electron shuttle (redox mediator) mediating the degradation of estrogens. DOM hindered enzyme-catalyzed removal of estrogens while enhanced their transformation during the simultaneous photo-enzymatic process. Membrane rejection of estrogens was pronounced for hydrophobic DOM with high aromaticity and phenolic moiety content. Elimination of estrogens via photolysis, biodegradation, enzymolysis and membrane rejection in the presence of DOM is initiated by sorption, accentuating the role of DOM as a mediator in regulating aquatic estrogen removal. Published by Elsevier B.V.

Complexation of Arsenite with Humic Acid in the Presence of Ferric Iron

PubMed Central

Liu, Guangliang; Fernandez, Aymara; Cai, Yong

2011-01-01

In the presence of iron (Fe), dissolved organic matter (DOM) may bind considerable amounts of arsenic (As), through formation of Fe-bridged As-Fe-DOM complexes and surface complexation of As on DOM-stabilized Fe-colloids (collectively referred to as As-Fe-DOM complexation). However, direct (e.g., chromatographic and spectroscopic) evidence and fundamental kinetic and stability constants have been rarely reported for this As-Fe-DOM complexation. Using a size exclusion chromatography (SEC)-UV-inductively coupled plasma mass spectrometry (ICP-MS) technique, arsenite (AsIII)-Fe-DOM complexation was investigated after adding AsIII into the priorly prepared Fe-DOM. A series of evidence, including coelution of As, Fe, and DOM from the SEC column and coretention of As, Fe, and DOM by 3 kDa MWCO centrifugal filtration membrane, demonstrated the occurrence of AsIII-Fe-DOM complexation. The kinetic data of AsIII-Fe-DOM complexation were well described by a pseudo-first order rate equation (R2 = 0.95), with the rate constant (k′) being 0.17±0.04 1/h. Stability of AsIII-Fe-DOM complexation was characterized by apparent stability constant (Ks) derived from two-site ligand binding model, with log Ks ranging from 4.4±0.2 to 5.6±0.4. Considering the kinetics (within hours) and stability (similar to typical metal-humates) of AsIII-Fe-DOM complexation, this complexation needs to be included when evaluating As mobility in Fe and DOM rich environments. PMID:21322632

Contrasting Effects of Dissolved Organic Matter on Mercury Methylation by Geobacter sulfurreducens PCA and Desulfovibrio desulfuricans ND132.

PubMed

Zhao, Linduo; Chen, Hongmei; Lu, Xia; Lin, Hui; Christensen, Geoff A; Pierce, Eric M; Gu, Baohua

2017-09-19

Natural dissolved organic matter (DOM) affects mercury (Hg) redox reactions and anaerobic microbial methylation in the environment. Several studies have shown that DOM can enhance Hg methylation, especially under sulfidic conditions, whereas others show that DOM inhibits Hg methylation due to strong Hg-DOM complexation. In this study, we investigated and compared the effects of DOM on Hg methylation by an iron-reducing bacterium Geobacter sulfurreducens PCA and a sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 under nonsulfidic conditions. The methylation experiment was performed with washed cells either in the absence or presence of DOM or glutathione, both of which form strong complexes with Hg via thiol-functional groups. DOM was found to greatly inhibit Hg methylation by G. Sulfurreducens PCA but enhance Hg methylation by D. desulfuricans ND132 cells with increasing DOM concentration. These strain-dependent opposing effects of DOM were also observed with glutathione, suggesting that thiols in DOM likely played an essential role in affecting microbial Hg uptake and methylation. Additionally, DOM and glutathione greatly decreased Hg sorption by G. sulfurreducens PCA but showed little effect on D. desulfuricans ND132 cells, demonstrating that ND132 has a higher affinity to sorb or take up Hg than the PCA strain. These observations indicate that DOM effects on Hg methylation are bacterial strain specific, depend on the DOM:Hg ratio or site-specific conditions, and may thus offer new insights into the role of DOM in methylmercury production in the environment.

Dissolved Organic Matter in Groundwater: a Shadow of its Former Self

NASA Astrophysics Data System (ADS)

Chapelle, F.

2017-12-01

The occurrence and dynamics of dissolved organic matter (DOM) are fundamentally different between ground- and surface water systems. The most obvious difference is that primary production, an important source of DOM to many surface waters, it is wholly absent from groundwater systems. Because of that, the composition and bioavailability of DOM is functionally linked to its residence time within the subsurface. While sorption/desorption processes segregate chemical fractions of DOM in both ground- and surface water systems, their effects are magnified by the much higher sediment/water mass ratio characteristic of groundwater systems. These differences, which often act in concert with each other, explain many observed characteristics of DOM in groundwater systems including (1) the low and nearly uniform DOM concentrations (0.5-1.0 mg/L) characteristic of many aquifers, (2) the progressive loss of carbohydrate and amino acid DOM and the enrichment of aromatic DOM, with increasing aquifer residence time (3) the progressive loss of VIS/UV absorption capacity (color) of DOM with increasing aquifer residence time, (4) the negative correlation between dissolved oxygen concentrations and DOM bioavailability, and (5) the positive correlation between DOM bioavailability and the final products of anoxic redox processes. Thus, while the principal sources of DOM to many groundwater systems are surface-derived, the dynamics unique to subsurface environments tend to render that DOM a shadow of its former self.

What Do We Know about DOM Chemical Composition Based on Its Optical Properties?

NASA Astrophysics Data System (ADS)

Aiken, G.

2016-02-01

Dissolved organic matter (DOM) optical measurements (UV-Vis light absorbance and fluorescence) provide useful information related to DOM composition and reactivity, and can serve as proxies for DOM concentration and the concentrations of some metals, such as mercury. While these measurements are useful for a range of objectives, they only measure aromatic molecules that absorb UV-Vis light and a smaller subset of these molecules that fluoresce. They provide no information about the substantial fraction of DOM that is non-chromophoric. Based on chromatographic fractionation on XAD resins, DOM optical properties measured on whole water samples strongly correlate with both the concentration and composition of the hydrophobic acid (HPOA) fraction of the DOM. In this presentation the results of DOM optical measurements, DOM fractionation analyses, and 13C-nuclear magnetic resonance (NMR) and ultrahigh-resolution mass spectrometry (FTICR_MS) of HPOA fractions obtained from a wide range a natural waters will be presented to examine the relationships between DOM optical properties and DOM chemical composition. The HPOA fractions within and between rivers exhibit a wide range of optical behaviors reflective of sources and transformations compared to other DOM fractions. While, 13C-NMR and FTICR-MS analyses generally show greater relative concentrations of aromatic molecules for those samples with strong optical signals, they also indicate that the HPOA fractions are mostly composed of a large number of non-chromophoric molecules, such as carbohydrates carboxyl-rich alicyclic molecules (CRAM), and other aliphatic molecules, all of which have implications regarding DOM reactivity, biolability, sources, and age. The utility and short-comings of employing optical data for assessing sources and transformations of DOM in natural waters will be examined using case studies involving organic matter in the Yukon River Basin and riverine export of DOM to the Gulf of Maine.

Removal of triazine-based pollutants from water by carbon nanotubes: Impact of dissolved organic matter (DOM) and solution chemistry.

PubMed

Engel, Maya; Chefetz, Benny

2016-12-01

Adsorption of organic pollutants by carbon nanotubes (CNTs) in the environment or removal of pollutants during water purification require deep understanding of the impacts of the presence of dissolved organic matter (DOM). DOM is an integral part of environmental systems and plays a key role affecting the behavior of organic pollutants. In this study, the effects of solution chemistry (pH and ionic strength) and the presence of DOM on the removal of atrazine and lamotrigine by single-walled CNTs (SWCNTs) was investigated. The solubility of atrazine slightly decreased (∼5%) in the presence of DOM, whereas that of lamotrigine was significantly enhanced (by up to ∼70%). Simultaneous introduction of DOM and pollutant resulted in suppression of removal of both atrazine and lamotrigine, which was attributed to DOM-pollutant competition or blockage of adsorption sites by DOM. However the decrease in removal of lamotrigine was also a result of its complexation with DOM. Pre-introduction of DOM significantly reduced pollutant adsorption by the SWCNTs, whereas introduction of DOM after the pollutant resulted in the release of adsorbed atrazine and lamotrigine from the SWCNTs. These data imply that DOM exhibits higher affinity for the adsorption sites than the triazine-based pollutants. In the absence of DOM atrazine was a more effective competitor than lamotrigine for adsorption sites in SWCNTs. However, competition between pollutants in the presence of DOM revealed lamotrigine as the better competitor. Our findings help unravel the complex DOM-organic pollutant-CNT system and will aid in CNT-implementation in water-purification technologies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Lability of High Molecular Weight Dissolved Organic Matter Polysaccharides Increases with Mild Acid or Base Treatment.

NASA Astrophysics Data System (ADS)

Pedler Sherwood, B.; Sosa, O.; Nelson, C. E.; Repeta, D.; DeLong, E.

2016-02-01

Approximately 662 Pg of dissolved organic carbon (DOC) has accumulated in the global ocean, yet the biological and chemical constraints on DOC turnover remain poorly understood. High molecular weight dissolved organic matter (HMWDOM) is largely comprised of semi-labile polysaccharides. These polysaccharides resist degradation even in the presence of nutrient amendments, suggesting unknown factors of polysaccharide composition affect microbial degradation. In a series of microcosm incubations conducted at station ALOHA in the North Pacific Subtropical Gyre, we tested the affect of mild base (KOH-DOM) and acid (HCl-DOM) treatments on polysaccharide lability. KOH-DOM, HCl-DOM, and untreated HMWDOM was added to seawater from the deep chlorophyll maximum and 200m. Microcosms amended with KOH-DOM and HCl-DOM yielded higher bacterial abundance and greater carbon drawdown relative to untreated HMWDOM and unamended controls. Microcosms amended with KOH-DOM and HCl-DOM also showed significant production of fluorescent DOM (fDOM), whereas untreated HMWDOM and unamended controls showed a net decrease in fDOM as measured by parallel factor analysis of DOM excitation-emission spectra. Metagenomic analyses revealed that microcosms amended with untreated HMWDOM and controls became dominated by Alteromonas genera ( 60% total sequence reads). In contrast, KOH-DOM and HCl-DOM amended microcosms yielded greater bacterial diversity; Alteromonas genera comprised 25% of sequence reads, with differences primarily accounted for by proportional increases in vibrio, roseobacter, rugeria and marinomonas clades. Transcriptomic analyses identified differential gene expression during growth on each DOM fraction. This study provides new insight into specific chemical moieties that may limit the bacterial degradation rate of semi-labile HMWDOM in the ocean.

A statistic-thermodynamic model for the DOM degradation in the estuary

NASA Astrophysics Data System (ADS)

Zheng, Quanan; Chen, Qin; Zhao, Haihong; Shi, Jiuxin; Cao, Yong; Wang, Dan

2008-03-01

This study aims to clarify the role of dissolved salts playing in the degradation process of terrestrial dissolved organic matter (DOM) at a scale of molecular movement. The molecular thermal movement is perpetual motion. In a multi-molecular system, this random motion also causes collision between the molecules. Seawater is a multi-molecular system consisting from water, salt, and terrestrial DOM molecules. This study attributes the DOM degradation in the estuary to the inelastic collision of DOM molecule with charged salt ions. From statistic-thermodynamic theories of molecular collision, the DOM degradation model and the DOM distribution model are derived. The models are validated by the field observations and satellite data. Thus, we conclude that the inelastic collision between the terrestrial DOM molecules and dissolved salt ions in seawater is a decisive dynamic mechanism for rapid loss of terrestrial DOM.

Tracking the evolution of stream DOM source during storm events using end member mixing analysis based on DOM quality

NASA Astrophysics Data System (ADS)

Yang, Liyang; Chang, Soon-Woong; Shin, Hyun-Sang; Hur, Jin

2015-04-01

The source of river dissolved organic matter (DOM) during storm events has not been well constrained, which is critical in determining the quality and reactivity of DOM. This study assessed temporal changes in the contributions of four end members (weeds, leaf litter, soil, and groundwater), which exist in a small forested watershed (the Ehwa Brook, South Korea), to the stream DOM during two storm events, using end member mixing analysis (EMMA) based on spectroscopic properties of DOM. The instantaneous export fluxes of dissolved organic carbon (DOC), chromophoric DOM (CDOM), and fluorescent components were all enhanced during peak flows. The DOC concentration increased with the flow rate, while CDOM and humic-like fluorescent components were diluted around the peak flows. Leaf litter was dominant for the DOM source in event 2 with a higher rainfall, although there were temporal variations in the contributions of the four end members to the stream DOM for both events. The contribution of leaf litter peaked while that of deeper soils decreased to minima at peak flows. Our results demonstrated that EMMA based on DOM properties could be used to trace the DOM source, which is of fundamental importance for understanding the factors responsible for river DOM dynamics during storm events.

Contrasting Effects of Dissolved Organic Matter on Mercury Methylation by G. sulfurreducens PCA and D. desulfuricans ND132

DOE PAGES

Zhao, Linduo; Chen, Hongmei; Lu, Xia; ...

2017-08-14

Natural dissolved organic matter (DOM) affects mercury (Hg) redox reactions and anaerobic microbial Hg methylation in the environment. Several studies have shown that DOM can enhance Hg methylation, especially under sulfidic conditions, whereas others show that DOM inhibits Hg methylation due to strong Hg-DOM complexation. Here, we investigated and compared the effects of DOM on Hg methylation by an iron-reducing bacterium Geobacter sulfurreducens PCA and a sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 under non-sulfidic conditions. The methylation experiment was performed with washed cells either in the absence or presence of DOM or glutathione, both of which form strong complexes with Hgmore » via thiol-functional groups. DOM was found to greatly inhibit Hg methylation by G. Sulfurreducens PCA but enhance Hg methylation by D. desulfuricans ND132 cells with increasing DOM concentration. Furthermore, these strain-dependent opposing effects of DOM were also observed with glutathione, suggesting that thiols in DOM likely played an essential role in affecting cell Hg uptake and methylation. Additionally, DOM and glutathione decreased Hg sorption by G. sulfurreducens PCA, but not by D. desulfuricans ND132 cells, demonstrating that ND132 has a higher affinity to sorb or take up Hg than the PCA strain. Finally, these observations indicate that DOM effects on Hg methylation are bacterial strain specific, depend on the DOM:Hg ratio or site-specific conditions, and may thus offer new insights into the role of DOM in methylmercury production in the environment.« less

Pre-treatments, characteristics, and biogeochemical dynamics of dissolved organic matter in sediments: A review.

PubMed

Chen, Meilian; Hur, Jin

2015-08-01

Dissolved organic matter (DOM) in sediments, termed here sediment DOM, plays a variety of important roles in global biogeochemical cycling of carbon and nutrients as well as in the fate and transport of xenobiotics. Here we reviewed sediment DOM, including pore waters and water extractable organic matter from inland and coastal sediments, based on recent literature (from 1996 to 2014). Sampling, pre-treatment, and characterization methods for sediment DOM were summarized. The characteristics of sediment DOM have been compared along an inland to coastal ecosystems gradient and also with the overlying DOM in water column to distinguish the unique nature of it. Dissolved organic carbon (DOC) from inland sediment DOM was generally higher than coastal areas, while no notable differences were found for their aromaticity and apparent molecular weight. Fluorescence index (FI) revealed that mixed sources are dominant for inland sediment DOM, but marine end-member prevails for coastal sediment DOM. Many reports showed that sediments operate as a net source of DOC and chromophoric DOM (CDOM) to the water column. Sediment DOM has shown more enrichment of nitrogen- and sulfur-containing compounds in the elemental signature than the overlying DOM. Fluorescent fingerprint investigated by excitation-emission matrix coupled with parallel factor analysis (EEM-PARAFAC) further demonstrated the characteristics of sediment DOM lacking in the photo-oxidized and the intermediate components, which are typically present in the overlying surface water. In addition, the biogeochemical changes in sediment DOM and the subsequent environmental implications were discussed with the focus on the binding and the complexation properties with pollutants. Copyright © 2015 Elsevier Ltd. All rights reserved.

Enhanced Production of Bioethanol by Fermentation of Autohydrolyzed and C4mimOAc-Treated Sugarcane Bagasse Employing Various Yeast Strains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hashmi, Muzna; Shah, Aamer; Hameed, Abdul

Natural dissolved organic matter (DOM) affects mercury (Hg) redox reactions and anaerobic microbial Hg methylation in the environment. Several studies have shown that DOM can enhance Hg methylation, especially under sulfidic conditions, whereas others show that DOM inhibits Hg methylation due to strong Hg-DOM complexation. Here, we investigated and compared the effects of DOM on Hg methylation by an iron-reducing bacterium Geobacter sulfurreducens PCA and a sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 under non-sulfidic conditions. The methylation experiment was performed with washed cells either in the absence or presence of DOM or glutathione, both of which form strong complexes with Hgmore » via thiol-functional groups. DOM was found to greatly inhibit Hg methylation by G. Sulfurreducens PCA but enhance Hg methylation by D. desulfuricans ND132 cells with increasing DOM concentration. These strain-dependent opposing effects of DOM were also observed with glutathione, suggesting that thiols in DOM likely played an essential role in affecting cell Hg uptake and methylation. Additionally, DOM and glutathione decreased Hg sorption by G. sulfurreducens PCA, but not by D. desulfuricans ND132 cells, demonstrating that ND132 has a higher affinity to sorb or take up Hg than the PCA strain. Our observations indicate that DOM effects on Hg methylation are bacterial strain specific, depend on the DOM:Hg ratio or site-specific conditions, and may thus offer new insights into the role of DOM in methylmercury production in the environment.« less

Impacts of global changes on the biogeochemistry and environmental effects of dissolved organic matter at the land-ocean interface: a review.

PubMed

Zhuang, Wan-E; Yang, Liyang

2018-02-01

Dissolved organic matter (DOM) is an important component in the biogeochemistry and ecosystem function of aquatic environments at the highly populated land-ocean interface. The mobilization and transformation of DOM at this critical interface are increasingly affected by a series of notable global changes such as the increasing storm events, intense human activities, and accelerating glacier loss. This review provides an overview of the changes in the quantity and quality of DOM under the influences of multiple global changes. The profound implications of changing DOM for aquatic ecosystem and human society are further discussed, and future research needs are suggested for filling current knowledge gaps. The fluvial export of DOM is strongly intensified during storm events, which is accompanied with notable changes in the chemical composition and reactivity of DOM. Land use not only changes the mobilization of natural DOM source pools within watersheds but also adds DOM of distinct chemical composition and reactivity from anthropogenic sources. Glacier loss brings highly biolabile DOM to downstream water bodies. The changing DOM leads to significant changes in heterotrophic activity, CO 2 out gassing, nutrient and pollutant biogeochemistry, and disinfection by-product formation. Further studies on the source, transformations, and downstream effects of storm DOM, temporal variations of DOM and its interactions with other pollutants in human-modified watersheds, photo-degradability of glacier DOM, and potential priming effects, are essential for better understanding the responses and feedbacks of DOM at the land-ocean interface under the impacts of global changes.

Enhanced Production of Bioethanol by Fermentation of Autohydrolyzed and C4mimOAc-Treated Sugarcane Bagasse Employing Various Yeast Strains

DOE PAGES

Hashmi, Muzna; Shah, Aamer; Hameed, Abdul; ...

2017-08-01

Natural dissolved organic matter (DOM) affects mercury (Hg) redox reactions and anaerobic microbial Hg methylation in the environment. Several studies have shown that DOM can enhance Hg methylation, especially under sulfidic conditions, whereas others show that DOM inhibits Hg methylation due to strong Hg-DOM complexation. Here, we investigated and compared the effects of DOM on Hg methylation by an iron-reducing bacterium Geobacter sulfurreducens PCA and a sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 under non-sulfidic conditions. The methylation experiment was performed with washed cells either in the absence or presence of DOM or glutathione, both of which form strong complexes with Hgmore » via thiol-functional groups. DOM was found to greatly inhibit Hg methylation by G. Sulfurreducens PCA but enhance Hg methylation by D. desulfuricans ND132 cells with increasing DOM concentration. These strain-dependent opposing effects of DOM were also observed with glutathione, suggesting that thiols in DOM likely played an essential role in affecting cell Hg uptake and methylation. Additionally, DOM and glutathione decreased Hg sorption by G. sulfurreducens PCA, but not by D. desulfuricans ND132 cells, demonstrating that ND132 has a higher affinity to sorb or take up Hg than the PCA strain. Our observations indicate that DOM effects on Hg methylation are bacterial strain specific, depend on the DOM:Hg ratio or site-specific conditions, and may thus offer new insights into the role of DOM in methylmercury production in the environment.« less

Contrasting Effects of Dissolved Organic Matter on Mercury Methylation by G. sulfurreducens PCA and D. desulfuricans ND132

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Linduo; Chen, Hongmei; Lu, Xia

Natural dissolved organic matter (DOM) affects mercury (Hg) redox reactions and anaerobic microbial Hg methylation in the environment. Several studies have shown that DOM can enhance Hg methylation, especially under sulfidic conditions, whereas others show that DOM inhibits Hg methylation due to strong Hg-DOM complexation. Here, we investigated and compared the effects of DOM on Hg methylation by an iron-reducing bacterium Geobacter sulfurreducens PCA and a sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 under non-sulfidic conditions. The methylation experiment was performed with washed cells either in the absence or presence of DOM or glutathione, both of which form strong complexes with Hgmore » via thiol-functional groups. DOM was found to greatly inhibit Hg methylation by G. Sulfurreducens PCA but enhance Hg methylation by D. desulfuricans ND132 cells with increasing DOM concentration. Furthermore, these strain-dependent opposing effects of DOM were also observed with glutathione, suggesting that thiols in DOM likely played an essential role in affecting cell Hg uptake and methylation. Additionally, DOM and glutathione decreased Hg sorption by G. sulfurreducens PCA, but not by D. desulfuricans ND132 cells, demonstrating that ND132 has a higher affinity to sorb or take up Hg than the PCA strain. Finally, these observations indicate that DOM effects on Hg methylation are bacterial strain specific, depend on the DOM:Hg ratio or site-specific conditions, and may thus offer new insights into the role of DOM in methylmercury production in the environment.« less

Changes in dissolved organic matter quality in a peatland and forest headwater stream as a function of seasonality and hydrologic conditions

NASA Astrophysics Data System (ADS)

Broder, Tanja; Knorr, Klaus-Holger; Biester, Harald

2017-04-01

Peatlands and peaty riparian zones are major sources of dissolved organic matter (DOM), but are poorly understood in terms of export dynamics and controls thereof. Thereby quality of DOM affects function and behavior of DOM in aquatic ecosystems, but DOM quality can also help to track DOM sources and their export dynamics under specific hydrologic preconditions. The objective of this study was to elucidate controls on temporal variability in DOM concentration and quality in stream water draining a bog and a forested peaty riparian zone, particularly considering drought and storm flow events. DOM quality was monitored using spectrofluorometric indices for aromaticity (SUVA254), apparent molecular size (SR) and precursor organic material (FI), as well as PARAFAC modeling of excitation emission matrices (EEMs). Indices for DOM quality exhibited major changes due to different hydrologic conditions, but patterns were also dependent on season. Stream water at the forested site with mineral, peaty soils generally exhibited higher variability in DOM concentrations and quality compared to the outflow of an ombrotrophic bog, where DOM was less susceptible to changes in hydrologic conditions. During snowmelt and spring events, near-surface protein-like DOM pools were exported. A microbial DOM fraction originating from groundwater and deep peat layers was increasing during drought, while a strongly microbially altered DOM fraction was also exported by discharge events with dry preconditions at the forested site. This might be due to accelerated microbial activity in the peaty riparian zone of the forested site under these preconditions. Our study demonstrated that DOM export dynamics are not only a passive mixing of different hydrological sources, but monitoring studies have to consider that DOM quality depends on hydrologic preconditions and season. Moreover, the forested peaty riparian zone generated the most variability in headwater DOM quantity and quality, as could be tracked by the used spectrofluorometric indices.

Molecular Insights on Dissolved Organic Matter Transformation by Supraglacial Microbial Communities.

PubMed

Antony, Runa; Willoughby, Amanda S; Grannas, Amanda M; Catanzano, Victoria; Sleighter, Rachel L; Thamban, Meloth; Hatcher, Patrick G; Nair, Shanta

2017-04-18

Snow overlays the majority of Antarctica and is an important repository of dissolved organic matter (DOM). DOM transformations by supraglacial microbes are not well understood. We use ultrahigh resolution mass spectrometry to elucidate molecular changes in snowpack DOM by in situ microbial processes (up to 55 days) in a coastal Antarctic site. Both autochthonous and allochthonous DOM is highly bioavailable and is transformed by resident microbial communities through parallel processes of degradation and synthesis. DOM thought to be of a more refractory nature, such as dissolved black carbon and carboxylic-rich alicyclic molecules, was also rapidly and extensively reworked. Microbially reworked DOM exhibits an increase in the number and magnitude of N-, S-, and P-containing formulas, is less oxygenated, and more aromatic when compared to the initial DOM. Shifts in the heteroatom composition suggest that microbial processes may be important in the cycling of not only C, but other elements such as N, S, and P. Microbial reworking also produces photoreactive compounds, with potential implications for DOM photochemistry. Refined measurements of supraglacial DOM and their cycling by microbes is critical for improving our understanding of supraglacial DOM cycling and the biogeochemical and ecological impacts of DOM export to downstream environments.

[Absorption and fluorescence characteristics of dissolved organic matter (DOM) in rainwater and sources analysis in summer and winter season].

PubMed

Liang, Jian; Jiang, Tao; WeiI, Shi-Qiang; Lu, Song; Yan, Jin-Long; Wang, Qi-Lei; Gao, Jie

2015-03-01

This study aimed at evaluating the variability of the optical properties including UV-Vis and fluorescence characteristics of dissolved organic matter (DOM) from rainwater in summer and winter seasons. UV-Vis and fluorescence spectroscopy, together with Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model and fire events map, were conducted to characterize DOM and investigate its sources and contributions. The results showed that as compared with aquatic and soil DOM, rainwater DOM showed similar spectral characteristics, suggesting DOM in precipitation was also an important contributor to DOM pool in terrestrial and aquatic systems. The concentrations of DOC in rainwater were 0.88-12.80 mg x L(-1), and the CDOM concentrations were 3.17-21.11 mg x L(-1). Differences of DOM samples between summer and winter were significant (P < 0.05). In comparison to summer, DOM samples in winter had lower molecular weight and aromaticity, and also lower humification. Input of DOM in winter was predominantly derived from local and short-distance distances, while non-special scattering sources were identified as the main contributors in summer. Although absorption and fluorescence spectroscopy could be used to identify DOM composition and sources, there were obvious differences in spectra and sources analysis between rainwater DOM and the others from other sources. Thus, the classic differentiation method by "allochthonous (terrigenous) and autochthonous (authigenic)" is possibly too simple and arbitrary for characterization of DOM in rainwater.

Concurrent photolytic degradation of aqueous methylmercury and dissolved organic matter

USGS Publications Warehouse

Fleck, Jacob A.; Gill, Gary W.; Bergamaschi, Brian A.; Kraus, Tamara E.C.; Downing, Bryan D.; Alpers, Charles N.

2014-01-01

Monomethyl mercury (MeHg) is a potent neurotoxin that threatens ecosystem viability and human health. In aquatic systems, the photolytic degradation of MeHg (photodemethylation) is an important component of the MeHg cycle. Dissolved organic matter (DOM) is also affected by exposure to solar radiation (light exposure) leading to changes in DOM composition that can affect its role in overall mercury (Hg) cycling. This study investigated changes in MeHg concentration, DOM concentration, and the optical signature of DOM caused by light exposure in a controlled field-based experiment using water samples collected from wetlands and rice fields. Filtered water from all sites showed a marked loss in MeHg concentration after light exposure. The rate of photodemethylation was 7.5 × 10-3 m2 mol-1 (s.d. 3.5 × 10-3) across all sites despite marked differences in DOM concentration and composition. Light exposure also caused changes in the optical signature of the DOM despite there being no change in DOM concentration, indicating specific structures within the DOM were affected by light exposure at different rates. MeHg concentrations were related to optical signatures of labile DOM whereas the percent loss of MeHg was related to optical signatures of less labile, humic DOM. Relationships between the loss of MeHg and specific areas of the DOM optical signature indicated that aromatic and quinoid structures within the DOM were the likely contributors to MeHg degradation, perhaps within the sphere of the Hg-DOM bond. Because MeHg photodegradation rates are relatively constant across freshwater habitats with natural Hg–DOM ratios, physical characteristics such as shading and hydrologic residence time largely determine the relative importance of photolytic processes on the MeHg budget in these mixed vegetated and open-water systems.

Concurrent photolytic degradation of aqueous methylmercury and dissolved organic matter.

PubMed

Fleck, Jacob A; Gill, Gary; Bergamaschi, Brian A; Kraus, Tamara E C; Downing, Bryan D; Alpers, Charles N

2014-06-15

Monomethyl mercury (MeHg) is a potent neurotoxin that threatens ecosystem viability and human health. In aquatic systems, the photolytic degradation of MeHg (photodemethylation) is an important component of the MeHg cycle. Dissolved organic matter (DOM) is also affected by exposure to solar radiation (light exposure) leading to changes in DOM composition that can affect its role in overall mercury (Hg) cycling. This study investigated changes in MeHg concentration, DOM concentration, and the optical signature of DOM caused by light exposure in a controlled field-based experiment using water samples collected from wetlands and rice fields. Filtered water from all sites showed a marked loss in MeHg concentration after light exposure. The rate of photodemethylation was 7.5×10(-3)m(2)mol(-1) (s.d. 3.5×10(-3)) across all sites despite marked differences in DOM concentration and composition. Light exposure also caused changes in the optical signature of the DOM despite there being no change in DOM concentration, indicating specific structures within the DOM were affected by light exposure at different rates. MeHg concentrations were related to optical signatures of labile DOM whereas the percent loss of MeHg was related to optical signatures of less labile, humic DOM. Relationships between the loss of MeHg and specific areas of the DOM optical signature indicated that aromatic and quinoid structures within the DOM were the likely contributors to MeHg degradation, perhaps within the sphere of the Hg-DOM bond. Because MeHg photodegradation rates are relatively constant across freshwater habitats with natural Hg-DOM ratios, physical characteristics such as shading and hydrologic residence time largely determine the relative importance of photolytic processes on the MeHg budget in these mixed vegetated and open-water systems. Published by Elsevier B.V.

Distribution, Source and Fate of Dissolved Organic Matter in Shelf Seas

NASA Astrophysics Data System (ADS)

Carr, N.; Mahaffey, C.; Hopkins, J.; Sharples, J.; Williams, R. G.; Davis, C. E.

2016-02-01

Dissolved organic matter (DOM) is a complex array of molecules containing carbon (DOC), nitrogen (DON) and phosphorous (DOP), and represents the largest pool of organic matter in the marine environment. DOM in the sea originates from a variety of sources, including allochthonous inputs of terrestrial DOM from land via rivers, and autochthonous inputs through in-situ biotic processes that include phytoplankton exudation, grazing and cell lysis. Marine DOM is a substrate for bacterial growth and can act as a source of nutrients for autotrophs. However, a large component of DOM is biologically refractory. This pool is carbon-rich and nutrient-poor, and can transport and store its compositional elements over large areas and on long time scales. The role of DOM in the shelf seas is currently unclear, despite these regions acting as conduits between the land and open ocean, and also being highly productive ecosystems. Using samples collected across the Northwest European Shelf Sea, we studied the distribution, source, seasonality and potential fate of DOM using a combination of analytical tools, including analysis of amino acids, DOM absorbance spectra and excitation emission matrices, in conjunction with parallel factor analysis (PARAFAC). Strong cross shelf and seasonal gradients in DOM source and lability were found. We observed a strong seasonally dependent significant correlation between salinity and terrestrial DOM in the bottom mixed layer, an enrichment of DOM at the shelf edge in winter and a three-fold increase in fresh marine DOM coinciding with the timing of a spring bloom. Together, our findings illustrate the dynamic nature of DOM in shelf seas over a seasonal cycle and, highlight the potential for DOM to play a key role in the carbon cycle in these regions.

Contrasting effects of photochemical and microbial degradation on Cu(II) binding with fluorescent DOM from different origins.

PubMed

Xu, Huacheng; Guan, Dong-Xing; Zou, Li; Lin, Hui; Guo, Laodong

2018-08-01

Effects of photochemical and microbial degradation on variations in composition and molecular-size of dissolved organic matter (DOM) from different sources (algal and soil) and the subsequent influence on Cu(II) binding were investigated using UV-Vis, fluorescence excitation-emission matrices coupled with parallel factor analysis, flow field-flow fractionation (FlFFF), and metal titration. The degradation processes resulted in an initial rapid decline in the bulk dissolved organic carbon and chromophoric and fluorescent DOM components, followed by a small or little decrease. Specifically, photochemical reaction decreased the aromaticity, humification and apparent molecular weights of all DOM samples, whereas a reverse trend was observed during microbial degradation. The FlFFF fractograms revealed that coagulation of both protein- and humic-like DOM induced an increase in molecular weights for algal-DOM, while the molecular weight enhancement for allochthonous soil samples was mainly attributed to the self-assembly of humic-like components. The Cu(II) binding capacity of algal-derived humic-like and fulvic-like DOM consistently increased during photo- and bio-degradation, while the soil-derived DOM exhibited a slight decline in Cu(II) binding capacity during photo-degradation but a substantial increase during microbial degradation, indicating source- and degradation-dependent metal binding heterogeneities. Pearson correlation analysis demonstrated that the Cu(II) binding potential was mostly related with aromaticity and molecular size for allochthonous soil-derived DOM, but was regulated by both DOM properties and specific degradation processes for autochthonous algal-derived DOM. This study highlighted the coupling role of inherent DOM properties and external environmental processes in regulating metal binding, and provided new insights into metal-DOM interactions and the behavior and fate of DOM-bound metals in aquatic environments. Copyright © 2018 Elsevier Ltd. All rights reserved.

Sorptive and desorptive fractionation of dissolved organic matter by mineral soil matrices.

PubMed

Oren, Adi; Chefetz, Benny

2012-01-01

Interactions of dissolved organic matter (DOM) with soil minerals, such as metal oxides and clays, involve various sorption mechanisms and may lead to sorptive fractionation of certain organic moieties. While sorption of DOM to soil minerals typically involves a degree of irreversibility, it is unclear which structural components of DOM correspond to the irreversibly bound fraction and which factors may be considered determinants. To assist in elucidating that, the current study aimed at investigating fractionation of DOM during sorption and desorption processes in soil. Batch DOM sorption and desorption experiments were conducted with organic matter poor, alkaline soils. Fourier-transform infrared (FTIR) and UV-Vis spectroscopy were used to analyze bulk DOM, sorbed DOM, and desorbed DOM fractions. Sorptive fractionation resulted mainly from the preferential uptake of aromatic, carboxylic, and phenolic moieties of DOM. Soil metal-oxide content positively affected DOM sorption and binding of some specific carboxylate and phenolate functional groups. Desorptive fractionation of DOM was expressed by the irreversible-binding nature of some carboxylic moieties, whereas other bound carboxylic moieties were readily desorbed. Inner-sphere, as opposed to outer-sphere, ligand-exchange complexation mechanisms may be responsible for these irreversible, as opposed to reversible, interactions, respectively. The interaction of aliphatic DOM constituents with soil, presumably through weak van der Waals forces, was minor and increased with increasing proportion of clay minerals in the soil. Revealing the nature of DOM-fractionation processes is of great importance to understanding carbon stabilization mechanisms in soils, as well as the overall fate of contaminants that might be associated with DOM. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Effects of dissolved organic matter (DOM) sources and nature of solid extraction sorbent on recoverable DOM composition: Implication into potential lability of different compound groups.

PubMed

Chen, Meilian; Kim, Sunghwan; Park, Jae-Eun; Kim, Hyun Sik; Hur, Jin

2016-07-01

Noting the source-dependent properties of dissolved organic matter (DOM), this study explored the recoverable compounds by solid phase extraction (SPE) of two common sorbents (C18 and PPL) eluted with methanol solvent for contrasting DOM sources via fluorescence excitation-emission matrix coupled with parallel factor analysis (EEM-PARAFAC) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Fresh algae and leaf litter extracts DOM, one riverine DOM, and one upstream lacustrine DOM were selected for the comparison. C18 sorbent was generally found to extract more diverse molecular formula, relatively higher molecular weight, and more heteroatomic DOM compounds within the studied mass range than PPL sorbent except for the leaf litter extract. Even with the same sorbent, the main molecular features of the two end member DOM were distributed on different sides of the axes of a multivariate ordination, indicating the source-dependent characteristics of the recoverable compounds by the sorbents. In addition, further examination of the molecular formula uniquely present in the two end members and the upstream lake DOM suggested that proteinaceous, tannin-like, and heteroatomic DOM constituents might be potential compound groups which are labile and easily degraded during their mobilization into downstream watershed. This study provides new insights into the sorbent selectivity of DOM from diverse sources and potential lability of various compound groups.

Biodegradation kinetics of dissolved organic matter chromatographic fractions in an intermittent river

NASA Astrophysics Data System (ADS)

Catalán, N.; Casas-Ruiz, J. P.; von Schiller, D.; Proia, L.; Obrador, B.; Zwirnmann, E.; Marcé, R.

2017-01-01

Controls on the degradation of dissolved organic matter (DOM) are complex but key to understand the role of freshwaters in the carbon cycle. Both the origin and previous degradation history have been suggested to determine DOM reactivity, but it is still a major challenge to understand the links between DOM composition and biodegradation kinetics. An appropriate context to study these links are intermittent rivers, as summer drought naturally diversifies DOM sources and sinks. Here we investigated the biodegradation kinetics of DOM in the main aquatic environments present in a temporary river. During dark incubations we traced the dynamics of bulk DOM and its main chromatographic fractions defined using LC-OCD: high molecular weight substances (HMWS), low molecular weight substances (LMWS), and humic substances and building blocks. Bulk DOM decay patterns were successfully fitted to the reactivity continuum (RC) biodegradation model. The RC parameters depicted running waters as the sites presenting a more reactive DOM, and temporary pools, enriched in leaf litter, as the ones with slowest DOM decay. The decay patterns of each DOM fraction were consistent throughout sites. LMWS and HMWS decayed in all cases and could be modeled using the RC model. Notably, the dynamics of LMWS controlled the bulk DOM kinetics. We discuss the mechanistic basis for the chromatographic fractions' kinetics during biodegradation and the implications that preconditioning and summer drought can have for DOM biodegradation in intermittent rivers.

Reactivity of Triplet Excited States of Dissolved Natural Organic Matter in Stormflow from Mixed-Use Watersheds.

PubMed

McCabe, Andrew J; Arnold, William A

2017-09-05

Dissolved organic matter (DOM) quantity and composition control the rate of formation (R f,T ) of triplet excited states of dissolved natural organic matter ( 3 DOM*) and the efficiency of 3 DOM* formation (the apparent quantum yield, AQY T ). Here, the reactivity of 3 DOM* in stormflow samples collected from watersheds with variable land covers is examined. Stormflow DOM reflects variability in DOM quantity and composition as a function of land cover and may be important in controlling the fate of cotransported pollutants. R f,T and AQY T were measured using 2,4,6-trimethylphenol in stormflow samples under simulated sunlight. The DOM source and composition was characterized using absorbance and fluorescence spectroscopies and high-resolution mass spectrometry. R f,T and the total rate of light absorption by the water samples (R a ) increased with the dissolved organic carbon (DOC) concentration. AQY T was independent of DOC concentration, but varied with DOM source: developed land cover (4-6%) ≈ open water > vegetated land cover (3%). AQY T was positively related to an index for microbial/algal DOM content and negatively related to DOM molecular weight, DOM aromaticity, and the content of polyphenols. This work demonstrates that TMP is an effective probe for the determination of R f,T and AQY T in whole water samples after accounting for the inhibition of TMP photodegradation by DOM.

Molecular-level dynamics of refractory dissolved organic matter

NASA Astrophysics Data System (ADS)

Niggemann, J.; Gerdts, G.; Dittmar, T.

2012-04-01

Refractory dissolved organic matter (DOM) accounts for most of the global oceanic organic carbon inventory. Processes leading to its formation and factors determining its stability are still largely unknown. We hypothesize that refractory DOM carries a universal molecular signature. Characterizing spatial and temporal variability in this universal signature is a key to understanding dynamics of refractory DOM. We present results from a long-term study of the DOM geo-metabolome in the open North Sea. Geo-metabolomics considers the entity of DOM as a population of compounds, each characterized by a specific function and reactivity in the cycling of energy and elements. Ten-thousands of molecular formulae were identified in DOM by ultrahigh resolution mass spectrometry analysis (FT-ICR-MS, Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry). The DOM pool in the North Sea was influenced by a complex interplay of processes that produced, transformed and degraded dissolved molecules. We identified a stable fraction in North Sea DOM with a molecular composition similar to deep ocean DOM. Molecular-level changes in this stable fraction provide novel information on dynamics and interactions of refractory DOM.

Photoreduction of Hg(II) and photodemethylation of methylmercury: the key role of thiol sites on dissolved organic matter

USGS Publications Warehouse

Jeremiason, Jeffrey D.; Portner, Joshua C.; Aiken, George R.; Hiranaka, Amber J.; Dvorak, Michelle T.; Tran, Khuyen T.; Latch, Douglas E.

2015-01-01

This study examined the kinetics of photoreduction of Hg(II) and photodemethylation of methylmercury (MeHg+) attached to, or in the presence of, dissolved organic matter (DOM). Both Hg(II) and MeHg+ are principally bound to reduced sulfur groups associated with DOM in many freshwater systems. We propose that a direct photolysis mechanism is plausible for reduction of Hg(II) bound to reduced sulfur groups on DOM while an indirect mechanism is supported for photodemethylation of MeHg+ bound to DOM. UV spectra of Hg(II) and MeHg+ bound to thiol containing molecules demonstrate that the Hg(II)–S bond is capable of absorbing UV-light in the solar spectrum to a much greater extent than MeHg+–S bonds. Experiments with chemically distinct DOM isolates suggest that concentration of DOM matters little in the photochemistry if there are enough reduced S sites present to strongly bind MeHg+ and Hg(II); DOM concentration does not play a prominent role in photodemethylation other than to screen light, which was demonstrated in a field experiment in the highly colored St. Louis River where photodemethylation was not observed at depths ≥10 cm. Experiments with thiol ligands yielded slower photodegradation rates for MeHg+ than in experiments with DOM and thiols; rates in the presence of DOM alone were the fastest supporting an intra-DOM mechanism. Hg(II) photoreduction rates, however, were similar in experiments with only DOM, thiols plus DOM, or only thiols suggesting a direct photolysis mechanism. Quenching experiments also support the existence of an intra-DOM photodemethylation mechanism for MeHg+. Utilizing the difference in photodemethylation rates measured for MeHg+ attached to DOM or thiol ligands, the binding constant for MeHg+ attached to thiol groups on DOM was estimated to be 1016.7.

Characterization and origin of polar dissolved organic matter from the Great Salt Lake

USGS Publications Warehouse

Leenheer, J.A.; Noyes, T.I.; Rostad, C.E.; Davisson, M.L.

2004-01-01

Polar dissolved organic matter (DOM) was isolated from a surface-water sample from the Great Salt Lake by separating it from colloidal organic matter by membrane dialysis, from less-polar DOM fractions by resin sorbents, and from inorganic salts by a combination of sodium cation exchange followed by precipitation of sodium salts by acetic acid during evaporative concentration. Polar DOM was the most abundant DOM fraction, accounting for 56% of the isolated DOM. Colloidal organic matter was 14C-age dated to be about 100% modern carbon and all of the DOM fractions were 14C-age dated to be between 94 and 95% modern carbon. Average structural models of each DOM fraction were derived that incorporated quantitative elemental and infrared, 13C-NMR, and electrospray/mass spectrometric data. The polar DOM model consisted of open-chain N-acetyl hydroxy carboxylic acids likely derived from N-acetyl heteropolysaccharides that constituted the colloidal organic matter. The less polar DOM fraction models consisted of aliphatic alicyclic ring structures substituted with carboxyl, hydroxyl, ether, ester, and methyl groups. These ring structures had characteristics similar to terpenoid precursors. All DOM fractions in the Great Salt Lake are derived from algae and bacteria that dominate DOM inputs in this lake.

Complete and Partial Photo-oxidation of Dissolved Organic Matter Draining Permafrost Soils.

PubMed

Ward, Collin P; Cory, Rose M

2016-04-05

Photochemical degradation of dissolved organic matter (DOM) to carbon dioxide (CO2) and partially oxidized compounds is an important component of the carbon cycle in the Arctic. Thawing permafrost soils will change the chemical composition of DOM exported to arctic surface waters, but the molecular controls on DOM photodegradation remain poorly understood, making it difficult to predict how inputs of thawing permafrost DOM may alter its photodegradation. To address this knowledge gap, we quantified the susceptibility of DOM draining the shallow organic mat and the deeper permafrost layer of arctic soils to complete and partial photo-oxidation and investigated changes in the chemical composition of each DOM source following sunlight exposure. Permafrost and organic mat DOM had similar lability to photomineralization despite substantial differences in initial chemical composition. Concurrent losses of carboxyl moieties and shifts in chemical composition during photodegradation indicated that photodecarboxylation could account for 40-90% of DOM photomineralized to CO2. Permafrost DOM had a higher susceptibility to partial photo-oxidation compared to organic mat DOM, potentially due to a lower abundance of phenolic moieties with antioxidant properties. These results suggest that photodegradation will likely continue to be an important control on DOM fate in arctic freshwaters as the climate warms and permafrost soils thaw.

Interactions between iron and organic matter may influence the fate of permafrost carbon in the Arctic

NASA Astrophysics Data System (ADS)

Cory, R. M.; Trusiak, A.; Ward, C.; Kling, G. W.; Tfaily, M.; Paša-Tolić, L.; Noel, V.; Bargar, J.

2017-12-01

The ongoing thawing of permafrost soils is the only environmental change that allows tremendous stores of organic carbon (C) to be converted into carbon dioxide (CO2) on decadal time scales, thus providing a positive and accelerating feedback to global warming. Evidence suggests that iron enhances abiotic reactions that convert dissolved organic matter (DOM) to CO2 in dark soils and in sunlit surface waters depending on its redox state and association with DOM (i.e., iron-DOM complexation). However, the complexation of iron in surface waters and soils remains too poorly understood to predict how iron influences the rates of oxidation of DOM to CO2. To address this knowledge gap, we characterized iron-DOM complexation in iron-rich soil and surface waters of the Arctic, in combination with measurements of DOM oxidation to CO2. These waters contain high concentrations of dissolved iron and DOM (up to 1 and 2 mM, respectively), and low concentrations of other potential ligands for iron such as sulfide, carbonate, chloride, or bromide. Ultra-high resolution mass spectrometry (FT-ICR MS) was used to identify ligands for iron within the DOM pool, and synchrotron based X-ray analysis (XAS and EXAFS) was used to assess iron's oxidation state, to detect iron complexation, and to constrain the chemical composition of the complexes. Across a natural gradient of dissolved iron and DOM concentrations, many potential ligands were identified within DOM that are expected to complex with iron (e.g., aromatic acids). EXAFS showed substantial complexation of reduced ferrous iron (Fe(II)) to DOM in arctic soil waters, on the basis of comparison to Fe(II)-DOM reference spectra. Identification of iron complexed to DOM in soil waters is consistent with strongly co-varying iron and DOM concentrations in arctic soil and surface waters, and supports our hypothesis that complexation of iron by DOM influences dark and light redox reactions that oxidize DOM to CO2. Understanding the molecular controls on the biogeochemical reactions that convert permafrost carbon to CO2 is critical for understanding the role of the Arctic in current and future climate change.

Application of fluorescence spectroscopy for dissolved organic matter characterization in constructed wetlands

NASA Astrophysics Data System (ADS)

Sardana, A.; Aziz, T. N.; Cottrell, B. A.

2017-12-01

In this presentation we will discuss our ongoing work to characterize the photochemical behavior of dissolved organic matter (DOM) from wastewater treated in constructed wetlands. We have used a suite of spectroscopic and chromatographic techniques to characterize the DOM and to quantify the potential production of reactive oxygenated species (ROS). In the present study, DOM was fractionated based on its hydrophobicity and both the natural water isolates and fractionated DOM were characterized using SUVA254, spectral slope ratios, excitation emission matrix fluorescence spectroscopy (EEMs) and proton nuclear magnetic resonance (1H NMR). Photodegradation of wetland DOM and the formation of the hydroxyl radical (*OH), singlet oxygen (1O2), and the triplet-excited state (3DOM*) was also determined to assess the reactivity of DOM. EEM spectra exhibited the four main fluorescence peaks that are characteristic of DOM: peak A humic-like DOM, Peak C (fulvic or chromophoric DOM), Peak M (marine-like DOM), and peak T (tryptophan or protein-like absorbance). Two additional observed peaks with shorter emission wavelengths (A' Ex/Em = 243/278 nm and T' Ex/Em = 272/319 nm) were attributed to the microbial DOM in wastewater effluent. The spectral slope ratios decreased from 1.46 at the wetland inlet to 0.89 at the wetland outlet. The protein-like Peak T fluorescence decreased from 50% at the wetland inlet to 6.7% at the Wetland 2 outlet. A negative correlation between the percent fluorescence of Peak T and Peaks A, C and M confirmed the transition from the spectrum of pure wastewater with a primarily protein-like signature to a spectrum characteristic of terrestrially derived DOM. This transition coincided with enhanced formation rates and steady state concentrations of photochemically produced reactive intermediates (PPRIs). Size Exclusion Chromatography demonstrated that the influent wastewater had a lower molecular weight as compared to downstream wetland locations. Fractionation of DOM based on hydrophobicity followed by 1H NMR analysis indicated an increase in the complexity and composition of wetland effluent DOM. This presentation will summarize these findings and present results from our new microcosm constructed wetlands built to develop insights into DOM production and photochemical characteristics.

DICOM index tracker enterprise: advanced system for enterprise-wide quality assurance and patient safety monitoring

NASA Astrophysics Data System (ADS)

Zhang, Min; Pavlicek, William; Panda, Anshuman; Langer, Steve G.; Morin, Richard; Fetterly, Kenneth A.; Paden, Robert; Hanson, James; Wu, Lin-Wei; Wu, Teresa

2015-03-01

DICOM Index Tracker (DIT) is an integrated platform to harvest rich information available from Digital Imaging and Communications in Medicine (DICOM) to improve quality assurance in radiology practices. It is designed to capture and maintain longitudinal patient-specific exam indices of interests for all diagnostic and procedural uses of imaging modalities. Thus, it effectively serves as a quality assurance and patient safety monitoring tool. The foundation of DIT is an intelligent database system which stores the information accepted and parsed via a DICOM receiver and parser. The database system enables the basic dosimetry analysis. The success of DIT implementation at Mayo Clinic Arizona calls for the DIT deployment at the enterprise level which requires significant improvements. First, for geographically distributed multi-site implementation, the first bottleneck is the communication (network) delay; the second is the scalability of the DICOM parser to handle the large volume of exams from different sites. To address this issue, DICOM receiver and parser are separated and decentralized by site. To facilitate the enterprise wide Quality Assurance (QA), a notable challenge is the great diversities of manufacturers, modalities and software versions, as the solution DIT Enterprise provides the standardization tool for device naming, protocol naming, physician naming across sites. Thirdly, advanced analytic engines are implemented online which support the proactive QA in DIT Enterprise.

The characteristics of dissolved organic matter (DOM) in storm sewer sediments and the binding interaction with Cu(II) in four typical regions in Beijing, China.

PubMed

Zhang, Ziyang; Li, Kun; Zhang, Xiaoran; Li, Haiyan

2017-07-01

In this work, dissolved organic matter (DOM) was extracted from storm sewer sediments collected in four typical regions (residential, campus, traffic and business regions) in Beijing, China. The basic characteristics of DOM were analyzed by UV-visible spectroscopy (UV-Vis), excitation-emission matrix Fluorescence Spectroscopy and Fourier Transform Infrared Spectroscopy. Furthermore, the complexation between DOM and Cu(II) were investigated. The results showed that there were large amount of aromatic structure in the DOM extracted from storm sewer sediments. The microbial activities had also made a contribution to the DOM in storm sewer sediments. The composition of DOM influenced the complexing capacity of Cu(II) greatly, which may be attributed to the protein-like and humic-like substances in storm sewer sediments. This study demonstrated valuable information on the structure present in the DOM of storm sewer sediments and provided new insight for exploring the relationship between DOM and co-existing heavy metals in storm sewer sediments.

Partitioning of the pesticide trifluralin between dissolved organic matter and water using automated SPME-GC/MS.

PubMed

Caupos, Emilie; Touffet, Arnaud; Mazellier, Patrick; Croue, Jean-Philippe

2015-03-01

Solid-phase microextraction (SPME) was used to determine the equilibrium association constant for a pesticide, trifluralin (TFR), with dissolved organic matter (DOM). After optimization of the SPME method for the analysis of TFR, partition coefficients (K DOM) with three different sources of DOM were determined in buffered solutions at pH 7. Commercial humic acids and DOM fractions isolated from two surface waters were used. The values of log K DOM varied from 4.3 to 5.8, depending on the nature of the organic material. A good correlation was established between log K DOM and DOM properties (as measured with the H/O atomic ratio and UV absorbance), in agreement with literature data. This is consistent with the effect of polarity and aromaticity for governing DOM-pollutant associations, regardless of the origin of DOM. This association phenomenon is relevant to better understand the behavior of pesticides in the environment since it controls part of pesticide leaching and fate in aquatic systems.

Ocean metabolism and dissolved organic matter: How do small dissolved molecules persist in the ocean?

NASA Astrophysics Data System (ADS)

Benner, Ronald

2010-05-01

The ocean reservoir of dissolved organic matter (DOM) is among the largest global reservoirs (~700 Pg C) of reactive organic carbon. Marine primary production (~50 Pg C/yr) by photosynthetic microalgae and cyanobacteria is the major source of organic matter to the ocean and the principal substrate supporting marine food webs. The direct release of DOM from phytoplankton and other organisms as well as a variety of other processes, such as predation and viral lysis, contribute to the ocean DOM reservoir. Continental runoff and atmospheric deposition are relatively minor sources of DOM to the ocean, but some components of this material appear to be resistant to decomposition and to have a long residence time in the ocean. Concentrations of DOM are highest in surface waters and decrease with depth, a pattern that reflects the sources and diagenesis of DOM in the upper ocean. Most (70-80%) marine DOM exists as small molecules of low molecular weight (<1 kDalton). Surprisingly, high-molecular-weight (>1 kDalton) DOM is relatively enriched in major biochemicals, such as combined neutral sugars and amino acids, and is more bioavailable than low-molecular-weight DOM. The observed relationships among the size, composition, and reactivity of DOM have led to the size-reactivity continuum model, which postulates that diagenetic processes lead to the production of smaller molecules that are structurally altered and resistant to microbial degradation. The radiocarbon content of these small dissolved molecules also indicates these are the most highly aged components of DOM. Chemical signatures of bacteria are abundant in DOM and increase during diagenesis, indicating bacteria are an important source of slowly cycling biochemicals. Recent analyses of DOM isolates by ultrahigh-resolution mass spectrometry have revealed an incredibly diverse mixture of molecules. Carboxyl-rich alicyclic molecules are abundant in DOM, and they appear to be derived from diagenetically-altered terpenoids, such as sterols and hopanoids. Thermally-altered molecules, including black carbon, also appear to be important components of DOM, but their origins are unclear. We are rapidly acquiring novel information about the composition and molecular identity of DOM, and novel insights about the origins, transformations and fates this vast reservoir of DOM are emerging. This presentation will review and synthesize this information for comparison with non-living organic matter in other systems.

Copper(II) binding by dissolved organic matter: Importance of the copper-to-dissolved organic matter ratio and implications for the Biotic Ligand Model

USGS Publications Warehouse

Craven, Alison M.; Aiken, George R.; Ryan, Joseph N.

2012-01-01

The ratio of copper to dissolved organic matter (DOM) is known to affect the strength of copper binding by DOM, but previous methods to determine the Cu2+–DOM binding strength have generally not measured binding constants over the same Cu:DOM ratios. In this study, we used a competitive ligand exchange–solid-phase extraction (CLE-SPE) method to determine conditional stability constants for Cu2+–DOM binding at pH 6.6 and 0.01 M ionic strength over a range of Cu:DOM ratios that bridge the detection windows of copper-ion-selective electrode and voltammetry measurements. As the Cu:DOM ratio increased from 0.0005 to 0.1 mg of Cu/mg of DOM, the measured conditional binding constant (cKCuDOM) decreased from 1011.5 to 105.6 M–1. A comparison of the binding constants measured by CLE-SPE with those measured by copper-ion-selective electrode and voltammetry demonstrates that the Cu:DOM ratio is an important factor controlling Cu2+–DOM binding strength even for DOM isolates of different types and different sources and for whole water samples. The results were modeled with Visual MINTEQ and compared to results from the biotic ligand model (BLM). The BLM was found to over-estimate Cu2+ at low total copper concentrations and under-estimate Cu2+ at high total copper concentrations.

Carotenoids are the likely precursor of a significant fraction of marine dissolved organic matter

PubMed Central

Arakawa, Neal; Aluwihare, Lihini I.; Simpson, Andre J.; Soong, Ronald; Stephens, Brandon M.; Lane-Coplen, Daniel

2017-01-01

The ocean’s biota sequester atmospheric carbon dioxide (CO2) in part by producing dissolved organic matter (DOM) that persists in the ocean for millennia. This long-term accumulation of carbon may be facilitated by abiotic and biotic production of chemical structures that resist degradation, consequently contributing disproportionately to refractory DOM. Compounds that are selectively preserved in seawater were identified in solid-phase extracted DOM (PPL-DOM) using comprehensive gas chromatography (GC) coupled to mass spectrometry (MS). These molecules contained cyclic head groups that were linked to isoprenoid tails, and their overall structures closely resembled carotenoid degradation products (CDP). The origin of these compounds in PPL-DOM was further confirmed with an in vitro β-carotene photooxidation experiment that generated water-soluble CDP with similar structural characteristics. The molecular-level identification linked at least 10% of PPL-DOM carbon, and thus 4% of total DOM carbon, to CDP. Nuclear magnetic resonance spectra of experimental CDP and environmental PPL-DOM overlapped considerably, which indicated that even a greater proportion of PPL-DOM was likely composed of CDP. The CDP-rich DOM fraction was depleted in radiocarbon (14C age > 1500 years), a finding that supports the possible long-term accumulation of CDP in seawater. By linking a specific class of widespread biochemicals to refractory DOM, this work provides a foundation for future studies that aim to examine how persistent DOM forms in the ocean. PMID:28959723

Influence of land use and land cover on the spatial variability of dissolved organic matter in multiple aquatic environments.

PubMed

Singh, Shatrughan; Dash, Padmanava; Silwal, Saurav; Feng, Gary; Adeli, Ardeshir; Moorhead, Robert J

2017-06-01

Water quality of lakes, estuaries, and coastal areas serves as an indicator of the overall health of aquatic ecosystems as well as the health of the terrestrial ecosystem that drains to the water body. Land use and land cover plays not only a significant role in controlling the quantity of the exported dissolved organic matter (DOM) but also influences the quality of DOM via various biogeochemical and biodegradation processes. We examined the characteristics and spatial distribution of DOM in five major lakes, in an estuary, and in the coastal waters of the Mississippi, USA, and investigated the influence of the land use and land cover of their watersheds on the DOM composition. We employed absorption and fluorescence spectroscopy including excitation-emission matrix (EEM) combined with parallel factor (PARAFAC) analysis modeling techniques to determine optical properties of DOM and its characteristics in this study. We developed a site-specific PARAFAC model to evaluate DOM characteristics resulting in five diverse DOM compositions that included two terrestrial humic-like (C1 and C3), two microbial humic-like (C2 and C5), and one protein-like (C4) DOM. Our results showed elevated fluorescence levels of microbial humic-like or protein-like DOM in the lakes and coastal waters, while the estuarine waters showed relatively high fluorescence levels of terrestrial humic-like DOM. The results also showed that percent forest and wetland coverage explained 68 and 82% variability, respectively, in terrestrial humic-like DOM exports, while 87% variability in microbially derived humiclike DOM was explained by percent agricultural lands. Strong correlations between microbial humic-like DOM and fluorescence-derived DOM indices such as biological index (BIX) and fluorescence index (FI) indicated autochthonous characteristics in the lakes, while the estuary showed largely allochthonous DOM of terrestrial origin. We also observed higher concentrations of total dissolved phosphorous (TDP) and ammonium nitrogen (NH 4 -N) in coastal waters potentially due to photodegradation of refractory DOM derived from the sediment-bound organic matter in the coastal wetlands. This study highlights the relationships between the DOM compositions in the water and the land use and land cover in the watershed. The spatial variability of DOM in three different types of aquatic environments enhances the understanding of the role of land use and land cover in carbon cycling through export of organic matter to the aquatic ecosystems..

Dom34 Links Translation to Protein O-mannosylation

PubMed Central

van Wijlick, Lasse; Geissen, René; Hilbig, Jessica S.; Lagadec, Quentin; Cantero, Pilar D.; Juchimiuk, Mateusz; Kluge, Sven; Wickert, Stephan; Alepuz, Paula; Ernst, Joachim F.

2016-01-01

In eukaryotes, Dom34 upregulates translation by securing levels of activatable ribosomal subunits. We found that in the yeast Saccharomyces cerevisiae and the human fungal pathogen Candida albicans, Dom34 interacts genetically with Pmt1, a major isoform of protein O-mannosyltransferase. In C. albicans, lack of Dom34 exacerbated defective phenotypes of pmt1 mutants, while they were ameliorated by Dom34 overproduction that enhanced Pmt1 protein but not PMT1 transcript levels. Translational effects of Dom34 required the 5′-UTR of the PMT1 transcript, which bound recombinant Dom34 directly at a CA/AC-rich sequence and regulated in vitro translation. Polysomal profiling revealed that Dom34 stimulates general translation moderately, but that it is especially required for translation of transcripts encoding Pmt isoforms 1, 4 and 6. Because defective protein N- or O-glycosylation upregulates transcription of PMT genes, it appears that Dom34-mediated specific translational upregulation of the PMT transcripts optimizes cellular responses to glycostress. Its translational function as an RNA binding protein acting at the 5′-UTR of specific transcripts adds another facet to the known ribosome-releasing functions of Dom34 at the 3′-UTR of transcripts. PMID:27768707

Dom34 Links Translation to Protein O-mannosylation.

PubMed

van Wijlick, Lasse; Geissen, René; Hilbig, Jessica S; Lagadec, Quentin; Cantero, Pilar D; Pfeifer, Eugen; Juchimiuk, Mateusz; Kluge, Sven; Wickert, Stephan; Alepuz, Paula; Ernst, Joachim F

2016-10-01

In eukaryotes, Dom34 upregulates translation by securing levels of activatable ribosomal subunits. We found that in the yeast Saccharomyces cerevisiae and the human fungal pathogen Candida albicans, Dom34 interacts genetically with Pmt1, a major isoform of protein O-mannosyltransferase. In C. albicans, lack of Dom34 exacerbated defective phenotypes of pmt1 mutants, while they were ameliorated by Dom34 overproduction that enhanced Pmt1 protein but not PMT1 transcript levels. Translational effects of Dom34 required the 5'-UTR of the PMT1 transcript, which bound recombinant Dom34 directly at a CA/AC-rich sequence and regulated in vitro translation. Polysomal profiling revealed that Dom34 stimulates general translation moderately, but that it is especially required for translation of transcripts encoding Pmt isoforms 1, 4 and 6. Because defective protein N- or O-glycosylation upregulates transcription of PMT genes, it appears that Dom34-mediated specific translational upregulation of the PMT transcripts optimizes cellular responses to glycostress. Its translational function as an RNA binding protein acting at the 5'-UTR of specific transcripts adds another facet to the known ribosome-releasing functions of Dom34 at the 3'-UTR of transcripts.

Stormwater dissolved organic matter: influence of land cover and environmental factors.

PubMed

McElmurry, Shawn P; Long, David T; Voice, Thomas C

2014-01-01

Dissolved organic matter (DOM) plays a major role in defining biological systems and it influences the fate and transport of many pollutants. Despite the importance of DOM, understanding of how environmental and anthropogenic factors influence its composition and characteristics is limited. This study focuses on DOM exported as stormwater from suburban and urban sources. Runoff was collected before entering surface waters and DOM was characterized using specific ultraviolet absorbance at 280 nm (a proxy for aromaticity), molecular weight, polydispersity and the fraction of DOM removed from solution via hydrophobic and H-bonding mechanisms. General linear models (GLMs) incorporating land cover, precipitation, solar radiation and selected aqueous chemical measurements explained variations in DOM properties. Results show (1) molecular characteristics of DOM differ as a function of land cover, (2) DOM produced by forested land is significantly different from other landscapes, particularly urban and suburban areas, and (3) DOM from land cover that contains paved surfaces and sewers is more hydrophobic than from other types of land cover. GLMs incorporating environmental factors and land cover accounted for up to 86% of the variability observed in DOM characteristics. Significant variables (p < 0.05) included solar radiation, water temperature and water conductivity.

Co-precipitation of dissolved organic matter by calcium carbonate in Pyramid Lake, Nevada

USGS Publications Warehouse

Leenheer, Jerry A.; Reddy, Michael M.

2008-01-01

Our previous research has demonstrated that dissolved organic matter (DOM) influences calcium carbonate mineral formation in surface and ground water. To better understand DOM mediation of carbonate precipitation and DOM co-precipitation and/or incorporation with carbonate minerals, we characterized the content and speciation of DOM in carbonate minerals and in the lake water of Pyramid Lake, Nevada, USA. A 400-gram block of precipitated calcium carbonate from the Pyramid Lake shore was dissolved in 8 liters of 10% acetic acid. Particulate matter not dissolved by acetic acid was removed by centrifugation. DOM from the carbonate rock was fractionated into nine portions using evaporation, dialysis, resin adsorption, and selective precipitations to remove acetic acid and inorganic constituents. The calcium carbonate rock contained 0.23% DOM by weight. This DOM was enriched in polycarboxylic proteinaceous acids and hydroxy-acids in comparison with the present lake water. DOM in lake water was composed of aliphatic, alicyclic polycarboxylic acids. These compound classes were found in previous studies to inhibit calcium carbonate precipitation. DOM fractions from the carbonate rock were 14C-age dated at about 3,100 to 3,500 years before present. The mechanism of DOM co-precipitation and/or physical incorporation in the calcium carbonate is believed to be due to formation of insoluble calcium complexes with polycarboxylic proteinaceous acids and hydroxy-acids that have moderately large stability constants at the alkaline pH of the lake. DOM co-precipitation with calcium carbonate and incorporation in precipitated carbonate minerals removes proteinaceous DOM, but nearly equivalent concentrations of neutral and acidic forms of organic nitrogen in DOM remain in solution. Calcium carbonate precipitation during lime softening pretreatment of drinking water may have practical applications for removal of proteinaceous disinfection by-product precursors.

How Reservoirs Alter DOM Amount and Composition: Sources, Sinks, and Transformations

NASA Astrophysics Data System (ADS)

Kraus, T. E.; Bergamaschi, B. A.; Hernes, P. J.; Doctor, D. H.; Kendall, C.; Losee, R. F.; Downing, B. D.

2011-12-01

Reservoirs are critical components of many water supply systems as they allow the storage of water when supply exceeds demand. However, during water storage biogeochemical processes can alter both the amount and composition of dissolved organic matter (DOM), which can in turn affect water quality. While the balance between production and loss determines whether a reservoir is a net sink or source of DOM, changes in chemical composition are also relevant as they affect DOM reactivity (e.g. persistence in the environment, removability during coagulation treatment, and potential to form toxic compounds during drinking water treatment). The composition of the DOM pool also provides information about the DOM sources and processing, which can inform reservoir management. We examined the concentration and composition of DOM in San Luis Reservoir (SLR), a large off-stream impoundment of the California State Water Project. We used an array of DOM chemical tracers including dissolved organic carbon (DOC) concentration, optical properties, isotopic composition, lignin phenol content, and structural groupings determined by 13C NMR. There were periods when the reservoir was i) a net source of DOM due to the predominance of algal production (summer), ii) a net sink due to the predominance of degradation (fall/winter), and iii) balanced between production and consumption (spring). Despite only moderate variation in bulk DOC concentration (3.0-3.6 mg C/L), substantial changes in DOM composition indicated that terrestrial-derived material entering the reservoir was being degraded and replaced by aquatic-derived DOM produced within the reservoir. Results suggest reservoirs have the potential to reduce DOM amount and reactivity via degradative processes, however, these benefits can be decreased or even negated by the production of algal-derived DOM.

Toward a theory of distributed word expert natural language parsing

NASA Technical Reports Server (NTRS)

Rieger, C.; Small, S.

1981-01-01

An approach to natural language meaning-based parsing in which the unit of linguistic knowledge is the word rather than the rewrite rule is described. In the word expert parser, knowledge about language is distributed across a population of procedural experts, each representing a word of the language, and each an expert at diagnosing that word's intended usage in context. The parser is structured around a coroutine control environment in which the generator-like word experts ask questions and exchange information in coming to collective agreement on sentence meaning. The word expert theory is advanced as a better cognitive model of human language expertise than the traditional rule-based approach. The technical discussion is organized around examples taken from the prototype LISP system which implements parts of the theory.

The power and limits of a rule-based morpho-semantic parser.

PubMed Central

Baud, R. H.; Rassinoux, A. M.; Ruch, P.; Lovis, C.; Scherrer, J. R.

1999-01-01

The venue of Electronic Patient Record (EPR) implies an increasing amount of medical texts readily available for processing, as soon as convenient tools are made available. The chief application is text analysis, from which one can drive other disciplines like indexing for retrieval, knowledge representation, translation and inferencing for medical intelligent systems. Prerequisites for a convenient analyzer of medical texts are: building the lexicon, developing semantic representation of the domain, having a large corpus of texts available for statistical analysis, and finally mastering robust and powerful parsing techniques in order to satisfy the constraints of the medical domain. This article aims at presenting an easy-to-use parser ready to be adapted in different settings. It describes its power together with its practical limitations as experienced by the authors. PMID:10566313

The power and limits of a rule-based morpho-semantic parser.

PubMed

Baud, R H; Rassinoux, A M; Ruch, P; Lovis, C; Scherrer, J R

1999-01-01

The venue of Electronic Patient Record (EPR) implies an increasing amount of medical texts readily available for processing, as soon as convenient tools are made available. The chief application is text analysis, from which one can drive other disciplines like indexing for retrieval, knowledge representation, translation and inferencing for medical intelligent systems. Prerequisites for a convenient analyzer of medical texts are: building the lexicon, developing semantic representation of the domain, having a large corpus of texts available for statistical analysis, and finally mastering robust and powerful parsing techniques in order to satisfy the constraints of the medical domain. This article aims at presenting an easy-to-use parser ready to be adapted in different settings. It describes its power together with its practical limitations as experienced by the authors.

Hydrological Controls on Dissolved Organic Matter Quality and Export in a Coastal River System in Southeastern USA

NASA Astrophysics Data System (ADS)

Bhattacharya, R.; Osburn, C. L.

2017-12-01

Dissolved organic matter (DOM) exported from river catchments can influence the biogeochemical processes in coastal environments with implications for water quality and carbon budget. High flow conditions are responsible for most DOM export ("pulses") from watersheds, and these events reduce DOM transformation and production by "shunting" DOM from river networks into coastal waters: the Pulse-Shunt Concept (PSC). Subsequently, the source and quality of DOM is also expected to change as a function of river flow. Here, we used stream dissolved organic carbon concentrations ([DOC]) along with DOM optical properties, such as absorbance at 350 nm (a350) and fluorescence excitation and emission matrices modeled by parallel factor analysis (PARAFAC), to characterize DOM source, quality and fluxes under variable flow conditions for the Neuse River, a coastal river system in the southeastern US. Observations were made at a flow gauged station above head of tide periodically between Aug 2011 and Feb 2013, which captured low flow periods in summer and several high flow events including Hurricane Irene. [DOC] and a350 were correlated and varied positively with river flow, implying that a large portion of the DOM was colored, humic and flow-mobilized. During high flow conditions, PARAFAC results demonstrated the higher influx of terrestrial humic DOM, and lower in-stream phytoplankton production or microbial degradation. However, during low flow, DOM transformation and production increased in response to higher residence times and elevated productivity. Further, 70% of the DOC was exported by above average flows, where 3-4 fold increases in DOC fluxes were observed during episodic events, consistent with PSC. These results imply that storms dramatically affects DOM export to coastal waters, whereby high river flow caused by episodic events primarily shunt terrestrial DOM to coastal waters, whereas low flow promotes in-stream DOM transformation and amendment with microbial DOM.

Temporal Changes in Photochemically Labile DOM and Implications for Carbon Budgets in Peatland Aquatic Systems

NASA Astrophysics Data System (ADS)

Pickard, A.

2015-12-01

Aquatic systems in peatland catchments are subject to high loading of dissolved organic matter (DOM) from surrounding terrestrial environments. However the significance of photochemical transformation of DOM in peatland carbon budgets remains poorly constrained. In this study UV irradiation experiments were conducted on water samples collected over one year from two contrasting systems in Scotland: a stream draining a peatland with high levels of DOM and a reservoir draining a peat catchment with low levels of DOM. Further samples were collected from the high DOM system during two storm events. After experimental exposure, optical and chemical analyses were employed to determine photochemical lability of the DOM pool. At both sites irradiation-induced decreases in dissolved organic carbon (DOC) as a percentage of the total carbon pool were greatest in winter, suggesting that DOM was depleted in photo-reactive molecules in summer. Seasonal variability in DOC was high at the stream site and was positively correlated with CO₂ and CO photoproduction (r2 = 0.81 and 0.83, respectively; p<0.05). Lignin phenol analyses indicate considerable contribution of peat to the DOM pool at the stream site, particularly during summer. Whilst DOC concentrations did not vary greatly during storm events, UV-Vis absorbance indicators did, signifying changing DOM source material from activation of different hydrological pathways. The most photo-reactive DOM occurred 5-10 hours after peak discharge, suggesting that storms replenish photochemically labile DOM in headwater streams. Conservative estimates using data from this study suggest that up to 7% of the DOM pool of peatland streams can be lost (primarily as CO₂ and CO) upon exposure to 8 hours of environmentally representative UV irradiation. Further investigation in field campaigns under natural UV exposure are underway to assess the importance of photodegradation of DOM as a loss pathway of carbon based gases from aquatic systems.

Dynamics of dissolved organic matter (DOM) in a typical inland lake of the Three Gorges Reservoir area: Fluorescent properties and their implications for dissolved mercury species.

PubMed

Jiang, Tao; Chen, Xueshuang; Wang, Dingyong; Liang, Jian; Bai, Weiyang; Zhang, Cheng; Wang, Qilei; Wei, Shiqiang

2018-01-15

Dissolved organic matter (DOM) plays an important environmental and ecological role in inland aquatic systems, including lakes. In this study, using fluorescence analysis, we investigated the seasonal dynamics of DOM characteristics in Changshou Lake, which is a typical inland lake in the Three Gorges Reservoir (TGR) area. We also discuss the environmental implications of DOM for mercury (Hg) dynamics. Based on the origins of two end-members, the variations in DOM observed in this study in Changshou Lake suggest that hydrological processes (e.g., terrestrial inputs resulting from runoff and humic-like component residences) and biological activities (e.g., microbial and algae growth) are the two main principal components controlling the seasonal dynamics of DOM characteristics. Furthermore, the dynamics of dissolved Hg co-varied with variations in DOM properties, rather than with dissolved organic carbon (DOC) concentrations. This indicates that the previously reported simple correlations between DOC and Hg were not comprehensive and may lead to misunderstanding the interactions between DOM and Hg. Therefore, we recommend that when using DOM-Hg correlations to evaluate the role of DOM in the environmental fate of Hg, especially in field investigations of the spatial and temporal distribution of Hg, the properties of DOM must be taken into account. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mixing and photoreactivity of dissolved organic matter in the Nelson/Hayes estuarine system (Hudson Bay, Canada)

NASA Astrophysics Data System (ADS)

Guéguen, C.; Mokhtar, M.; Perroud, A.; McCullough, G.; Papakyriakou, T.

2016-09-01

This work presents the results of a 4-year study (2009-2012) investigating the mixing and photoreactivity of dissolved organic matter (DOM) in the Nelson/Hayes estuary (Hudson Bay). Dissolved organic carbon (DOC), colored DOM, and humic-like DOM decreased with increasing salinity (r2 = 0.70-0.84). Removal of DOM was noticeable at low to mid salinity range, likely due to degradation and/or adsorption to particles. DOM photobleaching rates (i.e., decrease in DOM signal resulting from exposure to solar radiation) ranged from 0.005 to 0.030 h- 1, corresponding to half-lives of 4.9-9.9 days. Dissolved organic matter from the Nelson and Hayes Rivers was more photoreactive than from the estuary where the photodegradation of terrestrial DOM decreased with increasing salinity. Coincident with the loss of CDOM absorption was an increase in spectral slope S, suggesting a decrease in DOM molecular weight. Marked differences in photoreactivity of protein- and humic-like DOM were observed with highly humidified material being the most photosensitive. Information generated by our study will provide a valuable data set for better understanding the impacts of future hydroelectric development and climate change on DOM biogeochemical dynamics in the Nelson/Hayes estuary and coastal domain. This study will constitute a reference on terrestrial DOM fate prior to building additional generating capacity on the Nelson River.

Roxarsone binding to soil-derived dissolved organic matter: Insights from multi-spectroscopic techniques.

PubMed

Fu, Qing-Long; He, Jian-Zhou; Blaney, Lee; Zhou, Dong-Mei

2016-07-01

The fate and transport of roxarsone (ROX), a widely used organoarsenic feed additive, in soil is significantly influenced by the ubiquitous presence of soil-derived dissolved organic matter (DOM). In this study, fluorescence quenching titration and two-dimensional correlation spectroscopy (2D-COS) were employed to study ROX binding to DOM. Binding mechanisms were revealed by fluorescence lifetime measurement and Fourier transform infrared spectroscopy (FTIR). Humic- and protein-like fluorophores were identified in the excitation-emission matrix and synchronous fluorescence spectra of DOM. The conditional stability constant (log KC) for ROX binding to DOM was found to be 5.06, indicating that ROX was strongly bound to DOM. The binding order of ROX to DOM fluorophores revealed by 2D-COS followed the sequence of protein-like fluorophore ≈ the longer wavelength excited humic-like (L-humic-like) fluorophore > the shorter wavelength excited humic-like (S-humic-like) fluorophore. 2D-COS resolved issues with peak overlapping and allowed further exploration of the interaction between ROX and DOM. Results of fluorescence lifetime and FTIR spectra demonstrated that ROX interacted with DOM through the hydroxyl, amide II, carboxyl, aliphatic CH, and NO2 groups, yielding stable DOM-ROX complexes. The strong interaction between ROX and DOM implies that DOM plays an important role in the environmental fate of ROX in soil. Copyright © 2016 Elsevier Ltd. All rights reserved.

Constraining Biomarkers of Dissolved Organic Matter Sourcing Using Microbial Incubations of Vascular Plant Leachates of the California landscape

NASA Astrophysics Data System (ADS)

Harfmann, J.; Hernes, P.; Chuang, C. Y.; Kaiser, K.; Spencer, R. G.; Guillemette, F.

2017-12-01

Source origin of dissolved organic matter (DOM) is crucial in determining reactivity, driving chemical and biological processing of carbon. DOM source biomarkers such as lignin (a vascular plant marker) and D-amino acids (bacterial markers) are well-established tools in tracing DOM origin and fate. The development of high-resolution mass spectrometry and optical studies has expanded our toolkit; yet despite these advances, our understanding of DOM sources and fate remains largely qualitative. Quantitative data on DOM pools and fluxes become increasingly necessary as we refine our comprehension of its composition. In this study, we aim to calibrate and quantify DOM source endmembers by performing microbial incubations of multiple vascular plant leachates, where total DOM is constrained by initial vascular plant input and microbial production. Derived endmembers may be applied to endmember mixing models to quantify DOM source contributions in aquatic systems.

On the use of hydroxyl radical kinetics to assess the number-average molecular weight of dissolved organic matter.

PubMed

Appiani, Elena; Page, Sarah E; McNeill, Kristopher

2014-10-21

Dissolved organic matter (DOM) is involved in numerous environmental processes, and its molecular size is important in many of these processes, such as DOM bioavailability, DOM sorptive capacity, and the formation of disinfection byproducts during water treatment. The size and size distribution of the molecules composing DOM remains an open question. In this contribution, an indirect method to assess the average size of DOM is described, which is based on the reaction of hydroxyl radical (HO(•)) quenching by DOM. HO(•) is often assumed to be relatively unselective, reacting with nearly all organic molecules with similar rate constants. Literature values for HO(•) reaction with organic molecules were surveyed to assess the unselectivity of DOM and to determine a representative quenching rate constant (k(rep) = 5.6 × 10(9) M(-1) s(-1)). This value was used to assess the average molecular weight of various humic and fulvic acid isolates as model DOM, using literature HO(•) quenching constants, kC,DOM. The results obtained by this method were compared with previous estimates of average molecular weight. The average molecular weight (Mn) values obtained with this approach are lower than the Mn measured by other techniques such as size exclusion chromatography (SEC), vapor pressure osmometry (VPO), and flow field fractionation (FFF). This suggests that DOM is an especially good quencher for HO(•), reacting at rates close to the diffusion-control limit. It was further observed that humic acids generally react faster than fulvic acids. The high reactivity of humic acids toward HO(•) is in line with the antioxidant properties of DOM. The benefit of this method is that it provides a firm upper bound on the average molecular weight of DOM, based on the kinetic limits of the HO(•) reaction. The results indicate low average molecular weight values, which is most consistent with the recent understanding of DOM. A possible DOM size distribution is discussed to reconcile the small nature of DOM with the large-molecule behavior observed in other studies.

Modeling Effects of Lability on Microbial Uptake of DOM in River Reaches

NASA Astrophysics Data System (ADS)

Li, A.; Drummond, J. D.; Bowen, J. C.; Cory, R. M.; Kaplan, L.; Packman, A. I.

2017-12-01

Rivers are hotspots for biological degradation of dissolved organic matter (DOM), contributing to 1.8 petagrams of carbon emissions per year. DOM represents approximately 60% of the total mass of organic carbon transported within river networks, fueling stream ecosystem metabolism. Not all DOM is biodegradable, biodegradation rates vary based on lability, and lability decreases with reaction time. Fluorescent fractions of DOM (FDOM) are often used as proxies of DOM lability. Humic-like FDOM, previously considered recalcitrant and thought to contribute minimally to the biodegradable DOM pools, has recently been shown to contribute more than 50% to DOM uptake in bioreactor columns colonized by bacteria in stream water. Protein-like FDOM, a proxy for the biodegradable DOM pool, also contributes to the recalcitrant DOM pool in bioreactors. However, the contribution of different lability pools to DOM uptake at the reach scale remains elusive. Here we combine local-scale results from a bioreactor study and measures of stream geomorphology parameters to model reach-scale DOM uptake in White Clay Creek, a Pennsylvania piedmont stream with an intact, forested riparian zone and inputs from upland agriculture. Steady state modeling of a point-source, continuous injection of FDOM shows that humic-like FDOM contributes up to 80% of the total removal of FDOM at the reach scale, suggesting its importance to in-stream DOM uptake. Tryptophan-like FDOM, a protein-like FDOM, contributes to 80% of the remaining fraction of FDOM at the reach scale that incorporates longer timescales of transport and retention. This is consistent with recent local-scale findings that the lability of tryptophan-like FDOM decreases substantially with reaction time in bioreactors, such that it becomes much more recalcitrant as it travels downstream. Steady state modeling of a distributed source, continuous injection of FDOM shows that contributing sources distribute differently along the river reach for each FDOM component, due to their different uptake patterns. Thus, variations of DOM lability are important for estimating reach-scale microbial uptake and contributing sources of in-stream DOM.

Stream Dissolved Organic Matter Quantity and Quality Along a Wetland-Cropland Catchment Gradient

NASA Astrophysics Data System (ADS)

McDonough, O.; Hosen, J. D.; Lang, M. W.; Oesterling, R.; Palmer, M.

2012-12-01

Wetlands may be critical sources of dissolved organic matter (DOM) to stream networks. Yet, more than half of wetlands in the continental United States have been lost since European settlement, with the majority of loss attributed to agriculture. The degree to which agricultural loss of wetlands impacts stream DOM is largely unknown and may have important ecological implications. Using twenty headwater catchments on the Delmarva Peninsula (Maryland, USA), we investigated the seasonal influence of wetland and cropland coverage on downstream DOM quantity and quality. In addition to quantifying bulk downstream dissolved organic carbon (DOC) concentration, we used a suite of DOM UV-absorbance metrics and parallel factor analysis (PARAFAC) modeling of excitation-emission fluorescence spectra (EEMs) to characterize DOM composition. Percent bioavailable DOC (%BDOC) was measured during the Spring sampling using a 28-day incubation. Percent wetland coverage and % cropland within the watersheds were significantly negatively correlated (r = -0.93, p < 0.001). Results show that % wetland coverage was positively correlated with stream DOM concentration, molecular weight, aromaticity, humic-like fluorescence, and allochthonous origin. Conversely, increased wetland coverage was negatively correlated with stream DOM protein-like fluorescence. Percent BDOC decreased with DOM humic-like fluorescence and increased with protein-like fluorescence. We observed minimal seasonal interaction between % wetland coverage and DOM concentration and composition across Spring, Fall, and Winter sampling seasons. However, principal component analysis suggested more pronounced seasonal differences exist in stream DOM. This study highlights the influence of wetlands on downstream DOM in agriculturally impacted landscapes where loss of wetlands to cultivation may significantly alter stream DOM quantity and quality.

Spatial pattern of dissolved organic matter (DOM) along a stream drainage in a forested, Piedmont catchment

NASA Astrophysics Data System (ADS)

Inamdar, S. P.; Singh, S.

2013-12-01

Understanding how dissolved organic matter (DOM) varies spatially in catchments and the processes and mechanisms that regulate this variation is critical for developing accurate and reliable models of DOM. We determined the concentrations and composition of DOM at multiple locations along a stream drainage network in a 79 ha forested, Piedmont, watershed in Maryland, USA. DOM concentrations and composition was compared for five stream locations during baseflow (drainage areas - 0.62, 3.5, 4.5, 12 and 79 ha) and three locations (3.5, 12, 79 ha) for storm flow. Sampling was conducted by manual grab samples and automated ISCO samplers. DOM composition was characterized using a suite of spectrofluorometric indices which included - HIX, a254, and FI. A site-specific PARAFAC model was also developed for DOM fluorescence to determine the humic-, fulvic-, and protein-like DOM constituents. Hydrologic flow paths during baseflow and stormflow were characterized for all stream locations using an end-member mixing model (EMMA). DOM varied notably across the sampled positions for baseflow and stormflow. During baseflow, mean DOC concentrations for the sampled locations ranged between 0.99-3.1 mg/L whereas for stormflow the range was 5.22-8.11 mg/L. Not surprisingly, DOM was more humic and aromatic during stormflow versus baseflow. The 3.5 ha stream drainage location that contained a large wetland yielded the highest DOC concentration as well as the most humic and aromatic DOM, during both, baseflow and stormflow. In contrast, a headwater stream location (0.62 ha) that received runoff from a groundwater seep registered the highest mean value for % protein-like DOM (30%) and the lowest index for aromaticity (mean a254 = 6.52) during baseflow. During stormflow, the mean % protein-like DOM was highest at the largest 79 ha drainage location (mean = 11.8%) and this site also registered the lowest mean value for a254 (46.3). Stream drainage locations that received a larger proportion of runoff along surficial flow paths produced a more aromatic and humic DOM with high DOC concentrations; whereas those with a greater proportion of groundwater contributions produced DOM with greater % of protein-like content. Overall, our observations suggest that occurrence of wetlands and the nature of hydrologic flow paths were the key determinants for the spatial pattern of DOM.

Compositions and constituents of freshwater dissolved organic matter isolated by reverse osmosis.

PubMed

Zhang, Yulong; Huang, Wen; Ran, Yong; Mao, Jingdong

2014-08-15

Dissolved organic matter (DOM) from riverine and lacustrine water was isolated using a reverse osmosis (RO) system. Solid-state (13)C nuclear magnetic resonance ((13)C NMR) was used to quantitatively evaluate the compositions and constituents of DOM, which are compared with previous investigations on marine DOM. Results indicated that concentration factor (CF) was a key metric controlling yield and sorption of DOM on the RO system. The sorption was likely non-selective, based on the (13)C NMR and δ(13)C analyses. Carbohydrates and lipids accounted for 25.0-41.5% and 30.2-46.3% of the identifiable DOM, followed by proteins (18.2-19.8%) and lignin (7.17-12.8%). The freshwater DOM contained much higher alkyl and aromatic C but lower alkoxyl and carboxyl C than marine DOM. The structural difference was not completely accounted for by using structure of high molecular weight (HMW) DOM, suggesting a size change involved in transformations of DOM during the transport from rivers to oceans. Copyright © 2014 Elsevier Ltd. All rights reserved.

The impact of solar radiation on the use of dissolved organic matter in two Ozark Streams: Possible role of photo-enhanced humification

NASA Astrophysics Data System (ADS)

Townsend, S. L.; Ziegler, S. E.

2005-05-01

The effect of solar radiation on dissolved organic matter (DOM) utilization was studied in two contrasting streams from June 2002 through October 2004. Moores Creek is an agricultural stream with elevated nutrient and dissolved organic carbon (DOC) concentrations. Huey Hollow is a forested stream with low nutrient and DOC concentrations. A series of experiments were conducted seasonally to assess how solar radiation influenced DOM utilization. Exposure of DOM to solar radiation significantly decreased its utilization during most seasons in both streams. Each stream experienced one seasonal period when exposure of DOM significantly increased bacterial production; during these periods, DOM appeared to be the least bioavailable and most photochemically reactive. Interestingly, in spring when bioavailability of DOM was lowest in Moores Creek solar radiation exposure further reduced DOM bioavailability. Elevated ammonium concentrations during this spring experiment suggest photochemically-enhanced humification may have been an important mechanism influencing DOM cycling. Bioassays using 15N-labeled ammonium indicated no significant effect of elevated ammonium on the utilization of DOM in either stream in fall 2004. Detection of elevated 15N in the DOM fractions, however, would reveal light stimulated humification under elevated ammonium concentrations not detected with the bioassay.

Effects of dissolved organic matter from a eutrophic lake on the freely dissolved concentrations of emerging organic contaminants.

PubMed

Xiao, Yi-Hua; Huang, Qing-Hui; Vähätalo, Anssi V; Li, Fei-Peng; Chen, Ling

2014-08-01

The authors studied the effects of dissolved organic matter (DOM) on the bioavailability of bisphenol A (BPA) and chloramphenicol by measuring the freely dissolved concentrations of the contaminants in solutions containing DOM that had been isolated from a mesocosm in a eutrophic lake. The abundance and aromaticity of the chromophoric DOM increased over the 25-d mesocosm experiment. The BPA freely dissolved concentration was 72.3% lower and the chloramphenicol freely dissolved concentration was 56.2% lower using DOM collected on day 25 than using DOM collected on day 1 of the mesocosm experiment. The freely dissolved concentrations negatively correlated with the ultraviolent absorption coefficient at 254 nm and positively correlated with the spectral slope of chromophoric DOM, suggesting that the bioavailability of these emerging organic contaminants depends on the characteristics of the DOM present. The DOM-water partition coefficients (log KOC ) for the emerging organic contaminants positively correlated with the aromaticity of the DOM, measured as humic acid-like fluorescent components C1 (excitation/emission=250[313]/412 nm) and C2 (excitation/emission=268[379]/456 nm). The authors conclude that the bioavailability of emerging organic contaminants in eutrophic lakes can be affected by changes in the DOM. © 2014 SETAC.

Dissolved organic matter reduces algal accumulation of methylmercury

USGS Publications Warehouse

Luengen, Allison C.; Fisher, Nicholas S.; Bergamaschi, Brian A.

2012-01-01

Dissolved organic matter (DOM) significantly decreased accumulation of methylmercury (MeHg) by the diatom Cyclotella meneghiniana in laboratory experiments. Live diatom cells accumulated two to four times more MeHg than dead cells, indicating that accumulation may be partially an energy-requiring process. Methylmercury enrichment in diatoms relative to ambient water was measured by a volume concentration factor (VCF). Without added DOM, the maximum VCF was 32 x 104, and the average VCF (from 10 to 72 h) over all experiments was 12.6 x 104. At very low (1.5 mg/L) added DOM, VCFs dropped by approximately half. At very high (20 mg/L) added DOM, VCFs dropped 10-fold. Presumably, MeHg was bound to a variety of reduced sulfur sites on the DOM, making it unavailable for uptake. Diatoms accumulated significantly more MeHg when exposed to transphilic DOM extracts than hydrophobic ones. However, algal lysate, a labile type of DOM created by resuspending a marine diatom in freshwater, behaved similarly to a refractory DOM isolate from San Francisco Bay. Addition of 67 μM L-cysteine resulted in the largest drop in VCFs, to 0.28 x 104. Although the DOM composition influenced the availability of MeHg to some extent, total DOM concentration was the most important factor in determining algal bioaccumulation of MeHg.

Controls on the dynamics of dissolved organic matter in soils: A review

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kalbitz, K.; Solinger, S.; Park, J.H.

Dissolved organic matter (DOM) in soils plays an important role in the biogeochemistry of carbon, nitrogen, and phosphorus, in pedogenesis, and in the transport of pollutants in soils. The aim of this review is to summarize the recent literature about controls on DOM concentrations and fluxes in soils. The authors focus on comparing results between laboratory and field investigations and on the differences between the dynamics of dissolved organic carbon (DOC), nitrogen (DON), and phosphorus (DOP). Both laboratory and field studies show that litter and humus are the most important DOM sources in soils. However, it is impossible to quantifymore » the individual contributions of each of these sources to DOM release. In addition, it is not clear how changes in the pool sizes of litter or humus may affect DOM release. High microbial activity, high fungal abundance, and any conditions that enhance mineralization all promote high DOM concentrations. However, under field conditions, hydrologic variability in soil horizons with high carbon contents may be more important than biotic controls. In subsoil horizons with low carbon contents, DOM may be adsorbed strongly to mineral surfaces, resulting in low DOM concentrations in the soil solution. There are strong indications that microbial degradation of DOM also controls the fate of DOM in the soil.« less

Comprehensive assessment of precursors, diagenesis, and reactivity to water treatment of dissolved and colloidal organic matter

USGS Publications Warehouse

Leenheer, J.A.

2004-01-01

A comprehensive isolation, fractionation, and characterization research approach was developed for dissolved and colloidal organic matter (DOM) in water, and it was applied to various surface- and groundwaters to assess DOM precursors, DOM diagenesis, and DOM reactivity to water treatment processes. Major precursors for natural DOM are amino sugars, condensed tannins, and terpenoids. Amino sugar colloids derived from bacterial cell walls are incompletely removed by drinking water treatment and foul reverse osmosis membranes, but are nearly quantitatively removed by soil/aquifer treatment. When chlorinated, amino sugars produce low yields of regulated disinfection by-products (DBFs) but they produce significant chlorine demand that is likely caused by chlorination of free amino groups. Condensed tannins are major precursors for "blackwater" DOM such as that found in the Suwannee River. This DOM produces high yields of DBPs upon chorination, and is efficiently removed by coagulation/flocculation treatment. Terpenoid-derived DOM appears to be biologically refractory, infiltrates readily into groundwater with little removal by soil/aquifer treatment, gives low DBF-yields upon chlorination and is poorly removed by coagulation/flocculation treatments. Peptides derived from proteins are major components of the base DOM fraction (10% or less of the mass of DOM), and this fraction produces large yields of haloacetonitriles upon chorination.

Retrieval Interference in Syntactic Processing: The Case of Reflexive Binding in English.

PubMed

Patil, Umesh; Vasishth, Shravan; Lewis, Richard L

2016-01-01

It has been proposed that in online sentence comprehension the dependency between a reflexive pronoun such as himself/herself and its antecedent is resolved using exclusively syntactic constraints. Under this strictly syntactic search account, Principle A of the binding theory-which requires that the antecedent c-command the reflexive within the same clause that the reflexive occurs in-constrains the parser's search for an antecedent. The parser thus ignores candidate antecedents that might match agreement features of the reflexive (e.g., gender) but are ineligible as potential antecedents because they are in structurally illicit positions. An alternative possibility accords no special status to structural constraints: in addition to using Principle A, the parser also uses non-structural cues such as gender to access the antecedent. According to cue-based retrieval theories of memory (e.g., Lewis and Vasishth, 2005), the use of non-structural cues should result in increased retrieval times and occasional errors when candidates partially match the cues, even if the candidates are in structurally illicit positions. In this paper, we first show how the retrieval processes that underlie the reflexive binding are naturally realized in the Lewis and Vasishth (2005) model. We present the predictions of the model under the assumption that both structural and non-structural cues are used during retrieval, and provide a critical analysis of previous empirical studies that failed to find evidence for the use of non-structural cues, suggesting that these failures may be Type II errors. We use this analysis and the results of further modeling to motivate a new empirical design that we use in an eye tracking study. The results of this study confirm the key predictions of the model concerning the use of non-structural cues, and are inconsistent with the strictly syntactic search account. These results present a challenge for theories advocating the infallibility of the human parser in the case of reflexive resolution, and provide support for the inclusion of agreement features such as gender in the set of retrieval cues.

Retrieval Interference in Syntactic Processing: The Case of Reflexive Binding in English

PubMed Central

Patil, Umesh; Vasishth, Shravan; Lewis, Richard L.

2016-01-01

It has been proposed that in online sentence comprehension the dependency between a reflexive pronoun such as himself/herself and its antecedent is resolved using exclusively syntactic constraints. Under this strictly syntactic search account, Principle A of the binding theory—which requires that the antecedent c-command the reflexive within the same clause that the reflexive occurs in—constrains the parser's search for an antecedent. The parser thus ignores candidate antecedents that might match agreement features of the reflexive (e.g., gender) but are ineligible as potential antecedents because they are in structurally illicit positions. An alternative possibility accords no special status to structural constraints: in addition to using Principle A, the parser also uses non-structural cues such as gender to access the antecedent. According to cue-based retrieval theories of memory (e.g., Lewis and Vasishth, 2005), the use of non-structural cues should result in increased retrieval times and occasional errors when candidates partially match the cues, even if the candidates are in structurally illicit positions. In this paper, we first show how the retrieval processes that underlie the reflexive binding are naturally realized in the Lewis and Vasishth (2005) model. We present the predictions of the model under the assumption that both structural and non-structural cues are used during retrieval, and provide a critical analysis of previous empirical studies that failed to find evidence for the use of non-structural cues, suggesting that these failures may be Type II errors. We use this analysis and the results of further modeling to motivate a new empirical design that we use in an eye tracking study. The results of this study confirm the key predictions of the model concerning the use of non-structural cues, and are inconsistent with the strictly syntactic search account. These results present a challenge for theories advocating the infallibility of the human parser in the case of reflexive resolution, and provide support for the inclusion of agreement features such as gender in the set of retrieval cues. PMID:27303315

Electrochemically modified dissolved organic matter accelerates the combining photodegradation and biodegradation of 17α-ethinylestradiol in natural aquatic environment.

PubMed

He, Huan; Huang, Bin; Fu, Gen; Xiong, Dan; Xu, Zhixiang; Wu, Xinhao; Pan, Xuejun

2018-06-15

The photochemical conversion and microbial transformation of pollutants mediated by dissolved organic matter (DOM), including 17α-ethinylestradiol (EE2), are often accompanied in natural water. However, there are few studies to explore the connection and mechanism between the two processes. This research aims to investigate the mechanism of DOM after electrochemically modification mediated EE2 combining photodegradation and biodegradation in the environment and it want to explain the natural phenomena of DOM after electrochemical advanced treatment entering the water environment mediated EE2 natural degradation. The results showed that combining photodegradation with biodegradation rates of EE2 mediated by DOM and electrochemically modified DOM (E-DOM) were promoted obviously. The efficiency of EE2 biodegradation was shown to be strongly correlated with electron accepting capacity (EAC) of DOM. Electrochemical modification can increase the EAC of DOM leading to EE2 biodegradation accelerated, and it also can form more triplet-state DOM moieties to promote the EE2 photodegradation in irradiation conditions, due to the increasing of quinone-type structures in DOM. Moreover, cell polymeric secretion (CPS) secreted from the microorganism could be stimulated to an excited state by irradiation, and that also accelerated EE2 degradation. Photolysis combined with biochemical degradation yielded less toxic degradation products. This study shows that the emission of DOM in wastewater after electrochemical treatment could accelerate estrogen degradation and play a positive role on the pollutant transformation in the environment. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effects of quantity, quality, and contact time of dissolved organic matter on bioconcentration of benzo[a]pyrene in the nematode Caenorhabditis elegans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haitzer, M.; Hoess, S.; Burnison, B.K.

1999-03-01

Quantity and quality of dissolved organic matter (DOM) and the time allowed for DOM to interact with organic contaminants can influence their bioavailability. The authors studied the effect of natural aquatic DOM that had been in contact with benzo[a]pyrene (B[a]P) for 1 to 12 d on the bioconcentration of B[a]P in the nematode Caenorhabditis elegans. Dissolved organic matter quality and quantity was varied by using DOM from three different sources, each in three different concentrations. A model, based on the assumption that only freely dissolved B[a]P is bioavailable, was employed to estimate biologically determined partition coefficients [K{sub p}(biol.)]. Expressing themore » data for each combination of DOM source and contact time in a single K{sub p} (biol.) value allowed a direct comparison of the effects of different DOM qualities and contact times. The results show that the effect of DOM from a specific source was dependent on DOM quantity, but they also observed a distinct effect of DOM quality (represented by different sampling locations) on the bioconcentration of B[a]P. Contact time had no significant influence for the effects of two DOM sources on the bioconcentration of B[a]P. However, the third DOM source was significantly more effective with increased contact time, leading to lower B[a]P bioconcentration in the nematodes.« less

Association between arsenic and different-sized dissolved organic matter in the groundwater of black-foot disease area, Taiwan.

PubMed

Chen, Ting-Chien; Hseu, Zeng-Yei; Jean, Jiin-Shuh; Chou, Mon-Lin

2016-09-01

The formation of an arsenic (As)-dissolved organic matter (DOM) complex is important in driving the release of arsenic in groundwater. This study collected groundwater samples from a 20 m deep well throughout 2014 and separated each into three subsamples by ultrafiltration: high molecular weight-DOM (HDOM, 0.45 μm-10 kDa), medium molecular weight-DOM (MDOM, 10-1 kDa), and low molecular weight-DOM (LDOM, <1 kDa) solutions. The fractional DOM was measured with a three-dimensional excitation-emission matrix (EEM) via fluorescence spectroscopy. A fluorescence quenching method was used to calculate the apparent stability constant (Ks) between arsenic and the fractional DOM. Based on the EEM records, three fluorescence indicators were further calculated to characterize the DOM sources, including the fluorescence index (FI), the biological index (BI), and the humification index (HI). The experimental results indicated that arsenic in the groundwater was mainly partitioned into the MDOM and LDOM fractions. All fractional DOMs contained humic acid-like substances and were considered as microbial sources. LDOM had the highest humification degree and aromaticity, followed by MDOM and HDOM. The As and DOM association could be formed by a Fe-bridge, which was demonstrated by the Ks values and fourier transform infrared (FTIR) spectra of the DOM. The formation of AsFe-DOM complex was only significant in the MDOM and LDOM. Copyright © 2016 Elsevier Ltd. All rights reserved.

Temporal Dynamics in the Concentration, Flux, and Optical Properties of Tree-derived Dissolved Organic Matter (Tree-DOM) in an Epiphyte-laden Oak-cedar Forest.

NASA Astrophysics Data System (ADS)

Whitetree, A.; Van Stan, J. T., II; Wagner, S.; Guillemette, F.; Lewis, J.; Silva, L.; Stubbins, A.

2017-12-01

Studies on the fate and transport of dissolved organic matter (DOM) along the rainfall-to-discharge flow pathway typically begin in streams or soils, neglecting the initial enrichment of rainfall with DOM during contact with plant canopies. However, rain water can gather significant amounts of tree-derived DOM (tree-DOM) when it drains from the canopy, as throughfall, and down the stem, as stemflow. We examined the temporal variability of event-scale tree-DOM concentrations, yield, and optical (light absorbance and fluorescence) characteristics from an epiphyte-laden Quercus virginiana-Juniperus virginiana forest on Skidaway Island, Savannah, Georgia (USA). All tree-DOM fluxes were highly enriched compared to rainfall and epiphytes further increased concentrations. Stemflow DOC concentrations were greater than throughfall across study species, yet larger throughfall water yields produced greater DOC yields versus stemflow. Tree-DOM optical characteristics indicate it is aromatic-rich with FDOM dominated by humic-like fluorescence, containing 10-20% protein-like (tryptophan-like) fluorescence. Storm size was the only storm condition that strongly correlated with tree-DOM concentration and flux; however, throughfall and stemflow optical characteristics varied little across a wide range of storm conditions (from low magnitude events to intense tropical storms). Annual tree-DOM yields from the study forest (0.8-46 g-C m-2 yr-1) compared well to other yields along the rainfall-to- discharge flow pathway, exceeding DOM yields from some river watersheds.

Origins and bioavailability of dissolved organic matter in groundwater

USGS Publications Warehouse

Shen, Yuan; Chapelle, Francis H.; Strom, Eric W.; Benner, Ronald

2015-01-01

Dissolved organic matter (DOM) in groundwater influences water quality and fuels microbial metabolism, but its origins, bioavailability and chemical composition are poorly understood. The origins and concentrations of dissolved organic carbon (DOC) and bioavailable DOM were monitored during a long-term (2-year) study of groundwater in a fractured-rock aquifer in the Carolina slate belt. Surface precipitation was significantly correlated with groundwater concentrations of DOC, bioavailable DOM and chromophoric DOM, indicating strong hydrological connections between surface and ground waters. The physicochemical and biological processes shaping the concentrations and compositions of DOM during its passage through the soil column to the saturated zone are conceptualized in the regional chromatography model. The model provides a framework for linking hydrology with the processes affecting the transformation, remineralization and microbial production of DOM during passage through the soil column. Lignin-derived phenols were relatively depleted in groundwater DOM indicating substantial removal in the unsaturated zone, and optical properties of chromophoric DOM indicated lower molecular weight DOM in groundwater relative to surface water. The prevalence of glycine, γ-aminobutyric acid, and d-enantiomers of amino acids indicated the DOM was highly diagenetically altered. Bioassay experiments were used to establish DOC-normalized yields of amino acids as molecular indicators of DOM bioavailability in groundwater. A relatively small fraction (8 ± 4 %) of DOC in groundwater was bioavailable. The relatively high yields of specific d-enantiomers of amino acids indicated a substantial fraction (15–34 %) of groundwater DOC was of bacterial origin.

Extraneous dissolved organic matter enhanced adsorption of dibutyl phthalate in soils: Insights from kinetics and isotherms.

PubMed

Wu, Wei; Sheng, Hongjie; Gu, Chenggang; Song, Yang; Willbold, Sabine; Qiao, Yan; Liu, Guangxia; Zhao, Wei; Wang, Yu; Jiang, Xin; Wang, Fang

2018-08-01

The widespread use of plastic film, especially in agricultural practices, has resulted in phthalic acid esters (PAEs) pollution, which poses risks for greenhouse soils. Application of composted manure is a common agricultural practice that adds extraneous dissolved organic matter (DOM) to the soil, however, the effect of extraneous DOM on the behavior of PAEs in agricultural soil is not clear. Dibutyl phthalate (DBP) was used as a model compound to investigate the effect and mechanism of extraneous DOM on the adsorption kinetics and isotherms of PAEs in two types of soils, through batch experiments and characterization of extraneous DOM and soils using fourier transform infrared spectroscopy (FTIR) and nuclear magnetic resonance (NMR). The equilibrium adsorption amount of DBP in black soil was higher than in red soil regardless of the presence of extraneous DOM, due to the higher organic matter content of black soil. Hydrophobic partition played a dominant role in the DBP adsorption process of soils with and without extraneous DOM. The addition of DOM enhanced the adsorption capacity of DBP through partition in the two soils, especially at high DBP concentrations. Additions of a lower concentration of DOM better enhanced the adsorption effect than the higher concentrated DOM, due to an increase in water solubility of DBP resulted from excessive extraneous DOM in aqueous phase. Differences in mineral composition of soils led to diverse adsorption mechanisms of DBP as affected by additions of extraneous DOM. The FTIR spectra indicated that the intra-molecular and intermolecular hydrogen bond interactions of carboxylic acids, aromatic CC and CO in amides were involved in DBP adsorption in soils. Therefore, addition of DOM may increase adsorption of DBP in soils and thus influence its bioavailability and transformation in soils. Copyright © 2018 Elsevier B.V. All rights reserved.

The Effect of Increased Loads of Dissolved Organic Matter on Estuarine Microbial Community Composition and Function

PubMed Central

Traving, Sachia J.; Rowe, Owen; Jakobsen, Nina M.; Sørensen, Helle; Dinasquet, Julie; Stedmon, Colin A.; Andersson, Agneta; Riemann, Lasse

2017-01-01

Increased river loads are projected as one of the major consequences of climate change in the northern hemisphere, leading to elevated inputs of riverine dissolved organic matter (DOM) and inorganic nutrients to coastal ecosystems. The objective of this study was to investigate the effects of elevated DOM on a coastal pelagic food web from the coastal northern Baltic Sea, in a 32-day mesocosm experiment. In particular, the study addresses the response of bacterioplankton to differences in character and composition of supplied DOM. The supplied DOM differed in stoichiometry and quality and had pronounced effects on the recipient bacterioplankton, driving compositional changes in response to DOM type. The shifts in bacterioplankton community composition were especially driven by the proliferation of Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Alpha- and Betaproteobacteria populations. The DOM additions stimulated protease activity and a release of inorganic nutrients, suggesting that DOM was actively processed. However, no difference between DOM types was detected in these functions despite different community compositions. Extensive release of re-mineralized carbon, nitrogen and phosphorus was associated with the bacterial processing, corresponding to 25–85% of the supplied DOM. The DOM additions had a negative effect on phytoplankton with decreased Chl a and biomass, particularly during the first half of the experiment. However, the accumulating nutrients likely stimulated phytoplankton biomass which was observed to increase towards the end of the experiment. This suggests that the nutrient access partially outweighed the negative effect of increased light attenuation by accumulating DOM. Taken together, our experimental data suggest that parts of the future elevated riverine DOM supply to the Baltic Sea will be efficiently mineralized by microbes. This will have consequences for bacterioplankton and phytoplankton community composition and function, and significantly affect nutrient biogeochemistry. PMID:28337180

Evaluating oxidation-reduction properties of dissolved organic matter from Chinese milk vetch (Astragalus sinicus L.): a comprehensive multi-parametric study.

PubMed

Liu, Yong; Lou, Jun; Li, Fang-Bai; Xu, Jian-Ming; Yu, Xiong-Sheng; Zhu, Li-An; Wang, Feng

2014-08-01

Green manuring is a common practice in replenishment of soil organic matter and nutrients in rice paddy field. Owing to the complex interplay of multiple factors, the oxidation--reduction (redox) properties of dissolved organic matter (DOM) from green manure crops are presently not fully understood. In this study, a variety of surrogate parameters were used to evaluate the redox capacity and redox state of DOM derived from Chinese milk vetch (CMV, Astragalus sinicus L.) via microbial decomposition under continuously flooded (CF) and non-flooded (NF) conditions. Additionally, the correlation between the surrogate parameters of CMV-DOM and the kinetic parameters of relevant redox reactions was evaluated in a soil-water system containing CMV-DOM. Results showed that the redox properties of CMV-DOM were substantially different between the fresh and decomposed CMV-DOM treatments. Determination of the surrogate parameters via ultraviolet-visible/Fourier transform infrared absorption spectroscopy and gel permeation chromatography generally provided high-quality data for predicting the redox capacity of CMV-DOM, while the surrogate parameters determined by elemental analysis were suitable for predicting the redox state of CMV-DOM. Depending on the redox capacity and redox state of various moieties/components, NF-decomposed CMV-DOM could easily accelerate soil reduction by shuttling electrons to iron oxides, because it contained more reversible redox-active functional groups (e.g. quinone and hydroquinone pairs) than CF-decomposed CMV-DOM. This work demonstrates that a single index cannot interpret complex changes in multiple factors that jointly determine the redox reactivity of CMV-DOM. Thus, a multi-parametric study is needed for providing comprehensive information on the redox properties of green manure DOM.

How reservoirs alter drinking water quality: Organic matter sources, sinks, and transformations

USGS Publications Warehouse

Kraus, Tamara E.C.; Bergamaschi, Brian A.; Hernes, Peter J.; Doctor, Daniel H.; Kendall, Carol; Downing, Bryan D.; Losee, Richard F.

2011-01-01

Within reservoirs, production, transformation, and loss of dissolved organic matter (DOM) occur simultaneously. While the balance between production and loss determines whether a reservoir is a net sink or source of DOM, changes in chemical composition are also important because they affect DOM reactivity with respect to disinfection by-product (DBP) formation. The composition of the DOM pool also provides insight into DOM sources and processing, which can inform reservoir management. We examined the concentration and composition of DOM in San Luis Reservoir, a large off-stream impoundment of the California State Water Project. We used a wide array of DOM chemical tracers including dissolved organic carbon (DOC) concentration, trihalomethane and haloacetic acid formation potentials (THMFP and HAAFP, respectively), absorbance properties, isotopic composition, lignin phenol content, and structural groupings determined by 13C nuclear magnetic resonance (NMR). There were periods when the reservoir was a net source of DOC due to the predominance of algal production (summer), a net sink due to the predominance of degradation (fall–winter), and balanced between production and consumption (spring). Despite only moderate variation in bulk DOC concentration (3.0–3.6 mg C/L), changes in DOM composition indicated that terrestrial-derived material entering the reservoir was being degraded and replaced by aquatic-derived DOM produced within the reservoir. Substantial changes in the propensity of the DOM pool to form THMs and HAAs illustrate that the DBP precursor pool was not directly coupled to bulk DOC concentration and indicate that algal production is an important source of DBP precursors. Results suggest reservoirs have the potential to attenuate DOM amount and reactivity with respect to DBP precursors via degradative processes; however, these benefits can be decreased or even negated by the production of algal-derived DOM.

Human activities cause distinct dissolved organic matter composition across freshwater ecosystems.

PubMed

Williams, Clayton J; Frost, Paul C; Morales-Williams, Ana M; Larson, James H; Richardson, William B; Chiandet, Aisha S; Xenopoulos, Marguerite A

2016-02-01

Dissolved organic matter (DOM) composition in freshwater ecosystems is influenced by the interactions among physical, chemical, and biological processes that are controlled, at one level, by watershed landscape, hydrology, and their connections. Against this environmental template, humans may strongly influence DOM composition. Yet, we lack a comprehensive understanding of DOM composition variation across freshwater ecosystems differentially affected by human activity. Using optical properties, we described DOM variation across five ecosystem groups of the Laurentian Great Lakes region: large lakes, Kawartha Lakes, Experimental Lakes Area, urban stormwater ponds, and rivers (n = 184 sites). We determined how between ecosystem variation in DOM composition related to watershed size, land use and cover, water quality measures (conductivity, dissolved organic carbon (DOC), nutrient concentration, chlorophyll a), and human population density. The five freshwater ecosystem groups had distinctive DOM composition from each other. These significant differences were not explained completely through differences in watershed size nor spatial autocorrelation. Instead, multivariate partial least squares regression showed that DOM composition was related to differences in human impact across freshwater ecosystems. In particular, urban/developed watersheds with higher human population densities had a unique DOM composition with a clear anthropogenic influence that was distinct from DOM composition in natural land cover and/or agricultural watersheds. This nonagricultural, human developed impact on aquatic DOM was most evident through increased levels of a microbial, humic-like parallel factor analysis component (C6). Lotic and lentic ecosystems with low human population densities had DOM compositions more typical of clear water to humic-rich freshwater ecosystems but C6 was only present at trace to background levels. Consequently, humans are strongly altering the quality of DOM in waters nearby or flowing through highly populated areas, which may alter carbon cycles in anthropogenically disturbed ecosystems at broad scales. © 2015 John Wiley & Sons Ltd.

Evaluating the distribution of terrestrial dissolved organic matter in a complex coastal ecosystem using fluorescence spectroscopy

NASA Astrophysics Data System (ADS)

Yamashita, Youhei; Boyer, Joseph N.; Jaffé, Rudolf

2013-09-01

The coastal zone of the Florida Keys features the only living coral reef in the continental United States and as such represents a unique regional environmental resource. Anthropogenic pressures combined with climate disturbances such as hurricanes can affect the biogeochemistry of the region and threaten the health of this unique ecosystem. As such, water quality monitoring has historically been implemented in the Florida Keys, and six spatially distinct zones have been identified. In these studies however, dissolved organic matter (DOM) has only been studied as a quantitative parameter, and DOM composition can be a valuable biogeochemical parameter in assessing environmental change in coastal regions. Here we report the first data of its kind on the application of optical properties of DOM, in particular excitation emission matrix fluorescence with parallel factor analysis (EEM-PARAFAC), throughout these six Florida Keys regions in an attempt to assess spatial differences in DOM sources. Our data suggests that while DOM in the Florida Keys can be influenced by distant terrestrial environments such as the Everglades, spatial differences in DOM distribution were also controlled in part by local surface runoff/fringe mangroves, contributions from seasgrass communities, as well as the reefs and waters from the Florida Current. Application of principal component analysis (PCA) of the relative abundance of EEM-PARAFAC components allowed for a clear distinction between the sources of DOM (allochthonous vs. autochthonous), between different autochthonous sources and/or the diagenetic status of DOM, and further clarified contribution of terrestrial DOM in zones where levels of DOM were low in abundance. The combination between EEM-PARAFAC and PCA proved to be ideally suited to discern DOM composition and source differences in coastal zones with complex hydrology and multiple DOM sources.

Human activities cause distinct dissolved organic matter composition across freshwater ecosystems

USGS Publications Warehouse

Williams, Clayton J.; Frost, Paul C.; Morales-Williams, Ana M.; Larson, James H.; Richardson, William B.; Chiandet, Aisha S.; Xenopoulos, Marguerite A.

2016-01-01

Dissolved organic matter (DOM) composition in freshwater ecosystems is influenced by interactions between physical, chemical, and biological processes that are controlled, at one level, by watershed landscape, hydrology, and their connections. Against this environmental template, humans may strongly influence DOM composition. Yet, we lack a comprehensive understanding of DOM composition variation across freshwater ecosystems differentially affected by human activity. Using optical properties, we described DOM variation across five ecosystem groups of the Laurentian Great Lakes Region: large lakes, Kawartha Lakes, Experimental Lakes Area, urban stormwater ponds, and rivers (n = 184 sites). We determined how between ecosystem variation in DOM composition related to watershed size, land use and cover, water quality measures (conductivity, dissolved organic carbon (DOC), nutrient concentration, chlorophyll a), and human population density. The five freshwater ecosystem groups had distinctive DOM composition from each other. These significant differences were not explained completely through differences in watershed size nor spatial autocorrelation. Instead, multivariate partial least squares regression showed that DOM composition was related to differences in human impact across freshwater ecosystems. In particular, urban/developed watersheds with higher human population densities had a unique DOM composition with a clear anthropogenic influence that was distinct from DOM composition in natural land cover and/or agricultural watersheds. This nonagricultural, human developed impact on aquatic DOM was most evident through increased levels of a microbial, humic-like parallel factor analysis component (C6). Lotic and lentic ecosystems with low human population densities had DOM compositions more typical of clear water to humic-rich freshwater ecosystems but C6 was only present at trace to background levels. Consequently, humans are strongly altering the quality of DOM in waters nearby or flowing through highly populated areas, which may alter carbon cycles in anthropogenically disturbed ecosystems at broad scales.

Photodegradation of dissolved organic matter in ice under solar irradiation.

PubMed

Xue, Shuang; Wang, Chao; Zhang, Zhaohong; Song, Youtao; Liu, Qiang

2016-02-01

The photodegradation behavior of dissolved organic matter (DOM) with different origins in ice under solar irradiation was investigated. Exposure to sunlight at 2.7 × 10(5) J m(-2) resulted in dissolved organic carbon (DOC) reductions of 22.1-36.5% in ice. The naturally occurring DOM had higher photodegradation potentials than the wastewater-derived DOM in ice. Ultraviolet (UV)-absorbing compounds in DOM, regardless of DOM origin, had much higher photodegradation potentials than gross DOC in ice. The susceptibility of UV-absorbing compounds with natural origin to sunlight exposure in ice was higher than those derived from wastewater. Trihalomethane (THM) precursors were more susceptible to photochemical reactions than gross DOC and haloacetic acid (HAA) precursors in ice. THM precursors in naturally occurring DOM were more photoreactive than those in wastewater-derived DOM in ice, while the photoreactivity of HAA precursors in ice was independent of DOM origin. In ice, the photoreactivity of humic-like fluorescent materials, regardless of DOM origin, was higher than that of gross DOC and protein-like fluorescent materials. DOC reductions caused by sunlight irradiation were found to be negatively correlated to DOC levels, and positively correlated to the aromaticity of DOM. The photodegradation of both wastewater-derived and naturally occurring DOM in ice was significantly facilitated at both acid and alkaline pH, as compared to neutral pH. The photodegradation of DOM in ice, regardless of the origin, was facilitated by nitrate ion [Formula: see text] , nitrite ion [Formula: see text] , ferric ion (Fe(3+)) and ferrous ion (Fe(2+)), and on the other hand, was inhibited by chloridion ion (Cl(-)) and copper ion (Cu(2+)). Copyright © 2015 Elsevier Ltd. All rights reserved.

The effect of probe choice and solution conditions on the apparent photoreactivity of dissolved organic matter.

PubMed

Maizel, Andrew C; Remucal, Christina K

2017-08-16

Excited triplet states of dissolved organic matter ( 3 DOM) are quantified directly with the species-specific probes trans,trans-hexadienoic acid (HDA) and 2,4,6-trimethylphenol (TMP), and indirectly with the singlet oxygen ( 1 O 2 ) probe furfuryl alcohol (FFA). Although previous work suggests that these probe compounds may be sensitive to solution conditions, including dissolved organic carbon concentration ([DOC]) and pH, and may quantify different 3 DOM subpopulations, the probes have not been systematically compared. Therefore, we quantify the apparent photoreactivity of diverse environmental waters using HDA, TMP, and FFA. By conducting experiments under ambient [DOC] and pH, with standardized [DOC] and pH, and with solid phase extraction isolates, we demonstrate that much of the apparent dissimilarity in photochemical measurements is attributable to solution conditions, rather than intrinsic differences in 3 DOM production. In general, apparent quantum yields (Φ 1 O 2 ≥ Φ 3 DOM,TMP ≫ Φ 3 DOM,HDA ) and pseudo-steady state concentrations ([ 1 O 2 ] ss > [ 3 DOM] ss,TMP > [ 3 DOM] ss,HDA ) show consistent relationships in all waters under standardized conditions. However, intrinsic differences in 3 DOM photoreactivity are apparent between DOM from diverse sources, as seen in the higher Φ 1 O 2 and lower Φ 3 DOM,TMP of wastewater effluents compared with oligotrophic lakes. Additionally, while conflicting trends in photoreactivity are observed under ambient conditions, all probes observe quantum yields increasing from surface wetlands to terrestrially influenced waters to oligotrophic lakes under standardized conditions. This work elucidates how probe selection and solution conditions influence the apparent photoreactivity of environmental waters and confirms that 3 DOM or 1 O 2 probes cannot be used interchangeably in waters that vary in [DOC], pH, or DOM source.

Biochar amendment to soil changes dissolved organic matter content and composition.

PubMed

Smebye, Andreas; Alling, Vanja; Vogt, Rolf D; Gadmar, Tone C; Mulder, Jan; Cornelissen, Gerard; Hale, Sarah E

2016-01-01

Amendments of biochar, a product of pyrolysis of biomass, have been shown to increase fertility of acidic soils by enhancing soil properties such as pH, cation-exchange-capacity and water-holding-capacity. These parameters are important in the context of natural organic matter contained in soils, of which dissolved organic matter (DOM) is the mobile and most bioavailable fraction. The effect of biochar on the content and composition of DOM in soils has received little research attention. This study focuses on the effects of amendments of two different biochars to an acidic acrisol and a pH-neutral brown soil. A batch experiment showed that mixing biochar with the acrisols at a 10 wt.% dose increased the pH from 4.9 to 8.7, and this resulted in a 15-fold increase in the dissolved organic carbon concentration (from 4.5 to 69 mg L(-1)). The pH-increase followed the same trend as the release of DOM in the experiment, causing higher DOM solubility and desorption of DOM from mineral sites. The binding to biochar of several well-characterised reference DOM materials was also investigated and results showed a higher sorption of aliphatic DOM to biochar than aromatic DOM, with DOM-water partitioning coefficients (Kd-values) ranging from 0.2 to 590 L kg(-1). A size exclusion occurring in biochar's micropores, could result in a higher sorption of smaller aliphatic DOM molecules than larger aromatic ones. These findings indicate that biochar could increase the leaching of DOM from soil, as well as change the DOM composition towards molecules with a larger size and higher aromaticity. Copyright © 2015 Elsevier Ltd. All rights reserved.

The effect of dissolved organic matter (DOM) on sodium transport and nitrogenous waste excretion of the freshwater cladoceran (Daphnia magna) at circumneutral and low pH.

PubMed

Al-Reasi, Hassan A; Yusuf, Usman; Smith, D Scott; Wood, Chris M

2013-11-01

Dissolved organic matter (DOM), a heterogeneous substance found in all natural waters, has many documented abiotic roles, but recently, several possible direct influences of DOM on organism physiology have been reported. However, most studies have been carried out with a limited number of natural DOM isolates or were restricted to the use of commercial or artificial humic substances. We therefore employed three previously characterized, chemically-distinct natural DOMs, as well as a commercially available humic acid (Aldrich, AHA), at circumneutral (7-8) and acidic pH (~5), to examine DOM effects on whole-body Na(+) concentration, unidirectional influx and efflux rates of Na(+), and ammonia and urea excretion rates in Daphnia magna. Whole-body Na(+) concentration, Na(+) influx, and Na(+) efflux rates were all unaffected regardless of pH, suggesting no influence of the various natural DOMs on active uptake and passive diffusion of Na(+) in this organism. Ammonia and urea excretion rates were both increased by low pH. Ammonia excretion rates were reduced at circumneutral pH by the most highly colored, allochthonous DOM, and at low pH by all three natural DOMs, as well as by the commercial AHA. Urea excretion rates were not influenced by the presence of the various DOMs in circumneutral solutions, but were attenuated by the presence of two allochthonous DOM sources (isolated from Bannister Lake and Luther Marsh) at acidic pH. The observed reductions may be attributed partially to the higher buffering capacities of natural DOM sources, as well as their ability to interact with biological membranes as estimated by a new measure calculated from their acid-base titration characteristics, the Proton Binding Index (PBI). © 2013.

Source and Processes of Dissolved Organic Matter in a Bangladesh Groundwater

NASA Astrophysics Data System (ADS)

McKnight, D. M.; Simone, B. E.; Mladenov, N.; Zheng, Y.; Legg, T. M.; Nemergut, D.

2010-12-01

Arsenic contamination of groundwater is a global health crisis, especially in Bangladesh where an estimated 40 million people are at risk. The release of geogenic arsenic bound to sediments into groundwater is thought to be influenced by dissolved organic matter (DOM) through several biogeochemical processes. Abiotically, DOM can promote the release of sediment bound As through the formation of DOM-As complexes and competitive interactions between As and DOM for sorption sites on the sediment. Additionally, the labile portion of groundwater DOM can serve as an electron donor to support microbial growth and the more recalcitrant humic DOM may serve as an electron shuttle, facilitating the eventual reduction of ferric iron present as iron oxides in sediments and consequently the mobilization of sorbed As and organic material. The goal of this study is to understand the source of DOM in representative Bangladesh groundwaters and the DOM sorption processes that occur at depth. We report chemical characteristics of representative DOM from a surface water, a shallow low-As groundwater, mid-depth high-As groundwater from the Araihazar region of Bangladesh. The humic DOM from groundwater displayed a more terrestrial chemical signature, indicative of being derived from plant and soil precursor materials, while the surface water humic DOM had a more microbial signature, suggesting an anthropogenic influence. In terms of biogeochemical processes occurring in the groundwater system, there is evidence from a diverse set of chemical characteristics, ranging from 13C-NMR spectroscopy to the analysis of lignin phenols, for preferential sorption onto iron oxides influencing the chemistry and reactivity of humic DOM in high As groundwater in Bangladesh. Taken together, these results provide chemical evidence for anthropogenic influence and the importance of sorption reactions at depth controlling the water quality of high As groundwater in Bangladesh.

Composition, dynamics, and fate of leached dissolved organic matter in terrestrial ecosystems: Results from a decomposition experiment

USGS Publications Warehouse

Cleveland, C.C.; Neff, J.C.; Townsend, A.R.; Hood, E.

2004-01-01

Fluxes of dissolved organic matter (DOM) are an important vector for the movement of carbon (C) and nutrients both within and between ecosystems. However, although DOM fluxes from throughfall and through litterfall can be large, little is known about the fate of DOM leached from plant canopies, or from the litter layer into the soil horizon. In this study, our objectives were to determine the importance of plant-litter leachate as a vehicle for DOM movement, and to track DOM decomposition [including dissolve organic carbon (DOC) and dissolved organic nitrogen (DON) fractions], as well as DOM chemical and isotopic dynamics, during a long-term laboratory incubation experiment using fresh leaves and litter from several ecosystem types. The water-extractable fraction of organic C was high for all five plant species, as was the biodegradable fraction; in most cases, more than 70% of the initial DOM was decomposed in the first 10 days of the experiment. The chemical composition of the DOM changed as decomposition proceeded, with humic (hydrophobic) fractions becoming relatively more abundant than nonhumic (hydrophilic) fractions over time. However, in spite of proportional changes in humic and nonhumic fractions over time, our data suggest that both fractions are readily decomposed in the absence of physicochemical reactions with soil surfaces. Our data also showed no changes in the ??13C signature of DOM during decomposition, suggesting that isotopic fractionation during DOM uptake is not a significant process. These results suggest that soil microorganisms preferentially decompose more labile organic molecules in the DOM pool, which also tend to be isotopically heavier than more recalcitrant DOM fractions. We believe that the interaction between DOM decomposition dynamics and soil sorption processes contribute to the ??13C enrichment of soil organic matter commonly observed with depth in soil profiles.

Partitioning of dissolved organic matter-bound mercury between a hydrophobic surface and polysulfide-rubber polymer.

PubMed

Kim, Eun-Ah; Luthy, Richard G

2011-11-01

This study investigated the role of dissolved organic matter on mercury partitioning between a hydrophobic surface (polyethylene, PE) and a reduced sulfur-rich surface (polysulfide rubber, PSR). Comparative sorption studies employed polyethylene and polyethylene coated with PSR for reactions with DOM-bound mercuric ions. These studies revealed that PSR enhanced the Hg-DOM removal from water when DOM was Suwannee River natural organic matter (NOM), fulvic acid (FA), or humic acid (HA), while the same amount of 1,3-propanedithiol-bound mercuric ion was removed by both PE and PSR-PE. The differences for Hg-DOM removal efficiencies between PE and PSR-PE varied depending on which DOM was bound to mercuric ion as suggested by the PE/water and PSR-PE/water partition coefficients for mercury. The surface concentrations of mercury on PE and PSR-PE with the same DOM measured by x-ray photoelectron spectroscopy were similar, which indicated the comparable amounts of immobilized mercury on PE and PSR-PE being exposed to the aqueous phase. With these observations, two major pathways for the immobilization reactions between PSR-PE and Hg-DOM were examined: 1) adsorption of Hg-DOM on PE by hydrophobic interactions between DOM and PE, and 2) addition reaction of Hg-DOM onto PSR by a complexation reaction between Hg and PSR. The percent contribution of each pathway was derived from a mass balance and the ratios among aqueous mercury, PE-bound Hg-DOM, and PSR-bound Hg-DOM concentrations. The results indicate strong binding of mercuric ion with both dissolved organic matter and PSR polymer. The FT-IR examination of Hg-preloaded-PSR-PEs after the reaction with DOM corroborated a strong interaction between mercuric ion and 1,3-propanedithiol compared to Hg-HA, Hg-FA, or Hg-NOM interactions. Copyright © 2011 Elsevier Ltd. All rights reserved.

Composition and transformation of dissolved organic matter in the Baltic Sea

NASA Astrophysics Data System (ADS)

Seidel, Michael; Manecki, Marcus; Herlemann, Daniel P. R.; Deutsch, Barbara; Schulz-Bull, Detlef; Jürgens, Klaus; Dittmar, Thorsten

2017-05-01

The processing of terrestrial dissolved organic matter (DOM) in coastal shelf seas is an important part of the global carbon cycle, yet, it is still not well understood. One of the largest brackish shelf seas, the Baltic Sea in northern Europe, is characterized by high freshwater input from sub-arctic rivers and limited water exchange with the Atlantic Ocean via the North Sea. We studied the molecular and isotopic composition and turnover of solid-phase extractable (SPE) DOM and its transformation along the salinity and redox continuum of the Baltic Sea during spring and autumn. We applied ultrahigh-resolution mass spectrometry and other geochemical and biological approaches. Our data demonstrate a large influx of terrestrial riverine DOM, especially into the northern part of the Baltic Sea. The DOM composition in the central Baltic Sea changed seasonally and was mainly related to autochthonous production by phytoplankton in spring. Especially in the northern, river-dominated basins, a major fraction of riverine DOM was removed, likely by bio- and photo-degradation. We estimate that the removal rate of terrestrial DOM in the Baltic Sea (Bothnian Bay to the Danish Straits/Kattegat area) is 1.6 - 1.9 Tg C per year which is 43 to 51% of the total riverine input. The export of terrestrial DOM from the Danish Straits/Kattegat area towards the North Sea is 1.8 - 2.1 Tg C per year. Due to the long residence time of terrestrial DOM in the Baltic Sea (total of ca. 12 years), seasonal variations caused by bio- and photo-transformations and riverine discharge are dampened, resulting in a relatively invariant DOM molecular and isotopic signature exported to the North Sea. In the deep stagnant basins of the Baltic Sea, the DOM composition and dissolved organic nitrogen concentrations changed seasonally, likely because of vertical particle transport and subsequent degradation releasing DOM. DOM in the deep anoxic basins was also enriched in sulfur-containing organic molecules, pointing to abiotic sulfurization of DOM under sulfidic conditions.

Partitioning of dissolved organic matter-bound mercury between a hydrophobic surface and polysulfide-rubber polymer

PubMed Central

Kim, Eun-Ah

2011-01-01

This study investigated the role of dissolved organic matter on mercury partitioning between a hydrophobic surface (polyethylene, PE) and a reduced sulfur-rich surface (polysulfide rubber, PSR). Comparative sorption studies employed polyethylene and polyethylene coated with PSR for reactions with DOM-bound mercuric ions. These studies revealed that PSR enhanced the Hg-DOM removal from water when DOM was Suwannee River natural organic matter (NOM), fulvic acid (FA), or humic acid (HA), while the same amount of 1,3-propanedithiol-bound mercuric ion was removed by both PE and PSR-PE. The differences for Hg-DOM removal efficiencies between PE and PSR-PE varied depending on which DOM was bound to mercuric ion as suggested by the PE/water and PSR-PE/water partition coefficients for mercury. The surface concentrations of mercury on PE and PSR-PE with the same DOM measured by x-ray – photoelectron spectroscopy were similar, which indicated the comparable amounts of immobilized mercury on PE and PSR-PE being exposed to the aqueous phase. With these observations, two major pathways for the immobilization reactions between PSR-PE and Hg- DOM were examined: 1) adsorption of Hg-DOM on PE by hydrophobic interactions between DOM and PE, and 2) addition reaction of Hg-DOM onto PSR by a complexation reaction between Hg and PSR. The percent contribution of each pathway was derived from a mass balance and the ratios among aqueous mercury, PE-bound Hg-DOM, and PSR-bound Hg-DOM concentrations. The results indicate strong binding of mercuric ion with both dissolved organic matter and PSR polymer. The FT-IR examination of Hg-preloaded-PSR-PEs after the reaction with DOM corroborated a strong interaction between mercuric ion and 1,3-propanedithiol compared to Hg-HA, Hg-FA, or Hg-NOM interactions. PMID:21872900

Phototransformation of pesticides in prairie potholes: effect of dissolved organic matter in triplet-induced oxidation.

PubMed

Karpuzcu, M Ekrem; McCabe, Andrew J; Arnold, William A

2016-02-01

Photochemical reactions involving a variety of photosensitizers contribute to the abiotic transformation of pesticides in prairie pothole lakes (PPLs). Despite the fact that triplet excited state dissolved organic matter (DOM) enhances phototransformation of pesticides by acting as a photosensitizer, it may also decrease the overall phototransformation rate through various mechanisms. In this study, the effect of DOM on the phototransformation of four commonly applied pesticides in four different PPL waters was investigated under simulated sunlight using photoexcited benzophenone-4-carboxylate as the oxidant with DOM serving as an anti-oxidant. For atrazine and mesotrione, a decrease in phototransformation rates was observed, while phototransformations of metolachlor and isoproturon were not affected by DOM inhibition. Phototransformation rates and the extent of inhibition/enhancement by DOM varied spatially and temporally across the wetlands studied. Characterization of DOM from the sites and different seasons suggested that the DOM type and variations in the DOM structure are important factors controlling phototransformation rates of pesticides in PPLs.

Formation of nanocolloidal metacinnabar in mercury-DOM-sulfide systems

USGS Publications Warehouse

Gerbig, Chase A.; Kim, Christopher S.; Stegemeier, John P.; Ryan, Joseph N.; Aiken, George R.

2011-01-01

Direct determination of mercury (Hg) speciation in sulfide-containing environments is confounded by low mercury concentrations and poor analytical sensitivity. Here we report the results of experiments designed to assess mercury speciation at environmentally relevant ratios of mercury to dissolved organic matter (DOM) (i.e., <4 nmol Hg (mg DOM)−1) by combining solid phase extraction using C18 resin with extended X-ray absorption fine structure (EXAFS) spectroscopy. Aqueous Hg(II) and a DOM isolate were equilibrated in the presence and absence of 100 μM total sulfide. In the absence of sulfide, mercury adsorption to the resin increased as the Hg:DOM ratio decreased and as the strength of Hg-DOM binding increased. EXAFS analysis indicated that in the absence of sulfide, mercury bonds with an average of 2.4 ± 0.2 sulfur atoms with a bond length typical of mercury-organic thiol ligands (2.35 Å). In the presence of sulfide, mercury showed greater affinity for the C18 resin, and its chromatographic behavior was independent of Hg:DOM ratio. EXAFS analysis showed mercury–sulfur bonds with a longer interatomic distance (2.51–2.53 Å) similar to the mercury–sulfur bond distance in metacinnabar (2.53 Å) regardless of the Hg:DOM ratio. For all samples containing sulfide, the sulfur coordination number was below the ideal four-coordinate structure of metacinnabar. At a low Hg:DOM ratio where strong binding DOM sites may control mercury speciation (1.9 nmol mg–1) mercury was coordinated by 2.3 ± 0.2 sulfur atoms, and the coordination number rose with increasing Hg:DOM ratio. The less-than-ideal coordination numbers indicate metacinnabar-like species on the nanometer scale, and the positive correlation between Hg:DOM ratio and sulfur coordination number suggests progressively increasing particle size or crystalline order with increasing abundance of mercury with respect to DOM. In DOM-containing sulfidic systems nanocolloidal metacinnabar-like species may form, and these species need to be considered when addressing mercury biogeochemistry.

Transformations of DOM in forested catchments: the pathways of DOM from litter and soil to river export

NASA Astrophysics Data System (ADS)

Lajtha, K.; Yano, Y.; Crow, S.; Kaushal, S.

2006-12-01

Although the quality and quantity of DOM ultimately derives from plant detritus and soils in watersheds, three is substantial alteration of DOM as it passes from litter through the terrestrial landscape. As DOM is generated from plant and microbial detritus and processing, different fractions may be lost via respiration, form quasi-stable soil organic matter, or be temporarily sorbed to soil minerals. We followed the fate of DOC and DON from forested plots with experimentally altered detritus loads to determine the relative roles of original plant litter chemistry and soil transformations. Our study site was the DIRT (Detrital Input and Removal Treatment) plots at the H.J. Andrews Experimental Forest in Oregon, where treatments include detrital additions (wood vs. needle litter), litter exclusion, and root exclusions. Fractionation of detritus leachate solutions demonstrated significant differences in DOC chemistry from different detrital sources. Root leachates produced high quantities of hydrophilic neutral DOC, a fraction rich in labile sugars and polysaccharides; young wood extracts produced higher quantities of weak hydrophobic acids and hydrophobic neutrals (longer chain hydrocarbons); older wood had lower quantities of most labile constituents but was rich in strong hydrophobic acids. Although laboratory extracts of different litter types showed differences in DOM chemistry, soil solutions collected just below the forest floor from the differing detrital treatments were remarkably uniform and poor in labile constituents, suggesting microbial equalization of DOM leachate in the field. DOM quality and concentrations changed significantly with passage through soil profiles. DOC concentrations decreased through the soil profile in all plots to a greater degree than did dissolved organic nitrogen (DON), most likely due to preferential sorption of high C:N hydrophobic dissolved organic matter (DOM) in upper horizons. Percent hydrophobic DOM decreased significantly with depth, and the remaining hydrophilic DOM had a much lower and narrower C:N ratio than hydrophobic DOM. We also hypothesize that protein-reactive polyphenols, or tannins, may contribute to the decreased lability of N-rich DOM in soil solutions and thus significantly influence the quality of DOM delivered to streams.

The role of reactive oxygen species in the degradation of lignin derived dissolved organic matter

NASA Astrophysics Data System (ADS)

Waggoner, Derek C.; Wozniak, Andrew S.; Cory, Rose M.; Hatcher, Patrick G.

2017-07-01

Evidence suggests that reactive oxygen species (ROS) are important in transforming the chemical composition of the large pool of terrestrially-derived dissolved organic matter (DOM) exported from land to water annually. However, due to the challenges inherent in isolating the effects of individual ROS on DOM composition, the role of ROS in the photochemical alteration of DOM remains poorly characterized. In this work, terrestrial DOM was independently exposed to singlet oxygen (1O2), and superoxide (O2-rad under controlled laboratory conditions). Using ultra-high resolution mass spectrometry to track molecular level alterations of DOM by ROS, these findings suggest exposure to 1O2 (generated using Rose Bengal and visible light) removed formulas with an O/C > 0.3, and primarily resulted in DOM comprised of formulas with higher oxygen content, while O2-rad exposure (from KO2 in DMSO) removed formulas with O/C < 0.3 and produced aliphatic formulas (H/C > 1.5). Comparison of DOM altered by ROS in this study to riverine and coastal DOM showed that (20-80%) overlap in formulas, providing evidence for the role of ROS in shaping the composition of DOM exported from rivers to oceans.

The effect of source material in determining the photoreactivity of DOM in peatland aquatic systems

NASA Astrophysics Data System (ADS)

Pickard, Amy; Heal, Kate; McLeod, Andy; Dinsmore, Kerry

2016-04-01

Aquatic systems draining peatlands receive a high loading of dissolved organic matter (DOM) from surrounding terrestrial environments. However the fate of aquatic DOM remains poorly constrained, in part due to lack of knowledge regarding the photoreactivity of DOM and how this changes as a function of variability in source material. In this study water samples were collected monthly for a 13-month period from two contrasting aquatic systems in Scotland: a stream draining a peatland with high DOM concentrations (33.3 ± 14.2 mg DOC L-1) and a reservoir draining a peat catchment with low DOM concentrations (4.16 ± 0.91 mg DOC L-1). Controlled UV irradiation laboratory experiments were conducted on samples filtered to 0.2 μm in order to assess the photoreactivity of the DOM, measured as the unit mass of DOC lost upon irradiation. Experiments took place over 8h in temperature controlled conditions, with unirradiated samples used as controls. After exposure, a range of analytical techniques were used to characterise the DOM to yield information about its source material and to determine how this was related to the observed photoreactivity. Lignin phenol analyses indicate considerable contribution of Sphagnum to DOM at the stream site, particularly during summer, as demonstrated by high P-hydroxy/Vanillyl phenol ratios (P/V). Low P/V ratios were correlated with increased photoreactivity, (Pearson's: -0.410; p = 0.15, n = 13), suggesting that DOM from woody lignin sources within the catchment was more photolabile. Photoreactivity was also negatively correlated with Fluorescence Index (FI) values (Pearson's: -0.555; p = 0.055, n = 13), where low FI values are understood to indicate greater contribution of terrestrially derived material to aquatic DOM. Excitation-emission matrices (EEMs) indicate that DOM at the stream site was primarily comprised of a humic-like peak (Ex/Em = 340, 380/460 nm). However, there was also contribution from a protein-like peak (Ex/Em = 290, 320/350 nm), which was present in samples with lower photoreactivity. DOM at the reservoir site was primarily composed of the same identified protein-like peak, which may account for the lower observed photoreactivity of these samples. Although total DOC concentration is the dominant control on photo-induced DOC losses in peatland aquatic systems, these results show that organic matter characterisation can be used to further comprehend changes to DOM photoreactivity. Increased understanding of DOM processing in aquatic freshwater systems will allow the fate of DOM to be more accurately determined.

Investigating the effect of hardness cations on coagulation: The aspect of neutralisation through Al(III)-dissolved organic matter (DOM) binding.

PubMed

Zhou, Yuxuan; Yan, Mingquan; Liu, Ruiping; Wang, Dongsheng; Qu, Jiuhui

2017-05-15

Hardness cations are ubiquitous and abundant in source water, while the effect of hardness on the performance of coagulation for dissolved organic matter (DOM) removal in water treatment remains unclear due to the limitation of methods that can characterise the subtle interactions between DOM, coagulant and hardness cations. This work quantified the competition between coagulant Al 3+ and hardness cations to bind onto DOM using absorbance spectroscopy acquired at different Al 3+ concentrations in the absence and presence of Ca 2+ or Mg 2+ . The results indicate that, in the presence of either Mg 2+ or Ca 2+ , an increasing depression of the binding of Al 3+ -DOM could be observed in the differential spectra of DOM with the increasing of Mg 2+ or Ca 2+ at a level of 10, 100 and 1000 μM, with the observation being more significant at higher pH from 6.5 to 8.5. The results of zeta potentials of DOM indicate that the competition of hardness cations results in the negative DOM being less efficiently neutralised by Al 3+ . This study demonstrates that the removal of DOM by coagulation would significantly deteriorate with the presence of hardness cations, which would compete with coagulant Al 3+ to neutralise the unsaturated sites in DOM. Copyright © 2017 Elsevier Ltd. All rights reserved.

Fate of 14C-labeled dissolved organic matter in paddy and upland soils in responding to moisture.

PubMed

Chen, Xiangbi; Wang, Aihua; Li, Yang; Hu, Lening; Zheng, Hua; He, Xunyang; Ge, Tida; Wu, Jinshui; Kuzyakov, Yakov; Su, Yirong

2014-08-01

Soil organic matter (SOM) content in paddy soils is higher than that in upland soils in tropical and subtropical China. The dissolved organic matter (DOM) concentration, however, is lower in paddy soils. We hypothesize that soil moisture strongly controls the fate of DOM, and thereby leads to differences between the two agricultural soils under contrasting management regimens. A 100-day incubation experiment was conducted to trace the fate and biodegradability of DOM in paddy and upland soils under three moisture levels: 45%, 75%, and 105% of the water holding capacity (WHC). (14)C labeled DOM, extracted from the (14)C labeled rice plant material, was incubated in paddy and upland soils, and the mineralization to (14)CO2 and incorporation into microbial biomass were analyzed. Labile and refractory components of the initial (14)C labeled DOM and their respective half-lives were calculated by a double exponential model. During incubation, the mineralization of the initial (14)C labeled DOM in the paddy soils was more affected by moisture than in the upland soils. The amount of (14)C incorporated into the microbial biomass (2.4-11.0% of the initial DOM-(14)C activity) was less affected by moisture in the paddy soils than in the upland soils. At any of the moisture levels, 1) the mineralization of DOM to (14)CO2 within 100 days was 1.2-2.1-fold higher in the paddy soils (41.9-60.0% of the initial DOM-(14)C activity) than in the upland soils (28.7-35.7%), 2) (14)C activity remaining in solution was significantly lower in the paddy soils than in the upland soils, and 3) (14)C activity remaining in the same agricultural soil solution was not significantly different among the three moisture levels after 20 days. Therefore, moisture strongly controls DOM fate, but moisture was not the key factor in determining the lower DOM in the paddy soils than in the upland soils. The UV absorbance of DOM at 280 nm indicates less aromaticity of DOM from the paddy soils than from the upland soils. At any of the moisture levels, much more labile DOM was found in paddy soils (34.3-49.2% of the initial (14)C labeled DOM) compared with that in upland soils (19.4-23.9%). This demonstrates that the lower DOM content in the paddy soil compared with that in the upland soil is probably determined by the less complex components and structure of the DOM. Copyright © 2014 Elsevier B.V. All rights reserved.

Automatic Parsing of Parental Verbal Input

PubMed Central

Sagae, Kenji; MacWhinney, Brian; Lavie, Alon

2006-01-01

To evaluate theoretical proposals regarding the course of child language acquisition, researchers often need to rely on the processing of large numbers of syntactically parsed utterances, both from children and their parents. Because it is so difficult to do this by hand, there are currently no parsed corpora of child language input data. To automate this process, we developed a system that combined the MOR tagger, a rule-based parser, and statistical disambiguation techniques. The resultant system obtained nearly 80% correct parses for the sentences spoken to children. To achieve this level, we had to construct a particular processing sequence that minimizes problems caused by the coverage/ambiguity trade-off in parser design. These procedures are particularly appropriate for use with the CHILDES database, an international corpus of transcripts. The data and programs are now freely available over the Internet. PMID:15190707

Incremental Refinement of FAÇADE Models with Attribute Grammar from 3d Point Clouds

NASA Astrophysics Data System (ADS)

Dehbi, Y.; Staat, C.; Mandtler, L.; Pl¨umer, L.

2016-06-01

Data acquisition using unmanned aerial vehicles (UAVs) has gotten more and more attention over the last years. Especially in the field of building reconstruction the incremental interpretation of such data is a demanding task. In this context formal grammars play an important role for the top-down identification and reconstruction of building objects. Up to now, the available approaches expect offline data in order to parse an a-priori known grammar. For mapping on demand an on the fly reconstruction based on UAV data is required. An incremental interpretation of the data stream is inevitable. This paper presents an incremental parser of grammar rules for an automatic 3D building reconstruction. The parser enables a model refinement based on new observations with respect to a weighted attribute context-free grammar (WACFG). The falsification or rejection of hypotheses is supported as well. The parser can deal with and adapt available parse trees acquired from previous interpretations or predictions. Parse trees derived so far are updated in an iterative way using transformation rules. A diagnostic step searches for mismatches between current and new nodes. Prior knowledge on façades is incorporated. It is given by probability densities as well as architectural patterns. Since we cannot always assume normal distributions, the derivation of location and shape parameters of building objects is based on a kernel density estimation (KDE). While the level of detail is continuously improved, the geometrical, semantic and topological consistency is ensured.

Neuroanatomical term generation and comparison between two terminologies.

PubMed

Srinivas, Prashanti R; Gusfield, Daniel; Mason, Oliver; Gertz, Michael; Hogarth, Michael; Stone, James; Jones, Edward G; Gorin, Fredric A

2003-01-01

An approach and software tools are described for identifying and extracting compound terms (CTs), acronyms and their associated contexts from textual material that is associated with neuroanatomical atlases. A set of simple syntactic rules were appended to the output of a commercially available part of speech (POS) tagger (Qtag v 3.01) that extracts CTs and their associated context from the texts of neuroanatomical atlases. This "hybrid" parser. appears to be highly sensitive and recognized 96% of the potentially germane neuroanatomical CTs and acronyms present in the cat and primate thalamic atlases. A comparison of neuroanatomical CTs and acronymsbetween the cat and primate atlas texts was initially performed using exact-term matching. The implementation of string-matching algorithms significantly improved the identification of relevant terms and acronyms between the two domains. The End Gap Free string matcher identified 98% of CTs and the Needleman Wunsch (NW) string matcher matched 36% of acronyms between the two atlases. Combining several simple grammatical and lexical rules with the POS tagger ("hybrid parser") (1) extracted complex neuroanatomical terms and acronyms from selected cat and primate thalamic atlases and (2) and facilitated the semi-automated generation of a highly granular thalamic terminology. The implementation of string-matching algorithms (1) reconciled terminological errors generated by optical character recognition (OCR) software used to generate the neuroanatomical text information and (2) increased the sensitivity of matching neuroanatomical terms and acronyms between the two neuroanatomical domains that were generated by the "hybrid" parser.

GBParsy: a GenBank flatfile parser library with high speed.

PubMed

Lee, Tae-Ho; Kim, Yeon-Ki; Nahm, Baek Hie

2008-07-25

GenBank flatfile (GBF) format is one of the most popular sequence file formats because of its detailed sequence features and ease of readability. To use the data in the file by a computer, a parsing process is required and is performed according to a given grammar for the sequence and the description in a GBF. Currently, several parser libraries for the GBF have been developed. However, with the accumulation of DNA sequence information from eukaryotic chromosomes, parsing a eukaryotic genome sequence with these libraries inevitably takes a long time, due to the large GBF file and its correspondingly large genomic nucleotide sequence and related feature information. Thus, there is significant need to develop a parsing program with high speed and efficient use of system memory. We developed a library, GBParsy, which was C language-based and parses GBF files. The parsing speed was maximized by using content-specified functions in place of regular expressions that are flexible but slow. In addition, we optimized an algorithm related to memory usage so that it also increased parsing performance and efficiency of memory usage. GBParsy is at least 5-100x faster than current parsers in benchmark tests. GBParsy is estimated to extract annotated information from almost 100 Mb of a GenBank flatfile for chromosomal sequence information within a second. Thus, it should be used for a variety of applications such as on-time visualization of a genome at a web site.

Disambiguating the species of biomedical named entities using natural language parsers

PubMed Central

Wang, Xinglong; Tsujii, Jun'ichi; Ananiadou, Sophia

2010-01-01

Motivation: Text mining technologies have been shown to reduce the laborious work involved in organizing the vast amount of information hidden in the literature. One challenge in text mining is linking ambiguous word forms to unambiguous biological concepts. This article reports on a comprehensive study on resolving the ambiguity in mentions of biomedical named entities with respect to model organisms and presents an array of approaches, with focus on methods utilizing natural language parsers. Results: We build a corpus for organism disambiguation where every occurrence of protein/gene entity is manually tagged with a species ID, and evaluate a number of methods on it. Promising results are obtained by training a machine learning model on syntactic parse trees, which is then used to decide whether an entity belongs to the model organism denoted by a neighbouring species-indicating word (e.g. yeast). The parser-based approaches are also compared with a supervised classification method and results indicate that the former are a more favorable choice when domain portability is of concern. The best overall performance is obtained by combining the strengths of syntactic features and supervised classification. Availability: The corpus and demo are available at http://www.nactem.ac.uk/deca_details/start.cgi, and the software is freely available as U-Compare components (Kano et al., 2009): NaCTeM Species Word Detector and NaCTeM Species Disambiguator. U-Compare is available at http://-compare.org/ Contact: xinglong.wang@manchester.ac.uk PMID:20053840

High-frequency measurements reveal spatial and temporal patterns of dissolved organic matter in an urban water conveyance.

PubMed

Mihalevich, Bryce A; Horsburgh, Jeffery S; Melcher, Anthony A

2017-10-30

Stormwater runoff in urban areas can contribute high concentrations of dissolved organic matter (DOM) to receiving waters, potentially causing impairment to the aquatic ecosystem of urban streams and downstream water bodies. Compositional changes in DOM due to storm events in forested, agricultural, and urban landscapes have been well studied, but in situ sensors have not been widely applied to monitor stormwater contributions in urbanized areas, leaving the spatial and temporal characteristics of DOM within these systems poorly understood. We deployed fluorescent DOM (FDOM) sensors at upstream and downstream locations within a study reach to characterize the spatial and temporal changes in DOM quantity and sources within an urban water conveyance that receives stormwater runoff. Baseflow FDOM decreased over the summer season as seasonal flows upstream transported less DOM. FDOM fluctuated diurnally, the amplitude of which also declined as the summer season progressed. During storms, FDOM concentrations were rapidly elevated to values orders of magnitude greater than baseflow measurements, with greater concentrations at the downstream monitoring site, revealing high contributions from stormwater outfalls between the two locations. Observations from custom, in situ fluorometers resembled results obtained using laboratory methods for identifying DOM source material and indicated that DOM transitioned to a more microbially derived composition as the summer season progressed, while stormwater contributions contributed DOM from terrestrial sources. Deployment of a mobile sensing platform during varying flow conditions captured spatial changes in DOM concentration and composition and revealed contributions of DOM from outfalls during stormflows that would have otherwise been unobserved.

Chemical and optical changes in freshwater dissolved organic matter exposed to solar radiation

USGS Publications Warehouse

Osburn, C.L.; Morris, D.P.; Thorn, K.A.; Moeller, R.E.

2001-01-01

We studied the chemical and optical changes in the dissolved organic matter (DOM) from two freshwater lakes and a Sphagnum bog after exposure to solar radiation. Stable carbon isotopes and solid-state 13C-NMR spectra of DOM were used together with optical and chemical data to interpret results from experimental exposures of DOM to sunlight and from seasonal observations of two lakes in northeastern Pennsylvania. Solar photochemical oxidation of humic-rich bog DOM to smaller LMW compounds and to DIC was inferred from losses of UV absorbance, optical indices of molecular weight and changes in DOM chemistry. Experimentally, we observed a 1.2??? enrichment in ??13C and a 47% loss in aromatic C functionality in bog DOM samples exposed to solar UVR. Similar results were observed in the surface waters of both lakes. In late summer hypolimnetic water in humic Lake Lacawac, we observed 3 to 4.5??? enrichments in ??13C and a 30% increase in aromatic C relative to early spring values during spring mixing. These changes coincided with increases in molecular weight and UV absorbance. Anaerobic conditions of the hypolimnion in Lake Lacawac suggest that microbial metabolism may be turning over allochthonous C introduced during spring mixing, as well as autochthonous C. This metabolic activity produces HMW DOM during the summer, which is photochemically labile and isotopically distinct from allochthonous DOM or autochthonous DOM. These results suggest both photooxidation of allochthonous DOM in the epilimnion and autotrophic production of DOM by bacteria in the hypolimnion cause seasonal trends in the UV absorbance of lakes.

Relationships between land cover and dissolved organic matter change along the river to lake transition

USGS Publications Warehouse

Larson, James H.; Frost, Paul C.; Xenopoulos, Marguerite A.; Williams, Clayton J.; Morales-Williams, Ana M.; Vallazza, Jonathan M.; Nelson, J. C.; Richardson, William B.

2014-01-01

Dissolved organic matter (DOM) influences the physical, chemical, and biological properties of aquatic ecosystems. We hypothesized that controls over spatial variation in DOM quantity and composition (measured with DOM optical properties) differ based on the source of DOM to aquatic ecosystems. DOM quantity and composition should be better predicted by land cover in aquatic habitats with allochthonous DOM and related more strongly to nutrients in aquatic habitats with autochthonous DOM. Three habitat types [rivers (R), rivermouths (RM), and the nearshore zone (L)] associated with 23 tributaries of the Laurentian Great Lakes were sampled to test this prediction. Evidence from optical indices suggests that DOM in these habitats generally ranged from allochthonous (R sites) to a mix of allochthonous-like and autochthonous-like (L sites). Contrary to expectations, DOM properties such as the fluorescence index, humification index, and spectral slope ratio were only weakly related to land cover or nutrient data (Bayesian R 2 values were indistinguishable from zero). Strongly supported models in all habitat types linked DOM quantity (that is, dissolved organic carbon concentration [DOC]) to both land cover and nutrients (Bayesian R2 values ranging from 0.55 to 0.72). Strongly supported models predicting DOC changed with habitat type: The most important predictor in R sites was wetlands whereas the most important predictor at L sites was croplands. These results suggest that as the DOM pool becomes more autochthonous-like, croplands become a more important driver of spatial variation in DOC and wetlands become less important.

The chemical composition and source identification of soil dissolved organic matter in riparian buffer zones from Chongming Island, China.

PubMed

Wang, Yulai; Yang, Changming; Li, Jianhua; Shen, Shuo

2014-09-01

Dissolved organic matter (DOM) that is derived from the soil of riparian buffer zones has a complex chemical composition, and it plays an important role in the transport and transformation of pollutants. To identify the source of DOM and to better understand its chemical and structural properties, we collected 33 soil samples from zones with fluctuating water levels along the major rivers on Chongming Island, evaluated the DOM contents in riparian soil, analyzed the chemical composition and functional groups and traced DOM origins by using liquid chromatography quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS) combined with clustering analysis. All sampling sites were divided into four groups by principal component analysis (PCA) on the basis of the DOM molecules. The results showed that there was no significant difference in the DOM contents between every two groups; however, the DOM fractions differed significantly among the different site groups in the following order: Σ lipids and Σ proteins>Σ sugars and Σ fatty acids>Σ amino acids, Σ indoles and Σ alkaloids. DOM in the riparian buffer zones originated from riparian plants, domestic sewage and agricultural activities, and the hydrophobic and amphiphilic fractions accounting for over 60% of the identified molecules were the dominant fractions. Our study has confirmed the heterogeneous properties of DOM, and it is of vital importance to isolate and characterize the various DOM fractions at the molecular level for a better understanding of the behavior and roles of DOM in the natural environment. Copyright © 2014 Elsevier Ltd. All rights reserved.

Why dissolved organic matter (DOM) enhances photodegradation of methylmercury

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qian, Yun; Yin, Xiangping Lisa; Brooks, Scott C

2014-01-01

Methylmercury (MeHg) is known to degrade photochemically, but it remains unclear what roles naturally dissolved organic matter (DOM) and complexing organic ligands play in MeHg photodegradation. Here we investigate the rates and mechanisms of MeHg photodegradation using DOM samples with varying oxidation states and origins as well as organic ligands with known molecular structures. All DOM and organic ligands increased MeHg photodegradation under solar irradiation, but the first-order rate constants varied depending on the oxidation state of DOM and the type and concentration of the ligands. Compounds containing both thiols and aromatics (e.g., thiosalicylate and reduced DOM) increased MeHg degradationmore » rates far greater than those containing only aromatic or thiol functional groups (e.g., salicylate or glutathione). Our results suggest that, among other factors, the synergistic effects of thiolate and aromatic moieties in DOM greatly enhance MeHg photodegradation.« less

Pan-Arctic Distribution of Bioavailable Dissolved Organic Matter and Linkages With Productivity in Ocean Margins

NASA Astrophysics Data System (ADS)

Shen, Yuan; Benner, Ronald; Kaiser, Karl; Fichot, Cédric G.; Whitledge, Terry E.

2018-02-01

Rapid environmental changes in the Arctic Ocean affect plankton productivity and the bioavailability of dissolved organic matter (DOM) that supports microbial food webs. We report concentrations of dissolved organic carbon (DOC) and yields of amino acids (indicators of labile DOM) in surface waters across major Arctic margins. Concentrations of DOC and bioavailability of DOM showed large pan-Arctic variability that corresponded to varying hydrological conditions and ecosystem productivity, respectively. Widespread hot spots of labile DOM were observed over productive inflow shelves (Chukchi and Barents Seas), in contrast to oligotrophic interior margins (Kara, Laptev, East Siberian, and Beaufort Seas). Amino acid yields in outflow gateways (Canadian Archipelago and Baffin Bay) indicated the prevalence of semilabile DOM in sea ice covered regions and sporadic production of labile DOM in ice-free waters. Comparing these observations with surface circulation patterns indicated varying shelf subsidies of bioavailable DOM to Arctic deep basins.

Insights into the redox components of dissolved organic matters during stabilization process.

PubMed

Yuan, Ying; Xi, Bei-Dou; He, Xiao-Song; Ma, Yan; Zhang, Hui; Li, Dan; Zhao, Xin-Yu

2018-05-01

The changes of dissolved organic matter (DOM) components during stabilization process play significant effects on its redox properties but are little reported. Composting is a stabilization process of DOM, during which both the components and electron transfer capacities (ETCs) of DOM change. The redox components within compost-derived DOM during the stabilization process are investigated in this study. The results show that compost-derived DOM contained protein-like, fulvic-like, and humic-like components. The protein-like component decreases during composting, whereas the fulvic- and humic-like components increase during the process. The electron-donating capacity (EDC), electron-accepting capacity (EAC), and ETC of compost-derived DOM all increase during composting but their correlations with the components presented significant difference. The humic-like components were the main functional component responsible for both EDC and ETC, whereas the protein- and fluvic-like components show negative effects with the EAC, EDC, and ETC, suggesting that the components within DOM have specific redox properties during the stabilization process. These findings are very meaningful for better understanding the geochemical behaviors of DOM in the environment.

Molecular Features of Dissolved Organic Matter Produced by Picophytoplankton

NASA Astrophysics Data System (ADS)

Ma, X.; Coleman, M.; Waldbauer, J.

2016-02-01

Compounds derived from picophytoplankton through exudation, grazing and viral lysis contribute a large proportion of labile DOM to the ocean. This labile DOM is rapidly turned over by and exchanged among microbial communities. However, identifying labile DOM compounds and tracking their sources and sinks in ocean ecosystems is complicated by the presence of non-labile DOM which has a significantly larger reservoir size and longer residence time. This study focuses on investigating labile DOM produced by single-strain cyanobacteria isolates via different modes of release and varied nutrient conditions. DOM compounds are analyzed by high-resolution mass spectrometry. Statistical comparison between intracellular and extracellular molecular data of Synechococcus WH7803 revealed noticeable differences in terms of compound number, size and structure. Incubation experiments using combined whole seawater and diluent of grazer-free or viral-free water at the BATS time-series station in Sargasso Sea yielded complimentary data to be synthesized with data from lab cultures. The compositional features of each type of DOM could serve as future proxies for different modes of DOM production in the oceans.

Effects of iron on optical properties of dissolved organic matter.

PubMed

Poulin, Brett A; Ryan, Joseph N; Aiken, George R

2014-09-02

Iron is a source of interference in the spectroscopic analysis of dissolved organic matter (DOM); however, its effects on commonly employed ultraviolet and visible (UV-vis) light adsorption and fluorescence measurements are poorly defined. Here, we describe the effects of iron(II) and iron(III) on the UV-vis absorption and fluorescence of solutions containing two DOM fractions and two surface water samples. In each case, regardless of DOM composition, UV-vis absorption increased linearly with increasing iron(III). Correction factors were derived using iron(III) absorption coefficients determined at wavelengths commonly used to characterize DOM. Iron(III) addition increased specific UV absorbances (SUVA) and decreased the absorption ratios (E2:E3) and spectral slope ratios (SR) of DOM samples. Both iron(II) and iron(III) quenched DOM fluorescence at pH 6.7. The degree and region of fluorescence quenching varied with the iron:DOC concentration ratio, DOM composition, and pH. Regions of the fluorescence spectra associated with greater DOM conjugation were more susceptible to iron quenching, and DOM fluorescence indices were sensitive to the presence of both forms of iron. Analyses of the excitation-emission matrices using a 7- and 13-component parallel factor analysis (PARAFAC) model showed low PARAFAC sensitivity to iron addition.

Toxic metals (Ni2+, Pb2+, Hg2+) binding affinity of dissolved organic matter (DOM) derived from different ages municipal landfill leachate

NASA Astrophysics Data System (ADS)

Rikta, S. Y.; Tareq, Shafi M.; Uddin, M. Khabir

2018-03-01

Solid waste production is rapidly increasing in Bangladesh and landfill leachate is the consequence of the decomposition of this waste. These leachates contain heavy metals and significant amount of dissolved organic matter (DOM). DOM is known to have considerable role in heavy metals speciation. Hence, it is important to characterize DOM/leachate and evaluate toxic metals binding affinity of DOM. The objectives of this study were to characterize the DOM in landfill leachate through physico-chemical and optical analyses and to investigate the toxic metals (Ni2+, Pb2+ and Hg2+) binding affinity of three different ages (fresh sample L-1, young sample L-2 and mature sample L-3) DOM samples. Results suggested that leachate is a potential pollutant which contained very high organic pollutant load. Conditional stability constant (Log K) and percentages of fluorophores that correspond to metal binding (% f) values indicated that young DOM sample (L-2) had the highest binding affinity to all the three metals ions. In general, DOM samples showed the following order affinity to the metal ions; Ni2+ binding affinity: L-2 > L-3 > L-1, Pb2+ binding affinity: L-2 > L-3 > L-1 and Hg2+ binding affinity: L-2 > L-1 > L-3.

Spectroscopic study of interactions of lead (II) ions with dissolved organic matter: Evidence of preferential engagement of carboxylic groups

NASA Astrophysics Data System (ADS)

Lu, Yujuan; Yan, Mingquan; Korshin, Gregory V.

2017-09-01

The speciation, bioavailability and transport of Pb(II) in the environment are strongly affected by dissolved organic matter (DOM). Despite the importance of these interactions, the nature of Pb(II)-DOM binding is insufficiently attested. This study addressed this deficiency using the method of differential absorbance spectroscopy in combination with the non-ideal competitive adsorption (NICA)-Donnan model. Differential absorbance data allowed quantifying the interactions between Pb(II) and DOM in a wide range of pH values, ionic strengths and Pb(II) concentrations at an environmentally relevant DOM concentration (5 mg L-1). Changes of the slopes of the log-transformed absorbance spectra of DOM in the range of wavelength 242-262 and 350-400 nm were found to be predictive of the extent of Pb(II) bound by DOM carboxylic groups and of the total amount of DOM-bound Pb(II), respectively. The results also demonstrated the preferential involvement of DOM carboxylic groups in Pb(II) binding. The spectroscopic data allowed optimizing selected Pb(II)-DOM complexation constants used in the NICA-Donnan Model. This resulted in a markedly improved performance of that model when it was applied to interpret previously published Pb(II)-fulvic acid datasets.

Effects of iron on optical properties of dissolved organic matter

USGS Publications Warehouse

Poulin, Brett; Ryan, Joseph N.; Aiken, George R.

2014-01-01

Iron is a source of interference in the spectroscopic analysis of dissolved organic matter (DOM); however, its effects on commonly employed ultraviolet and visible (UV–vis) light adsorption and fluorescence measurements are poorly defined. Here, we describe the effects of iron(II) and iron(III) on the UV–vis absorption and fluorescence of solutions containing two DOM fractions and two surface water samples. In each case, regardless of DOM composition, UV–vis absorption increased linearly with increasing iron(III). Correction factors were derived using iron(III) absorption coefficients determined at wavelengths commonly used to characterize DOM. Iron(III) addition increased specific UV absorbances (SUVA) and decreased the absorption ratios (E2:E3) and spectral slope ratios (SR) of DOM samples. Both iron(II) and iron(III) quenched DOM fluorescence at pH 6.7. The degree and region of fluorescence quenching varied with the iron:DOC concentration ratio, DOM composition, and pH. Regions of the fluorescence spectra associated with greater DOM conjugation were more susceptible to iron quenching, and DOM fluorescence indices were sensitive to the presence of both forms of iron. Analyses of the excitation–emission matrices using a 7- and 13-component parallel factor analysis (PARAFAC) model showed low PARAFAC sensitivity to iron addition.

Evaluating Activated Carbon Adsorption of Dissolved Organic Matter and Micropollutants Using Fluorescence Spectroscopy.

PubMed

Shimabuku, Kyle K; Kennedy, Anthony M; Mulhern, Riley E; Summers, R Scott

2017-03-07

Dissolved organic matter (DOM) negatively impacts granular activated carbon (GAC) adsorption of micropollutants and is a disinfection byproduct precursor. DOM from surface waters, wastewater effluent, and 1 kDa size fractions were adsorbed by GAC and characterized using fluorescence spectroscopy, UV-absorption, and size exclusion chromatography (SEC). Fluorescing DOM was preferentially adsorbed relative to UV-absorbing DOM. Humic-like fluorescence (peaks A and C) was selectively adsorbed relative to polyphenol-like fluorescence (peaks T and B) potentially due to size exclusion effects. In the surface waters and size fractions, peak C was preferentially removed relative to peak A, whereas the reverse was found in wastewater effluent, indicating that humic-like fluorescence is associated with different compounds depending on DOM source. Based on specific UV-absorption (SUVA), aromatic DOM was preferentially adsorbed. The fluorescence index (FI), if interpreted as an indicator of aromaticity, indicated the opposite but exhibited a strong relationship with average molecular weight, suggesting that FI might be a better indicator of DOM size than aromaticity. The influence of DOM intermolecular interactions on adsorption were minimal based on SEC analysis. Fluorescence parameters captured the impact of DOM size on the fouling of 2-methylisoborneol and warfarin adsorption and correlated with direct competition and pore blockage indicators.

Ecosystem consequences of changing inputs of terrestrial dissolved organic matter to lakes: current knowledge and future challenges

USGS Publications Warehouse

Solomon, Christopher T.; Jones, Stuart E.; Weidel, Brian C.; Buffam, Ishi; Fork, Megan L; Karlsson, Jan; Larsen, Soren; Lennon, Jay T.; Read, Jordan S.; Sadro, Steven; Saros, Jasmine E.

2015-01-01

Lake ecosystems and the services that they provide to people are profoundly influenced by dissolved organic matter derived from terrestrial plant tissues. These terrestrial dissolved organic matter (tDOM) inputs to lakes have changed substantially in recent decades, and will likely continue to change. In this paper, we first briefly review the substantial literature describing tDOM effects on lakes and ongoing changes in tDOM inputs. We then identify and provide examples of four major challenges which limit predictions about the implications of tDOM change for lakes, as follows: First, it is currently difficult to forecast future tDOM inputs for particular lakes or lake regions. Second, tDOM influences ecosystems via complex, interacting, physical-chemical-biological effects and our holistic understanding of those effects is still rudimentary. Third, non-linearities and thresholds in relationships between tDOM inputs and ecosystem processes have not been well described. Fourth, much understanding of tDOM effects is built on comparative studies across space that may not capture likely responses through time. We conclude by identifying research approaches that may be important for overcoming those challenges in order to provide policy- and management-relevant predictions about the implications of changing tDOM inputs for lakes.

Bioavailability of atrazine, pyrene and benzo[a]pyrene in European river waters

USGS Publications Warehouse

Akkanen, J.; Penttinen, S.; Haitzer, M.; Kukkonen, J.V.K.

2001-01-01

Thirteen river waters and one humic lake water were characterized. The effects of dissolved organic matter (DOM) on the bioavailability of atrazine, pyrene and benzo[a]pyrene (B[a]P) was evaluated. Binding of the chemicals by DOM was analyzed with the equilibrium dialysis technique. For each of the water samples, 24 h bioconcentration factors (BCFs) of the chemicals were measured in Daphnia magna. The relationship between DOM and other water characteristics (including conductivity, water hardness and pH), and bioavailability of the chemicals was studied by performing several statistical analyses, including multiple regression analyses, to determine how much of the variation of BCF values could be explained by the quantity and quality of DOM. The bioavailability of atrazine was not affected by DOM or any other water characteristics. Although equilibrium dialysis showed binding of pyrene to DOM, the bioavailability of pyrene was not significantly affected by DOM. The bioavailability of B[a]P was significantly affected by both the quality and quantity of DOM. Multiple regression analyses, using the quality (ABS270 and HbA%) and quantity of DOM as variables, explainedup to 70% of the variation in BCF of B[a]P in the waters studied. ?? 2001 Elsevier Science Ltd. All rights reserved.

Structural stability of coprecipitated natural organic matter and ferric iron under reducing conditions

USGS Publications Warehouse

Henneberry, Yumiko K.; Kraus, Tamara E.C.; Nico, Peter S.; Horwath, William R.

2012-01-01

The objective was to assess the interaction of Fe coprecipitated with dissolved organic matter (DOM) and its effect on Fe (hydr)oxide crystallinity and DOM retention under abiotic reducing conditions. A Fe-based coagulant was reacted with DOM from an agricultural drain and the resulting precipitate (floc) was exposed to S(-II) and Fe(II). Solution concentrations of Fe(II/III) and DOM were monitored, floc crystallinity was determined using X-ray diffraction, and the composition and distribution of functional groups were assessed using scanning transmission X-ray microscopy (STXM) and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. Results indicate coprecipitation of Fe(III) with DOM forms a non-crystalline floc that withstands crystallization regardless of change in pH, Fe:DOM ratio and type of reductant added. There was no evidence that exposure to reducing conditions led to release of DOM from the floc, indicating that coprecipitation with complex natural DOM in aquatic environments may stabilize Fe (hydr)oxides against crystallization upon reaction with reduced species and lead to long term sequestration of the DOM. STXM analysis identified spatially distinct regions with remarkable functional group purity, contrary to the model of DOM as a relatively uniform complex polymer lacking identifiable organic compounds. Polysaccharide-like OM was strongly and directly correlated with the presence of Fe but showed different Fe binding strength depending on the presence of carboxylic acid functional groups, whereas amide and aromatic functional groups were inversely correlated with Fe content.

Modelling the interactions between DOM and bacteria in marine ecosystems: state of the art and future prospective

NASA Astrophysics Data System (ADS)

polimene, Luca

2014-05-01

Marine dissolved organic matter (DOM) is the main source of carbon, nutrients and energy for marine prokaryotes, the most abundant life form in the oceans. Only a fraction of assimilated DOM is used by prokaryotes to synthesise new biomass (particulate organic matter, POM), while the rest is used for respiration or is excreted back into the environment as recalcitrant DOM (RDOM). The relative proportions of assimilated DOM that is distributed either to POM, respiration or RDOM is not constant but highly variable depending on the environmental conditions (e.g. nutrient availability, quality/quantity of DOM, temperature). This metabolic plasticity allows bacteria to shape the biogeochemistry of the surrounding waters by modulating three key carbon/energy fluxes fundamental for the functioning of the marine ecosystem: i) the transition from DOM to POM, ii) the remineralisation of carbon and nutrients, and iii) the transformation of labile DOM into recalcitrant DOM. The explicit representation of these processes (and their relative efficiency) in marine ecosystem models is a crucial (and challenging) issue which cannot be overlooked if we want to properly simulate marine biogeochemical cycles under present and climate changing conditions. This talk will provide an overview of how state of the art marine ecosystem models represent the interactions between DOM and bacteria, highlighting strengths and limits of the approaches currently used. A summary of future developments along with issues still open on the topic will also be presented and discussed.

A Transformational Journey: Compositional Changes in Organic Matter during Desorption from Sediments

NASA Astrophysics Data System (ADS)

Matiasek, S. J.; Pellerin, B. A.; Spencer, R.; Bergamaschi, B. A.; Hernes, P.

2016-12-01

The release of organic matter (OM) from suspended particles via desorption is a critical component of OM cycling since dissolved OM (DOM) fuels aquatic ecosystems and is a precursor for disinfection by-products formation. This study assessed the elemental and molecular composition of DOM desorbed abiotically from sediments and soils of an irrigated agricultural watershed of northern California. Relative to mineral-bound OM, the released DOM was nitrogen-poor (lower carbon:nitrogen ratios) and depleted in amino acids and lignin phenols (lower carbon-normalized yields). Water-extracted DOM appeared substantially more degraded than its parent particulate OM with increased molar contributions of acidic amino acids, non-protein amino acids, and acidic lignin phenols, all molecular indicators of a more extensively processed OM pool. Desorption processes also significantly altered lignin compositional ratios which help distinguish vascular-plant sources of DOM. Specific optical parameters, including spectral slope, specific UV absorbance at 254 nm (SUVA254), and fluorescence index (FI), did not constitute useful proxies for the desorbed DOM pool, while absorption coefficients and fluorescence peak intensities were strongly correlated with extracted DOM concentrations and composition. This study highlights the profound impact of desorption on DOM composition which, if unaccounted for, could lead to misinterpretations of common biomarkers and optical proxies used to predict DOM sources and reactivity. Our findings suggest that sediments contribute a biogeochemically distinct source of DOM to surface waters, with potential impacts on aquatic health and drinking water quality.

Shift in the chemical composition of dissolved organic matter in the Congo River network

NASA Astrophysics Data System (ADS)

Lambert, Thibault; Bouillon, Steven; Darchambeau, François; Massicotte, Philippe; Borges, Alberto V.

2016-09-01

The processing of terrestrially derived dissolved organic matter (DOM) during downstream transport in fluvial networks is poorly understood. Here, we report a dataset of dissolved organic carbon (DOC) concentrations and DOM composition (stable carbon isotope ratios, absorption and fluorescence properties) acquired along a 1700 km transect in the middle reach of the Congo River basin. Samples were collected in the mainstem and its tributaries during high-water (HW) and falling-water (FW) periods. DOC concentrations and DOM composition along the mainstem were found to differ between the two periods because of a reduced lateral mixing between the central water masses of the Congo River and DOM-rich waters from tributaries and also likely because of a greater photodegradation during FW as water residence time (WRT) increased. Although the Cuvette Centrale wetland (one of the world's largest flooded forests) continuously releases highly aromatic DOM in streams and rivers of the Congo Basin, the downstream transport of DOM was found to result in an along-stream gradient from aromatic to aliphatic compounds. The characterization of DOM through parallel factor analysis (PARAFAC) suggests that this transition results from (1) the losses of aromatic compounds by photodegradation and (2) the production of aliphatic compounds by biological reworking of terrestrial DOM. Finally, this study highlights the critical importance of the river-floodplain connectivity in tropical rivers in controlling DOM biogeochemistry at a large spatial scale and suggests that the degree of DOM processing during downstream transport is a function of landscape characteristics and WRT.

Relationships between dissolved organic matter and discharge: New insights from in-situ measurements in a northern forested watershed

NASA Astrophysics Data System (ADS)

Pellerin, B. A.; Shanley, J. B.; Saraceno, J.; Aiken, G.; Sebestyen, S. D.; Bergamaschi, B. A.

2012-12-01

Quantifying the fundamental linkages between hydrology and dissolved organic matter (DOM) dynamics in streams and rivers is critical for understanding carbon loads, ecosystem food webs and metal transport. Accurately assessing this relationship is difficult, however, given that rapid changes in water flow paths and associated DOM sources are often not captured by traditional discrete sampling intervals of weeks to months. We explored DOM - discharge relationships at Sleepers River below a 40.5 hectare USGS research watershed in northern Vermont by making 30 minute chromophoric DOM fluorescence (FDOM) measurements in-situ since October 2008 along with periodic discrete sampling for dissolved organic carbon. There is a tight coupling between the timing of increases in FDOM and discharge at Sleepers during events, but the ratio of FDOM to discharge exhibited considerable variability across seasons and events, as did FDOM-discharge hysteresis (FDOM variously peaked 1-4 hours after streamflow). Discrete DOM quality indicators (spectral slope, fluorescence index, SUVA) indicate DOM was predominantly terrestrial at all but the lowest flows, highlighting the important role of DOM-rich terrestrial flow paths as the primary source of stream DOM. Our results suggest that changes in flow paths are likely to be the primary drivers of future changes in DOM transport from this site rather than changes in DOM quality. Overcoming significant challenges inherent in continuous sensor deployments in watersheds (e.g. ice cover, suspended particles, remote communication and power) will allow for new insights into watershed biogeochemistry.

FLIP for FLAG model visualization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wooten, Hasani Omar

A graphical user interface has been developed for FLAG users. FLIP (FLAG Input deck Parser) provides users with an organized view of FLAG models and a means for efficiently and easily navigating and editing nodes, parameters, and variables.

Python/Lua Benchmarks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Busby, L.

This is an adaptation of the pre-existing Scimark benchmark code to a variety of Python and Lua implementations. It also measures performance of the Fparser expression parser and C and C++ code on a variety of simple scientific expressions.

Variable C : N : P stoichiometry of dissolved organic matter cycling in the Community Earth System Model

DOE PAGES

Letscher, R. T.; Moore, J. K.; Teng, Y. -C.; ...

2014-06-16

Dissolved organic matter (DOM) plays an important role in the ocean's biological carbon pump by providing an advective/mixing pathway for ~ 20% of export production. DOM is known to have a stoichiometry depleted in nitrogen (N) and phosphorus (P) compared to the particulate organic matter pool, a~fact that is often omitted from biogeochemical-ocean general circulation models. However the variable C : N : P stoichiometry of DOM becomes important when quantifying carbon export from the upper ocean and linking the nutrient cycles of N and P with that of carbon. Here we utilize recent advances in DOM observational data coveragemore » and offline tracer-modeling techniques to objectively constrain the variable production and remineralization rates of the DOM C / N / P pools in a simple biogeochemical-ocean model of DOM cycling. The optimized DOM cycling parameters are then incorporated within the Biogeochemical Elemental Cycling (BEC) component of the Community Earth System Model and validated against the compilation of marine DOM observations. The optimized BEC simulation including variable DOM C : N : P cycling was found to better reproduce the observed DOM spatial gradients than simulations that used the canonical Redfield ratio. Global annual average export of dissolved organic C, N, and P below 100 m was found to be 2.28 Pg C yr -1 (143 Tmol C yr -1), 16.4 Tmol N yr -1, and 1 Tmol P yr -1, respectively with an average export C : N : P stoichiometry of 225 : 19 : 1 for the semilabile (degradable) DOM pool. DOC export contributed ~ 25% of the combined organic C export to depths greater than 100 m.« less

Variable C : N : P stoichiometry of dissolved organic matter cycling in the Community Earth System Model

DOE PAGES

Letscher, R. T.; Moore, J. K.; Teng, Y. -C.; ...

2015-01-12

Dissolved organic matter (DOM) plays an important role in the ocean's biological carbon pump by providing an advective/mixing pathway for ~ 20% of export production. DOM is known to have a stoichiometry depleted in nitrogen (N) and phosphorus (P) compared to the particulate organic matter pool, a fact that is often omitted from biogeochemical ocean general circulation models. However the variable C : N : P stoichiometry of DOM becomes important when quantifying carbon export from the upper ocean and linking the nutrient cycles of N and P with that of carbon. Here we utilize recent advances in DOM observationalmore » data coverage and offline tracer-modeling techniques to objectively constrain the variable production and remineralization rates of the DOM C : N : P pools in a simple biogeochemical-ocean model of DOM cycling. The optimized DOM cycling parameters are then incorporated within the Biogeochemical Elemental Cycling (BEC) component of the Community Earth System Model (CESM) and validated against the compilation of marine DOM observations. The optimized BEC simulation including variable DOM C : N : P cycling was found to better reproduce the observed DOM spatial gradients than simulations that used the canonical Redfield ratio. Global annual average export of dissolved organic C, N, and P below 100 m was found to be 2.28 Pg C yr -1 (143 Tmol C yr -1, 16.4 Tmol N yr -1, and 1 Tmol P yr -1, respectively, with an average export C : N : P stoichiometry of 225 : 19 : 1 for the semilabile (degradable) DOM pool. Dissolved organic carbon (DOC) export contributed ~ 25% of the combined organic C export to depths greater than 100 m.« less

Differences in dissolved organic matter lability between alpine glaciers and alpine rock glaciers of the American West

NASA Astrophysics Data System (ADS)

Hall, E.; Fegel, T. S., II; Baron, J.; Boot, C. M.

2015-12-01

While alpine glaciers in montane regions represent the largest flux of dissolved organic matter (DOM) from global ice melt no research has examined the bioavailability of DOM melted out of glacial ice in the western continental United States. Furthermore, rock glaciers are an order of magnitude more abundant than ice glaciers in U.S., yet are not included in budgets for perennial ice carbon stores. Our research aims to understand differences in the bioavailability of carbon from ice glaciers and rock glaciers along the Central Rocky Mountains of Colorado. Identical microbial communities were fed standardized amounts of DOM from four different ice glacier-rock glaciers pairs. Using laboratory incubations, paired with mass spectrometry based metabolomics and 16S gene sequencing; we were able to examine functional definitions of DOM lability in glacial ice. We hypothesized that even though DOM quantities are similar in the outputs of both glacial types in our study area, ice glacial DOM would be more bioavailable than DOM from rock glaciers due to higher proportions of byproducts from microbial metabolism than rock glacier DOM, which has higher amounts of "recalcitrant" plant material. Our results show that DOM from ice glaciers is more labile than DOM from geologically and geographically similar paired rock glaciers. Ice glacier DOM represents an important pool of labile carbon to headwater ecosystems of the Rocky Mountains. Metabolomic analysis shows numerous compounds from varying metabolite pathways, including byproducts of nitrification before and after incubation, meaning that, similar to large maritime glaciers in Alaska and Europe, subglacial environments in the mountain ranges of the United States are hotspots for biological activity and processing of organic carbon.

Molecular Hysteresis of Dissolved Organic Matter in the Connecticut River Watershed

NASA Astrophysics Data System (ADS)

Wagner, S.; Hoyle, J. B.; Matt, S.; Raymond, P. A.; Saiers, J. E.; Dittmar, T.; Stubbins, A.

2017-12-01

Rainfall-runoff processes have emerged as key controllers of the quantity and quality of terrestrial dissolved organic matter (DOM) exported from the landscape to inland waters. Hydrological events result in increased river discharge and a concomitant release of large amounts of DOM into fluvial networks. This study is part of a Macrosystems project which aims to test the Pulse-Shunt Concept: where rivers are converted from active to passive pipes during high discharge events ("pulse"), transporting labile, terrestrial DOM downstream ("shunt"), and relocating biogeochemical hotspots for DOM from the upper to the lower reaches of the watershed. The primary objective of our study was to track hysteretic changes in riverine DOM molecular composition over the course of a storm event. Samples were collected from nested watersheds in the Passumpsic River catchment, a tributary of the Connecticut River (USA). High resolution monitoring (via in-situ sondes) and high frequency collection of discreet samples (for FT-ICR/MS and other analyses) was necessary to capture short-term, hydrologically-driven variations in DOM concentration and composition. At the onset of the discharge event, we observed a unique DOM signature, enriched in aliphatic, and potentially biolabile, DOM. During peak discharge, and along the falling limb of the hydrograph, an aromatic, terrestrial-type DOM signature was more prevalent. These initial findings support the pulse-shunt hypothesis, providing evidence for the release of labile forms of DOM into rivers during the onset of a storm event, which apparently persists across low-to-high stream orders. Insights into the molecular hysteresis of fluvial DOM spotlights the impact of watershed hydrology on biogeochemical cycling in river networks.

Further insight into the roles of the chemical composition of dissolved organic matter (DOM) on ultrafiltration membranes as revealed by multiple advanced DOM characterization tools.

PubMed

Ly, Quang Viet; Hur, Jin

2018-06-01

This study assessed the relative contributions of different constitutes in dissolved organic matter (DOM) with two different sources (i.e., urban river and effluent) to membrane fouling on three types of ultrafiltration (UF) membranes via excitation emission matrix - parallel factor analysis (EEM-PARAFAC), size exclusion chromatography (SEC), and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Two polyethersulfone membranes with different pore sizes and one regenerated cellulose membrane were used as representative hydrophobic (HPO) and hydrophilic (HPI) UF membranes, respectively. Although size exclusion effect was found to be the most prevailing rejection mechanism, the behaviors of individual fluorescent components (one tryptophan-like, one microbial-humic-like, and terrestrial humic-like) and different size fractions upon the UF filtration revealed that chemical interactions (e.g., hydrophobic interactions and hydrogen bonding) between DOM and membrane might play important roles in UF membrane fouling, especially for small sized DOM molecules. Based on the molecular level composition determined by FT-ICR-MS, the CHOS formula group showed a greater removal tendency toward the HPO membrane, while the CHONS group was prone to be removed by the HPI membrane. The changes in the overall molecular composition of DOM upon UF filtration were highly dependent on the sources of DOM. The molecules of more acidic nature tended to remain in the permeate of effluent DOM, while the river DOM was shifted into more nitrogen-enriched composition after filtration. Regardless of the DOM sources, the HPO membrane with a smaller pore size led to the most pronounced changes in the molecular composition of DOM. Copyright © 2018 Elsevier Ltd. All rights reserved.

Urbanization and agriculture increase exports and differentially alter elemental stoichiometry of dissolved organic matter (DOM) from tropical catchments.

PubMed

Gücker, Björn; Silva, Ricky C S; Graeber, Daniel; Monteiro, José A F; Boëchat, Iola G

2016-04-15

Many tropical biomes are threatened by rapid land-use change, but its catchment-wide biogeochemical effects are poorly understood. The few previous studies on DOM in tropical catchments suggest that deforestation and subsequent land use increase stream water dissolved organic carbon (DOC) concentrations, but consistent effects on DOM elemental stoichiometry have not yet been reported. Here, we studied stream water DOC concentrations, catchment DOC exports, and DOM elemental stoichiometry in 20 tropical catchments at the Cerrado-Atlantic rainforest transition, dominated by natural vegetation, pasture, intensive agriculture, and urban land cover. Streams draining pasture could be distinguished from those draining natural catchments by their lower DOC concentrations, with lower DOM C:N and C:P ratios. Catchments with intensive agriculture had higher DOC exports and lower DOM C:P ratios than natural catchments. Finally, with the highest DOC concentrations and exports, as well as the highest DOM C:P and N:P ratios, but the lowest C:N ratios among all land-use types, urbanized catchments had the strongest effects on catchment DOM. Thus, urbanization may have alleviated N limitation of heterotrophic DOM decomposition, but increased P limitation. Land use-especially urbanization-also affected the seasonality of catchment biogeochemistry. While natural catchments exhibited high DOC exports and concentrations, with high DOM C:P ratios in the rainy season only, urbanized catchments had high values in these variables throughout the year. Our results suggest that urbanization and pastoral land use exerted the strongest impacts on DOM biogeochemistry in the investigated tropical catchments and should thus be important targets for management and mitigation efforts. Copyright © 2016 Elsevier B.V. All rights reserved.

Revealing Sources and Distribution Changes of Dissolved Organic Matter (DOM) in Pore Water of Sediment from the Yangtze Estuary

PubMed Central

Wang, Ying; Zhang, Di; Shen, Zhenyao; Feng, Chenghong; Chen, Jing

2013-01-01

Dissolved organic matter (DOM) in sediment pore waters from Yangtze estuary of China based on abundance, UV absorbance, molecular weight distribution and fluorescence were investigated using a combination of various parameters of DOM as well as 3D fluorescence excitation emission matrix spectra (F-EEMS) with the parallel factor and principal component analysis (PARAFAC-PCA). The results indicated that DOM in pore water of Yangtze estuary was very variable which mainly composed of low aromaticity and molecular weight materials. Three humic-like substances (C1, C2, C4) and one protein-like substance (C3) were identified by PARAFAC model. C1, C2 and C4 exhibited same trends and were very similar. The separation of samples on both axes of the PCA showed the difference in DOM properties. C1, C2 and C4 concurrently showed higher positive factor 1 loadings, while C3 showed highly positive factor 2 loadings. The PCA analysis showed a combination contribution of microbial DOM signal and terrestrial DOM signal in the Yangtze estuary. Higher and more variable DOM abundance, aromaticity and molecular weight of surface sediment pore water DOM can be found in the southern nearshore than the other regions primarily due to the influence of frequent and intensive human activities and tributaries inflow in this area. The DOM abundance, aromaticity, molecular weight and fluorescence intensity in core of different depth were relative constant and increased gradually with depth. DOM in core was mainly composed of humic-like material, which was due to higher release of the sedimentary organic material into the porewater during early diagenesis. PMID:24155904

Characterization of spectral responses of dissolved organic matter (DOM) for atrazine binding during the sorption process onto black soil.

PubMed

Wang, Yifan; Zhang, Xinyuan; Zhang, Xing; Meng, Qingjuan; Gao, Fengjie; Zhang, Ying

2017-08-01

This study was aim to investigate the interaction between soil-derived dissolved organic matter (DOM) and atrazine as a kind of pesticides during the sorption process onto black soil. According to the experimental data, the adsorption capacity of Soil + DOM, Soil and DOM were 41.80, 31.45 and 9.35 mg kg -1 , separately, which indicated that DOM significantly enhanced the adsorption efficiency of atrazine by soil. Data implied that the pseudo-second-order kinetic equation could well explain the adsorption process. The adsorption isotherms (R 2  > 0.99) had a satisfactory fit in both Langmuir and Freundlich models. Three-dimensional excitation-emission matrix (3D-EEM), synchronous fluorescence, two-dimensional correlation spectroscopy (2D-COS) and Fourier transform infrared spectroscopy (FT-IR) were selected to analyze the interaction between DOM and atrazine. 3D-EEM showed that humic acid-like substances were the main component of DOM. The fluorescence of DOM samples were gradually quenched with the increased of atrazine concentrations. Synchronous fluorescence spectra showed that static fluorescence quenching was the main quenching process. 2D-COS indicated that the order of the spectral changes were as following: 336 nm > 282 nm. Furthermore, the fluorescence quenching of humic-like fraction occurred earlier than that of protein-like fraction under atrazine surroundings. FT-IR spectra indicated that main compositions of soil DOM include proteins, polysaccharides and humic substances. The findings of this study are significant to reveal DOM played an important role in the environmental fate of pesticides during sorption process onto black soil and also provide more useful information for understanding the interaction between DOM and pesticides by using spectral responses. Copyright © 2017. Published by Elsevier Ltd.

Characterization of binding site heterogeneity for copper within dissolved organic matter fractions using two-dimensional correlation fluorescence spectroscopy.

PubMed

Hur, Jin; Lee, Bo-Mi

2011-06-01

The heterogeneity of copper binding characteristics for dissolved organic matter (DOM) fractions was investigated based on the fluorescence quenching of the synchronous fluorescence spectra upon the addition of copper and two-dimensional correlation spectroscopy (2D-COS). Hydrophobic acid (HoA) and hydrophilic (Hi) fractions of two different DOM (algal and leaf litter DOM) were used for this study. For both DOM, fluorescence quenching occurred at a wider range of wavelengths for the HoA fractions compared to the Hi fractions. The combined information of the synchronous and asynchronous maps derived from 2D-COS provided a clear picture of the heterogeneous distribution of the copper binding sites within each DOM fraction, which was not readily recognized by a simple comparison of the changes in the synchronous fluorescence spectra upon the addition of copper. For the algal DOM, higher stability constants were exhibited for the HoA versus the Hi fractions. The logarithms of the stability constants ranged from 4.8 to 6.1 and from 4.5 to 5.0 for the HoA and the Hi fractions of the algal DOM, respectively, depending on the associated wavelength and the fitted models. In contrast, no distinctive difference in the binding characteristics was found between the two fractions of the leaf litter DOM. This suggests that influences of the structural and chemical properties of DOM on copper binding may differ for DOM from different sources. The relative difference of the calculated stability constants within the DOM fractions were consistent with the sequential orders interpreted from the asynchronous 2D-COS. It is expected that 2D-COS will be widely applied to other DOM studies requiring detailed information on the heterogeneous nature and subsequent effects under a range of environmental conditions. Copyright © 2011 Elsevier Ltd. All rights reserved.

Diurnal variability in riverine dissolved organic matter composition determined by in situ optical measurement in the San Joaquin River (California, USA)

USGS Publications Warehouse

Spencer, R.G.M.; Pellerin, B.A.; Bergamaschi, B.A.; Downing, B.D.; Kraus, T.E.C.; Smart, D.R.; Dahlgren, R.A.; Hernes, P.J.

2007-01-01

Dissolved organic matter (DOM) concentration and composition in riverine and stream systems are known to vary with hydrological and productivity cycles over the annual and interannual time scales. Rivers are commonly perceived as homogeneous with respect to DOM concentration and composition, particularly under steady flow conditions over short time periods. However, few studies have evaluated the impact of short term variability ( < 1 day) on DOM dynamics. This study examined whether diurnal processes measurably altered DOM concentration and composition in the hypereutrophic San Joaquin River (California) during a relatively quiescent period. We evaluated the efficacy of using optical in situ measurements to reveal changes in DOM which may not be evident from bulk dissolved organic carbon (DOC) measurement alone. The in situ optical measurements described in this study clearly showed for the first time diurnal variations in DOM measurements, which have previously been related to both composition and concentration, even though diurnal changes were not well reflected in bulk DOC concentrations. An apparent asynchronous trend of DOM absorbance and chlorophyll-a in comparison to chromophoric dissolved organic matter (CDOM) fluorescence and spectral slope S290-350 suggests that no one specific CDOM spectrophotometric measurement explains absolutely DOM diurnal variation in this system; the measurement of multiple optical parameters is therefore recommended. The observed diurnal changes in DOM composition, measured by in situ optical instrumentation likely reflect both photochemical and biologically-mediated processes. The results of this study highlight that short-term variability in DOM composition may complicate trends for studies aiming to distinguish different DOM sources in riverine systems and emphasizes the importance of sampling specific study sites to be compared at the same time of day. The utilization of in situ optical technology allows short-term variability in DOM dynamics to be monitored and serves to increase our understanding of its processing and fundamental role in the aquatic environment. Copyright ?? 2007 John Wiley & Sons, Ltd.

Understanding microbial/DOM interactions using fluorescence and flow cytometry

NASA Astrophysics Data System (ADS)

Fox, Bethany; Rushworth, Cathy; Attridge, John; Anesio, Alexandre; Cox, Tim; Reynolds, Darren

2015-04-01

The transformation and movement of dissolved organic carbon (DOC) within freshwater aquatic systems is an important factor in the global cycling of carbon. DOC within aquatic systems is known to underpin the microbial food web and therefore plays an essential role in supporting and maintaining the aquatic ecosystem. Despite this the interactions between bacteria and dissolved organic matter (DOM) are not well understood, although the literature indicates that the microbial processing of bioavailable DOM is essential during the production of autochthonous, labile, DOM. DOM can be broadly characterised by its fluorescing properties and Coble et al. (2014) define terrestrially derived DOM as exhibiting "peak C" fluorescence, whilst labile microbially derived DOM is defined as showing "peak T" fluorescence. Our work explores the microbial/DOM interactions by analysing aquatic samples using fluorescence excitation and emission matrices (EEMs) in conjunction with microbial consumption of dissolved oxygen. Environmental and synthetic water samples were subjected to fluorescence characterisation using both fluorescence spectroscopy and in situ fluorescence sensors (Chelsea Technologies Group Ltd.). PARAFAC analysis and peak picking were performed on EEMs and compared with flow cytometry data, used to quantify bacterial numbers present within samples. Synthetic samples were created using glucose, glutamic acid, nutrient-rich water and a standard bacterial seed. Synthetic samples were provided with terrestrially derived DOM via the addition of an aliquot of environmental water. Using a closed system approach, samples were incubated over time (up to a maximum of 20 days) and analysed at pre-defined intervals. The main focus of our work is to improve our understanding of microbial/DOM interactions and how these interactions affect both the DOM characteristics and microbial food web in freshwater aquatic systems. The information gained, in relation to the origin, microbial processing and subsequent production of DOM, will inform the development of a new generation of in situ fluorescence sensors. Ultimately, our aim is develop a novel technology that enables the monitoring of ecosystem health in freshwater aquatic systems.

Photochemical reactivities of dissolved organic matter (DOM) in a sub-alpine lake revealed by EEM-PARAFAC: An insight into the fate of allochthonous DOM in alpine lakes affected by climate change.

PubMed

Du, Yingxun; Zhang, Yuanyuan; Chen, Feizhou; Chang, Yuguang; Liu, Zhengwen

2016-10-15

Due to climate change, tree line advance is occurring in many alpine regions. Within the next 50 to 100years, alpine lake catchments are expected to develop increased vegetation cover similar to that of sub-alpine lake catchments which currently exist below the tree line. Such changes in vegetation could trigger increased allochthonous DOM inputs to alpine lakes. To understand the fate of allochthonous DOM in alpine lakes impacted by climate change, the photochemical reactivity of DOM in sub-alpine Lake Tiancai (located 200m below the tree line) was investigated by excitation emission matrix fluorescence combined with parallel factor analysis (EEM-PARAFAC) and UV-Vis spectra analysis. With photo-exposure, a decrease in apparent DOM molecular weight was observed and 32% DOM was photomineralized to CO2. Interestingly, the aromaticity of DOM increased after photodegradation, as evidenced by increases in both the specific UV absorbance at 254nm (SUVA254) and the humification index (HIX). Five EEM-PARAFAC components were identified, including four terrestrially-derived substances (C1, C2, C3 and C4; allochthonous) and one tryptophan-like substance (C5; autochthonous). Generally, allochthonous DOM represented by C2 and C3 exhibited greater photoreactivity than autochthonous DOM represented by C5. C4 was identified as a possible photoproduct with relatively high aromaticity and photorefractive tendencies and contributed to the observed increase in SUVA254 and HIX. UV light facilitated the photodegradation of DOM and had the greatest effect on the removal of C3. This study provides information on the transformation of EEM-PARAFAC components in a sub-alpine lake, which is important in understanding the fate of increased allochthonous DOM inputs to alpine lakes impacted by climate change. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular characteristics of continuously released DOM during one year of root and leaf litter decomposition

NASA Astrophysics Data System (ADS)

Altmann, Jens; Jansen, Boris; Kalbitz, Karsten; Filley, Timothy

2013-04-01

Dissolved organic matter (DOM) is one of the most dynamic carbon pools linking the terrestrial with the aquatic carbon cycle. Besides the insecure contribution of terrestrial DOM to the greenhouse effect, DOM also plays an important role for the mobility and availability of heavy metals and organic pollutants in soils. These processes depend very much on the molecular characteristics of the DOM. Surprisingly the processes that determine the molecular composition of DOM are only poorly understood. DOM can originate from various sources, which influence its molecular composition. It has been recognized that DOM formation is not a static process and DOM characteristics vary not only between different carbon sources. However, molecular characteristics of DOM extracts have scarcely been studied continuously over a longer period of time. Due to constant molecular changes of the parent litter material or soil organic matter during microbial degradation, we assumed that also the molecular characteristics of litter derived DOM varies at different stages during root and needle decomposition. For this study we analyzed the chemical composition of root and leaf samples of 6 temperate tree species during one year of litter decomposition in a laboratory incubation. During this long-term experiment we measured continuously carbon and nitrogen contents of the water extracts and the remaining residues, C mineralization rates, and the chemical composition of water extracts and residues by Curie-point pyrolysis mass spectrometry with TMAH We focused on the following questions: (I) How mobile are molecules derived from plant polymers like tannin, lignin, suberin and cutin? (II) How does the composition of root and leaf derived DOM change over time in dependence on the stage of decomposition and species? Litter derived DOM was generally dominated by aromatic compounds. Substituded fatty acids as typically cutin or suberin derived were not detected in the water extracts. Fresh leaf and needle samples released a much higher amount of tannins than fresh root samples. At later litter decomposition stages the influence of tannins decreased and lignin derived phenols dominated the extracts. With ongoing litter degradation the degree of oxidation for the litter material increased, which was also reflected by the water extracted molecules.

Molecular signatures of biogeochemical transformations in dissolved organic matter from ten World Rivers

NASA Astrophysics Data System (ADS)

Riedel, Thomas; Zark, Maren; Vähätalo, Anssi; Niggemann, Jutta; Spencer, Robert; Hernes, Peter; Dittmar, Thorsten

2016-09-01

Rivers carry large amounts of dissolved organic matter (DOM) to the oceans thereby connecting terrestrial and marine element cycles. Photo-degradation in conjunction with microbial turnover is considered a major pathway by which terrigenous DOM is decomposed. To reveal globally relevant patterns behind this process, we performed photo-degradation experiments and year-long bio-assays on DOM from ten of the largest world rivers that collectively account for more than one-third of the fresh water discharge to the global ocean. We furthermore tested the hypothesis that the terrigenous component in deep ocean DOM may be far higher than biomarker studies suggest, because of the selective photochemical destruction of characteristic biomolecules from vascular plants. DOM was molecularly characterized by a combination of non-targeted ultrahigh-resolution mass spectrometry and quantitative molecular tracer analyses. We show that the reactivity of DOM is globally related to broad catchment properties. Basins that are dominated by forest and grassland export more photo-degradable DOM than other rivers. Chromophoric compounds are mainly vascular plant-derived polyphenols, and partially carry a pyrogenic signature from vegetation fires. These forest and grassland dominated rivers lost up to 50% of dissolved organic carbon (DOC) during irradiation, and up to 85% of DOC was lost in total if subsequently bio-incubated for one year. Basins covered by cropland, on the other hand, export DOM with a higher proportion of photo-resistant and bio-available DOM which is enriched in nitrogen. In these rivers, 30% or less of DOC was photodegraded. Consistent with previous studies, we found that riverine DOM resembled marine DOM in its broad molecular composition after extensive degradation, mainly due to almost complete removal of aromatics. More detailed molecular fingerprinting analysis (based on the relative abundance of >4000 DOM molecular formulae), however, revealed clear differences between degraded riverine and deep-sea DOM (molecular Bray-Curtis dissimilarity of 50%). None of our experimental treatments enhanced the molecular similarity between the rivers and the deep ocean. We conclude that terrigenous DOM retains a specific molecular signature during photo-degradation on much longer time scales than previously assumed and that substantial, thus far unknown, molecular transformations occur prior to downward convection into the deep oceanic basins.

Design, fabrication, and testing of nanostructured carbons and composites

NASA Astrophysics Data System (ADS)

Wang, Zhiyong

Many applications, such as catalysis, sensing, separation and energy storage and conversion, will benefit from the miniaturization of materials to nanometer length scales. This dissertation details my study of nanocomposites based on three-dimensionally ordered macroporous (3DOM) carbons and zirconia, and three-dimensionally ordered macroporous/mesoporous (3DOM/m) carbons. The macropores of these materials were produced using colloidal crystal templates while the mesopores were generated using surfactant templates. These solids are composed of close-packed and three-dimensionally interconnected spherical macropores surrounded by nanoscale solid or mesoporous wall skeletons. This unique architecture offers large surface areas, pore volumes, and good access into the bulk via a macroporous network. 3DOM carbons have been demonstrated as promising electrode materials for lithium ion batteries and sensors, but their electrochemical performance still needs to be improved. As a model system for the modification of the electrode, 3DOM C/TiO2 was synthesized by fabricating a conformal coating of TiO2 nanoparticles on the macropore walls of 3DOM C. My research further extended the micro-structural design of monolithic carbon from 3DOM to 3DOM/m. 3DOM/m C monoliths with high surface areas, controllable mesopore sizes, and mesopore ordering, were synthesized by three methods. One of the methods is simpler and more environment benign than previously reported methods. The mesopores in 3DOM/m C-based electrode provide room to accommodate secondary phases, such as graphitic carbon, SnO2 and Si which can improve the conductivity or lithium capacity of the electrode. Owing to this advantage, 3DOM/m C/C and 3DOM/m C/SnO2 exhibited significantly improved rate performance, lithium capacity and cycleability, compared with 3DOM C. To meet the demands of nano-sized functional materials in applications such as nano-device fabrication and drug delivery, mesoporous carbon nanoparticles with cubic, spherical and tetrapod shapes were also synthesized. In addition, new methods were developed to assemble nanocomposites of bifunctional catalyst components. These materials were designed for the potential direct conversion of synthesis gas to clean liquid fuels. Coatings of zeolite and cobalt nanoparticles were fabricated on 3DOM promoted zirconia. The 3DOM zirconia-based nanocomposites were characterized by a wide variety of techniques to illustrate their morphologies, internal structures, chemical compositions, porosity, and crystallographic phases.

Factorial analysis of the trihalomethane formation in the reaction of colloidal, hydrophobic, and transphilic fractions of DOM with free chlorine.

PubMed

Platikanov, Stefan; Tauler, Roma; Rodrigues, Pedro M S M; Antunes, Maria Cristina G; Pereira, Dilson; Esteves da Silva, Joaquim C G

2010-09-01

This study focuses on the factors that affect trihalomethane (THMs) formation when dissolved organic matter (DOM) fractions (colloidal, hydrophobic, and transphilic fractions) in aqueous solutions were disinfected with chlorine. DOM fractions were isolated and fractionated from filtered lake water and were characterized by elemental analysis. The investigation involved a screening Placket-Burman factorial analysis design of five factors (DOM concentration, chlorine dose, temperature, pH, and bromide concentration) and a Box-Behnken design for a detailed assessment of the three most important factor effects (DOM concentration, chlorine dose, and temperature). The results showed that colloidal fraction has a relatively low contribution to THM formation; transphilic fraction was responsible for about 50% of the chloroform generation, and the hydrophobic fraction was the most important to the brominated THM formation. When colloidal and hydrophobic fraction solutions were disinfected, the most significant factors were the following: higher DOM fraction concentration led to higher THM concentration, an increase of pH corresponded to higher concentration levels of chloroform and reduced bromoform, higher levels of chlorine dose and temperature produced a rise in the total THM formation, especially of the chlorinated THMs; higher bromide concentration generates higher concentrations of brominated THMs. Moreover, linear models were implemented and response surface plots were obtained for the four THM concentrations and their total sum in the disinfection solution as a function of the DOM concentration, chlorine dose, and temperature. Overall, results indicated that THM formation models were very complex due to individual factor effects and significant interactions among the factors. In order to reduce the concentration of THMs in drinking water, DOM concentrations must be reduced in the water prior to the disinfection. Fractionation of DOM, together with an elemental analysis of the fractions, is important issue in the revealing of the quality and quantity characteristics of DOM. Systematic study composed from DOM fraction investigation and factorial analysis of the responsible parameters in the THM formation reaction can, after an evaluation of the adjustment of the models with the reality, serves well for the evaluation of the spatial and temporal variability in the THM formation in dependence of DOM. However, taking into consideration the natural complexity of DOM, different operations and a strict control of them (like coagulation/flocculation and filtration) has to be used to quantitatively remove DOM from the raw water. Assuming that this study represents a local case study, similar experiments can be easily applied and will supply with relevant information every local water treatment plant meeting problems with THM formation. The coagulation/flocculation and the filtration stages are the main mechanisms to remove DOM, particularly the colloidal DOM fraction. With the objective to minimize THMs generation, different unit operation designed to quantitatively remove DOM from water must be optimized.

The Relationship Between Dissolved Organic Matter Composition and Organic Matter Optical Properties in Freshwaters

NASA Astrophysics Data System (ADS)

Aiken, G.; Spencer, R. G.; Butler, K.

2010-12-01

Dissolved organic matter (DOM) chemistry and flux are potentially useful, albeit, underutilized, indicators of watershed characteristics, climate influences on watershed hydrology and soils, and changes associated with resource management. Source materials, watershed geochemistry, oxidative processes and hydrology exert strong influences on the nature and reactivity of DOM in aquatic systems. The molecules that comprise DOM, in turn, control a number of environmental processes important for ecosystem function including light penetration and photochemistry, microbial activity, mineral dissolution/precipitation, and the transport and reactivity of hydrophobic compounds and metals (e.g. Hg). In particular, aromatic molecules derived from higher plants exert strong controls on aquatic photochemistry, and on the transport and biogeochemistry of metals. Assessment of DOM composition and transport, therefore, can provide a basis for understanding watershed processes and biogeochemistry of rivers and streams. Here we present results of multi-year studies designed to assess the seasonal and spatial variability of DOM quantity and quality for 57 North American Rivers. DOM concentrations and composition, based on DOM fractionation on XAD resins, ultraviolet (UV)/visible absorption and fluorescence spectroscopic analyses, and specific compound analyses, varied greatly both between sites and seasonally within a given site. DOM in these rivers exhibited a wide range of concentration (<80 to >4000 µM C* L-1) and specific ultra-violet absorbance at 254 nm (SUVA254) (0.6 to 5 L *mg C-1 *m-1), an optical measurement that is an indicator of aromatic carbon content. In almost all systems, UV absorbance measured at specific wavelengths (e.g. 254 nm) correlated strongly with DOM and hydrophobic organic acid (HPOA) content (aquatic humic substances). The relationships between dissolved organic carbon (DOC) concentration and absorbance for the range of systems were quite variable due to variation in the fraction of non-chromophoric DOM. However, the relationship between HPOA content and UV absorbance was stronger and more consistent because the HPOA fraction contains a greater percentage of UV absorbing compounds than other fractions of the DOM. These results demonstrate that optical properties, such as UV absorbance, are excellent proxies for DOC and HPOA concentrations within a given system. For a limited set of samples, we observed that optical measurements were strongly correlated with lignin phenols, a biomarker indicative of higher plant sources of DOM, and with Hg, which interacts strongly with DOM. Optical measurements are relatively inexpensive to obtain, provide critical information related to DOM composition and reactivity, and can be measured in situ. When combined with discharge data, optical measurements allow estimation of both DOM flux and reactivity in streams and rivers. The link between the nature and reactivity of DOM and its optical properties can be exploited to provide powerful monitoring tools to assess the impacts of climate change and management practices on overall water quality, on DOM transport and transformation, and on the transport of other chemical constituents of interest.

The Effects of Biodegradation and Photodegradation on DOM Optical Properties: Controlled Laboratory Study Using Plant, Soil and Algal Leachates

NASA Astrophysics Data System (ADS)

Hansen, A. M.; Kraus, T. E. C.; Pellerin, B. A.; Fleck, J.

2014-12-01

Many studies use optical properties to infer dissolved organic matter (DOM) composition and origin; however, there are few controlled studies which examine the effects of environmental processing on different DOM sources. Our goal was to better understand the roles DOM plays in wetland environments of the Sacramento-San Joaquin Delta. Therefore, five endmember sources of DOM from this region were selected for use in this study: peat soil (euic, thermic Typic Medisaprists); three aquatic macrophytes (white rice (Oryza sativa); tule (Schoenoplectus acutus); cattail (Typha spp.)); and one diatom (Thalassiosira weissflogii). We measured DOM concentrations (mg C/L) and optical properties (absorbance and fluorescence) of these sources following biological and photochemical degradation over a three month period. DOM concentration decreased by over 90% in plant and algal leachates following 3 months of biodegradation, while photoexposure had negligible effects. The fluorescence index (FI), humic index (HI), specific UV absorbance at 254 nm (SUVA), and carbon-normalized fluorescence of Peaks C and A increased with biodegradation, whereas Peak T decreased. Photoexposure resulted in a decrease of the FI, HI and SUVA values. Our results emphasize the need to better understand how environmental processing affects DOM properties in aquatic environments; the frequently opposing effects of biodegradation and photodegradation, which occur simultaneously in nature, make it challenging to decipher the original DOM source without considering multiple parameters. This dataset can help us better identify which optical properties, either individual or in combination, can provide insight into how biogeochemical processes affect DOM in aquatic environments.

Fluorescence Excitation-Emission Matrix Regional Integration to Quantify Spectra for Dissolved Organic Matter

USGS Publications Warehouse

Chen, W.; Westerhoff, P.; Leenheer, J.A.; Booksh, K.

2003-01-01

Excitation-emission matrix (EEM) fluorescence spectroscopy has been widely used to characterize dissolved organic matter (DOM) in water and soil. However, interpreting the >10,000 wavelength-dependent fluorescence intensity data points represented in EEMs has posed a significant challenge. Fluorescence regional integration, a quantitative technique that integrates the volume beneath an EEM, was developed to analyze EEMs. EEMs were delineated into five excitation-emission regions based on fluorescence of model compounds, DOM fractions, and marine waters or freshwaters. Volumetric integration under the EEM within each region, normalized to the projected excitation-emission area within that region and dissolved organic carbon concentration, resulted in a normalized region-specific EEM volume (??i,n). Solid-state carbon nuclear magnetic resonance (13C NMR), Fourier transform infrared (FTIR) analysis, ultraviolet-visible absorption spectra, and EEMs were obtained for standard Suwannee River fulvic acid and 15 hydrophobic or hydrophilic acid, neutral, and base DOM fractions plus nonfractionated DOM from wastewater effluents and rivers in the southwestern United States. DOM fractions fluoresced in one or more EEM regions. The highest cumulative EEM volume (??T,n = ????i,n) was observed for hydrophobic neutral DOM fractions, followed by lower ??T,n values for hydrophobic acid, base, and hydrophilic acid DOM fractions, respectively. An extracted wastewater biomass DOM sample contained aromatic protein- and humic-like material and was characteristic of bacterial-soluble microbial products. Aromatic carbon and the presence of specific aromatic compounds (as indicated by solid-state 13C NMR and FTIR data) resulted in EEMs that aided in differentiating wastewater effluent DOM from drinking water DOM.

Light limitation plays a central role in regulating DOM reactions in temperate watersheds

NASA Astrophysics Data System (ADS)

Yoon, B.; Hosen, J. D.; Kyzivat, E.; Fair, J. H.; Weber, L.; Aho, K. S.; Stubbins, A.; Lowenthal, R. S.; Raymond, P. A.

2017-12-01

Biological uptake and photochemical oxidation determine how much dissolved organic matter (DOM) can be removed and exported from inland waters. It is thus critical to understand the control on the biological and photochemical oxidation of DOM, and identify potential synergy between these two DOM removal processes. Yet, the variability of biological and photochemical lability, and the prevalence of priming effects between the two removal mechanisms are poorly understood at larger spatiotemporal scale. To address this knowledge gap, we analyzed the lability of 900 samples collected throughout the Connecticut River across two years (n = 510 for biolability, n=394 for photolability). Furthermore, we measured the effect of photochemical priming for biological removal and of biological priming for photochemical removal (n= 151, n=146, respectively). Our results show that photolability is on average 5 times greater than biolability, and that the mass of photolabile DOM can be predicted from UV absorbance at 254 nm. Photochemical DOM removal also led to additional "unlocking" of previously bio-recalcitrant DOM in 80% of the samples, and increased the biological lability by threefold on average. Scaling further, we extrapolate our model to estimate that the DOM fluxes leaving the Connecticut River and the Mississippi River are 49% and 45% photolabile, respectively. The significant photoreactivity observed across the samples and the subsequent increase in biolability demonstrate that sunlight is a more potent agent of DOM removal than the biological reactions. Yet, the photolability of DOM fluxes leaving the Connecticut River and Mississippi River indicates that the full photo-oxidation potential is not achieved due to light limitation.

Comparison of the discriminative stimulus effects of dimethyltryptamine with different classes of psychoactive compounds in rats.

PubMed

Gatch, Michael B; Rutledge, Margaret A; Carbonaro, Theresa; Forster, Michael J

2009-07-01

There has been increased recreational use of dimethyltryptamine (DMT), but little is known of its discriminative stimulus effects. The present study assessed the similarity of the discriminative stimulus effects of DMT to other types of hallucinogens and to psychostimulants. Rats were trained to discriminate DMT from saline. To test the similarity of DMT to known hallucinogens, the ability of (+)-lysergic acid diethylamide (LSD), (-)-2,5-dimethoxy-4-methylamphetamine (DOM), (+)-methamphetamine, or (+/-)3,4-methylenedioxymethyl amphetamine (MDMA) to substitute in DMT-trained rats was tested. The ability of DMT to substitute in rats trained to discriminate each of these compounds was also tested. To assess the degree of similarity in discriminative stimulus effects, each of the compounds was tested for substitution in all of the other training groups. LSD, DOM, and MDMA all fully substituted in DMT-trained rats, whereas DMT fully substituted only in DOM-trained rats. Full cross-substitution occurred between DMT and DOM, LSD and DOM, and (+)-methamphetamine and MDMA. MDMA fully substituted for (+)-methamphetamine, DOM, and DMT, but only partially for LSD. In MDMA-trained rats, LSD and (+)-methamphetamine fully substituted, whereas DMT and DOM did not fully substitute. No cross-substitution was evident between (+)-methamphetamine and DMT, LSD, or DOM. DMT produces discriminative stimulus effects most similar to those of DOM, with some similarity to the discriminative stimulus effects of LSD and MDMA. Like DOM and LSD, DMT seems to produce predominately hallucinogenic-like discriminative stimulus effects and minimal psychostimulant effects, in contrast to MDMA which produced hallucinogen- and psychostimulant-like effects.

Hydrologic Controls on In-Stream Optical Dissolved Organic Matter Characteristics in an Old-Growth Forest of the Oregon Cascades

NASA Astrophysics Data System (ADS)

Lajtha, K.; Lee, B. S.

2015-12-01

Dissolved organic matter (DOM) is a critical component of the carbon cycle linking terrestrial and aquatic ecosystems, yet DOM composition representative of DOM sources at headwater catchments in the western U.S is poorly understood. This study examined the effect of forest management history and hydrologic patterns on DOM chemistry at nine experimental watersheds located in the H.J. Andrews Long Term Ecological Research Experimental Forest of the Oregon Cascades. Stream water samples representing a three-week composite of each watershed were collected between May 2013 and February 2015 (32 events). DOM chemistry was characterized by examining UV and fluorescent properties of stream samples. Specific UV absorbance at 254 nm (SUVA254; Weishaar et al. 2003), generally indicative of aromaticity, showed the lowest value at the high elevation clear-cut site (watershed 6, 1,030 m) and the highest value at the low elevation clear-cut site (watershed 10, 680 m) throughout the study period. DOM fluorescent components, identified by this study using a multivariate statistical model, Parallel Factor Analysis (PARAFAC), did not differ significantly among experimental watersheds with varying forest management history. However, a protein-like DOM component exhibited temporal variations. Correlation analysis between the protein-like DOM and hydrologic patterns indicate that stream water during dry seasons come from protein-rich groundwater sources. This study shows UV and fluorescent spectroscopy DOM characterization is a viable finger printing method to detect DOM sources in pristine headwater streams at the western Cascades of Oregon where characterization of the stream water source with low DOC and DON concentrations is difficult.

Actinide Sorption in Rainier Mesa Tunnel Waters from the Nevada Test Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, P; Zavarin, M; Leif, R

2007-12-17

The sorption behavior of americium (Am), plutonium (Pu), neptunium (Np), and uranium (U) in perched Rainier Mesa tunnel water was investigated. Both volcanic zeolitized tuff samples and groundwater samples were collected from Rainier Mesa, Nevada Test Site, NV for a series of batch sorption experiments. Sorption in groundwater with and without the presence of dissolved organic matter (DOM) was investigated. Am(III) and Pu(IV) are more soluble in groundwater that has high concentrations of DOM. The sorption K{sub d} for Am(III) and Pu(IV) on volcanic zeolitized tuff was up to two orders of magnitude lower in samples with high DOM (15more » to 19 mg C/L) compared to samples with DOM removed (< 0.4 mg C/L) or samples with naturally low DOM (0.2 mg C/L). In contrast, Np(V) and U(VI) sorption to zeolitized tuff was much less affected by the presence of DOM. The Np(V) and U(VI) sorption Kds were low under all conditions. Importantly, the DOM was not found to significantly sorb to the zeolitized tuff during these experiment. The concentration of DOM in groundwater affects the transport behavior of actinides in the subsurface. The mobility of Am(III) and Pu(IV) is significantly higher in groundwater with elevated levels of DOM resulting in potentially enhanced transport. To accurately model the transport behavior of actinides in groundwater at Rainier Mesa, the low actinide Kd values measured in groundwater with high DOM concentrations must be incorporated in predictive transport models.« less

DOM composition and transformation in boreal forest soils: The effects of temperature and organic-horizon decomposition state

USGS Publications Warehouse

O’Donnell, Jonathan A.; Aiken, George R.; Butler, Kenna D.; Guillemette, Francois; Podgorski, David C.; Spencer, Robert G. M.

2016-01-01

The boreal region stores large amounts of organic carbon (C) in organic-soil horizons, which are vulnerable to destabilization via warming and disturbance. Decomposition of soil organic matter (SOM) contributes to the production and turnover of dissolved organic matter (DOM). While temperature is a primary control on rates of SOM and DOM cycling, little is known about temperature effects on DOM composition in soil leachate. Here we conducted a 30 day incubation to examine the effects of temperature (20 versus 5°C) and SOM decomposition state (moss versus fibric versus amorphous horizons) on DOM composition in organic soils of interior Alaska. We characterized DOM using bulk dissolved organic C (DOC) concentration, chemical fractionation, optical properties, and ultrahigh-resolution mass spectrometry. We observed an increase in DOC concentration and DOM aromaticity in the 20°C treatment compared to the 5°C treatment. Leachate from fibric horizons had higher DOC concentration than shallow moss or deep amorphous horizons. We also observed chemical shifts in DOM leachate over time, including increases in hydrophobic organic acids, polyphenols, and condensed aromatics and decreases in low-molecular weight hydrophilic compounds and aliphatics. We compared ultrahigh-resolution mass spectrometry and optical data and observed strong correlations between polyphenols, condensed aromatics, SUVA254, and humic-like fluorescence intensities. These findings suggest that biolabile DOM was preferentially mineralized, and the magnitude of this transformation was determined by kinetics (i.e., temperature) and substrate quality (i.e., soil horizon). With future warming, our findings indicate that organic soils may release higher concentrations of aromatic DOM to aquatic ecosystems.

Temporal Dynamics in the Concentration, Flux, and Optical Properties of Tree-Derived Dissolved Organic Matter in an Epiphyte-Laden Oak-Cedar Forest

NASA Astrophysics Data System (ADS)

Van Stan, John T.; Wagner, Sasha; Guillemette, François; Whitetree, Ansley; Lewis, Julius; Silva, Leticia; Stubbins, Aron

2017-11-01

Studies on the fate and transport of dissolved organic matter (DOM) along the rainfall-to-discharge flow pathway typically begin in streams or soils, neglecting the initial enrichment of rainfall with DOM during contact with plant canopies. However, rain water can gather significant amounts of tree-derived DOM (tree-DOM) when it drains from the canopy, as throughfall, and down the stem, as stemflow. We examined the temporal variability of event-scale tree-DOM concentrations, yield, and optical (light absorbance and fluorescence) characteristics from an epiphyte-laden Quercus virginiana-Juniperus virginiana forest on Skidaway Island, Savannah, Georgia (USA). All tree-DOM fluxes were highly enriched in dissolved organic carbon (DOC) compared to rainfall, and epiphytes further increased concentrations. Stemflow DOC concentrations were greater than throughfall across study species, yet larger throughfall water yields produced greater DOC yields versus stemflow. Tree-DOM optical characteristics indicate it is aromatic-rich with fluorescent DOM dominated by humic-like fluorescence, containing 10-20% protein-like (tryptophan-like) fluorescence. Storm size was the only storm condition that strongly correlated with tree-DOM concentration and flux; however, throughfall and stemflow optical characteristics varied little across a wide range of storm conditions (from low magnitude events to intense tropical storms). Annual tree-DOM yields from the study forest (0.8-46 g C m-2 yr-1) were similar to other yields from discrete down-gradient fluxes (litter leachates, soil leachates, and stream discharge) along the rainfall-to-discharge flow path.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schumacher,M.; Christl, I.; Vogt, R.

The chemical composition and carbon isotope signature of aquatic dissolved organic matter (DOM) in five boreal forest catchments in Scandinavia were investigated. The DOM was isolated during spring and fall seasons using a reverse osmosis technique. The DOM samples were analyzed by elemental analysis, FT-IR, solid-state CP-MAS {sup 13}C-NMR, and C-1s NEXAFS spectroscopy. In addition, the relative abundance of carbon isotopes ({sup 12}C, {sup 13}C, {sup 14}C) in the samples was measured. There were no significant differences in the chemical composition or carbon isotope signature of the DOM sampled in spring and fall seasons. Also, differences in DOM composition betweenmore » the five catchments were minor. Compared to reference peat fulvic and humic acids, all DOM samples were richer in O-alkyl carbon and contained less aromatic and phenolic carbon, as shown by FT-IR, {sup 13}C-NMR, and C-1s NEXAFS spectroscopy. The DOM was clearly enriched in {sup 14}C relative to the NBS oxalic acid standard of 1950, indicating that the aquatic DOM contained considerable amounts of organic carbon younger than about 50 years. The weight-based C:N ratios of 31 {+-} 6 and the {delta}{sup 13}Cvalues of -29 {+-} 2{per_thousand}indicate that the isolated DOM is of terrestrial rather than aquatic origin. We conclude that young, hydrophilic carbon compounds of terrestrial origin are predominant in the samples investigated, and that the composition of the aquatic DOM in the studied boreal forest catchments is rather stable during low to intermediate flow conditions.« less

A translator writing system for microcomputer high-level languages and assemblers

NASA Technical Reports Server (NTRS)

Collins, W. R.; Knight, J. C.; Noonan, R. E.

1980-01-01

In order to implement high level languages whenever possible, a translator writing system of advanced design was developed. It is intended for routine production use by many programmers working on different projects. As well as a fairly conventional parser generator, it includes a system for the rapid generation of table driven code generators. The parser generator was developed from a prototype version. The translator writing system includes various tools for the management of the source text of a compiler under construction. In addition, it supplies various default source code sections so that its output is always compilable and executable. The system thereby encourages iterative enhancement as a development methodology by ensuring an executable program from the earliest stages of a compiler development project. The translator writing system includes PASCAL/48 compiler, three assemblers, and two compilers for a subset of HAL/S.

Characterization and Fate of Dissolved Organic Matter in the Lena Delta Region, Siberia

NASA Astrophysics Data System (ADS)

Goncalves-Araujo, R.; Stedmon, C. A.; Heim, B.; Dubinenkov, I.; Kraberg, A.; Moiseev, D.; Bracher, A.

2016-02-01

Connectivity between the terrestrial and marine environment in the Artic is changing as a result of climate change, influencing both freshwater budgets and the supply of carbon to the sea. This study characterizes the optical properties of dissolved organic matter (DOM) within the Lena Delta region and evaluates the behavior of DOM across the fresh water-marine gradient. Six fluorescent components (four humic-like; one marine humic-like; one protein-like) were identified by Parallel Factor Analysis (PARAFAC) with a clear dominance of allochthonous humic-like signals. Colored DOM (CDOM) and dissolved organic carbon (DOC) were highly correlated and had their distribution coupled with hydrographical conditions. Higher DOM concentration and degree of humification were associated with the low salinity waters of the Lena River. Values decreased towards the higher salinity Laptev Sea shelf waters. Results demonstrate different responses of DOM mixing in relation to the vertical structure of the water column, as reflecting the hydrographical dynamics in the region. Two mixing curves for DOM were apparent. In surface waters above the pycnocline there was a sharper decrease in DOM concentration in relation to salinity indicating removal. In the bottom water layer the DOM decrease within salinity was less. We propose there is a removal of DOM occurring primarily at the surface layer, which is likely driven by photodegradation and flocculation.

Spatial and seasonal variations in stream water delta34S-dissolved organic matter in northern Sweden.

PubMed

Giesler, Reiner; Björkvald, Louise; Laudon, Hoalmar; Mörth, Carl-Magnus

2009-01-15

The discharge of terrestrial dissolved organic matter (DOM) by streams is an important cross-system linkage that strongly influences downstream aquatic ecosystems. Isotopic tracers are important tools that can help to unravel the source of DOM from different terrestrial compartments in the landscape. Here we demonstrate the spatial and seasonal variation of delta34S of DOM in 10 boreal streams to test if the tracer could provide new insights into the origin of DOM. We found large spatial and seasonal variations in stream water delta34S-DOM values ranging from -5.2 per thousand to +9.6 per thousand with an average of +4.0 +/- 0.6 (N = 62; average and 95% confidence interval). Large seasonal variations were found in stream water delta34S-DOM values: for example, a shift of more than 10 per thousand during the spring snowmelt in a wetland-dominated stream. Spatial differences were also observed during the winter base flow with higher delta34S-DOM values in the fourth-order Krycklan stream at the outlet of the 68 km2 catchment compared to the small (< 1 km2) headwater streams. Our data clearly show that the delta34S-DOM values have the potential to be used as a tracer to identify and generate new insights about terrestrial DOM sources in the boreal landscape.

Variation of organic matter quantity and quality in streams at Critical Zone Observatory watersheds

USGS Publications Warehouse

Miller, Matthew P.; Boyer, Elizabeth W.; McKnight, Diane M.; Brown, Michael G.; Gabor, Rachel S.; Hunsaker, Carolyn T.; Iavorivska , Lidiia; Inamdar, Shreeram; Kaplan, Louis A.; Johnson, Dale W.; Lin, Henry; McDowell, William H.; Perdrial, Julia N.

2016-01-01

The quantity and chemical composition of dissolved organic matter (DOM) in surface waters influence ecosystem processes and anthropogenic use of freshwater. However, despite the importance of understanding spatial and temporal patterns in DOM, measures of DOM quality are not routinely included as part of large-scale ecosystem monitoring programs and variations in analytical procedures can introduce artifacts. In this study, we used consistent sampling and analytical methods to meet the objective of defining variability in DOM quantity and quality and other measures of water quality in streamflow issuing from small forested watersheds located within five Critical Zone Observatory sites representing contrasting environmental conditions. Results show distinct separations among sites as a function of water quality constituents. Relationships among rates of atmospheric deposition, water quality conditions, and stream DOM quantity and quality are consistent with the notion that areas with relatively high rates of atmospheric nitrogen and sulfur deposition and high concentrations of divalent cations result in selective transport of DOM derived from microbial sources, including in-stream microbial phototrophs. We suggest that the critical zone as a whole strongly influences the origin, composition, and fate of DOM in streams. This study highlights the value of consistent DOM characterization methods included as part of long-term monitoring programs for improving our understanding of interactions among ecosystem processes as controls on DOM biogeochemistry.

Effects of molecular weight on the diffusion coefficient of aquatic dissolved organic matter and humic substances.

PubMed

Balch, J; Guéguen, C

2015-01-01

In situ measurements of labile metal species using diffusive gradients in thin films (DGT) passive samplers are based on the diffusion rates of individual species. Although most studies have dealt with chemically isolated humic substances, the diffusion of dissolved organic matter (DOM) across the hydrogel is not well understood. In this study, the diffusion coefficient (D) and molecular weight (MW) of 11 aquatic DOM and 4 humic substances (HS) were determined. Natural, unaltered aquatic DOM was capable of diffusing across the diffusive gel membrane with D values ranging from 2.48×10(-6) to 5.31×10(-6) cm(2) s(-1). Humic substances had diffusion coefficient values ranging from 3.48×10(-6) to 6.05×10(-6) cm(2) s(-1), congruent with previous studies. Molecular weight of aquatic DOM and HS samples (∼500-1750 Da) measured using asymmetrical flow field-flow fractionation (AF4) strongly influenced D, with larger molecular weight DOM having lower D values. No noticeable changes in DOM size properties were observed during the diffusion process, suggesting that DOM remains intact following diffusion across the diffusive gel. The influence of molecular weight on DOM mobility will assist in further understanding and development of the DGT technique and the uptake and mobility of contaminants associated with DOM in aquatic environments. Copyright © 2014 Elsevier Ltd. All rights reserved.

Spatial and temporal variations in DOM composition in ecosystems: The importance of long-term monitoring of optical properties

Treesearch

R. Jaffe; D. McKnight; N. Maie; R. Cory; W. H. McDowell; J.L. Campbell

2008-01-01

Source, transformation, and preservation mechanisms of dissolved organic matter (DOM) remain elemental questions in contemporary marine and aquatic sciences and represent a missing link in models of global elemental cycles. Although the chemical character of DOM is central to its fate in the global carbon cycle, DOM characterizations in long-term ecological research...

The river as a chemostat: fresh perspectives on dissolved organic matter flowing down the river continuum

USGS Publications Warehouse

Creed, Irena F.; McKnight, Diane M.; Pellerin, Brian; Green, Mark B.; Bergamaschi, Brian; Aiken, George R.; Burns, Douglas A.; Findlay, Stuart E G; Shanley, James B.; Striegl, Robert G.; Aulenbach, Brent T.; Clow, David W.; Laudon, Hjalmar; McGlynn, Brian L.; McGuire, Kevin J.; Smith, Richard A.; Stackpoole, Sarah M.

2015-01-01

A better understanding is needed of how hydrological and biogeochemical processes control dissolved organic carbon (DOC) concentrations and dissolved organic matter (DOM) composition from headwaters downstream to large rivers. We examined a large DOM dataset from the National Water Information System of the US Geological Survey, which represents approximately 100 000 measurements of DOC concentration and DOM composition at many sites along rivers across the United States. Application of quantile regression revealed a tendency towards downstream spatial and temporal homogenization of DOC concentrations and a shift from dominance of aromatic DOM in headwaters to more aliphatic DOM downstream. The DOC concentration–discharge (C-Q) relationships at each site revealed a downstream tendency towards a slope of zero. We propose that despite complexities in river networks that have driven many revisions to the River Continuum Concept, rivers show a tendency towards chemostasis (C-Q slope of zero) because of a downstream shift from a dominance of hydrologic drivers that connect terrestrial DOM sources to streams in the headwaters towards a dominance of instream and near-stream biogeochemical processes that result in preferential losses of aromatic DOM and preferential gains of aliphatic DOM.

Spatial dependence of reduced sulfur in Everglades dissolved organic matter controlled by sulfate enrichment

USGS Publications Warehouse

Poulin, Brett A.; Ryan, Joseph N.; Nagy, Kathryn L.; Stubbins, Aron; Dittmar, Thorsten; Orem, William H.; Krabbenhoft, David P.; Aiken, George R.

2017-01-01

Sulfate inputs to the Florida Everglades stimulate sulfidic conditions in freshwater wetland sediments that affect ecological and biogeochemical processes. An unexplored implication of sulfate enrichment is alteration of the content and speciation of sulfur in dissolved organic matter (DOM), which influences the reactivity of DOM with trace metals. Here, we describe the vertical and lateral spatial dependence of sulfur chemistry in the hydrophobic organic acid fraction of DOM from unimpacted and sulfate-impacted Everglades wetlands using X-ray absorption spectroscopy and ultrahigh-resolution mass spectrometry. Spatial variation in DOM sulfur content and speciation reflects the degree of sulfate enrichment and resulting sulfide concentrations in sediment pore waters. Sulfur is incorporated into DOM predominantly as highly reduced species in sulfidic pore waters. Sulfur-enriched DOM in sediment pore waters exchanges with overlying surface waters and the sulfur likely undergoes oxidative transformations in the water column. Across all wetland sites and depths, the total sulfur content of DOM correlated with the relative abundance of highly reduced sulfur functionality. The results identify sulfate input as a primary determinant on DOM sulfur chemistry to be considered in the context of wetland restoration and sulfur and trace metal cycling.

Metabolomics Reveal Optimal Grain Preprocessing (Milling) toward Rice Koji Fermentation.

PubMed

Lee, Sunmin; Lee, Da Eun; Singh, Digar; Lee, Choong Hwan

2018-03-21

A time-correlated mass spectrometry (MS)-based metabolic profiling was performed for rice koji made using the substrates with varying degrees of milling (DOM). Overall, 67 primary and secondary metabolites were observed as significantly discriminant among different samples. Notably, a higher abundance of carbohydrate (sugars, sugar alcohols, organic acids, and phenolic acids) and lipid (fatty acids and lysophospholipids) derived metabolites with enhanced hydrolytic enzyme activities were observed for koji made with DOM of 5-7 substrates at 36 h. The antioxidant secondary metabolites (flavonoids and phenolic acid) were relatively higher in koji with DOM of 0 substrates, followed by DOM of 5 > DOM of 7 > DOM of 9 and 11 at 96 h. Hence, we conjecture that the rice substrate preprocessing between DOM of 5 and 7 was potentially optimal toward koji fermentation, with the end product being rich in distinctive organoleptic, nutritional, and functional metabolites. The study rationalizes the substrate preprocessing steps vital for commercial koji making.

Fractions and biodegradability of dissolved organic matter derived from different composts.

PubMed

Wei, Zimin; Zhang, Xu; Wei, Yuquan; Wen, Xin; Shi, Jianhong; Wu, Junqiu; Zhao, Yue; Xi, Beidou

2014-06-01

An experiment was conducted to determine the fractions of molecular weights (MW) and the biodegradability of dissolved organic matter (DOM) in mature composts derived from dairy cattle manure (DCM), kitchen waste (KW), cabbage waste (CW), tomato stem waste (TSW), municipal solid waste (MSW), green waste (GW), chicken manure (CM), sludge (S), and mushroom culture waste (MCW). There were distinct differences in the concentration and MW fractions of DOM, and the two measures were correlated. Fraction MW>5kDa was the major component of DOM in all mature composts. Determined 5day biochemical oxygen demand (BOD5) of DOM was correlated to the concentration of DOM and all MW fractions except MW>5kDa, indicating that the biodegradability of DOM was a function of the content and proportion of fraction MW<5kDa. This study suggests that the amount and distribution of low MW fractions affect DOM biodegradability. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evaluation of passive samplers for the collection of dissolved organic matter in streams.

PubMed

Warner, Daniel L; Oviedo-Vargas, Diana; Royer, Todd V

2015-01-01

Traditional sampling methods for dissolved organic matter (DOM) in streams limit opportunities for long-term studies due to time and cost constraints. Passive DOM samplers were constructed following a design proposed previously which utilizes diethylaminoethyl (DEAE) cellulose as a sampling medium, and they were deployed throughout a temperate stream network in Indiana. Two deployments of the passive samplers were conducted, during which grab samples were frequently collected for comparison. Differences in DOM quality between sites and sampling methods were assessed using several common optical analyses. The analyses revealed significant differences in optical properties between sampling methods, with the passive samplers preferentially collecting terrestrial, humic-like DOM. We assert that the differences in DOM composition from each sampling method were caused by preferential binding of complex humic compounds to the DEAE cellulose in the passive samplers. Nonetheless, the passive samplers may provide a cost-effective, integrated sample of DOM in situations where the bulk DOM pool is composed mainly of terrestrial, humic-like compounds.

Spatio-temporal variability of the molecular fingerprint of soil dissolved organic matter in a headwater agricultural catchment

NASA Astrophysics Data System (ADS)

Jeanneau, Laurent; Pierson-Wickmann, Anne-Catherine; Jaffrezic, Anne; Lambert, Thibault; Gruau, Gérard

2013-04-01

Dissolved organic matter (DOM) is implied in (i) ecosystem services such as the support of biodiversity, (ii) the alteration of the drinkable water quality by formation of trihalomethane and (iii) the transfer of micropollutants from soils to rivers. Moreover, since DOM connects soils and oceans that are interacting with the atmosphere, understanding its biogeochemistry will help in investigating the carbon cycle and in creating strategies to mitigate climate change. DOM in headwater stream ecosystems is mainly inherited from allochtonous inputs with different reservoirs being mobilized during storm and interstorm events at the scale of an hydrological year. Those changes in DOM reservoirs, if accompanied by composition and reactivity changes, may impact DOM ecosystem services and drinking water production processes. Elucidating the compositional changes due to changes in the source of DOM in rivers has thus become a important axis of DOM research. The aim of this study is to test the ability of the molecular tools of the organic geochemistry and more specifically the combination of thermochemiolysis and gas chromatography - mass spectrometry (THM-GC-MS) to (i) link the variability of the river DOM composition to different DOM reservoirs in catchment soils and (ii) provide hypothesis on the nature and the mechanisms of formation (microbial growth, litter decomposition) of those reservoirs. This analytical method seems particularly adapted since it allows the differentiation between vegetal and microbial inputs and the determination of the extent of the biodegradation process of biomolecules such as lignin. To test this method, the molecular fingerprint of soil DOM has been investigated in the wetland area of a small (500 ha) agricultural catchment (the so-called Kervidy-Naizin catchment) located in Brittany, western France. The soil DOM was sampled fortnightly at three depths using zero-tension lysimeters during the hydrological year 2010-2011. The samples were freeze-dried and analyzed for their molecular composition using THM-GC-MS. Three chemical classes of compounds were investigated including lignin, polysaccharides and fatty acids. The combination of those results at the molecular scale with the results of investigations on spectroscopic (specific UV absorbance at 254 nm, SUVA) fingerprints, the isotopic (d13C) fingerprint of DOM and the hydrological data (water table depth) has highlighted (i) the correlation between molecular and bulk scales investigated using the SUVA and the proportion of lignin markers and (ii) the evolution of the molecular composition of soil DOM related to the changes of the water table depth, which could be linked to the mobilization of different reservoirs and/or to the succession of different mechanisms of production governed by the changes in hydrological regimes. This study highlights THM-GC-MS as a valuable tool to investigate the molecular composition of DOM. By differentiating the vegetal and the microbial components of DOM, it allows the investigation of the sources and mechanisms of DOM formation. Finally, its application to a catchment with hydrological data emphasizes the hydrological regime as a main driver of the evolution of the molecular composition of DOM.

Core-size regulated aggregation/disaggregation of citrate-coated gold nanoparticles (5-50 nm) and dissolved organic matter: Extinction, emission, and scattering evidence

NASA Astrophysics Data System (ADS)

Esfahani, Milad Rabbani; Pallem, Vasanta L.; Stretz, Holly A.; Wells, Martha J. M.

2018-01-01

Knowledge of the interactions between gold nanoparticles (GNPs) and dissolved organic matter (DOM) is significant in the development of detection devices for environmental sensing, studies of environmental fate and transport, and advances in antifouling water treatment membranes. The specific objective of this research was to spectroscopically investigate the fundamental interactions between citrate-stabilized gold nanoparticles (CT-GNPs) and DOM. Studies indicated that 30 and 50 nm diameter GNPs promoted disaggregation of the DOM. This result-disaggregation of an environmentally important polyelectrolyte-will be quite useful regarding antifouling properties in water treatment and water-based sensing applications. Furthermore, resonance Rayleigh scattering results showed significant enhancement in the UV range which can be useful to characterize DOM and can be exploited as an analytical tool to better sense and improve our comprehension of nanomaterial interactions with environmental systems. CT-GNPs having core size diameters of 5, 10, 30, and 50 nm were studied in the absence and presence of added DOM at 2 and 8 ppm at low ionic strength and near neutral pH (6.0-6.5) approximating surface water conditions. Interactions were monitored by cross-interpretation among ultraviolet (UV)-visible extinction spectroscopy, excitation-emission matrix (EEM) spectroscopy (emission and Rayleigh scattering), and dynamic light scattering (DLS). This comprehensive combination of spectroscopic analyses lends new insights into the antifouling behavior of GNPs. The CT-GNP-5 and -10 controls emitted light and aggregated. In contrast, the CT-GNP-30 and CT-GNP-50 controls scattered light intensely, but did not aggregate and did not emit light. The presence of any CT-GNP did not affect the extinction spectra of DOM, and the presence of DOM did not affect the extinction spectra of the CT-GNPs. The emission spectra (visible range) differed only slightly between calculated and actual mixtures of CT-GNP-5 or -10 with DOM, whereas emissions for mixtures of CT-GNP-30 or -50 with DOM were enhanced at the surface plasmon resonance (SPR) wavelength. The emission spectra (ultraviolet range) for protein-like constituents of DOM were quenched. Resonance Rayleigh scattering (RRS) was more intense for the CT-GNP-30 and -50 than for the CT-GNP-5 and -10 controls. Intensity-based DLS particle size distributions (PSDs) of DOM controls, CT-GNP-5 and -10 nm controls, and 5- and 10 nm GNP-DOM mixtures exhibited multimodal aggregation. Analyses of CT-GNP-5 and CT-GNP-10 nm mixtures with DOM indicated overcoating of DOM molecules occurred in close proximity (< 10 nm) to GNPs, whereas similar overcoating was not supported for the CT-GNP-30 or -50 mixtures with DOM. These fundamental observations can be exploited to improve our comprehension of nanomaterial interactions with environmental systems.

Unraveling signatures of biogeochemical processes and the depositional setting in the molecular composition of pore water DOM across different marine environments

NASA Astrophysics Data System (ADS)

Schmidt, Frauke; Koch, Boris P.; Goldhammer, Tobias; Elvert, Marcus; Witt, Matthias; Lin, Yu-Shih; Wendt, Jenny; Zabel, Matthias; Heuer, Verena B.; Hinrichs, Kai-Uwe

2017-06-01

Dissolved organic matter (DOM) in marine sediment pore waters derives largely from decomposition of particulate organic matter and its composition is influenced by various biogeochemical and oceanographic processes in yet undetermined ways. Here, we determine the molecular inventory of pore water DOM in marine sediments of contrasting depositional regimes with ultrahigh-resolution mass spectrometry and complementary bulk chemical analyses in order to elucidate the factors that shape DOM composition. Our sample sets from the Mediterranean, Marmara and Black Seas covered different sediment depths, ages and a range of marine environments with different (i) organic matter sources, (ii) balances of organic matter production and preservation, and (iii) geochemical conditions in sediment and water column including anoxic, sulfidic and hypersaline conditions. Pore water DOM had a higher molecular formula richness than overlying water with up to 11,295 vs. 2114 different molecular formulas in the mass range of 299-600 Da and covered a broader range of element ratios (H/C = 0.35-2.19, O/C = 0.03-1.19 vs. H/C = 0.56-2.13, O/C = 0.15-1.14). Formula richness was independent of concentrations of DOC and TOC. Near-surface pore water DOM was more similar to water column DOM than to deep pore water DOM from the same core with respect to formula richness and the molecular composition, suggesting exchange at the sediment-water interface. The DOM composition in the deeper sediments was controlled by organic matter source, selective decomposition of specific DOM fractions and early diagenetic molecule transformations. Compounds in pelagic sediment pore waters were predominantly highly unsaturated and N-bearing formulas, whereas oxygen-rich CHO-formulas and aromatic compounds were more abundant in pore water DOM from terrigenous sediments. The increase of S-bearing molecular formulas in the water column and pore waters of the Black Sea and the Mediterranean Discovery Basin was consistent with elevated HS- concentrations reflecting the incorporation of sulfur into biomolecules during early diagenesis. Sulfurization resulted in an increased average molecular mass of DOM and higher formula richness (up to 5899 formulas per sample). In sediments from the methanogenic zone in the Black Sea, the DOM pool was distinctly more reduced than overlying sediments from the sulfate-reducing zone. Bottom and pore water DOM from the Discovery Basin contained the highest abundances of aliphatic compounds in the entire dataset; a large fraction of abundant N-bearing formulas possibly represented peptide and nucleotide formulas suggesting preservation of these molecules in the life inhibiting environment of the Discovery Basin. Our unique data set provides the basis for a comprehensive understanding of the molecular signatures in pore water DOM and the turnover of sedimentary organic matter in marine sediments.

Inhibition of precipitation and aggregation of metacinnabar (mercuric sulfide) by dissolved organic matter isolated from the Florida Everglades

USGS Publications Warehouse

Ravichandran, M.; Aiken, G.R.; Ryan, J.N.; Reddy, M.M.

1999-01-01

Precipitation and aggregation of metacinnabar (black HgS) was inhibited in the presence of low concentrations (???3 mg C/L) of humic fractions of dissolved organic matter (DOM) isolated from the Florida Everglades. At low Hg concentrations (??? x 10-8 M), DOM prevented the precipitation of metacinnabar. At moderate Hg concentrations (5 x 10-5 M), DOM inhibited the aggregation of colloidal metacinnabar (Hg passed through a 0.1 ??m filter but was removed by centrifugation). At Hg concentrations greater than 5 x 10-4 M, mercury formed solid metacinnabar particles that were removed from solution by a 0.1 ??m filter. Organic matter rich in aromatic moleties was preferentially removed with the solid. Hydrophobic organic acids (humic and fulvic acids) inhibited aggregation better than hydrophilic organic acids. The presence of chloride, acetate, salicylate, EDTA, and cysteine did not inhibit the precipitation or aggregation of metacinnabar. Calcium enhanced metacinnabar aggregation even in the presence of DOM, but the magnitude of the effect was dependent on the concentrations of DOM, Hg, and Ca. Inhibition of metacinnabar precipitation appears to be a result of strong DOM-Hg binding. Prevention of aggregation of colloidal particles appears to be caused by adsorption of DOM and electrostatic repulsion.Precipitation and aggregation of metacinnabar (black HgS) was inhibited in the presence of low concentrations (???3 mg C/L) of humic fractions of dissolved organic matter (DOM) isolated from the Florida Everglades. At low Hg concentrations (???5??10-8 M), DOM prevented the precipitation of metacinnabar. At moderate Hg concentrations (5??10-5 M), DOM inhibited the aggregation of colloidal metacinnabar (Hg passed through a 0.1 ??m filter but was removed by centrifugation). At Hg concentrations greater than 5??10-4 M, mercury formed solid metacinnabar particles that were removed from solution by a 0.1 ??m filter. Organic matter rich in aromatic moieties was preferentially removed with the solid. Hydrophobic organic acids (humic and fulvic acids) inhibited aggregation better than hydrophilic organic acids. The presence of chloride, acetate, salicylate, EDTA, and cysteine did not inhibit the precipitation or aggregation of metacinnabar. Calcium enhanced metacinnabar aggregation even in the presence of DOM, but the magnitude of the effect was dependent on the concentrations of DOM, Hg, and Ca. Inhibition of metacinnabar precipitation appears to be a result of strong DOM-Hg binding. Prevention of aggregation of colloidal particles appears to be caused by adsorption of DOM and electrostatic repulsion.

Spatio-seasonal variability in dissolved organic matter optical properties and its bioavailability in a subalpine lake

NASA Astrophysics Data System (ADS)

Stadler, Masumi; Ejarque, Elisabet; Kainz, Martin J.

2017-04-01

Allochthonous and autochothonous dissolved organic matter (DOM) in lakes mainly originate from terrestrial and aquatic primary production, respectively. Due to their differing biochemical composition the degradability of DOM by microorganisms is expected to vary. The carbon use efficiency of bacteria and DOM biodegradability determine whether the consumed DOM is incorporated into microbial biomass or respired to CO2 and ultimately emitted into the atmosphere. Thus, understanding the interaction of biodegradable DOM and its consumers is crucial to increase our knowledge on the role of lakes in the global carbon cycling. However, interactions of specific aquatic DOM signatures and the microbial population still remain widely debated. The aim of this study was to explore how DOM biodegradability changes along a stream-lake continuum at different seasons of the year. We monitored DOM quantity and its optical properties, inorganic nutrients, CO2 and bacterial growth over 20 days in dark bioassays with water from the inflow, outflow and at three layers of an oligotrophic subalpine lake. Preliminary results reveal highest microbial abundance in the metalimnion in winter and summer (0.7 106 and 2.5 106 cells mL-1, respectively) and the inflow in spring and autumn (1 106 and 1.4 106 cells mL-1, respectively) after 20 days. Surprisingly, with the exception of winter samples final inflow bacterial abundance results high, despite its lowest initial natural cell concentration, providing evidence for effective utilisation of terrestrial DOM, even with its high humic signature as indicated by the humification index (HIX). Nonetheless, after a microbial biomass peak with the inflow yielding mostly highest after three days, at the final experimental stage microbial biomass does only marginally differ between all sites with the exception of autumn samples where outflow and metalimnion turn out most productive. Even though the DOM of all lake sites and the lake outflow were characterised by lower molecular weight (indicated by the slope ratio (SR)) and a higher autochthonous signature (BIX) in all seasons, rapid growth of inflow bacteria highlight the potential of terrestrially-derived DOM to support bacterial growth, and challenge previous ideas that autchthonously-produced DOM would be more labile than DOM of terrestrial origin.

A DOM Odyssey: The Tale of Molecular Transformations in an Aquifer near Bemidji, MN

NASA Astrophysics Data System (ADS)

Podgorski, D. C.; Zito, P.; Smith, D. F.; Cao, X.; Schmidt-Rohr, K.; Wagner, S.; Stubbins, A.; Aiken, G.; Cozzarelli, I.; Bekins, B. A.; Spencer, R. G.

2017-12-01

Analytical methods including fluorescence spectroscopy, NMR spectroscopy, and ultrahigh resolution mass spectrometry have significantly advanced the understanding of compositional controls on dissolved organic matter (DOM) processing and fate. Yet, we still heavily rely on extrapolation of chemical changes identified at the edges of the compositional continuum (i.e., endmembers) to assess DOM reactivity and stability. While extrapolation of chemical transformations is useful for determining relative changes in DOM composition, a comprehensive understanding of the underlying core structures and composition is required to develop advanced biogeochemical models. Studying DOM from natural systems is complicated by many variables associated with an open system including input from multiple sources, simultaneous photo-alteration and microbial processing, and obtaining samples that cover high spatial and temporal resolution. A 38-year biodegradation study at the National Crude Oil Spill Research site near Bemidji, MN provides a unique opportunity to monitor DOM in a relatively closed system. An extensively characterized 1 m thick oil body is confined to a 25 x 75 m2 area at the water table in the aquifer. Oxidized metabolites partition from the oil into the underlying aquifer increase the DOC concentration to > 100 ppm from < 2 ppm up-gradient from the oil body. This newly produced DOM is comprised of aliphatic compounds with high H/C, low O/C and blue-shifted fluorescence, similar in composition to permafrost- and algal-derived DOM. The aliphatic DOM is transported laterally from the oil pool by groundwater, creating a plume that ultimately discharges into the Unnamed Lake 325 m downgradient. More than 10 years later and hundreds of meters downgradient from the oil body, the DOC concentration has decreased to 3-5 ppm and the DOM is compositionally non-distinct. Microbes have left behind degradation products and selectively preserved compounds that exhibit red-shifted fluorescence and molecular formulas with O/C and H/C similar to those associated with the `island of stability'. Samples collected spatially from the DOM plume between these two endmembers provide sufficient temporal resolution to model both DOC concentration and DOM composition as a result of biodegradation.

Catchment scale molecular composition of hydrologically mobilized dissolved organic matter

NASA Astrophysics Data System (ADS)

Raeke, Julia; Lechtenfeld, Oliver J.; Oosterwoud, Marieke R.; Bornmann, Katrin; Tittel, Jörg; Reemtsma, Thorsten

2016-04-01

Increasing concentrations of dissolved organic matter (DOM) in rivers of temperate catchments in Europe and North Amerika impose new technical challenges for drinking water production. The driving factors for this decadal increase in DOM concentration are not conclusive and changes in annual temperatures, precipitation and atmospheric deposition are intensely discussed. It is known that the majority of DOM is released by few but large hydrologic events, mobilizing DOM from riparian wetlands for export by rivers and streams. The mechanisms of this mobilization and the resulting molecular composition of the released DOM may be used to infer long-term changes in the biogeochemistry of the respective catchment. Event-based samples collected over two years from streams in three temperate catchments in the German mid-range mountains were analyzed after solid-phase extraction of DOM for their molecular composition by ultra-high resolution mass spectrometry (FT-ICR MS). Hydrologic conditions, land use and water chemistry parameters were used to complement the molecular analysis. The molecular composition of the riverine DOM was strongly dependent on the magnitude of the hydrologic events, with unsaturated, oxygen-enriched compounds being preferentially mobilized by large events. This pattern is consistent with an increase in dissolved iron and aluminum concentrations. In contrast, the relative proportions of nitrogen and sulfur bearing compounds increased with an increased agricultural land use but were less affected by the mobilization events. Co-precipitation experiments with colloidal aluminum showed that unsaturated and oxygen-rich compounds are preferentially removed from the dissolved phase. The precipitated compounds thus had similar chemical characteristics as compared to the mobilized DOM from heavy rain events. Radiocarbon analyses also indicated that this precipitated fraction of DOM was of comparably young radiocarbon age. DOM radiocarbon from field samples showed that also the event-mobilized DOM had higher radiocarbon content. Overall, hydrology not only controls the quantity of exported carbon from temperate catchments but also strongly influences the molecular composition by mobilizing distinct compound classes in conjunction with dissolved iron and aluminum. From these results future compositional changes in temperate river DOM can be assessed, given an expected increase in the magnitude of hydrologic events, and technical advice for drinking water production may be inferred.

Nematode feeding strategies and the fate of dissolved organic matter carbon in different deep-sea sedimentary environments

NASA Astrophysics Data System (ADS)

Pape, Ellen; van Oevelen, Dick; Moodley, Leon; Soetaert, Karline; Vanreusel, Ann

2013-10-01

Sediments sampled from the Galicia Bank seamount and the adjacent slope (northeast Atlantic), and from a western Mediterranean slope site, were injected onboard with 13C-enriched dissolved organic matter (DOM) to evaluate nematode feeding strategies and the fate of DOM carbon in different benthic environments. We hypothesized that nematode 13C label assimilation resulted from either direct DOM uptake or feeding on 13C labeled bacteria. Slope sediments were injected with glucose ("simple" DOM) or "complex" diatom-derived DOM to investigate the influence of DOM composition on carbon assimilation. The time-series (1, 7 and 14 days) experiment at the seamount site was the first study to reveal a higher 13C enrichment of nematodes than bacteria and sediments after 7 days. Although isotope dynamics indicated that both DOM and bacteria were plausible candidate food sources, the contribution to nematode secondary production and metabolic requirements (estimated from biomass-dependent respiration rates) was higher for bacteria than for DOM at all sites. The seamount nematode community showed higher carbon assimilation rates than the slope assemblages, which may reflect an adaptation to the food-poor environment. Our results suggested that the trophic importance of bacteria did not depend on the amount of labile sedimentary organic matter. Furthermore, there was a discrepancy between carbon assimilation rates observed in the experiments and the feeding type classification, based on buccal morphology. Sites with a similar feeding type composition (i.e. the northeast Atlantic sites) showed large differences in uptake, whilst the nematode assemblages at the two slope sites, which had a differing trophic structure, took up similar amounts of the DOM associated carbon. Our results did not indicate substantial differences in carbon processing related to the complexity of the DOM substrate. The quantity of processed carbon (5-42% of added DOM) was determined by the bacteria, and was primarily respired. The bulk of the added 13C-DOM was not ingested by the benthic biota under study, and a considerable fraction was possibly adsorbed onto the sediment grains.

Molecular and optical properties of tree-derived dissolved organic matter in throughfall and stemflow from live oaks and eastern red cedar

NASA Astrophysics Data System (ADS)

Stubbins, Aron; Silva, Leticia M.; Dittmar, Thorsten; Van Stan, John T.

2017-03-01

Studies of dissolved organic matter (DOM) transport through terrestrial aquatic systems usually start at the stream. However, the interception of rainwater by vegetation marks the beginning of the terrestrial hydrological cycle making trees the headwaters of aquatic carbon cycling. Rainwater interacts with trees picking up tree-DOM, which is then exported from the tree in stemflow and throughfall. Stemflow denotes water flowing down the tree trunk, while throughfall is the water that drips through the leaves of the canopy. We report the concentrations, optical properties (light absorbance) and molecular signatures (ultrahigh resolution mass spectrometry) of tree-DOM in throughfall and stemflow from two tree species (live oak and eastern red cedar) with varying epiphyte cover on Skidaway Island, Savannah, Georgia, USA. Both stemflow and throughfall were enriched in DOM compared to rainwater, indicating trees were a significant source of DOM. The optical and molecular properties of tree-DOM were broadly consistent with those of DOM in other aquatic ecosystems. Stemflow was enriched in highly colored DOM compared to throughfall. Elemental formulas identified clustered the samples into three groups: oak stemflow, oak throughfall and cedar. The molecular properties of each cluster are consistent with an autochthonous aromatic-rich source associated with the trees, their epiphytes and the microhabitats they support. Elemental formulas enriched in oak stemflow were more diverse, enriched in aromatic formulas, and of higher molecular mass than for other tree-DOM classes, suggesting greater contributions from fresh and partially modified plant-derived organics. Oak throughfall was enriched in lower molecular weight, aliphatic and sugar formulas, suggesting greater contributions from foliar surfaces. While the optical properties and the majority of the elemental formulas within tree-DOM were consistent with vascular plant-derived organics, condensed aromatic formulas were also identified. As condensed aromatics are generally interpreted as deriving from partially combusted organics, some of the tree-DOM may have derived from the atmospheric deposition of thermogenic and other windblown organics. These initial findings should prove useful as future studies seek to track tree-DOM across the aquatic gradient from canopy roof, through soils and into fluvial networks.

Similarities in Photodegradation of Cyanobacteria-Derived and Marine Fluorescent Dissolved Organic Matter

NASA Astrophysics Data System (ADS)

Ianiri, H. L.; Timko, S.; Gonsior, M.

2016-02-01

Marine dissolved organic matter (DOM) is one of the largest reduced carbon reservoirs on Earth, yet we only have a limited understanding of its production, cycling, degradation, and overall structure. It was previously believed that a significant portion of refractory dissolved organic carbon (RDOC) in the ocean was derived from terrestrial sources, however recent studies indicated that the majority of marine DOM might be produced in situ by marine biota. Previous research has found that terrestrial and microbial DOM fluorescent signatures are similar, complicating the identification of the origins of marine fluorescent DOM (FDOM). However, photodegradation kinetics of terrestrial and microbial-derived DOM are expected to be different due to their assumed different chemical compositions. In this study we analyzed for the first time the photodegradation kinetics of microbial-derived DOM originating from different cyanobacteria strains. Cyanobacterial-derived DOM were exposed to simulated sunlight for a total of 20 hours while recording excitation emission matrix (EEM) fluorescence every twenty minutes to observe the photodegradation of this specific FDOM. Parallel Factor Analysis (PARAFAC) was applied to deconvolute the EEM matrices into six separate components. The photodegradation kinetics was then calculated for each component and compared with previously obtained photodegradation data of marine and terrestrial FDOM. This six component PARAFAC model was similar to those generated from open ocean data and global DOM data sets. The "humic-like" FDOM was also found in cyanobacteria FDOM and showed similar fluorescence intensities and percent fluorescence loss when compared to marine DOM. The degradation kinetics of the "humic-like" component of microbial-derived DOM was faster than that of terrestrial-derived DOM, and marine FDOM samples showed degradation kinetics more similar to microbial-derived FDOM. This indicates marine FDOM is more similar in chemical composition to microbial-derived FDOM than terrestrial-derived FDOM, supporting the hypothesis that the majority of marine FDOM is produced in situ.

Export of pre-aged, labile DOM from a central California coastal upwelling system: Insights from D/L amino acids and Δ14C signatures

NASA Astrophysics Data System (ADS)

Walker, B. D.; Shen, Y.; Benner, R. H.; Druffel, E. R. M.

2014-12-01

Coastal upwelling zones are among the most productive regions in the world and play a major role in global carbon and nitrogen cycles. Recent research suggests that a substantial fraction of newly fixed organic matter is exported offshore in the form of dissolved organic matter (DOM). However, to date only a few studies have examined DOM composition in the context of production and export from upwelling systems. The ultimate fate and geochemical impact of coastal DOM exported to offshore and mesopelagic ecosystems also remains largely unknown. Between 2007-2009 we conducted a high-resolution biogeochemical time series at the Granite Canyon Marine Pollution Studies Lab in part to evaluate the seasonal production and export of DOM from the Central CA coast. Our previous work demonstrated substantial, albeit disparate, seasonal production of dissolved organic carbon and nitrogen (DOC, DON) - with high DON (and low C:N ratios) produced during upwelling and high DOC produced during summer/fall water column stratification (Walker and McCarthy, 2012). Here we present new total dissolved D/L amino acid (TDAA) and UV-oxidizable DOC radiocarbon (Δ14C) data with the goal of determining the relative sources (heterotrophic vs. autotrophic), bioavailability, microbial processing and 14C-ages of C-rich vs. N-rich DOM exported from this upwelling system. Our results suggest that C-rich DOM produced during water column stratification carries a large microbial signature (i.e. high D/L AA ratios and non-protein AA abundance), whereas N-rich DOM produced during upwelling appears to be fresh, autotrophic DOM (i.e. lowest D/L AA ratios and highest TDAA abundance). DOM Δ14C signatures also did not approximate in situ dissolved inorganic carbon (DIC), and instead were far more negative and highly correlated to water mass density. Together our results indicate a previously unrecognized source of highly labile yet pre-aged DOM potentially impacting offshore and mesopelagic ecosystems.

Trials and Tribulations of Fluorescent Dissolved Organic Matter Chemical Interpretations: A case study of polar ice cores

NASA Astrophysics Data System (ADS)

D'Andrilli, J.

2017-12-01

Excitation emission matrix fluorescence spectroscopy is widely applied for rapid dissolved organic matter (DOM) characterization in aquatic systems. Fluorescent DOM surveys are booming, not only as a central focus in aquatic environments, but also as an important addition to interdisciplinary research (e.g., DOM analysis in concert with ice core paleoclimate reconstructions, stream metabolism, hydrologic regimes, agricultural developments, and biological activity), opening new doors, not just for novelty, but also for more challenges with chemical interpretations. Recently, the commonly used protein- versus humic-like classifications of DOM have been ineffective at describing DOM chemistry in various systems (e.g., ice cores, wastewaters, incubations/engineered). Moreover, the oversimplification of such classifications used to describe fluorescing components, without further scrutiny, has become commonplace, ultimately producing vague reporting. For example, West Antarctic ice core DOM was shown to contain fluorescence in the low excitation/emission wavelength region, however resolved fluorophores depicting tyrosine- and tryptophan-like DOM were not observed. At first, as literature suggested, we reported this result as protein-like, and concluded that microbial contributions were dominant in deep ice. That initial interpretation would disintegrate the conservation paradigm of atmospheric composition during deposition, the crux of ice core research, and contradict other lines of evidence. This begged the question, "How can we describe DOM chemistry without distinct fluorophores?" Antarctic ice core DOM was dominated by neither tyrosine- nor tryptophan-like fluorescence, causing "unusual" looking fluorescent components. After further examination, deep ice DOM was reported to contain fluorescent species most similar to monolignols and tannin-like phenols, describing the precursors of lignin from low carbon producing environments, consistent with marine sediment records. Currently, we are working towards more detailed descriptions of fluorescence, thus accepting variation in and around protein- and humic-like regions, and achieving robust chemical interpretations of DOM chemistry, ultimately providing insight to its interwoven nature in the environment.

Different effects of plant-derived dissolved organic matter (DOM) and urea on the priming of soil organic carbon.

PubMed

Qiu, Qingyan; Wu, Lanfang; Ouyang, Zhu; Li, Binbin; Xu, Yanyan

2016-03-01

Soil organic carbon (SOC) mineralization is important for the regulation of the global climate and soil fertility. Decomposition of SOC may be significantly affected by the supply of plant-derived labile carbon (C). To investigate the impact of plant-derived dissolved organic matter (DOM) and urea (N) additions on the decomposition of native SOC as well as to elucidate the underlying mechanisms of priming effects (PEs), a batch of incubation experiments was conducted for 250 days by application of (13)C-labeled plant-derived DOM and urea to soils. The direction of PE induced by the addition of DOM was different from the addition of N, i.e. it switched from negative to positive in DOM-amended soils, whereas in the N-treated soil it switched from positive to negative. Adding DOM alone was favorable for soil C sequestration (59 ± 5 mg C per kg soil), whereas adding N alone or together with DOM accelerated the decomposition of native SOC, causing net C losses (-62 ± 4 and -34 ± 31 mg C per kg soil, respectively). These findings indicate that N addition and its interaction with DOM are not favorable for soil C sequestration. Adding DOM alone increased the level of dissolved organic carbon (DOC), but it did not increase the level of soil mineral N. Changes in the ratio of microbial biomass carbon (MBC) to microbial biomass nitrogen (MBN) and microbial metabolic quotient (qCO2) after the addition of DOM and N suggest that a possible shift in the microbial community composition may occur in the present study. Adding DOM with or without N increased the activities of β-glucosidase and urease. Changes in the direction and magnitude of PE were closely related to changes in soil C and N availability. Soil C and N availability might influence the PE through affecting the microbial biomass and extracellular enzyme activity as well as causing a possible shift in the microbial community composition.

Dissolved organic matter and aluminum oxide nanoparticles synergistically cause cellular responses in freshwater microalgae.

PubMed

Ye, Nan; Wang, Zhuang; Wang, Se; Fang, Hao; Wang, Degao

2018-06-07

This study investigated the impact of dissolved organic matters (DOM) on the ecological toxicity of aluminum oxide nanoparticles (Al 2 O 3 NPs) at a relatively low exposure concentration (1 mg L -1 ). The unicellular green alga Scenedesmus obliquus was exposed to Al 2 O 3 NP suspensions in the presence of DOM (fulvic acid) at various concentrations (1, 10, and 40 mg L -1 ). The results show that the presence of DOM elevated the growth inhibition toxicity of Al 2 O 3 NPs towards S. obliquus in a dose-dependent manner. Moreover, the combination of DOM at 40 mg L -1 and Al 2 O 3 NPs resulted in a synergistic effect. The relative contribution of Al-ions released from Al 2 O 3 NPs to toxicity was lower than 5%, indicating that the presence of the particles instead of the dissolved ions in the suspensions was the major toxicity sources, regardless of the presence of DOM. Furthermore, DOM at 10 and 40 mg L -1 and Al 2 O 3 NPs synergistically induced the upregulation of intercellular reactive oxygen species levels and superoxide dismutase activities. Analysis of the plasma malondialdehyde concentrations and the observation of superficial structures of S. obliquus indicated that the mixtures of DOM and Al 2 O 3 NPs showed no significant effect on membrane lipid peroxidation damage. In addition, the presence of both DOM and Al 2 O 3 NPs contributed to an enhancement in both the mitochondrial membrane potential and the cell membrane permeability (CMP) in S. obliquus. In particular, Al 2 O 3 NPs in the presence of 10 and 40 mg L -1 DOM caused a greater increase in CMP compared to Al 2 O 3 NPs and DOM alone treatments. In conclusion, these findings suggest that DOM at high concentrations and Al 2 O 3 NPs synergistically interrupted cell membrane functions and triggered subsequent growth inhibition toxicity.

Dissolved organic matter enhances microbial mercury methylation under sulfidic conditions

USGS Publications Warehouse

Graham, Andrew M.; Aiken, George R.; Gilmour, Cynthia

2012-01-01

Dissolved organic matter (DOM) is generally thought to lower metal bioavailability in aquatic systems due to the formation of metal–DOM complexes that reduce free metal ion concentrations. However, this model may not be pertinent for metal nanoparticles, which are now understood to be ubiquitous, sometimes dominant, metal species in the environment. The influence of DOM on Hg bioavailability to microorganisms was examined under conditions (0.5–5.0 nM Hg and 2–10 μM sulfide) that favor the formation of β-HgS(s) (metacinnabar) nanoparticles. We used the methylation of stable-isotope enriched 201HgCl2 by Desulfovibrio desulfuricans ND132 in short-term washed cell assays as a sensitive, environmentally significant proxy for Hg uptake. Suwannee River humic acid (SRHA) and Williams Lake hydrophobic acid (WLHPoA) substantially enhanced (2- to 38-fold) the bioavailability of Hg to ND132 over a wide range of Hg/DOM ratios (9.4 pmol/mg DOM to 9.4 nmol/mg DOM), including environmentally relevant ratios. Methylmercury (MeHg) production by ND132 increased linearly with either SRHA or WLHPoA concentration, but SRHA, a terrestrially derived DOM, was far more effective at enhancing Hg-methylation than WLHPoA, an aquatic DOM dominated by autochthonous sources. No DOM-dependent enhancement in Hg methylation was observed in Hg–DOM–sulfide solutions amended with sufficient l-cysteine to prevent β-HgS(s) formation. We hypothesize that small HgS particles, stabilized against aggregation by DOM, are bioavailable to Hg-methylating bacteria. Our laboratory experiments provide a mechanism for the positive correlations between DOC and MeHg production observed in many aquatic sediments and wetland soils.

Comparison of the Discriminative Stimulus Effects of Dimethyltryptamine with Different Classes of Psychoactive Compounds in Rats

PubMed Central

Gatch, Michael B.; Rutledge, Margaret A.; Carbonaro, Theresa; Forster, Michael J.

2010-01-01

Rationale There has been increased recreational use of dimethyltryptamine (DMT), but little is known of its discriminative stimulus effects. Objectives The present study assessed the similarity of the discriminative stimulus effects of DMT to other types of hallucinogens and to psychostimulants. Methods Rats were trained to discriminate DMT from saline. To test the similarity of DMT to known hallucinogens, the ability of (+)-lysergic acid diethylamide (LSD), (−)-2,5-dimethoxy-4-methylamphetamine (DOM), (+)-methamphetamine, or (±)3,4-methylenedioxymethyl-amphetamine (MDMA) to substitute in DMT-trained rats was tested. The ability of DMT to substitute in rats trained to discriminate each of these compounds was also tested. To assess the degree of similarity in discriminative stimulus effects, each of the compounds was tested for substitution in all of the other training groups. Results LSD, DOM, and MDMA all fully substituted in DMT-trained rats, whereas DMT fully substituted only in DOM-trained rats. Full cross-substitution occurred between DMT and DOM, LSD and DOM, and (+)-methamphetamine and MDMA. MDMA fully substituted for (+)-methamphetamine, DOM, and DMT, but only partially for LSD. In MDMA-trained rats, LSD and (+)-methamphetamine fully substituted, whereas DMT and DOM did not fully substitute. No cross-substitution was evident between (+)-methamphetamine and DMT, LSD, or DOM. Conclusions DMT produces discriminative stimulus effects most similar to those of DOM, with some similarity to the discriminative stimulus effects of LSD and MDMA. Like DOM and LSD, DMT seems to produce predominately hallucinogenic-like discriminative stimulus effects and minimal psychostimulant effects, in contrast to MDMA which produced hallucinogen- and psychostimulant-like effects. PMID:19288085

Dissolved organic matter (DOM) in pore water of Arctic Ocean sediments: linking DOM molecular composition with microbial community structure

NASA Astrophysics Data System (ADS)

Rossel, P. E.; Bienhold, C.; Boetius, A.; Dittmar, T.

2016-02-01

Marine organic matter (OM) that sinks from surface waters to the seafloor is the energy and carbon source for benthic communities. These communities produce dissolved organic matter (DOM) in the process of remineralization, enriching the sediment porewater with fresh DOM compounds. In the Arctic Ocean, primary production is limited by nutrients and light and is thus strongly influenced by sea ice cover. Ice cover is expected to further decrease due to global warming, which may have important consequences for primary production and the quantity and quality of OM exported to the seafloor. This study focused on: 1) the molecular composition of the DOM in sediment pore waters of the deep Eurasian Arctic basins, 2) whether there is any relation between Arctic Ocean ice cover and DOM composition and 3) whether the DOM composition correlates with microbial community structure. Molecular data, obtained via 15 Tesla Fourier transform ion cyclotron resonance mass spectrometry, were statistically correlated with environmental parameters. The productive ice margin stations showed higher abundances of molecular formulae of peptides, unsaturated aliphatics and saturated fatty acids. This molecular trend is indicative of fresh OM and phytodetritus deposition, compared to the northernmost, ice-covered stations which had stronger aromatic signals. Benthic bacterial community structure, as assessed with the fingerprinting method ARISA, was significantly correlated with DOM molecular composition. Further analyses using Illumina next-generation sequencing will enable the taxonomic identification of specific bacterial groups and their interdependence with DOM compounds. This study contributes to the understanding of the coupling between Arctic Ocean productivity and its depositional regime, and provides first insights into potential links between microbial community structure and DOM molecular composition in Arctic sediments

Assessment of the content, structure, and source of soil dissolved organic matter in the coastal wetlands of Jiaozhou Bay, China

NASA Astrophysics Data System (ADS)

Xi, Min; Zi, Yuanyuan; Wang, Qinggai; Wang, Sen; Cui, Guolu; Kong, Fanlong

2018-02-01

The contents and the spectral analysis of dissolved organic matter (DOM) in four typical wetlands, such as naked tidal, suaeda salsa, reed and spartina, were conducted to investigate the content, structure, and source of DOM in coastal wetland soil. The soil samples were obtained from Jiaozhou Bay in January, April, July, and October of 2014. Results showed that the DOM contents in soil of four typical wetland were in order of spartina wetland > naked tidal > suaeda salsa wetland > reed wetland in horizontal direction, and decreased with the increase of soil depth on vertical section. In addition, the DOM contents changed with the seasons, in order of spring > summer > autumn > winter. The structural characteristics of DOM in Jiaozhou Bay wetland, such as aromaticity, hydrophobicity, molecular weight, polymerization degree of benzene ring carbon frame structure and so on were in order of spartina wetland > naked tidal > suaeda salsa wetland > reed wetland in the horizontal direction. On the vertical direction, they showed a decreasing trend with the increase of soil depth. The results of three dimensional fluorescence spectra and fluorescence spectrum parameters (FI, HIX, and BIX) indicated that the DOM in Jiaozhou Bay was mainly derived from the biological activities. The contents and structure of DOM had certain relevance, but the contents and source as well as the structure and source of DOM had no significant correlation. The external pollution including domestic sewage, industrial wastewater, and aquaculture sewage affected the correlation among the content, structure and source of DOM by influencing the percentage of non-fluorescent substance in DOM and disturbing the determination of protein-like fluorescence.

The effect of advanced secondary municipal wastewater treatment on the molecular composition of dissolved organic matter.

PubMed

Maizel, Andrew C; Remucal, Christina K

2017-10-01

There is a growing interest in water reuse and in recovery of nutrients from wastewater. Because many advanced treatment processes are designed to remove organic matter, a better understanding of the composition of dissolved organic matter (DOM) in wastewater is needed. To that end, we assessed DOM in the Nine Springs Wastewater Treatment Plant in Madison, Wisconsin by UV-visible spectroscopy and Fourier transform-ion cyclotron resonance mass spectrometry. Samples were collected from the influent and effluent of two different secondary treatment processes and their respective secondary clarifiers, the UV disinfection unit, and an Ostara treatment system, which produces struvite via chemical precipitation. The optical properties reveal that DOM throughout the plant is relatively aliphatic and is low in molecular weight compared to DOM in freshwater systems. Furthermore, the DOM is rich in heteroatoms (e.g., N, S, P, and Cl) and its molecular formulas are present in the lipid-, protein-, carbohydrate-, and lignin-like regions of van Krevelen diagrams. Secondary treatment produces DOM that is more aromatic and more complex, as shown by the loss of highly saturated formulas and the increase in the number of CHO, CHON, and CHOP formulas. The two secondary treatment processes produce DOM with distinct molecular compositions, while the secondary clarifiers and UV disinfection unit result in minimal changes in DOM composition. The Ostara process decreases the molecular weight of DOM, but does not otherwise alter its composition. The optical properties agree with trends in the molecular composition of DOM within the main treatment train of the Nine Springs plant. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ultrafiltration for the Determination of Cu Complexed with Dissolved Organic Matters of Different Molecular Weight from a Eutrophic River, China.

PubMed

Li, Anding; Zhang, Yan; Zhou, Beihai; Xin, Kailing; Gu, Yingnan; Xu, Weijie; Tian, Jie

2018-05-21

The molecular weight of dissolved organic matter (DOM) is one of the essential factors controlling the properties of metal complexes. A continuous ultrafiltration experiment was designed to study the properties of Cu complexes with different molecular weights in a river before and after eutrophication. The results showed that the concentration of DOM increased from 26.47 to 38.20 mg/L during the eutrophication process, however, DOM was still dominated by the small molecular weight fraction before and after eutrophication. The amount of Cu-DOM complexes increased with the increasing of molecular weight, however, the amounts of DOM-Cu complexes before eutrophication were higher than those after eutrophication. This is because DOM contained more -COOH and -OH before eutrophication and these functional groups are the active sites complexed with Cu.

Solid-state 13C NMR studies of dissolved organic matter in pore waters from different depositional environments

USGS Publications Warehouse

Orem, W.H.; Hatcher, P.G.

1987-01-01

Dissolved organic matter (DOM) in pore waters from sediments of a number of different depositional environments was isolated by ultrafiltration using membranes with a nominal molecular weight cutoff of 500. This > 500 molecular weight DOM represents 70-98% of the total DOM in these pore waters. We determined the gross chemical structure of this material using both solid-state 13C nuclear magnetic resonance spectroscopy and elemental analysis. Our results show that the DOM in these pore waters appears to exist as two major types: one type dominated by carbohydrates and paraffinic structures and the second dominated by paraffinic and aromatic structures. We suggest that the dominance of one or the other structural type of DOM in the pore water depends on the relative oxidizing/reducing nature of the sediments as well as the source of the detrital organic matter. Under dominantly anaerobic conditions carbohydrates in the sediments are degraded by bacteria and accumulate in the pore water as DOM. However, little or no degradation of lignin occurs under these conditions. In contrast, sediments thought to be predominantly aerobic in character have DOM with diminished carbohydrate and enhanced aromatic character. The aromatic structures in the DOM from these sediments are thought to arise from the degradation of lignin. The large amounts of paraffinic structures in both types of DOM may be due to the degradation of unidentified paraffinic materials in algal or bacterial remains. ?? 1987.

Influence of dissolved organic matter and activated carbon pore characteristics on organic micropollutant desorption.

PubMed

Aschermann, Geert; Zietzschmann, Frederik; Jekel, Martin

2018-04-15

By simulating decreasing inflow concentrations, the extent of desorption of organic micropollutants (OMP) from three activated carbons (AC) was examined in laboratory batch tests. The tested AC showed strong differences in pore size distribution and could therefore be characterized as typical micro-, meso- and macroporous AC, respectively. Adsorption and desorption conditions were varied by using drinking water (containing dissolved organic matter (DOM)) and DOM-free pure water as background solutions to examine the influence of DOM on OMP desorption for the different AC. Under ideal conditions (adsorption and desorption in pure water) adsorption of the tested OMP was found to be highly up to completely reversible for all tested AC. Under real conditions (adsorption and desorption in drinking water) additional DOM adsorption affects desorption in different ways depending on the AC pore structure. For the micro- and mesoporous AC, an increased irreversibility of OMP adsorption was found, which shows that DOM adsorption prevents OMP desorption. This could be referred to pore blockage effects that occur during the parallel adsorption of DOM and OMP. For the macroporous AC, DOM adsorption led to an enhanced OMP desorption which could be attributed to displacement processes. These results show that smaller pores tend to be blocked by DOM which hinders OMP from desorption. The overall larger pores of the macroporous AC do not get blocked which could allow (i) OMP to desorb and (ii) DOM to enter and displace OMP. Copyright © 2018 Elsevier Ltd. All rights reserved.

Dominant vs. non-dominant shoulder morphology in volleyball players and associations with shoulder pain and spike speed.

PubMed

Challoumas, Dimitrios; Artemiou, Andreas; Dimitrakakis, Georgios

2017-01-01

The aims of our study were to compare the dominant (DOM) and non-dominant (NDOM) shoulders of high-level volleyball athletes and identify possible associations of shoulder adaptations with spike speed (SS) and shoulder pathology. A total of 22 male volleyball players from two teams participating in the first division of the Cypriot championship underwent clinical shoulder tests and simple measurements around their shoulder girdle joints bilaterally. SS was measured with the use of a sports speed radar. Compared with the NDOM side, the DOM scapula was more lateralised, the DOM dorsal capsule demonstrated greater laxity, the DOM dorsal muscles stretching ability was compromised, and the DOM pectoralis muscle was more lengthened. Players with present or past DOM shoulder pain demonstrated greater laxity in their DOM dorsal capsule, tightening of their DOM inferior capsule, and lower SS compared with those without shoulder pain. Dorsal capsule measurements bilaterally were significant predictors of SS. None of the shoulder measurements was associated with team roles or infraspinatus atrophy, while scapular lateralisation was more pronounced with increasing years of experience, and scapular antetilting was greater with increasing age. Adaptations of the DOM shoulder may be linked to pathology and performance. We describe simple shoulder measurements that may have the potential to predict chronic shoulder injury and become part of injury prevention programmes. Detailed biomechanical and large prospective studies are warranted to assess the validity of our findings and reach more definitive conclusions.

Effects of aeration strategy on the evolution of dissolved organic matter (DOM) and microbial community structure during sludge bio-drying.

PubMed

Zhang, Junya; Cai, Xing; Qi, Lu; Shao, Chunyan; Lin, Yang; Zhang, Jin; Zhang, Yuanli; Shen, Peihong; Wei, Yuansong

2015-09-01

Sludge bio-drying in which sludge is dried by means of the heat generated by the aerobic degradation of its own organic substances has been widely used for sludge treatment. A better understanding of the evolution of dissolved organic matter (DOM) and its degradation drivers during sludge bio-drying could facilitate its control. Aeration is one of the key factors that affect sludge bio-drying performance. In this study, two aeration strategies (pile I-the optimized and pile II-the current) were established to investigate their impacts on the evolution of DOM and the microbial community in a full-scale sludge bio-drying plant. A higher pile temperature in pile I caused pile I to enter the DOM and microbiology stable stage approximately2 days earlier than pile II. The degradation of easily degradable components in the DOM primarily occurred in the thermophilic phase; after that degradation, the DOM components changed a little. Along with the evolution of the DOM, its main degradation driver, the microbial community, changed considerably. Phyla Firmicutes and Proteobacteria were dominant in the thermophilic stage, and genus Ureibacillus, which was the primary thermophilic bacteria, was closely associated with the degradation of the DOM. In the mesophilic stage, the microbial community changed significantly at first and subsequently stabilized, and the genus Parapedobacter, which belongs to Bacteriodetes, became dominant. This study elucidates the interplay between the DOM and microbial community during sludge bio-drying.

Phylogenetic and structural response of heterotrophic bacteria to dissolved organic matter of different chemical composition in a continuous culture study.

PubMed

Landa, M; Cottrell, M T; Kirchman, D L; Kaiser, K; Medeiros, P M; Tremblay, L; Batailler, N; Caparros, J; Catala, P; Escoubeyrou, K; Oriol, L; Blain, S; Obernosterer, I

2014-06-01

Dissolved organic matter (DOM) and heterotrophic bacteria are highly diverse components of the ocean system, and their interactions are key in regulating the biogeochemical cycles of major elements. How chemical and phylogenetic diversity are linked remains largely unexplored to date. To investigate interactions between bacterial diversity and DOM, we followed the response of natural bacterial communities to two sources of phytoplankton-derived DOM over six bacterial generation times in continuous cultures. Analyses of total hydrolysable neutral sugars and amino acids, and ultrahigh resolution mass spectrometry revealed large differences in the chemical composition of the two DOM sources. According to 454 pyrosequences of 16S ribosomal ribonucleic acid genes, diatom-derived DOM sustained higher levels of bacterial richness, evenness and phylogenetic diversity than cyanobacteria-derived DOM. These distinct community structures were, however, not associated with specific taxa. Grazing pressure affected bacterial community composition without changing the overall pattern of bacterial diversity levels set by DOM. Our results demonstrate that resource composition can shape several facets of bacterial diversity without influencing the phylogenetic composition of bacterial communities, suggesting functional redundancy at different taxonomic levels for the degradation of phytoplankton-derived DOM. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Influence of dissolved organic matter concentration and composition on the removal efficiency of perfluoroalkyl substances (PFASs) during drinking water treatment.

PubMed

Kothawala, Dolly N; Köhler, Stephan J; Östlund, Anna; Wiberg, Karin; Ahrens, Lutz

2017-09-15

Drinking water treatment plants (DWTPs) are constantly adapting to a host of emerging threats including the removal of micro-pollutants like perfluoroalkyl substances (PFASs), while concurrently considering how background levels of dissolved organic matter (DOM) influences their removal efficiency. Two adsorbents, namely anion exchange (AE) and granulated active carbon (GAC) have shown particular promise for PFAS removal, yet the influence of background levels of DOM remains poorly explored. Here we considered how the removal efficiency of 13 PFASs are influenced by two contrasting types of DOM at four concentrations, using both AE (Purolite A-600 ® ) and GAC (Filtrasorb 400 ® ). We placed emphasis on the pre-equilibrium conditions to gain better mechanistic insight into the dynamics between DOM, PFASs and adsorbents. We found AE to be very effective at removing both PFASs and DOM, while largely remaining resistant to even high levels of background DOM (8 mg carbon L -1 ) and surprisingly found that smaller PFASs were removed slightly more efficiently than longer chained counterparts, In contrast, PFAS removal efficiency with GAC was highly variable with PFAS chain length, often improving in the presence of DOM, but with variable response based on the type of DOM and PFAS chain length. Copyright © 2017 Elsevier Ltd. All rights reserved.

Optical properties and molecular diversity of dissolved organic matter in the Bering Strait and Chukchi Sea

NASA Astrophysics Data System (ADS)

Gonsior, Michael; Luek, Jenna; Schmitt-Kopplin, Philippe; Grebmeier, Jacqueline M.; Cooper, Lee W.

2017-10-01

Changes in the molecular composition of dissolved organic matter (DOM) and its light absorbing chromophoric component (CDOM) are of particular interest in the Arctic region because of climate change effects that lead to warmer sea surface temperatures and longer exposure to sunlight. We used continuous UV-vis (UV-vis) spectroscopy, excitation emission matrix fluorescence and ultrahigh resolution mass spectrometry during a transect from the Aleutian Islands in the Bering Sea to the Chukchi Sea ice edge through Bering Strait to determine the variability of DOM and CDOM. These data were combined with discrete sampling for stable oxygen isotopes of seawater, in order to evaluate the contributions of melted sea ice versus runoff to the DOM and CDOM components. This study demonstrated that high geographical resolution of optical properties in conjunction with stable oxygen ratios and non-targeted ultrahigh resolution mass spectrometry was able to distinguish between different DOM sources in the Arctic, including identification of labile DOM sources in Bering Strait associated with high algal blooms and sampling locations influenced by terrestrially-derived DOM, such as the terrestrial DOM signal originating from Arctic rivers and dirty/anchor sea ice. Results of this study also revealed the overall variability and chemodiversity of Arctic DOM present in the Bering and Chukchi Seas.

High-pressure size exclusion chromatography analysis of dissolved organic matter isolated by tangential-flow ultra filtration

USGS Publications Warehouse

Everett, C.R.; Chin, Y.-P.; Aiken, G.R.

1999-01-01

A 1,000-Dalton tangential-flow ultrafiltration (TFUF) membrane was used to isolate dissolved organic matter (DOM) from several freshwater environments. The TFUF unit used in this study was able to completely retain a polystyrene sulfonate 1,800-Dalton standard. Unaltered and TFUF-fractionated DOM molecular weights were assayed by high-pressure size exclusion chromatography (HPSEC). The weight-averaged molecular weights of the retentates were larger than those of the raw water samples, whereas the filtrates were all significantly smaller and approximately the same size or smaller than the manufacturer-specified pore size of the membrane. Moreover, at 280 nm the molar absorptivity of the DOM retained by the ultrafilter is significantly larger than the material in the filtrate. This observation suggests that most of the chromophoric components are associated with the higher molecular weight fraction of the DOM pool. Multivalent metals in the aqueous matrix also affected the molecular weights of the DOM molecules. Typically, proton-exchanged DOM retentates were smaller than untreated samples. This TFUF system appears to be an effective means of isolating aquatic DOM by size, but the ultimate size of the retentates may be affected by the presence of metals and by configurational properties unique to the DOM phase.

Cadmium accumulation in zebrafish (Danio rerio) eggs is modulated by dissolved organic matter (DOM).

PubMed

Burnison, B Kent; Meinelt, Thomas; Playle, Richard; Pietrock, Michael; Wienke, Andreas; Steinberg, Christian E W

2006-08-23

Experiments were conducted to investigate factors influencing the accumulation of cadmium (Cd(2+)) into zebrafish (Danio rerio) eggs. The accumulation of (109)Cd was affected by: (1) concentration, (2) time, (3) presence of dissolved organic material (DOM), (4) different origin of DOM and (5) different parts of fish eggs. Over a 5-h exposure, zebrafish eggs showed a steady increase in Cd-accumulation. DOM-concentrations over 15ppm carbon (C) decreased Cd-uptake significantly. Both samples of DOM, brown water marsh (LM) and a eutrophic pond (SP), at 16.9ppmC, reduced the Cd-accumulation in the chorion, perivitelline liquid and the embryo. Cd was mainly accumulated in the egg's outer shell chorion (61%) and only small amounts passed through the chorion into the perivitelline liquid (38%) and embryo (1%). In the presence of LM-DOM, the accumulation of Cd into the egg components was decreased by 43% (chorion), 52% (perivitelline liquid) and 52% (embryo), respectively, compared with the control group. Similarly, the presence of SP-DOM reduced the Cd-accumulation by 29% (chorion), 61% (perivitelline liquid) and 60% (embryo), respectively, compared with the controls. DOM-concentration should be taken into consideration when determining ecotoxicological effects of Cd on fish populations.

Continuous summer export of nitrogen-rich organic matter from the Greenland Ice Sheet inferred by ultrahigh resolution mass spectrometry.

PubMed

Lawson, Emily C; Bhatia, Maya P; Wadham, Jemma L; Kujawinski, Elizabeth B

2014-12-16

Runoff from glaciers and ice sheets has been acknowledged as a potential source of bioavailable dissolved organic matter (DOM) to downstream ecosystems. This source may become increasingly significant as glacial melt rates increase in response to future climate change. Recent work has identified significant concentrations of bioavailable carbon and iron in Greenland Ice Sheet (GrIS) runoff. The flux characteristics and export of N-rich DOM are poorly understood. Here, we employed electrospray ionization (ESI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to determine the elemental compositions of DOM molecules in supraglacial water and subglacial runoff from a large GrIS outlet glacier. We provide the first detailed temporal analysis of the molecular composition of DOM exported over a full melt season. We find that DOM pools in supraglacial and subglacial runoff are compositionally diverse and that N-rich material is continuously exported throughout the melt season, as the snowline retreats further inland. Identification of protein-like compounds and a high proportion of N-rich DOM, accounting for 27-41% of the DOM molecules identified by ESI FT-ICR MS, may suggest a microbial provenance and high bioavailability of glacially exported DOM to downstream microbial communities.

[Using ultraviolet-visible ( UV-Vis) absorption spectrum to estimate the dissolved organic matter (DOM) concentration in water, soils and sediments of typical water-level fluctuation zones of the Three Gorges Reservoir areas].

PubMed

Li, Lu-lu; Jiang, Tao; Lu, Song; Yan, Jin-long; Gao, Jie; Wei, Shi-qiang; Wang, Ding-yong; Guo, Nian; Zhao, Zhena

2014-09-01

Dissolved organic matter (DOM) is a very important component in terrestrial ecosystem. Chromophoric dissolved organic matter (CDOM) is a significant constituent of DOM, which can be measured by ultraviolet-visible (UV-Vis) absorption spectrum. Thus the relationship between CDOM and DOM was investigated and established by several types of models including single-wavelength model, double-wavelength model, absorption spectrum slope (S value) model and three-wavelength model, based on the UV-Vis absorption coefficients of soil and sediment samples (sampled in July of 2012) and water samples (sampled in November of 2012) respectively. The results suggested that the three-wavelength model was the best for fitting, and the determination coefficients of water, soil and sediment data were 0. 788, 0. 933 and 0. 856, respectively. Meanwhile, the nominal best model was validated with the UV-Vis data of 32 soil samples and 36 water samples randomly collected in 2013, showing the RRMSE and MRE were 16. 5% and 16. 9% respectively for soil DOM samples, 10. 32% and 9. 06% respectively for water DOM samples, which further suggested the prediction accuracy was higher in water DOM samples as compared with that in soil DOM samples.

Dissolved organic matter composition drives the marine production of brominated very short-lived substances.

PubMed

Liu, Yina; Thornton, Daniel C O; Bianchi, Thomas S; Arnold, William A; Shields, Michael R; Chen, Jie; Yvon-Lewis, Shari A

2015-03-17

Brominated very short-lived substances (BrVSLS), such as bromoform, are important trace gases for stratospheric ozone chemistry. These naturally derived trace gases are formed via bromoperoxidase-mediated halogenation of dissolved organic matter (DOM) in seawater. Information on DOM type in relation to the observed BrVSLS concentrations in seawater, however, is scarce. We examined the sensitivity of BrVSLS production in relation to the presence of specific DOM moieties. A total of 28 model DOM compounds in artificial seawater were treated with vanadium bromoperoxidase (V-BrPO). Our results show a clear dependence of BrVSLS production on DOM type. In general, molecules that comprise a large fraction of the bulk DOM pool did not noticeably affect BrVSLS production. Only specific cell metabolites and humic acid appeared to significantly enhance BrVSLS production. Amino acids and lignin phenols suppressed enzyme-mediated BrVSLS production and may instead have formed halogenated nonvolatile molecules. Dibromomethane production was not observed in any experiments, suggesting it is not produced by the same pathway as the other BrVSLS. Our results suggest that regional differences in DOM composition may explain the observed BrVSLS concentration variability in the global ocean. Ultimately, BrVSLS production and concentrations are likely affected by DOM composition, reactivity, and cycling in the ocean.

Insights into the binding interactions of autochthonous dissolved organic matter released from Microcystis aeruginosa with pyrene using spectroscopy.

PubMed

Yang, Chenghu; Liu, Yangzhi; Zhu, Yaxian; Zhang, Yong

2016-03-15

The autochthonous dissolved organic matter (DOM) released by Microcystis aeruginosa (M. aeruginosa-DOM) during its growth period was characterized by spectroscopy. Furthermore, the relationships between the M. aeruginosa-DOM spectroscopic descriptors and the pyrene binding coefficient (KDOC) values were explored. The results showed that the spectroscopic characteristics of the M. aeruginosa-DOM and the binding properties of pyrene were dynamically changed along with the algae growth. Pearson correlation analysis demonstrated that a higher pyrene KDOC value was observed for the M. aeruginosa-DOM that has a higher humification index (HIX) value, a lower biological index (BIX) value and a lower absorption ratio (E2/E3). The presence of protein-like and long-wavelength-excited humic-like components may impose negative and positive effects on binding of pyrene by the M. aeruginosa-DOM, respectively. Principal component analysis (PCA) further supported that the binding affinity of pyrene may be primarily influenced by the humification degree of the M. aeruginosa-DOM. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular-Scale Investigation with ESI-FT-ICR-MS on Fractionation of Dissolved Organic Matter Induced by Adsorption on Iron Oxyhydroxides.

PubMed

Lv, Jitao; Zhang, Shuzhen; Wang, Songshan; Luo, Lei; Cao, Dong; Christie, Peter

2016-03-01

Adsorption by minerals is a common geochemical process of dissolved organic matter (DOM) which may induce fractionation of DOM at the mineral-water interface. Here, we examine the molecular fractionation of DOM induced by adsorption onto three common iron oxyhydroxides using electrospray ionization coupled with Fourier-transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS). Ferrihydrite exhibited higher affinity to DOM and induced more pronounced molecular fractionation of DOM than did goethite or lepidocrocite. High molecular weight (>500 Da) compounds and compounds high in unsaturation or rich in oxygen including polycyclic aromatics, polyphenols and carboxylic compounds had higher affinity to iron oxyhydroxides and especially to ferrihydrite. Low molecular weight compounds and compounds low in unsaturation or containing few oxygenated groups (mainly alcohols and ethers) were preferentially maintained in solution. This study confirms that the double bond equivalence and the number of oxygen atoms are valuable parameters indicating the selective fractionation of DOM at mineral and water interfaces. The results of this study provide important information for further understanding the behavior of DOM in the natural environment.

Composition and Biolability of Dissolved Organic Matter Leached from the Dominant Endmembers of the Siberian Arctic

NASA Astrophysics Data System (ADS)

Borgen, M.; Spencer, R. G.; Mann, P. J.; Vonk, J. E.; Bulygina, E. B.; Holmes, R. M.

2012-12-01

Terrigenous dissolved organic matter (DOM) has historically been thought to be refractory as it is mobilized into and transported through Arctic fluvial networks. However, a growing body of evidence suggests that this DOM, largely leached from vegetation, soils, and litter during the annual freshet, is highly biolabile. This study examined DOM leached from these dominant endmembers of the Kolyma River watershed in the Siberian Arctic. As leachates progressed through time, measurements of dissolved organic carbon (DOC), optical parameters to assess DOM composition, and biodegradation incubations were undertaken. This suite of measurements allowed examination of the rate and composition of leached DOC into the aquatic system and quantification of the biolability of the DOM from the diverse range of endmembers examined. Of all the endmembers, vascular plants leached the greatest amount of DOC and results will be presented relating DOC concentration and DOM composition to initial source material. Furthermore, controls on DOM biolability, enzymatic activity, and the ultimate fate of terriginous DOC in Siberian fluvial systems will be discussed.

Rising trends of dissolved organic matter in drinking-water reservoirs as a result of recovery from acidification in the Ore Mts., Czech Republic.

PubMed

Oulehle, Filip; Hruska, Jakub

2009-12-01

The concentration of chemical oxygen demand (COD), a common proxy for dissolved organic matter (DOM), was measured at seven drinking-water reservoirs and four streams between 1969 and 2006. Nine of them showed significant DOM increases (median COD change +0.08 mg L(-1) yr(-1)). Several potential drivers of these trends were considered, including air temperature, rainfall, land-use and water sulfate concentration. Temperature and precipitation influenced inter-annual variations, but not long-term trends. The long-term DOM increase was significantly associated with declines of acidic deposition, especially sulfur deposition. Surface water sulfate concentrations decreased from a median of 62 mg L(-1)-27 mg L(-1) since 1980. The magnitude of DOM increase was positively correlated with average DOM concentration (R(2) = 0.79, p < 0.001). Simultaneously, DOM concentration was positively correlated with the proportion of Histosols within the catchments (R(2) = 0.79, p < 0.001). A focus on the direct removal of DOM by water treatment procedures rather than catchment remediation is needed.

Dissolved Organic Matter Composition and Export from U.S. Rivers

NASA Astrophysics Data System (ADS)

Aiken, G.; Butman, D. E.; Spencer, R. G.; Raymond, P.

2012-12-01

Dissolved organic matter (DOM) chemistry and flux are potentially useful indicators of watershed characteristics, climate influences on watershed hydrology and soils, and changes associated with water and land resource management. Organic source materials, watershed geochemistry, oxidative processes and hydrology strongly influence the nature and reactivity of DOM in aquatic systems. The molecules that comprise DOM, in turn, control a number of environmental processes important for ecosystem function including light penetration and photochemistry, microbial activity, mineral dissolution/precipitation, and the transport and reactivity of hydrophobic compounds and metals. In particular, aromatic molecules derived from higher plants exert strong controls on aquatic photochemistry, and on the transport and biogeochemistry of metals. Assessment of DOM composition and transport, therefore, can provide a basis for understanding watershed processes and biogeochemistry of rivers and streams. Here we present results of a multi-year study designed to assess the seasonal and spatial variability of DOM quantity and quality for 15 large North American river basins. Samples were collected from the mouths of the rivers using a sampling program designed to capture hydrologic and seasonal variability of DOM export. DOM concentrations and composition, based on DOM fractionation on XAD resins, chromophoric dissolved organic matter (CDOM) parameters (ultraviolet /visible absorption and fluorescence spectroscopy), specific compound analyses, and DO14C content varied greatly both between sites and seasonally within a given site. DOM in these rivers exhibited a wide range of concentration and carbon specific ultra-violet absorbance at 254 nm (SUVA254), an optical measurement that is an indicator of DOM aromatic carbon content. In almost all systems, CDOM optical parameters correlated strongly with DOC concentration and hydrophobic organic acid (HPOA) content (aquatic humic substances). In particular, SUVA254 was found to correlate strongly with the proportion of HPOA and Δ14C. Relationships between dissolved organic carbon (DOC) concentration and absorbance for individual rivers were quite variable due to differences in the fraction of non-chromophoric DOM. Notably, the relationship between UV absorption coefficients and DOC concentration for four rivers that drain arid regions and/or are heavily influenced by impoundments were statistically weak.although similar trends for these rivers were not observed for Δ14C. Basins with high discharge, high density of vegetation cover, and low population densities exported younger, more aromatic DOM. Conversely, old DOM was exported from low discharge watersheds draining arid regions and watersheds impacted by high population densities. While individual watershed characteristics control DOC concentrations, CDOM parameters and DO14C content, overall discharge dominated the flux of both CDOM and DO14C to coastal waters. The link between the nature and reactivity of DOM and its optical properties can be exploited to provide powerful monitoring tools to assess the impacts of climate change, land-use change, and management practices on overall water quality and on DOM transport and transformation.

Nature and transformation of dissolved organic matter in treatment wetlands

USGS Publications Warehouse

Barber, L.B.; Leenheer, J.A.; Noyes, T.I.; Stiles, E.A.

2001-01-01

This investigation into the occurrence, character, and transformation of dissolved organic matter (DOM) in treatment wetlands in the western United States shows that (i) the nature of DOM in the source water has a major influence on transformations that occur during treatment, (ii) the climate factors have a secondary effect on transformations, (iii) the wetlands receiving treated wastewater can produce a net increase in DOM, and (iv) the hierarchical analytical approach used in this study can measure the subtle DOM transformations that occur. As wastewater treatment plant effluent passes through treatment wetlands, the DOM undergoes transformation to become more aromatic and oxygenated. Autochthonous sources are contributed to the DOM, the nature of which is governed by the developmental stage of the wetland system as well as vegetation patterns. Concentrations of specific wastewaterderived organic contaminants such as linear alkylbenzene sulfonate, caffeine, and ethylenediaminetetraacetic acid were significantly attenuated by wetland treatment and were not contributed by internal loading.

Biogeochemical and Optical Analysis of Coastal DOM for Satellite Retrieval of Terrigenous DOM in the U.S. Middle Atlantic Bight

NASA Technical Reports Server (NTRS)

Mannino, A.; Dyda, R. Y.; Hernes, P. J.; Hooker, Stan; Hyde, Kim; Novak, Mike

2012-01-01

Estuaries and coastal ocean waters experience a high degree of variability in the composition and concentration of particulate and dissolved organic matter (DOM) as a consequence of riverine/estuarine fluxes of terrigenous DOM, sediments, detritus and nutrients into coastal waters and associated phytoplankton blooms. Our approach integrates biogeochemical measurements (elemental content, molecular analyses), optical properties (absorption) and remote sensing to examine terrestrial DOM contributions into the U.S. Middle Atlantic Bight (MAB). We measured lignin phenol composition, DOC and CDOM absorption within the Chesapeake and Delaware Bay mouths, plumes and adjacent coastal ocean waters to derive empirical relationships between CDOM and biogeochemical measurements for satellite remote sensing application. Lignin ranged from 0.03 to 6.6 ug/L between estuarine and outer shelf waters. Our results demonstrate that satellite-derived CDOM is useful as a tracer of terrigenous DOM in the coastal ocean

Validation of a simple liquid chromatographic method for determination and quantitation of residual ivermectin and doramectin in pig liver.

PubMed

Knold, Lone; Reitov, Marianne; Mortensen, Anna Birthe; Hansen-Møller, Jens

2002-01-01

A rapid and quantitative method for the extraction, derivatization, and liquid chromatography with fluorescence detection of ivermectin (IVM) and doramectin (DOM) residues in porcine liver was developed and validated. IVM and DOM were extracted from the liver samples with acetonitrile, the supernatant was evaporated to dryness at 37 degrees C under nitrogen, and the residue was reconstituted in 1-methylimidazole solution. After 2 min at room temperature, IVM and DOM were converted to a fluorescent derivative and then separated on a Hypersil ODS column. The derivatives of IVM and DOM were detected and quantitated with high specificity by fluorescence (excitation: 365 nm, emission: 475 nm). Abamectin was used as an internal standard. The mean extraction efficiencies from fortified samples (15 ng/g) were 75% for IVM and 70% for DOM. The limit of detection was 0.8 ng/g for both IVM and DOM.

Chromophoric Dissolved Organic Matter in Southwestern Greenland Lakes

NASA Astrophysics Data System (ADS)

Osburn, C. L.; Giles, M. E.; Underwood, G. J. C.

2014-12-01

Dissolved organic matter (DOM) is an important property of Arctic lake ecosystems, originating from allochthonous inputs from catchments and autochthonous production by plankton in the water column. Little is known about the quality of DOM in Arctic lakes that lack substantial inputs from catchments and such lakes are abundant in southwestern Greenland. Colored dissolved organic matter (CDOM), the fraction that absorbs ultraviolet (UV) and visible light, is the controlling factor for the optical properties of many surface waters and as well informs on the quality of DOM. We examined the quality of CDOM in 21 lakes in southwestern Greenland, from the ice sheet to the coast, as part of a larger study examining the role of DOM in regulating microbial communities in these lakes. DOM was size fractioned and absorbance and fluorescence was measured on each size fraction, as well as on bulk DOM. The specific ultraviolet absorbance (SUVA) at 254 nm (SUVA254), computed by normalizing absorption (a254) to dissolved organic carbon (DOC) concentration, provided an estimate of the aromatic carbon content of DOM. SUVA values were generally <2, indicating low aromatic content. Parallel factor analysis (PARAFAC) of CDOM fluorescence was used to determine the relative abundance of allochthonous and autochthonous DOM in all size fractions. Younger lakes near the ice sheet and lakes near the coast had lower amounts of CDOM and appeared more microbial in quality. However, lakes centrally located between the ice sheet and the coast had the highest CDOM concentrations and exhibited strong humic fluorescence. Overall distinct differences in CDOM quality were observed between lake locations and among DOM size fractions.

Metabolism of Deoxynivalenol and Deepoxy-Deoxynivalenol in Broiler Chickens, Pullets, Roosters and Turkeys

PubMed Central

Schwartz-Zimmermann, Heidi E.; Fruhmann, Philipp; Dänicke, Sven; Wiesenberger, Gerlinde; Caha, Sylvia; Weber, Julia; Berthiller, Franz

2015-01-01

Recently, deoxynivalenol-3-sulfate (DON-3-sulfate) was proposed as a major DON metabolite in poultry. In the present work, the first LC-MS/MS based method for determination of DON-3-sulfate, deepoxy-DON-3-sulfate (DOM-3-sulfate), DON, DOM, DON sulfonates 1, 2, 3, and DOM sulfonate 2 in excreta samples of chickens and turkeys was developed and validated. To this end, DOM-3-sulfate was chemically synthesized and characterized by NMR and LC-HR-MS/MS measurements. Application of the method to excreta and chyme samples of four feeding trials with turkeys, chickens, pullets, and roosters confirmed DON-3-sulfate as the major DON metabolite in all poultry species studied. Analogously to DON-3-sulfate, DOM-3-sulfate was formed after oral administration of DOM both in turkeys and in chickens. In addition, pullets and roosters metabolized DON into DOM-3-sulfate. In vitro transcription/translation assays revealed DOM-3-sulfate to be 2000 times less toxic on the ribosome than DON. Biological recoveries of DON and DOM orally administered to broiler chickens, turkeys, and pullets were 74%–106% (chickens), 51%–72% (roosters), and 131%–151% (pullets). In pullets, DON-3-sulfate concentrations increased from jejunum chyme samples to excreta samples by a factor of 60. This result, put into context with earlier studies, indicates fast and efficient absorption of DON between crop and jejunum, conversion to DON-3-sulfate in intestinal mucosa, liver, and possibly kidney, and rapid elimination into excreta via bile and urine. PMID:26569307

Spatial patterns of DOC concentration and DOM optical properties in a Brazilian tropical river-wetland system

NASA Astrophysics Data System (ADS)

Dalmagro, Higo J.; Johnson, Mark S.; de Musis, Carlo R.; Lathuillière, Michael J.; Graesser, Jordan; Pinto-Júnior, Osvaldo B.; Couto, Eduardo G.

2017-08-01

The Cerrado (savanna) and Pantanal (wetland) biomes of Central Western Brazil have experienced significant development activity in recent decades, including extensive land cover conversion from natural ecosystems to agriculture and urban expansion. The Cuiabá River transects the Cerrado biome prior to inundating large areas of the Pantanal, creating one of the largest biodiversity hot spots in the world. We measured dissolved organic carbon (DOC) and the optical absorbance and fluorescence properties of dissolved organic matter (DOM) from 40 sampling locations spanning Cerrado and Pantanal biomes during wet and dry seasons. In the upper, more agricultural region of the basin, DOC concentrations were highest in the rainy season with more aromatic and humified DOM. In contrast, DOC concentrations and DOM optical properties were more uniform for the more urbanized middle region of the basin between wet and dry seasons, as well as across sample locations. In the lower region of the basin, wet season connectivity between the river and the Pantanal floodplain led to high DOC concentrations, a fourfold increase in humification index (HIX) (an indicator of DOM humification), and a 50% reduction in the spectral slope (SR). Basin-wide, wet season values for SR, HIX, and FI (fluorescence index) indicated an increasing representation of terrestrially derived DOM that was more humified. Parallel factor analysis identified two terrestrially derived components (C1 and C2) representing 77% of total fluorescing DOM (fDOM). A third, protein-like fDOM component increased markedly during the wet season within the more urban-impacted region.

Controls on dissolved organic matter (DOM) degradation in a headwater stream: the influence of photochemical and hydrological conditions in determining light-limitation or substrate-limitation of photo-degradation

NASA Astrophysics Data System (ADS)

Cory, R. M.; Harrold, K. H.; Neilson, B. T.; Kling, G. W.

2015-11-01

We investigated how absorption of sunlight by chromophoric dissolved organic matter (CDOM) controls the degradation and export of DOM from Imnavait Creek, a beaded stream in the Alaskan Arctic. We measured concentrations of dissolved organic carbon (DOC), as well as concentrations and characteristics of CDOM and fluorescent dissolved organic matter (FDOM), during ice-free periods of 2011-2012 in the pools of Imnavait Creek and in soil waters draining to the creek. Spatial and temporal patterns in CDOM and FDOM in Imnavait Creek were analyzed in conjunction with measures of DOM degradation by sunlight and bacteria and assessments of hydrologic residence times and in situ UV exposure. CDOM was the dominant light attenuating constituent in the UV and visible portion of the solar spectrum, with high attenuation coefficients ranging from 86 ± 12 m-1 at 305 nm to 3 ± 1 m-1 in the photosynthetically active region (PAR). High rates of light absorption and thus light attenuation by CDOM contributed to thermal stratification in the majority of pools in Imnavait Creek under low-flow conditions. In turn, thermal stratification increased the residence time of water and DOM, and resulted in a separation of water masses distinguished by contrasting UV exposure (i.e., UV attenuation by CDOM with depth resulted in bottom waters receiving less UV than surface waters). When the pools in Imnavait Creek were stratified, DOM in the pool bottom water closely resembled soil water DOM in character, while the concentration and character of DOM in surface water was reproduced by experimental photo-degradation of bottom water. These results, in combination with water column rates of DOM degradation by sunlight and bacteria, suggest that photo-degradation is the dominant process controlling DOM fate and export in Imnavait Creek. A conceptual model is presented showing how CDOM amount and lability interact with incident UV light and water residence time to determine whether photo-degradation is "light-limited" or "substrate-limited". We suggest that degradation of DOM in CDOM-rich streams or ponds similar to Imnavait is typically light-limited under most flow conditions. Thus, export of DOM from this stream will be less under conditions that increase the light available for DOM photo-degradation (i.e., low flows, sunny days).

Using Three-Dimensional Fluorescence Spectrum Technology to Analyze the Effects of Natural Dissolved Organic Matter on the Pesticide Residues in the Soil.

PubMed

Lei, Hong-jun; Han, Yu-ping; Liu, Xin; Xu, Jian-xin

2015-07-01

The behavior of pesticide in soil is influenced by dissolved organic matter (DOM) through competition adsorption, adsorption, solubilization, accelerated degradation, and so on. Thus DOM and its components play an important role in the environmental risk in the soil ecosystem and groundwater environment. Currently, most studies focused on the short-term effect of high concentration of DOM on the pesticide residues. However, soil DOM is mainly at low level. Therefore, there is of some practical significance to probe into the environmental behavior of soil pesticides under natural level of DOM. Thus a site investigation was conducted in the farmland with long-term application history of pesticide. By using the three dimensional excitation-emission fluorescence matrix (3D-EEM) technology, together with the fluorescence regional integration (FRI) quantitative method, the long-term effects of pesticide residues under low concentration of natural DOM were analyzed. Results showed that: (1) The long-term effects of the natural DOM components on the environment behavior of most soil organochlorine pesticides were not significant except for a few pesticides such as y-HCH, p, p'-DDE, etc. (2) The influencing effects of DOM components on different type of pesticides were varied. Among which, the content of tyrosine component showed a significantly negative correlation (p < 0.05) with the concentration of y-HCH and p, p'-DDE. There were significant positive correlations (p < 0.05) between the byproducts of microbial degradation in DOM components and the concentration of heptachlor. There were also a significant positive correlation (p < 0.05) between the content of active humus component of humic acid in the DOM and the concentration of heptachlor epoxide. These results suggested that the distribution of different types of pesticides residue in the soil was influenced by different components at different levels of significance. (3) The humification degree of soil organic matter showed minor effect of DOM on the pesticide residues in the soil. In this study, 3D-EEM and FRI technology were firstly coupled in use for studying the influence of different components of DOM in soil on the environmental behavior of pesticides, which provides a new idea for the research on the mechanism of pesticides transportation and transformation in soil and groundwater environment.

Dissolved Organic Matter in the Gulf of Maine: Implications for Blue Carbon Cycling in Coastal Waters

NASA Astrophysics Data System (ADS)

Aiken, G.

2016-12-01

Nutrients and dissolved organic matter (DOM) delivered from terrestrial sources to coastal oceans are critical for ocean productivity and the blue carbon cycle. Assessing influences of these inputs on marine productivity is difficult due to the difficulty in monitoring the processes controlling carbon cycling over short time frames, as well as the lack of historical data to assess possible trends. In this presentation, results of a long-term study designed to assess productivity and water quality in the Gulf of Maine (GoM), and waters delivering terrestrially derived DOM to the GoM are presented. DOM in the major tributaries and discrete samples collected along transects in the GoM were characterized by many analytical approaches including measurement of DOM optical properties, DOM fractionation, isotopic , 13C-NMR and FTICR-MS analyses. The compositional information provided by these was combined with optical data obtained by an in-situ glider and remotely sensed satellite data. Results indicate that DOM associated with inflowing waters to the GoM is rich in aromatic compounds resulting in a large influx of terrestrially derived, chromophoric DOM. The net result of these inflows is that DOM in the GoM is more chromophoric than samples from the Sargasso Sea and mid-Pacific Ocean. Hydrologic analyses using discharge:concentration relationships along with historical river discharge data indicate that the amount of DOM from rivers to the GoM has increased over the past 80 years leading to a `yellowing' of the waters in the GoM. Indeed, comparisons of ocean color between the present study and observations made by Henry Bigelow in 1912-1913 using the Forel-Ule color scale indicate an increase in chromophoric DOM in the past century. Chromophoric DOM influences the productivity of aquatic systems by reducing light available for phytoplankton photosynthesis and growth. Over the course of this study, a decline in primary productivity was also observed, perhaps resulting from increased DOM fluxes to the GoM. Climate and hydrologic models predict increasing precipitation and runoff in the GoM watershed during this century, possibly resulting in an increase of terrestrial OM delivered to the GoM of 30% during the next 80 years. This could potentially influence productivity and blue carbon cycling in this marine system.

Qualitative changes of riverine dissolved organic matter at low salinities due to flocculation

NASA Astrophysics Data System (ADS)

Asmala, Eero; Bowers, David G.; Autio, Riitta; Kaartokallio, Hermanni; Thomas, David N.

2014-10-01

The flocculation of dissolved organic matter (DOM) was studied along transects through three boreal estuaries. Besides the bulk concentration parameters, a suite of DOM quality parameters were investigated, including colored DOM (CDOM), fluorescent DOM, and the molecular weight of DOM as well as associated dissolved iron concentrations. We observed significant deviations from conservative mixing at low salinities (<2) in the estuarine samples of dissolved organic carbon (DOC), UV absorption (a(CDOM254)), and humic-like fluorescence. The maximum deviation from conservative mixing for DOC concentration was -16%, at salinities between 1 and 2. An associated laboratory experiment was conducted where an artificial salinity gradient between 0 and 6 was created. The experiment confirmed the findings from the estuarine transects, since part of the DOC and dissolved iron pools were transformed to particulate fraction (>0.2 µm) and thereby removing them from the dissolved phase. We also measured flocculation of CDOM, especially in the UV region of the absorption spectrum. Protein-like fluorescence of DOM decreased, while humic-like fluorescence increased because of salt-induced flocculation. Additionally, there was a decrease in molecular weight of DOM. Consequently, the quantity and quality of the remaining DOM pool was significantly changed after influenced to flocculation. Based on these results, we constructed a mechanistic, two-component flocculation model. Our findings underline the importance of the coastal filter, where riverine organic matter is flocculated and exported to the sediments.

Microbial Community Response to Terrestrially Derived Dissolved Organic Matter in the Coastal Arctic.

PubMed

Sipler, Rachel E; Kellogg, Colleen T E; Connelly, Tara L; Roberts, Quinn N; Yager, Patricia L; Bronk, Deborah A

2017-01-01

Warming at nearly twice the global rate, higher than average air temperatures are the new 'normal' for Arctic ecosystems. This rise in temperature has triggered hydrological and geochemical changes that increasingly release carbon-rich water into the coastal ocean via increased riverine discharge, coastal erosion, and the thawing of the semi-permanent permafrost ubiquitous in the region. To determine the biogeochemical impacts of terrestrially derived dissolved organic matter (tDOM) on marine ecosystems we compared the nutrient stocks and bacterial communities present under ice-covered and ice-free conditions, assessed the lability of Arctic tDOM to coastal microbial communities from the Chukchi Sea, and identified bacterial taxa that respond to rapid increases in tDOM. Once thought to be predominantly refractory, we found that ∼7% of dissolved organic carbon and ∼38% of dissolved organic nitrogen from tDOM was bioavailable to receiving marine microbial communities on short 4 - 6 day time scales. The addition of tDOM shifted bacterial community structure toward more copiotrophic taxa and away from more oligotrophic taxa. Although no single order was found to respond universally (positively or negatively) to the tDOM addition, this study identified 20 indicator species as possible sentinels for increased tDOM. These data suggest the true ecological impact of tDOM will be widespread across many bacterial taxa and that shifts in coastal microbial community composition should be anticipated.

Aquatic photochemistry of sulfamethazine: multivariate effects of main water constituents and mechanisms.

PubMed

Li, Yingjie; Liu, Xiangliang; Zhang, Biaojun; Zhao, Qun; Ning, Ping; Tian, Senlin

2018-03-01

The ubiquity of sulfonamides (SAs) in natural waters requires insight into their environmental fate for ecological risk assessment. Extensive studies focused on the effect of univariate water constituents on the photochemical fate of SAs, yet the multivariate effects of water constituents in environmentally relevant concentrations on SA photodegradation are poorly understood. Here, response surface methodology was employed to explore the integrative effects of main water constituents (dissolved organic matter (DOM), NO 3 - , HCO 3 - , Cu 2+ ) on the photodegradation of a representative SA (sulfamethazine). Results showed that besides single factors, interaction of factors also significantly impacted the photodegradation. Radical scavenging experiments indicated that triplet-excited DOM ( 3 DOM*) was responsible for the enhancing effect of DOM on the photodegradation. Additionally, DOM may also quench the 3 DOM*-mediated oxidation intermediate of sulfamethazine causing the inhibiting effect of DOM-DOM interaction. We also found that HCO 3 - was oxidized by triplet-excited sulfamethazine producing CO 3 ˙ - , and the high reactivity of CO 3 ˙ - with sulfamethazine (second-order rate constant 2.2 × 10 8 M -1 s -1 ) determined by laser flash photolysis revealed the enhancing photodegradation mechanism of HCO 3 - . This study is among the first attempts to probe the photodegradation of SAs considering the integrative effects of water constituents, which is important in accurate ecological risk assessment of organic pollutants in the aquatic environment.

Effects of molecular size fraction of DOM on photodegradation of aqueous methylmercury.

PubMed

Kim, Moon-Kyung; Won, A-Young; Zoh, Kyung-Duk

2017-05-01

This study investigated the photodegradation kinetics of MeHg in the presence of various size fractions of dissolved organic matter (DOM) with MW < 3.5 kDa, 3.5 < MW < 10 kDa, and MW > 10 kDa. The DOM fraction with MW < 3.5 kDa was most effective in MeHg photodegradation. Increasing UV intensity resulted in the increase of photodegradation rate of the MeHg in all size of DOM fractions. Higher rates of MeHg degradation was observed at higher pH. For the portion of MW < 3.5 kDa, the photodegradation rate of MeHg increased with increasing DOM concentration, indicating that radicals such as singlet oxygen ( 1 O 2 ) radicals can be effectively produced by DOM. At higher portion of MW > 3.5 kDa, the inhibition of MeHg degradation was observed due to the effect of DOM photo-attenuation. Our result indicates that radical mediated reaction is the main mechanism of photodegradation of MeHg especially in the presence of MW < 3.5 kDa. Our results imply that the smaller molecular weight fraction (MW < 3.5 kDa) of DOM mainly increased the photodegradation rate of MeHg. Copyright © 2017 Elsevier Ltd. All rights reserved.

Snowmelt-driven changes in dissolved organic matter and bacterioplankton communities in the Heilongjiang watershed of China.

PubMed

Qiu, Linlin; Cui, Hongyang; Wu, Junqiu; Wang, Baijie; Zhao, Yue; Li, Jiming; Jia, Liming; Wei, Zimin

2016-06-15

Bacterioplankton plays a significant role in the circulation of materials and ecosystem function in the biosphere. Dissolved organic matter (DOM) from dead plant material and surface soil leaches into water bodies when snow melts. In our study, water samples from nine sampling sites along the Heilongjiang watershed were collected in February and June 2014 during which period snowmelt occurred. The goal of this study was to characterize changes in DOM and bacterioplankton community composition (BCC) associated with snowmelt, the effects of DOM, environmental and geographical factors on the distribution of BCC and interactions of aquatic bacterioplankton populations with different sources of DOM in the Heilongjiang watershed. BCC was measured by denaturing gradient gel electrophoresis (DGGE). DOM was measured by excitation-emission matrix (EEM) fluorescence spectroscopy. Bacterioplankton exhibited a distinct seasonal change in community composition due to snowmelt at all sampling points except for EG. Redundancy analysis (RDA) indicated that BCC was more closely related to DOM (Components 1 and 4, dissolved organic carbon, biochemical oxygen demand and chlorophyll a) and environmental factors (water temperature and nitrate nitrogen) than geographical factors. Furthermore, DOM had a greater impact on BCC than environmental factors (29.80 vs. 15.90% of the variation). Overall, spring snowmelt played an important role in altering the quality and quantity of DOM and BCC in the Heilongjiang watershed. Copyright © 2016 Elsevier B.V. All rights reserved.

Illuminating the dark side of DOM: A bottom up approach to understanding the structure and composition of DOM.

NASA Astrophysics Data System (ADS)

Zito, P.; Tarr, M. A.; Spencer, R. G.; Podgorski, D. C.

2017-12-01

Dissolved organic matter (DOM) is one of the most complex natural mixtures on Earth. It is generally comprised of hydrocarbons incorporating a diverse subset of oxygen-containing functional groups along with a small amount of nitrogen, sulfur and phosphorous heteroatoms all of which make it very difficult to chromatographically separate. The only way to directly characterize and quantify these structural and compositional changes is by separating the DOM continuum into defined bins of structure and chemistry. In this study, we take an alternate bottom-up approach that utilizes petroleum to work toward identifying the molecular structures of DOM. Although petroleum is the most structurally diverse mixture in nature, it is almost exclusively comprised of hydrocarbons with only trace quantities of heteroatoms, including oxygen. Here, crude oil was chromatographically separated into bins based on the number of aromatic rings to be used as a starting carbon source. Photochemically produced DOM from these aromatic ring bins provides unique opportunities to gain insight in the compositional controls associated with transport, processing and fate of DOM in natural systems. Here, we present EEMs data from individual ring fractions that were subjected to 24 hours of sunlight to use as a model to fingerprint specific aromatic regions in the DOM fraction. Results illustrate that the 1-, 2-, 3-, 4- and 5- ring fractions exhibit a wide range of structurally dependent excitation and emission spectra. A well-known red-shift in the emission and excitation occurs as the number of rings increase. In order to understand changes in the elemental composition of the data, ultra high-resolution mass spectrometry was used to obtain molecular level information. Together, these data will provide a tool to help understand the relationship of the composition and structure of DOM released into the environment in terms of aromaticity. It is well known that aromaticity is an important indicator of the chemical characteristics of DOM and can be used to explain the role of DOM in environmental processes. Thus, identifying these compounds in terms of aromaticity after photodegradation will provide information about the fate, transport and mechanisms of the photolabile and recalcitrant compounds in the environment.

Spatial variation of dissolved organic matter composition and characteristics in an urbanized watershed

NASA Astrophysics Data System (ADS)

Hsieh, C.; Li, M.

2013-12-01

Dissolved organic matter (DOM) is a chemically complex mixture of organic polymers that plays an important role in river ecosystems and originates from various sources. Some DOMs are autochthonous originating through phytoplankton and microbial activity in situ. On the other hand, some DOMs are allochthonous which are transported to river from the surrounding watershed by natural or anthropogenic activities. The studies of DOM in river are usually conducted at the watershed scale; however, factors of local spatial scale affecting DOM composition also need to take into consideration for the study of DOM in an urbanized watershed. Through increasing urbanization, changes in a watershed occur not only in land use patterns but also in river channel characteristics. The objective of this study is to investigate effects of different river channel characteristics and patterns on changes in DOM source and composition. In this study, we chose three tributaries of Tamsui river in Taiwan according to its land use pattern and river channel characteristics. At each sub-basin, river water samples were sampled from three study sites. River water DOM was measured by using optical measurements of UV absorption and fluorescence spectroscopy. Water samples were also collected for laboratory analysis of different water quality parameters. From our study sites, they are from three sub-basins which are in the similar physical environments but with different river channel types: the highly channelized Keelung river, the less channelized Xindian river, and less channelized Dahan river with five human-made wetlands. From the upstream to the urbanized downstream, composition of DOM showed variation among different sampled sites. In all three sub-basins, the trends of 5-day biochemical oxygen demand (BOD5) and suspended solids (SS) are also different. The changes in DOM source and composition as well as different water quality parmaters occur at the local spatial-scale depended on their river channel characters in urbanized watersheds. Based on our result, it indicates river channel characters which can have effects on biogeochemical processes of DOM. This knowledge can help us in understanding biogeochemical processes controlled or manipulated by anthropogenic activities at different spatial scales, and help us to make an integrative river health management in a watershed.

Composition of dissolved organic matter (DOM) from periodically submerged soils in the Three Gorges Reservoir areas as determined by elemental and optical analysis, infrared spectroscopy, pyrolysis-GC-MS and thermally assisted hydrolysis and methylation.

PubMed

Jiang, Tao; Kaal, Joeri; Liang, Jian; Zhang, Yaoling; Wei, Shiqiang; Wang, Dingyong; Green, Nelson W

2017-12-15

Soil-derived dissolved organic matter (DOM) has a major influence in biogeochemical processes related to contaminant dynamics and greenhouse gas emissions, due to its reactivity and its bridging role between the soil and aquatic systems. Within the Three Gorges Reservoir (TGR, China) area, an extensive water-fluctuation zone periodically submerges the surrounding soils. Here we report a characterization study of soil-derived DOM across the TGR areas, using elemental and optical analysis, infrared spectroscopy (FTIR), pyrolysis-GC-MS (Py-GC-MS) and thermally assisted hydrolysis and methylation (THM-GC-MS). The results showed that the soil DOM from the TGR area is a mixture of "allochthonous" (i.e., plant-derived/terrigenous) and "autochthonous" (i.e., microbial) origins. The terrigenous DOM is composed primarily of phenolic and aliphatic structures from lignin and aliphatic biopolymers (i.e. cutin, suberin), respectively. Multivariate statistics differentiated between two fractions of the microbial DOM, i.e. chitin-derived, perhaps from fungi and arthropods in soil, and protein-derived, partially sourced from algal or aquatic organisms. Molecular proxies of source and degradation state were in good agreement with optical parameters such as SUVA 254 , the fluorescence index (FI) and the humification index (HIX). The combined use of elemental analysis, fluorescence spectroscopy, and Py-GC-MS provides rigorous and detailed DOM characterization, whereas THM-GC-MS is useful for more precise but qualitative identification of the different phenolic (cinnamyl, p-hydroxyphenyl, guaiacyl, syringyl and tannin-derived) and aliphatic materials. With the multi-methodological approach used in this study, FTIR was the least informative, in part, because of the interference of inorganic matter in the soil DOM samples. The soil DOM from the TGR's water fluctuation zone exhibited considerable compositional diversity, mainly related to the balance between DOM source (microbial- or plant-derived), local vegetation and anthropogenic activities (e.g., agriculture). Finally, the relationship between DOM composition and its potential reactivity with substances of environmental concerns in the TGR area are also discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Application of UV-visible absorption spectroscopy combined with two-dimensional correlation for insight into DOM fractions from native halophyte soils in a larger estuarine delta.

PubMed

Wei, Huaibin; Yu, Huibin; Pan, Hongwei; Gao, Hongjie

2018-05-01

UV-visible absorption spectroscopy combined with principal component analysis (PCA) and two-dimensional correlation (2D correlation) is used to trace components of dissolved organic matter (DOM) extracted from soils in a larger estuarine delta and to investigate spatial variations of DOM fractions. Soil samples of different depths were collected from native halophyte soils along a saline gradient, i.e., Suaeda salsa Comm. (SSC), Chenopodium album Comm. (CAC), Phragmites australis Comm. (PAC), and Artemisia selengensis Comm. (ASC). Molecular weights of DOM within the SSC soil profile were the lowest, followed by the CAC, PAC, and ASC soil profiles. Humification degree of DOM within the ASC soil profile was the highest, followed by the PAC, SSC, and CAC soil profiles. DOM within the soil profiles mainly contained phenolic, carboxylic, microbial products, and aromatic and alkyl groups through the PCA, which presented the significant differentiation among the four native halophyte soil profiles. The 2D UV correlation spectra of DOM within the SSC soil profile indicated that the variations of the phenolic groups were the largest, followed by the carboxylic groups, microbial products, and humified organic materials according to the band changing order of 285 → 365 → 425 → 520 nm. The 2D UV correlation spectra of DOM within the CAC soil profiles determined that the decreasing order of the variations was phenolic groups > carboxylic groups > microbial products according the band changing order of 285 → 365 → 425 nm. The 2D UV correlation spectra of DOM within the PAC soil profile proved that the variations of the phenolic groups were larger than those of the carboxylic groups according to the band changing order of 285 → 365 nm. The 2D UV correlation spectra of DOM within the ASC soil profile demonstrated that the variations of the phenolic groups were larger than those of the other DOM fractions according to the broad cross-peak at 285/365-700 nm.

Reducement of cadmium adsorption on clay minerals by the presence of dissolved organic matter from animal manure.

PubMed

Zhou, Wenjun; Ren, Lingwei; Zhu, Lizhong

2017-04-01

Clay minerals are the most popular adsorbents/amendments for immobilizing heavy metals in contaminated soils, but the dissolved organic matter (DOM) in soil environment would potentially affect the adsorption/immobilization capacity of clay minerals for heavy metals. In this study, the effects of DOM derived from chicken manure (CM) on the adsorption of cadmium (Cd 2+ ) on two clay minerals, bentonite and zeolite, were investigated. The equilibrium data for Cd 2+ sorption in the absence or presence of CM-DOM could be well-fitted to the Langmuir equation (R 2  > 0.97). The presence of CM-DOM in the aqueous solution was found to greatly reduce the adsorption capacity of both minerals for Cd 2+ , in particular zeolite, and the percentage decreases for Cd 2+ sorption increased with increasing concentrations of Cd 2+ as well as CM-DOM in aqueous solutions. The adsorption of CM-DOM on zeolite was greater than that on bentonite in the absence of Cd 2+ , however, a sharp increase was observed for CM-DOM sorption on bentonite with increasing Cd 2+ concentrations but little change for that on zeolite, which can be attributed to the different ternary structures on mineral surface. The CM-DOM modified clay minerals were utilized to investigate the effect of mineral-adsorbed CM-DOM on Cd 2+ sorption. The adsorbed form was found to inhibit Cd 2+ sorption, and further calculation suggested it primarily responsible for the overall decrease in Cd 2+ sorption on clay minerals in the presence of CM-DOM in aqueous solutions. An investigation for the mineral surface morphology suggested that the mineral-adsorbed CM-DOM decreased Cd 2+ sorption on bentonite mainly through barrier effect, while in the case of zeolite, it was the combination of active sites occupation and barrier effect. These results can serve as a guide for evaluating the performance of clay minerals in immobilizing heavy metals when animal manure is present in contaminated soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Evolution of Dissolved Organic Matter Properties in a Constructed Wetland of Xiao River, Hebei].

PubMed

Ma, Li-na; Zhang, Hui; Tan, Wen-bing; Yu, Min-da; Huang, Zhi-gang; Gao, Ru-tai; Xi, Bei-dou; He, Xiao-song

2016-01-01

The evolution of water DOC and COD, and the source, chemical structure, humification degree and redox of dissolved organic matter (DOM) in a constructed wetland of Xiao River, Hebei, was investigated by 3D excitation--emission matrix fluorescence spectroscopy coupled with ultraviolet spectroscopy and chemical reduction, in order to explore the geochemical processes and environmental effects of DOM. Although DOC contributes at least 60% to COD, its decrease in the constructed wetland is mainly caused by the more extensive degradation of elements N, H, S, and P than C in DOM, and 65% is contributed from the former. DOM is mainly consisted of microbial products based on proxies f470/520 and BIX, indicating that DOM in water is apparently affected by microbial degradation. The result based on PARAFAC model shows that DOM in the constructed wetland contains protein-like and humus-like components, and Fulvic- and humic-like components are relatively easier to degrade than protein-like components. Fulvic- and humic-like components undergo similar decomposition in the constructed wetland. A common source of chromophoric dissolved organic matter (CDOM) and fluorescent dissolved organic matter (FDOM) exists; both CDOM and FDOM are mainly composed of a humus-like material and do not exhibit selective degradation in the constructed wetland. The proxies E2 /E3, A240-400, r(A, C) and HIX in water have no changes after flowing into the constructed wetland, implying that the humification degree of DOM in water is hardly affected by wet constructed wetland. However, the constructed wetland environment is not only beneficial in forming the reduced state of DOM, but also facilitates the reduction of ferric. It can also improve the capability of DOM to function as an electron shuttle. This result may be related to the condition that the aromatic carbon of DOM can be stabilized well in the constructed wetland.

Spatiotemporal variations in the abundance and composition of bulk and chromophoric dissolved organic matter in seasonally hypoxia-influenced Green Bay, Lake Michigan, USA.

PubMed

DeVilbiss, Stephen E; Zhou, Zhengzhen; Klump, J Val; Guo, Laodong

2016-09-15

Green Bay, Lake Michigan, USA, is the largest freshwater estuary in the Laurentian Great Lakes and receives disproportional terrestrial inputs as a result of a high watershed to bay surface area ratio. While seasonal hypoxia and the formation of "dead zones" in Green Bay have received increasing attention, there are no systematic studies on the dynamics of dissolved organic matter (DOM) and its linkage to the development of hypoxia. During summer 2014, bulk dissolved organic carbon (DOC) analysis, UV-vis spectroscopy, and fluorescence excitation-emission matrices (EEMs) coupled with PARAFAC analysis were used to quantify the abundance, composition and source of DOM and their spatiotemporal variations in Green Bay, Lake Michigan. Concentrations of DOC ranged from 202 to 571μM-C (average=361±73μM-C) in June and from 279 to 610μM-C (average=349±64μM-C) in August. In both months, absorption coefficient at 254nm (a254) was strongly correlated to bulk DOC and was most abundant in the Fox River, attesting a dominant terrestrial input. Non-chromophoric DOC comprised, on average, ~32% of bulk DOC in June with higher terrestrial DOM and ~47% in August with higher aquagenic DOM, indicating that autochthonous and more degraded DOM is of lower optical activity. PARAFAC modeling on EEM data resulted in four major fluorescent DOM components, including two terrestrial humic-like, one aquagenic humic-like, and one protein-like component. Variations in the abundance of DOM components further supported changes in DOM sources. Mixing behavior of DOM components also indicated that while bulk DOM behaved quasi-conservatively, significant compositional changes occurred during transport from the Fox River to the open bay. Copyright © 2016 Elsevier B.V. All rights reserved.

The composition and character of DOM from an upland peat catchment - sources, roles and fate

NASA Astrophysics Data System (ADS)

Worrall, F.; Moody, C.; Clay, G.; Boothroyd, I.; Burt, T. P.

2017-12-01

The fluvial fluxes of dissolved organic carbon (DOC) from peatlands form an important part of that ecosystem's carbon cycle, contributing approximately 35% of the overall peatland carbon budget. The source, role and fate of this component of the carbon cycle was explored for a peat covered catchment in the north east of England with dissolved organic matter (DOM) being sampled from both a first-order peat-hosted stream and soil water at two depths within the peat profile. All DOM samples were analysed within the context of analysing the particulate organic matter (POM) from the catchment; the peat profile; and biomass. All samples were analysed using: elemental analysis (C, H, N, O, P and S); bomb calorimetry; thermogravimetric analysis (TGA); 13C solid state NMR; and S isotopes. Furthermore, the degradation of fresh DOC was examined over periods of 70 hours every month for 23 months. The analysis has shown that: DOM is highly oxidised compared to all other organic in the ecosystem and DOM did not exist until [C]/[O] < 1.44. The DOM was dominantly the product of lignin breakdown and not the processing of proteins or carbohydrates, i.e. it was not an intermediate of oxidation to CO2. DOM could only be sourced from high in the peat profile at most above 41 cm depth. Thermodynamic inhibition shows that only DOM from the surface layers could be reactive in the catotelmic layers of the peat. There was a significant role for the composition of the DOM in controlling degradation with degradation rates significantly increasing with the proportion of aldehyde and carboxylic acid functional groups but decreasing with the proportion of N-alkyl functional groups. The study meant that is was possible to consider the behaviour of DOM in terms of its thermodynamic properties (DH, DS & DG) for both formation and reaction.

Pain-evoked trunk muscle activity changes during fatigue and DOMS.

PubMed

Larsen, L H; Hirata, R P; Graven-Nielsen, T

2017-05-01

Muscle pain may reorganize trunk muscle activity but interactions with exercise-related muscle fatigue and delayed onset muscle soreness (DOMS) is to be clarified. In 19 healthy participants, the trunk muscle activity during 20 multi-directional unpredictable surface perturbations were recorded after bilateral isotonic saline injections (control) and during unilateral and bilateral hypertonic saline-induced low back pain (LBP) in conditions of back muscle fatigue (Day-1) and DOMS (Day-2). Pain intensity and distribution were assessed by visual analogue scale (VAS) scores and pain drawings. The degree of fatigue and DOMS were assessed by Likert scale scores. Root-mean-square electromyographic (RMS-EMG) signals were recorded post-perturbation from six bilateral trunk muscles and the difference from baseline conditions (Delta-RMS-EMG) was extracted and averaged across abdominal and back muscles. In DOMS, peak VAS scores were higher during bilateral control and bilateral saline-induced pain than fatigue (p < 0.001) and during bilateral compared with unilateral pain (p < 0.001). The saline-induced pain areas were larger during DOMS than fatigue (p < 0.01). In response to surface perturbations during fatigue and DOMS, the back muscle Delta-RMS-EMG increased during bilateral compared with unilateral pain and control injections (p < 0.001) and decreased during unilateral pain compared with control injections (p < 0.04). In DOMS compared with fatigue, the post-perturbation Delta-RMS-EMG in back muscles was higher during bilateral pain and lower during unilateral pain (p < 0.001). The abdominal Delta-RMS-EMG was not significantly affected. Facilitated and attenuated back muscle responses to surface perturbations in bilateral and unilateral LBP, respectively, was more expressed during exercise-induced back muscle soreness compared with fatigue. Back muscle activity decreased during unilateral and increased during bilateral pain after unpredictable surface perturbations during muscle fatigue and DOMS. Accumulation effects of DOMS on pain intensity and spreading and trunk muscle activity after pain-induction. © 2017 European Pain Federation - EFIC®.

Testing the application of Teflon/quartz soil solution samplers for DOM sampling in the Critical Zone: Field and laboratory approaches

NASA Astrophysics Data System (ADS)

Dolan, E. M.; Perdrial, J. N.; Vazquez, A.; Hernández, S.; Chorover, J.

2010-12-01

Elizabeth Dolan1,2, Julia Perdrial3, Angélica Vázquez-Ortega3, Selene Hernández-Ruiz3, Jon Chorover3 1Deptartment of Soil, Environmental, and Atmospheric Science, University of Missouri. 2Biosphere 2, University of Arizona. 3Deptartment of Soil, Water, and Environmental Science, University of Arizona. Abstract: The behavior of dissolved organic matter (DOM) in soil is important to many biogeochemical processes. Extraction methods to obtain DOM from the unsaturated zone remain a current focus of research as different methods can influence the type and concentration of DOM obtained. Thus, the present comparison study involves three methods for soil solution sampling to assess their impact on DOM quantity and quality: 1) aqueous soil extracts, 2) solution yielded from laboratory installed suction cup samplers and 3) solutions from field installed suction cup samplers. All samples were analyzed for dissolved organic carbon and total nitrogen concentrations. Moreover, DOM quality was analyzed using fluorescence, UV-Vis and FTIR spectroscopies. Results indicate higher DOC values for laboratory extracted DOM: 20 mg/L for aqueous soil extracts and 31 mg/L for lab installed samplers compared to 12 mg/L for field installed samplers. Large variations in C/N ratios were also observed ranging from 1.5 in laboratory extracted DOM to 11 in field samples. Fluorescence excitation-emission matrices of DOM solutions obtained for the laboratory extraction methods showed higher intensities in regions typical for fulvic and humic acid-like materials relative to those extracted in the field. Similarly, the molar absorptivity calculated from DOC concentration normalization of UV-Vis absorbance of the laboratory-derived solutions was significantly higher as well, indicating greater aromaticity. The observed differences can be attributed to soil disturbance associated with obtaining laboratory derived solution samples. Our results indicate that laboratory extraction methods are not comparable to in-situ field soil solution extraction in terms of DOM.

Domesticated, Genetically Engineered, and Wild Plant Relatives Exhibit Unintended Phenotypic Differences: A Comparative Meta-Analysis Profiling Rice, Canola, Maize, Sunflower, and Pumpkin

PubMed Central

Hernández-Terán, Alejandra; Wegier, Ana; Benítez, Mariana; Lira, Rafael; Escalante, Ana E.

2017-01-01

Agronomic management of plants is a powerful evolutionary force acting on their populations. The management of cultivated plants is carried out by the traditional process of human selection or plant breeding and, more recently, by the technologies used in genetic engineering (GE). Even though crop modification through GE is aimed at specific traits, it is possible that other non-target traits can be affected by genetic modification due to the complex regulatory processes of plant metabolism and development. In this study, we conducted a meta-analysis profiling the phenotypic consequences of plant breeding and GE, and compared modified cultivars with wild relatives in five crops of global economic and cultural importance: rice, maize, canola, sunflower, and pumpkin. For these five species, we analyzed the literature with documentation of phenotypic traits that are potentially related to fitness for the same species in comparable conditions. The information was analyzed to evaluate whether the different processes of modification had influenced the phenotype in such a way as to cause statistical differences in the state of specific phenotypic traits or grouping of the organisms depending on their genetic origin [wild, domesticated with genetic engineering (domGE), and domesticated without genetic engineering (domNGE)]. In addition, we tested the hypothesis that, given that transgenic plants are a construct designed to impact, in many cases, a single trait of the plant (e.g., lepidopteran resistance), the phenotypic differences between domGE and domNGE would be either less (or inexistent) than between the wild and domesticated relatives (either domGE or domNGE). We conclude that (1) genetic modification (either by selective breeding or GE) can be traced phenotypically when comparing wild relatives with their domesticated relatives (domGE and domNGE) and (2) the existence and the magnitude of the phenotypic differences between domGE and domNGE of the same crop suggest consequences of genetic modification beyond the target trait(s). PMID:29259610

Analysing Submarine Groundwater Discharge (SGD)-borne Dissolved Organic Matter (DOM) in a karstic aquifer, Co. Galway, Ireland.

NASA Astrophysics Data System (ADS)

Kelly, Tara; Rocha, Carlos

2014-05-01

Submarine Groundwater Discharge (SGD) constitutes an "invisible" link between land and sea, transporting allochthonous and autochthonous dissolved organic matter (DOM), nutrients and metals to the ocean via the subterranean estuary. The latter acts as a powerful bioreactor where groundwater, in transit from land to sea, mixes with seawater leading to active modulation of both DOM content and chemical makeup of SGD. DOM in freshwater systems is a key component of the global carbon cycle. Climate change may hence increase the concentration of allochthonous carbon entering the oceans as terrestrial DOC is released from soils at higher temperatures, and transported via SGD. Presently, little is known about the effects of SGD-borne DOM on coastal carbon cycling. SGD therefore represents a dynamic reservoir and analysis is critical to forecast future environmental management programmes, both on a local and global scale. Labile DOM plays a crucial role in microbial remineralisation processes, and as it breaks down it contributes to the groundwater nutrient pool. Locally, this could add to eutrophication. However, if refractory carbon is present, it will be recalcitrant to mineralisation in transit and at the subterranean estuary. This putative additional input will thus imply the contribution of SGD to oceanic carbon storage. This study is focused on Kinvara Bay (Galway, western Ireland), the focal point for waters discharging from the Gort-Kinvara karstic aquifer. This aquifer represents the ideal study location for evaluation of SGD contribution to the coastal DOM pool, as SGD is focused in the bay, surface drainage is very limited, and groundwater travels across a large catchment area with a short residence time, minimising DOM modification in transit. DOM samples collected in the field have been analysed using Three-Dimensional Excitation Emission Matrix Fluorescence (3D-EEMF) and High Temperature Catalytic Oxidation. PARAFAC is subsequently used as a tool to elucidate the types, sources (marine vs terrigeneous) and fractional composition of DOM, both in SGD plumes and in surface waters.

After the flood: consistency in DOM response to the 2010/2011 Australian floods

NASA Astrophysics Data System (ADS)

Shutova, Y.; Baker, A.; Bridgeman, J.; Henderson, R.

2014-12-01

The 2010/2011 floods in Eastern Australia were one of the worst on record, causing more than one billion AUD of damages and killing 35 people. This field campaign, monitoring raw water DOM concentration and character on three contrasting rivers across the region captured the late recession curve (October 2011- September 2012). DOM was characterized using fluorescence excitation-emission matrix (EEM) spectra with PARAFAC analysis; δ 13C-DOC; and molecular size using liquid chromatography with organic carbon, UV254 and nitrogen detection (LC-OCD) to identify DOC fractions: biopolymers, humic substance (HS), building blocks (BB), low molecular weight acids, and low molecular weight neutrals. Despite the difference in catchment and climatic zones, similar trends were observed in all three rivers, where DOC concentrations gradually decreased in river streams over a year from 8-11 mgCL-1 to 3-4 mgCL-1, followed by similar changes of HS, BB and fluorescent terrestrially delivered DOM components (C1-C3). In Allyn and Patterson rivers the proportion of HS, fluorescent terrestrially delivered DOM components (C1, C2) in DOC have decreased, in contrast to Logan River, where the ratio of HS/DOC was highly variable and showed no particular trends. The proportion of other DOC components remained almost the same. Molecular weight of the HS declined from 700 gmol-1 to 610 gmol-1 in all sites. δ 13C-DOC increased during monitoring, this could be linked to general decrease of DOM proportion delivered from C4 type plants after the flood. Overall, although DOC concentration decreased over the year post flood at all sites, most importantly the composition of DOM changed, with major changes occurring in proportion of humic-like and fluorescent terrestrially delivered DOM. Therefore it is important to monitor DOM character to be able to assess the impact of climate change and extreme weather events on the DOM transport and transformation.

Cascading influence of inorganic nitrogen sources on DOM production, composition, lability and microbial community structure in the open ocean.

PubMed

Goldberg, S J; Nelson, C E; Viviani, D A; Shulse, C N; Church, M J

2017-09-01

Nitrogen frequently limits oceanic photosynthesis and the availability of inorganic nitrogen sources in the surface oceans is shifting with global change. We evaluated the potential for abrupt increases in inorganic N sources to induce cascading effects on dissolved organic matter (DOM) and microbial communities in the surface ocean. We collected water from 5 m depth in the central North Pacific and amended duplicate 20 liter polycarbonate carboys with nitrate or ammonium, tracking planktonic carbon fixation, DOM production, DOM composition and microbial community structure responses over 1 week relative to controls. Both nitrogen sources stimulated bulk phytoplankton, bacterial and DOM production and enriched Synechococcus and Flavobacteriaceae; ammonium enriched for oligotrophic Actinobacteria OM1 and Gammaproteobacteria KI89A clades while nitrate enriched Gammaproteobacteria SAR86, SAR92 and OM60 clades. DOM resulting from both N enrichments was more labile and stimulated growth of copiotrophic Gammaproteobacteria (Alteromonadaceae and Oceanospirillaceae) and Alphaproteobacteria (Rhodobacteraceae and Hyphomonadaceae) in weeklong dark incubations relative to controls. Our study illustrates how nitrogen pulses may have direct and cascading effects on DOM composition and microbial community dynamics in the open ocean. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Properties and evolution of dissolved organic matter during co-composting of dairy manure and Chinese herbal residues.

PubMed

Li, Qunliang; Lu, Yanyu; Guo, Xiaobo; Shan, Guangchun; Huang, Junhao

2017-03-01

Composting is an effective method in treating solid organic wastes, in which dissolved organic matter (DOM) plays an important role in transformation of organic matter and microbial activity. Therefore, an understanding of the properties and evolution of DOM during composting is crucial. In this study, DOM was studied using elemental analysis, spectroscopic analysis (UV-vis, FTIR, and pyrolysis-GC/MS), and colloidal analysis during a 120-day composting. Results showed that the content of N and O in DOM increased while C and H content declined progressively over the composting time. Aliphatic C-H stretching, aromatic C=C or C=O stretching of amide groups, and C-O stretch (carbohydrates) showed an obvious decrease, while COO- and C-N groups had a significant increase. The evolution of DOM indicated a gradual decrease of the lipid and polysaccharide fractions, whereas an increase of aromatic and nitrogenous compounds was observed. The DOM also showed a more stable status, and an accumulation of small molecular compounds occurred with composting proceeded. Taken together, these results shed a good insight into the properties and evolution of DOM during a composting process.

Optical properties of dissolved organic matter (DOM): Effects of biological and photolytic degradation

USGS Publications Warehouse

Hansen, Angela; Kraus, Tamara; Pellerin, Brian; Fleck, Jacob; Downing, Bryan D.; Bergamaschi, Brian

2016-01-01

Advances in spectroscopic techniques have led to an increase in the use of optical properties (absorbance and fluorescence) to assess dissolved organic matter (DOM) composition and infer sources and processing. However, little information is available to assess the impact of biological and photolytic processing on the optical properties of original DOM source materials. We measured changes in commonly used optical properties and indices in DOM leached from peat soil, plants, and algae following biological and photochemical degradation to determine whether they provide unique signatures that can be linked to original DOM source. Changes in individual optical parameters varied by source material and process, with biodegradation and photodegradation often causing values to shift in opposite directions. Although values for different source materials overlapped at the end of the 111-day lab experiment, multivariate statistical analyses showed that unique optical signatures could be linked to original DOM source material even after degradation, with 17 optical properties determined by discriminant analysis to be significant (p<0.05) in distinguishing between DOM source and environmental processing. These results demonstrate that inferring the source material from optical properties is possible when parameters are evaluated in combination even after extensive biological and photochemical alteration.

Characterization of dissolved organic matter in Dongjianghu Lake by UV-visible absorption spectroscopy with multivariate analysis.

PubMed

Zhu, Yanzhong; Song, Yonghui; Yu, Huibin; Liu, Ruixia; Liu, Lusan; Lv, Chunjian

2017-08-08

UV-visible absorption spectroscopy coupled with principal component analysis (PCA) and hierarchical cluster analysis (HCA) was applied to characterize spectroscopic components, detect latent factors, and investigate spatial variations of dissolved organic matter (DOM) in a large-scale lake. Twelve surface water samples were collected from Dongjianghu Lake in China. DOM contained lignin and quinine moieties, carboxylic acid, microbial products, and aromatic and alkyl groups, which in the northern part of the lake was largely different from the southern part. Fifteen spectroscopic indices were deduced from the absorption spectra to indicate molecular weight or humification degree of DOM. The northern part of the lake presented the smaller molecular weight or the lower humification degree of DOM than the southern part. E 2/4 , E 3/4 , E 2/3 , and S 2 were latent factors of characterizing the molecular weight of DOM, while E 2/5 , E 3/5 , E 2/6 , E 4/5 , E 3/6 , and A 2/1 were latent factors of evaluating the humification degree of DOM. The UV-visible absorption spectroscopy combined with PCA and HCA may not only characterize DOM fractions of lakes, but may be transferred to other types of waterscape.

The Influences of Dissolved Organic Matter on Mercury Biogeochemistry in Mesocosm Experiments in the Florida Everglades

NASA Astrophysics Data System (ADS)

Aiken, G. R.; Gilmour, C. A.; Krabbenhoft, D. P.; Orem, W.

2007-12-01

Interactions of mercury (Hg) with dissolved organic matter (DOM) play important roles in controlling reactivity, bioavailability and transport of Hg in aquatic systems. Laboratory experiments using a variety of organic matter isolates from surface waters in the Florida Everglades indicate that DOM binds Hg very strongly and is the dominant ligand for Hg in the absence of sulfide. These experiments have also shown that the presence of DOM influences the geochemical behavior of cinnabar (HgS) through the stabilization of nanocolloidal HgS resulting in relatively high Hg concentrations under supersaturated conditions with respect to HgS, a common condition in waters containing measurable sulfide concentrations. In this paper, the results of in-situ mesocosm experiments designed to directly measure the effects of DOM -Hg interactions on Hg biogeochemistry will be described. In these experiments, mesocosms (wetland enclosures), located in the central Everglades region of Water Conservation Area 3A (WCA 3A15), were amended with isotopically enriched Hg (200Hg, 202Hg), sulfate (SO4=) and the hydrophobic organic acid (HPOA) fraction of DOM from a site (F1) in the eutrophic northern Everglades. The use of stable isotope spikes in these studies allowed us to examine the delivery of Hg to surface soils (which are the predominant zones of methylation); partitioning of Hg and MeHg among phases (which impacts bioavailability); net MeHg production; loss of Hg and MeHg through photodemethylation, reduction and volatization; and bioaccumulation. The F1 HPOA isolate, obtained using XAD resins, was more aromatic, had a greater specific ultra-violet absorbance and had previously been shown to be more reactive with Hg than the DOM present at the 3A15 site. The F1 HPOA isolate formed strong DOM-Hg complexes (KDOM') = 1023.2 L kg-1 at pH = 7.0 and I = 0.1) and effectively inhibited the precipitation of HgS in laboratory experiments. Select mesocosms were amended with either F1-HPOA or SO4= resulting in a range of concentrations for each constituent. For the DOM amended mesocosms, DOC concentrations increased from 50-100% and the overall SUVA increased from 2.9 to 3.7 L mg C-1 m-1 relative to control mesocosms, indicating that both the concentration and overall reactivity of the DOM in the amended mesocosms had been altered substantially. In these mesocosms, the concentrations of both ambient and isotopically enriched dissolved Hg increased significantly compared to controls. Greater concentrations of both dissolved ambient and labeled methylmercury were also observed in the DOM amended mesocosms indicating that the added DOM increased Hg bioavailabilty of both Hg pools for methylation. In addition, DOM shielded Hg and MeHg from photodemethylation and volatilization, however, it inhibited subsequent MeHg bioaccumulation. Overall, the addition of DOM resulted in increased concentrations of labeled methylmercury comparable to those measured in mesocosms amended with SO4= suggesting that DOM is an important constituent influencing the methylation of Hg. This effect is likely due to increased concentrations of dissolved Hg in the DOM amended mesocosms.

Interactive Cohort Identification of Sleep Disorder Patients Using Natural Language Processing and i2b2.

PubMed

Chen, W; Kowatch, R; Lin, S; Splaingard, M; Huang, Y

2015-01-01

Nationwide Children's Hospital established an i2b2 (Informatics for Integrating Biology & the Bedside) application for sleep disorder cohort identification. Discrete data were gleaned from semistructured sleep study reports. The system showed to work more efficiently than the traditional manual chart review method, and it also enabled searching capabilities that were previously not possible. We report on the development and implementation of the sleep disorder i2b2 cohort identification system using natural language processing of semi-structured documents. We developed a natural language processing approach to automatically parse concepts and their values from semi-structured sleep study documents. Two parsers were developed: a regular expression parser for extracting numeric concepts and a NLP based tree parser for extracting textual concepts. Concepts were further organized into i2b2 ontologies based on document structures and in-domain knowledge. 26,550 concepts were extracted with 99% being textual concepts. 1.01 million facts were extracted from sleep study documents such as demographic information, sleep study lab results, medications, procedures, diagnoses, among others. The average accuracy of terminology parsing was over 83% when comparing against those by experts. The system is capable of capturing both standard and non-standard terminologies. The time for cohort identification has been reduced significantly from a few weeks to a few seconds. Natural language processing was shown to be powerful for quickly converting large amount of semi-structured or unstructured clinical data into discrete concepts, which in combination of intuitive domain specific ontologies, allows fast and effective interactive cohort identification through the i2b2 platform for research and clinical use.

Wh-filler-gap dependency formation guides reflexive antecedent search

PubMed Central

Frazier, Michael; Ackerman, Lauren; Baumann, Peter; Potter, David; Yoshida, Masaya

2015-01-01

Prior studies on online sentence processing have shown that the parser can resolve non-local dependencies rapidly and accurately. This study investigates the interaction between the processing of two such non-local dependencies: wh-filler-gap dependencies (WhFGD) and reflexive-antecedent dependencies. We show that reflexive-antecedent dependency resolution is sensitive to the presence of a WhFGD, and argue that the filler-gap dependency established by WhFGD resolution is selected online as the antecedent of a reflexive dependency. We investigate the processing of constructions like (1), where two NPs might be possible antecedents for the reflexive, namely which cowgirl and Mary. Even though Mary is linearly closer to the reflexive, the only grammatically licit antecedent for the reflexive is the more distant wh-NP, which cowgirl. (1). Which cowgirl did Mary expect to have injured herself due to negligence? Four eye-tracking text-reading experiments were conducted on examples like (1), differing in whether the embedded clause was non-finite (1 and 3) or finite (2 and 4), and in whether the tail of the wh-dependency intervened between the reflexive and its closest overt antecedent (1 and 2) or the wh-dependency was associated with a position earlier in the sentence (3 and 4). The results of Experiments 1 and 2 indicate the parser accesses the result of WhFGD formation during reflexive antecedent search. The resolution of a wh-dependency alters the representation that reflexive antecedent search operates over, allowing the grammatical but linearly distant antecedent to be accessed rapidly. In the absence of a long-distance WhFGD (Experiments 3 and 4), wh-NPs were not found to impact reading times of the reflexive, indicating that the parser's ability to select distant wh-NPs as reflexive antecedents crucially involves syntactic structure. PMID:26500579

Interactive Cohort Identification of Sleep Disorder Patients Using Natural Language Processing and i2b2

PubMed Central

Chen, W.; Kowatch, R.; Lin, S.; Splaingard, M.

2015-01-01

Summary Nationwide Children’s Hospital established an i2b2 (Informatics for Integrating Biology & the Bedside) application for sleep disorder cohort identification. Discrete data were gleaned from semistructured sleep study reports. The system showed to work more efficiently than the traditional manual chart review method, and it also enabled searching capabilities that were previously not possible. Objective We report on the development and implementation of the sleep disorder i2b2 cohort identification system using natural language processing of semi-structured documents. Methods We developed a natural language processing approach to automatically parse concepts and their values from semi-structured sleep study documents. Two parsers were developed: a regular expression parser for extracting numeric concepts and a NLP based tree parser for extracting textual concepts. Concepts were further organized into i2b2 ontologies based on document structures and in-domain knowledge. Results 26,550 concepts were extracted with 99% being textual concepts. 1.01 million facts were extracted from sleep study documents such as demographic information, sleep study lab results, medications, procedures, diagnoses, among others. The average accuracy of terminology parsing was over 83% when comparing against those by experts. The system is capable of capturing both standard and non-standard terminologies. The time for cohort identification has been reduced significantly from a few weeks to a few seconds. Conclusion Natural language processing was shown to be powerful for quickly converting large amount of semi-structured or unstructured clinical data into discrete concepts, which in combination of intuitive domain specific ontologies, allows fast and effective interactive cohort identification through the i2b2 platform for research and clinical use. PMID:26171080

The state and profile of open source software projects in health and medical informatics.

PubMed

Janamanchi, Balaji; Katsamakas, Evangelos; Raghupathi, Wullianallur; Gao, Wei

2009-07-01

Little has been published about the application profiles and development patterns of open source software (OSS) in health and medical informatics. This study explores these issues with an analysis of health and medical informatics related OSS projects on SourceForge, a large repository of open source projects. A search was conducted on the SourceForge website during the period from May 1 to 15, 2007, to identify health and medical informatics OSS projects. This search resulted in a sample of 174 projects. A Java-based parser was written to extract data for several of the key variables of each project. Several visually descriptive statistics were generated to analyze the profiles of the OSS projects. Many of the projects have sponsors, implying a growing interest in OSS among organizations. Sponsorship, we discovered, has a significant impact on project success metrics. Nearly two-thirds of the projects have a restrictive license type. Restrictive licensing may indicate tighter control over the development process. Our sample includes a wide range of projects that are at various stages of development (status). Projects targeted towards the advanced end user are primarily focused on bio-informatics, data formats, database and medical science applications. We conclude that there exists an active and thriving OSS development community that is focusing on health and medical informatics. A wide range of OSS applications are in development, from bio-informatics to hospital information systems. A profile of OSS in health and medical informatics emerges that is distinct and unique to the health care field. Future research can focus on OSS acceptance and diffusion and impact on cost, efficiency and quality of health care.

Photochemical Production of Singlet Oxygen from Dissolved Organic Matter in Ice.

PubMed

Fede, Alexis; Grannas, Amanda M

2015-11-03

Dissolved natural organic matter (DOM) is a ubiquitous component of natural waters and an important photosensitizer. A variety of reactive oxygen species (ROS) are known to be produced from DOM photochemistry, including singlet oxygen, 1O2. Recently, it has been determined that humic-like substances and unknown organic chromophores are significant contributors to sunlight absorption in snowpack; however, DOM photochemistry in snow/ice has received little attention in the literature. We recently showed that DOM plays an important role in indirect photolysis processes in ice, producing ROS and leading to the efficient photodegradation of a probe hydrophobic organic pollutant, aldrin.1 ROS scavenger experiments indicated that 1O2 played a significant role in the indirect photodegradation of aldrin. Here we quantitatively examine 1O2 photochemically produced from DOM in frozen and liquid aqueous solutions. Steady-state 1O2 production is enhanced up to nearly 1000 times in frozen DOM samples compared to liquid samples. 1O2 production is dependent on the concentration of DOM, but the nature of the DOM source (terrestrial vs microbial) does not have a significant effect on 1O2 production in liquid or frozen samples, with different source types producing similar steady-state concentrations of 1O2. The temperature of frozen samples also has a significant effect on steady-state 1O2 production in the range of 228-262 K, with colder samples producing more steady-state 1O2. The large enhancement in 1O2 in frozen samples suggests that it may play a significant role in the photochemical processes that occur in snow and ice, and DOM could be a significant, but to date poorly understood, oxidant source in snow and ice.

Spatial and Temporal Patterns of Dissolved Organic Matter Characteristics in the Upper Willamette River Basin, Oregon

NASA Astrophysics Data System (ADS)

Lee, B. S.; Lajtha, K.

2014-12-01

Dissolved organic matter (DOM) leaching through soil affects soil carbon sequestration and the carbon metabolism of receiving water bodies. Improving our understanding of the sources and fate of DOM at varying spatial and temporal patterns is crucial for land management decisions. However, little is known about how DOM sources change with land use types and seasonal flow patterns. In the Willamette River Basin (WRB), which is home to Oregon's major cities including Portland and Salem, forested headwaters transition to agricultural and urban land. The climate of WRB has a distinctive seasonal pattern with dry warm summers and wet winters driven by winter precipitation and snowmelt runoff between November and March. This study examined DOM fluorescence characteristic in stream water from 21 locations collected monthly and 16 locations collected seasonally to identify the sources and fate of DOM in the upper WRB in contrasting land uses. DOC and dissolved organic nitrogen concentrations increased as the flow rate increased during winter precipitation at all sites. This indicates that increased flow rate increased the connectivity between land and nearby water bodies. DOM fluorescent properties varied among land use types. During the first precipitation event after a long dry summer, a microbial DOM signature in agricultural areas increased along with nitrate concentrations. This may be because accumulated nutrients on land during the dry season flowed to nearby streams during the first rain event and promoted microbial growth in the streams. During the month of the highest flow rate in 2014, sampling sites near forest showed evidence of a greater terrestrial DOM signature compared to its signature during the dry season. This indicates fluorescent DOM characteristics in streams vary as the flow connectivity changes even within the same land type.

Molecular size-dependent abundance and composition of dissolved organic matter in river, lake and sea waters.

PubMed

Xu, Huacheng; Guo, Laodong

2017-06-15

Dissolved organic matter (DOM) is ubiquitous in natural waters. The ecological role and environmental fate of DOM are highly related to the chemical composition and size distribution. To evaluate size-dependent DOM quantity and quality, water samples were collected from river, lake, and coastal marine environments and size fractionated through a series of micro- and ultra-filtrations with different membranes having different pore-sizes/cutoffs, including 0.7, 0.4, and 0.2 μm and 100, 10, 3, and 1 kDa. Abundance of dissolved organic carbon, total carbohydrates, chromophoric and fluorescent components in the filtrates decreased consistently with decreasing filter/membrane cutoffs, but with a rapid decline when the filter cutoff reached 3 kDa, showing an evident size-dependent DOM abundance and composition. About 70% of carbohydrates and 90% of humic- and protein-like components were measured in the <3 kDa fraction in freshwater samples, but these percentages were higher in the seawater sample. Spectroscopic properties of DOM, such as specific ultraviolet absorbance, spectral slope, and biological and humification indices also varied significantly with membrane cutoffs. In addition, different ultrafiltration membranes with the same manufacture-rated cutoff also gave rise to different DOM retention efficiencies and thus different colloidal abundances and size spectra. Thus, the size-dependent DOM properties were related to both sample types and membranes used. Our results here provide not only baseline data for filter pore-size selection when exploring DOM ecological and environmental roles, but also new insights into better understanding the physical definition of DOM and its size continuum in quantity and quality in aquatic environments. Copyright © 2017 Elsevier Ltd. All rights reserved.

[The Influence of Runoff Pollution to DOM Features in an Urban Wastewater Treatment Plant].

PubMed

He, Li; Ji, Fang-ying; Lai, Ming-sheng; Xu, Xuan; Zhou, Wei-wei; Mao, Bo-lin; Yang, Ming-jia

2015-03-01

Combined with wastewater treatment process, the sewage in sunny and rainy day was collected from a wastewater treatment plant in Chongqing. Three-dimensional fluorescence spectra was used to investigate the characteristic fluorescence of dissolved organic matter (DOM). DOM dissolved organic carbon (DOC), chemical oxygen demand (COD), fluorescence index (ƒ450/500) and fluorescence intensity ratio γ (A, C) of fulvic acid in ultraviolet and visible region were used to analyze the impact of rain runoff pollution on sewage DOM. According to the experimental data, the DOM fluorescence fingerprints of this wastewater treatment plant were quite different from typical municipal sewage, and the main component was tryptophan with low excitation wavelength (Peak S), then the tryptophan with long wavelength excitation (Peak T) followed. A2/O process had an approximative degradation of the protein-like both in sunny day and rainy day, but had a better degradation of fulvic-like, DOC and COD in rainy day than that in sunny day. Morever, the fluorescence peaks got red-shifted after the biological treatment. The differences of DOM fluorescence fingerprint between sunny and rainy day were significant, the fluorescence center of UV fulvic (Peak A) in rainy day getting blue-shifted obviously, shifting from 240 - 248/390 - 440 to 240 - 250/370 - 400 nm. Although the DOM types in sunny and rainy day were the same, the source of fulvic got more complex by runoff and the component ratio of DOM also changed. Compared with the sunny day, the proportion of Peak S in DOM dereased by 10%, and the proportion of Peak A increased by 7% in rainy day.

Cation-induced coagulation of aquatic plant-derived dissolved organic matter: Investigation by EEM-PARAFAC and FT-IR spectroscopy.

PubMed

Liu, Shasha; Zhu, Yuanrong; Liu, Leizhen; He, Zhongqi; Giesy, John P; Bai, Yingchen; Sun, Fuhong; Wu, Fengchang

2018-03-01

Complexation and coagulation of plant-derived dissolved organic matter (DOM) by metal cations are important biogeochemical processes of organic matter in aquatic systems. Thus, coagulation and fractionation of DOM derived from aquatic plants by Ca(II), Al(III), and Fe(III) ions were investigated. Metal ion-induced removal of DOM was determined by analyzing dissolved organic carbon in supernatants after addition of these metal cations individually. After additions of metal ions, both dissolved and coagulated organic fractions were characterized by use of fluorescence excitation emission matrix-parallel factor (EEM-PARAFAC) analysis and Fourier transform infrared (FT-IR) spectroscopy. Addition of Ca(II), Fe(III) or Al(III) resulted in net removal of aquatic plant-derived DOM. Efficiencies of removal of DOM by Fe(III) or Al(III) were greater than that by Ca(II). However, capacities to remove plant-derived DOM by the three metals were less than which had been previously reported for humic materials. Molecular and structural features of plant-derived DOM fractions in associations with metal cations were characterized by changes in fluorescent components and infrared absorption peaks. Both aromatic and carboxylic-like organic matters could be removed by Ca(II), Al(III) or Fe(III) ions. Whereas organic matters containing amides were preferentially removed by Ca(II), and phenolic materials were selectively removed by Fe(III) or Al(III). These observations indicated that plant-derived DOM might have a long-lasting effect on water quality and organisms due to its poor coagulation with metal cations in aquatic ecosystems. Plant-derived DOM is of different character than natural organic matter and it is not advisable to attempt removal through addition of metal salts during treatment of sewage. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular fractionation of dissolved organic matter with metal salts.

PubMed

Riedel, Thomas; Biester, Harald; Dittmar, Thorsten

2012-04-17

Coagulation of dissolved organic matter (DOM) by hydrolyzing metals is an important environmental process with particular relevance, e.g., for the cycling of organic matter in metal-rich aquatic systems or the flocculation of organic matter in wastewater treatment plants. Often, a nonremovable fraction of DOM remains in solution even at low DOM/metal ratios. Because coagulation by metals results from interactions with functional groups, we hypothesize that noncoagulating fractions have a distinct molecular composition. To test the hypothesis, we analyzed peat-derived dissolved organic matter remaining in solution after mixing with salts of Ca, Al, and Fe using 15 T Electrospray Ionization Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (ESI-FT-ICR-MS). Addition of metals resulted in a net removal of DOM. Also a reduction of molecular diversity was observed, as the number of peaks from the ESI-FT-ICR-MS spectra decreased. At DOM/metal ratios of ∼9 Ca did not show any preference for distinct molecular fractions, while Fe and Al removed preferentially the most oxidized compounds (O/C ratio >0.4) of the peat leachate. Lowering DOM/metal ratios to ∼1 resulted in further removal of less oxidized as well as more aromatic compounds ("black carbon"). Molecular composition in the residual solution after coagulation was more saturated, less polar, and less oxidized compared to the original peat leachate and exhibited a surprising similarity with DOM of marine origin. By identifying more than 9200 molecular formulas we can show that structural properties (saturation and aromaticity) and oxygen content of individual DOM molecules play an important role in coagulation with metals. We conclude that polyvalent cations not only alter the net mobility but also the very molecular composition of DOM in aquatic environments.

Clearing the waters: Evaluating the need for site-specific field fluorescence corrections based on turbidity measurements

USGS Publications Warehouse

Saraceno, John F.; Shanley, James B.; Downing, Bryan D.; Pellerin, Brian A.

2017-01-01

In situ fluorescent dissolved organic matter (fDOM) measurements have gained increasing popularity as a proxy for dissolved organic carbon (DOC) concentrations in streams. One challenge to accurate fDOM measurements in many streams is light attenuation due to suspended particles. Downing et al. (2012) evaluated the need for corrections to compensate for particle interference on fDOM measurements using a single sediment standard in a laboratory study. The application of those results to a large river improved unfiltered field fDOM accuracy. We tested the same correction equation in a headwater tropical stream and found that it overcompensated fDOM when turbidity exceeded ∼300 formazin nephelometric units (FNU). Therefore, we developed a site-specific, field-based fDOM correction equation through paired in situ fDOM measurements of filtered and unfiltered streamwater. The site-specific correction increased fDOM accuracy up to a turbidity as high as 700 FNU, the maximum observed in this study. The difference in performance between the laboratory-based correction equation of Downing et al. (2012) and our site-specific, field-based correction equation likely arises from differences in particle size distribution between the sediment standard used in the lab (silt) and that observed in our study (fine to medium sand), particularly during high flows. Therefore, a particle interference correction equation based on a single sediment type may not be ideal when field sediment size is significantly different. Given that field fDOM corrections for particle interference under turbid conditions are a critical component in generating accurate DOC estimates, we describe a way to develop site-specific corrections.

Photochemical behavior of dissolved and colloidal organic matter in estuarine and oceanic waters.

PubMed

Zhu, Wen-Zhuo; Yang, Gui-Peng; Zhang, Hong-Hai

2017-12-31

Chromophoric dissolved organic matter (CDOM), carbohydrates, and amino acids were analyzed to investigate the photochemistry of total dissolved (<0.22μm) organic matter (DOM), high-molecular-weight (HMW, 1kDa-0.22μm) DOM and low-molecular-weight (LMW, <1kDa) DOM at stations in the Yangtze River and its coastal area, and in the Western Pacific Ocean. Results revealed that the humic-like and tryptophan-like CDOM fluorescent components in riverine, coastal, and oceanic surface waters were photodegraded during irradiation. However, the photochemical behavior of tyrosine-like component was obscured by the excessive fluorescence intensities of humic- and tryptophan-like fluorescent components. Light sensitivity varied depending on the source material; terrestrially derived DOM was more susceptible to irradiation than autochthonous DOM. In contrast to the expected photodegradation of CDOM, photo-induced synthetic reaction transformed the LMW matters to polysaccharides (PCHO) and degradation reaction decomposed the HMW DOM to Monosaccharides. Colloidal DOM preferentially underwent photodegradation, whereas permeate DOM mainly photosynthesized PCHO. The total hydrolysable amino acid (THAA) pool changed because of the additional input by the photodegradation of DOM or THAA itself. The compositions of THAA changed during the irradiation experiments, indicating that the different photochemical behavior of individual amino acids were related to their different original photoreactivities; the relatively stable amino acids (e.g., Ser and Gly) significantly accumulated during irradiation, whereas photo-active aromatic amino acids (e.g. Tyr and His) were prone to photodegradation. The data presented here demonstrated that irradiation significantly influence the conversion between dissolved and colloid organic matter. These results can promote the understanding of irradiation effect on the carbon and nitrogen cycle in riverine, estuarine and oceanic ecosystems. Copyright © 2017 Elsevier B.V. All rights reserved.

Dissolved organic matter in the unsaturated zone: the view from the cave

NASA Astrophysics Data System (ADS)

Baker, A.; Duan, W.; Rutlidge, H.; McDonough, L.; Oudone, P.; Meredith, K.; Andersen, M. S.; O'Carroll, D. M.; Coleborn, K.; Treble, P. C.

2017-12-01

Soil organic matter content is typically a few percent of the total soil composition. Diffuse recharge can mobilise some of this soil-derived organic matter. While soil pore water dissolved organic matter (DOM) concentrations are up to 100 ppm, the resulting groundwater dissolved organic matter concentration is typically less than 2ppm. Dissolved organic matter transported from the soil can be both biodegraded and sorbed to minerals, and the relative importance of these two processes in the unsaturated zone is poorly understood. Caves in karstified limestone uniquely provide direct access to water percolating from the soil to the groundwater. Cave percolation waters can be analysed for their DOM concentration and character. This provides insights into the extent and type of biological and chemical processing of DOM during transport from the soil to the groundwater. We determine the concentration and characteristics of DOM in cave percolation waters using liquid chromatography (LC-OCD) and optical spectrophotometry (fluorescence and absorbance). We sample DOM from multiple caves in SE Australia (Cathedral Cave, Wellington; South Glory and Harrie Wood Caves, Yarrangobilly), permitting comparison of unsaturated zone DOM properties at different depths (up to 30m below land surface) and different climate zones (montane and temperate). We use caves with long-term hydrological monitoring programs so that DOM in waters of contrasting residence times can be compared. Additionally, we compare these cave percolation water DOM characteristics to those from local and regional groundwater, sampled from nearby wells. Our results will help improve our understanding of how DOM is processed from soil to groundwater, and is also relevant to speleothem scientists interested in using organic matter preserved in speleothems as a paleoclimate or paleoenvironmental proxy.

Constants for mercury binding by organic matter isolates from the Florida Everglades

USGS Publications Warehouse

Benoit, J.M.; Mason, R.P.; Gilmour, C.C.; Aiken, G.R.

2001-01-01

Dissolved organic matter (DOM) has been implicated as an important complexing agent for Hg that can affect its mobility and bioavailability in aquatic ecosystems. However, binding constants for natural Hg-DOM complexes are not well known. We employed a competitive ligand approach to estimate conditional stability constants for Hg complexes with DOM isolates collected from Florida Everglades surface waters. The isolates examined were the hydrophobic fraction of DOM from a eutrophic, sulfidic site (F1-HPoA) and the hydrophilic fraction from an oligotrophic, low-sulfide site (2BS-HPiA). Our experimental determinations utilized overall octanol-water partitioning coefficients (Dow) for 203Hg at 0.01 M chloride and across pH and DOM concentration gradients. Use of this radioisotope allowed rapid determinations of Hg concentrations in both water and octanol phases without problems of matrix interference. Conditional stability constants (1 = 0.06, 23??C) were log K??? = 11.8 for F1-HPoA and log K' = 10.6 for 2BS-HPiA. These are similar to previously published stability constants for Hg binding to low-molecular-weight thiols. Further, F1-HPoA showed a pH-dependent decline in Dow that was consistent with models of Hg complexation with thiol groups as the dominant Hg binding sites in DOM. These experiments demonstrate that the DOM isolates are stronger ligands for Hg than chloride ion or ethylenediamine-tetraacetic acid. Speciation calculations indicate that at the DOM concentrations frequently measured in Everglades, 20 to 40 ??M, significant complexation of Hg by DOM would be expected in aerobic (sulfide-free) surface waters. Copyright ?? 2001 Elsevier Science Ltd.

Source to sink characterization of dissolved organic matter in a tropical karst system

NASA Astrophysics Data System (ADS)

Lechleitner, Franziska; Lang, Susan Q.; McIntyre, Cameron; Baldini, James U. L.; Dittmar, Thorsten; Eglinton, Timothy I.

2016-04-01

Karst systems are widespread surface features present on all continents. They are characterized by complex hydrology with a multitude of possible flow regimes, from diffuse seepage through the host rock to fracture flow in larger conduits. As stalagmite proxy records are important indicators of past terrestrial climate conditions, detailed understanding of the biogeochemistry of cave systems and their relationships to the overlying karst network is crucial. Microbial communities that drive the carbon cycle in caves are nourished by dissolved organic matter (DOM) carried with water into the cave system. Water samples from the Yok Balum cave in Belize were collected for DOM analysis, including soil waters, drip waters and pool waters from inside the cave. Additionally, DOM extracts from a stalagmite from the same cave were analysed to examine DOM signatures and test their applicability for reconstruction of environmental conditions. Ultrahigh-resolution mass spectrometry (via the ESI-FT-ICR-MS technique) yielded detailed molecular fingerprints on DOM from these samples. Several thousand molecular formulae of DOM compounds were identified. In addition, radiocarbon analyses were performed on the DOM samples to gain information on karst turnover times. A principal component analysis of the molecular data revealed a clear gradient between soil waters and cave waters, as soil waters were enriched in highly unsaturated oxygen-rich compounds (typical for vascular plants), which were much less abundant in drip waters. Conversely, peptides, which can originate from bacterial processes, were present only in the drip waters. Our data clearly show connectivity between the cave and overlaying soils, and reworking of DOM by the cave bacterial community. Furthermore, we found molecular evidence for the selective removal of vascular plant-derived DOM in the caves, possibly due to abiotic interactions with minerals.

Assessing the utility of dissolved organic matter photoreactivity as a predictor of in situ methylmercury concentration.

PubMed

Klapstein, Sara J; Ziegler, Susan E; Risk, David A; O'Driscoll, Nelson J

2018-06-01

Methylmercury (MeHg) bioaccumulation is a growing concern in ecosystems worldwide. The absorption of solar radiation by dissolved organic matter (DOM) and other photoreactive ligands can convert MeHg into less toxic forms of mercury through photodemethylation. In this study, spectral changes and photoreactivity of DOM were measured to assess the potential to control photoreactions and predict in situ MeHg concentration. Water samples collected from a series of lakes in southwestern Nova Scotia in June, August, and September were exposed to controlled ultraviolet-A (UV-A) radiation for up to 24hr. Dissolved organic matter photoreactivity, measured as the loss of absorbance at 350nm at constant UV-A irradiation, was positively dependent on the initial DOM concentration in lake waters (r 2 =0.94). This relationship was consistent over time with both DOM concentration and photoreactivity increasing from summer into fall across lakes. Lake in situ MeHg concentration was positively correlated with DOM concentration and likely catchment transport in June (r=0.77) but not the other sampling months. Despite a consistent seasonal variation in both DOM and Fe, and their respective correlations with MeHg, no discernable seasonal trend in MeHg was observed. However, a 3-year dataset from the 6 study lakes revealed a positive correlation between DOM concentration and both Fe (r=0.91) and MeHg concentrations (r=0.51) suggesting a more dominant landscape mobility control on MeHg. The DOM-MeHg relationships observed in these lakes highlights the need to examine DOM photoreactivity controls on MeHg transport and availability in natural waters particularly given future climate perturbations. Copyright © 2018. Published by Elsevier B.V.

Hydrological changes of DOM composition and biodegradability of rivers in temperate monsoon climates

NASA Astrophysics Data System (ADS)

Shin, Yera; Lee, Eun-Ju; Jeon, Young-Joon; Hur, Jin; Oh, Neung-Hwan

2016-09-01

The spatial and hydrological dynamics of dissolved organic matter (DOM) composition and biodegradability were investigated for the five largest rivers in the Republic of Korea (South Korea) during the years 2012-2013 using incubation experiments and spectroscopic measurements, which included parallel factor analysis (PARAFAC). The lower reaches of the five rivers were selected as windows showing the integrated effects of basin biogeochemistry of different land use under Asian monsoon climates, providing an insight on consistency of DOM dynamics across multiple sites which could be difficult to obtain from a study on an individual river. The mean dissolved organic carbon (DOC) concentrations of the five rivers were relatively low, ranging from 1.4 to 3.4 mg L-1, due to the high slope and low percentage of wetland cover in the basin. Terrestrial humic- and fulvic-like components were dominant in all the rivers except for one, where protein-like compounds were up to ∼80%. However, terrestrial components became dominant in all five of the rivers after high precipitation during the summer monsoon season, indicating the strong role of hydrology on riverine DOM compositions for the basins under Asian monsoon climates. Considering that 64% of South Korea is forested, our results suggest that the forests could be a large source of riverine DOM, elevating the DOM loads during monsoon rainfall. Although more DOM was degraded when DOM input increased, regardless of its sources, the percent biodegradability was reduced with increased proportions of terrestrially derived aromatic compounds. The shift in DOM quality towards higher percentages of aromatic terrestrial compounds may alter the balance of the carbon cycle of coastal ecosystems by changing microbial metabolic processes if climate extremes such as heavy storms and typhoons become more frequent due to climate change.

Molecular alteration of marine dissolved organic matter under experimental hydrothermal conditions

NASA Astrophysics Data System (ADS)

Hawkes, Jeffrey A.; Hansen, Christian T.; Goldhammer, Tobias; Bach, Wolfgang; Dittmar, Thorsten

2016-02-01

Marine dissolved organic matter (DOM) is a large (660 Pg) pool of reduced carbon that is subject to thermal alteration in hydrothermal systems and sedimentary basins. In natural high-temperature hydrothermal systems, DOM is almost completely removed, but the mechanism and temperature dependence of this removal have not been studied to date. We investigated molecular-level changes to DOM that was solid-phase extracted (SPE-DOM) from the deep ocean of the North Pacific Ocean. This complex molecular mixture was experimentally exposed to temperatures between 100 and 380 °C over the course of two weeks in artificial seawater, and was then characterised on a molecular level via ultrahigh-resolution Fourier-transform ion cyclotron mass spectrometry (FT-ICR-MS). Almost 93% of SPE-DOM was removed by the treatment at 380 °C, and this removal was accompanied by a consistent pattern of SPE-DOM alteration across the temperatures studied. Higher molecular weight and more oxygen rich compounds were preferentially removed, suggesting that decarboxylation and dehydration of carboxylic acid and alcohol groups are the most rapid degradation mechanisms. Nitrogen containing compounds followed the same overall trends as those containing just C, H and O up to 300 °C. Above this temperature, the most highly altered samples contained very little of the original character of marine DOM, instead being mainly composed of very low intensity N- and S- containing molecules with a high H/C ratio (>1.5). Our results suggest that abiotic hydrothermal alteration of SPE-DOM may already occur at temperatures above 68 °C. Our experiments were conducted without a sedimentary or mineral phase, and demonstrate that profound molecular alteration and almost complete removal of marine SPE-DOM requires nothing more than heating in a seawater matrix.

Dissolution of cinnabar (HgS) in the presence of natural organic matter

USGS Publications Warehouse

Waples, J.S.; Nagy, K.L.; Aiken, G.R.; Ryan, J.N.

2005-01-01

Cinnabar (HgS) dissolution rates were measured in the presence of 12 different natural dissolved organic matter (DOM) isolates including humic, fulvic, and hydrophobic acid fractions. Initial dissolution rates varied by 1.3 orders of magnitude, from 2.31 ?? 10-13 to 7.16 ?? 10-12 mol Hg (mg C)-1 m-2 s-1. Rates correlate positively with three DOM characteristics: specific ultraviolet absorbance (R2 = 0.88), aromaticity (R2 = 0.80), and molecular weight (R2 = 0.76). Three experimental observations demonstrate that dissolution was controlled by the interaction of DOM with the cinnabar surface: (1) linear rates of Hg release with time, (2) significantly reduced rates when DOM was physically separated from the surface by dialysis membranes, and (3) rates that approached constant values at a specific ratio of DOM concentration to cinnabar surface area, suggesting a maximum surface coverage by dissolution-reactive DOM. Dissolution rates for the hydrophobic acid fractions correlate negatively with sorbed DOM concentrations, indicating the presence of a DOM component that reduced the surface area of cinnabar that can be dissolved. When two hydrophobic acid isolates that enhanced dissolution to different extents were mixed equally, a 20% reduction in rate occurred compared to the rate with the more dissolution-enhancing isolate alone. Rates in the presence of the more dissolution-enhancing isolate were reduced by as much as 60% when cinnabar was prereacted with the isolate that enhanced dissolution to a lesser extent. The data, taken together, imply that the property of DOM that enhances cinnabar dissolution is distinct from the property that causes it to sorb irreversibly to the cinnabar surface. Copyright ?? 2005 Elsevier Ltd.

Turnover time of fluorescent dissolved organic matter in the dark global ocean.

PubMed

Catalá, Teresa S; Reche, Isabel; Fuentes-Lema, Antonio; Romera-Castillo, Cristina; Nieto-Cid, Mar; Ortega-Retuerta, Eva; Calvo, Eva; Álvarez, Marta; Marrasé, Cèlia; Stedmon, Colin A; Álvarez-Salgado, X Antón

2015-01-29

Marine dissolved organic matter (DOM) is one of the largest reservoirs of reduced carbon on Earth. In the dark ocean (>200 m), most of this carbon is refractory DOM. This refractory DOM, largely produced during microbial mineralization of organic matter, includes humic-like substances generated in situ and detectable by fluorescence spectroscopy. Here we show two ubiquitous humic-like fluorophores with turnover times of 435±41 and 610±55 years, which persist significantly longer than the ~350 years that the dark global ocean takes to renew. In parallel, decay of a tyrosine-like fluorophore with a turnover time of 379±103 years is also detected. We propose the use of DOM fluorescence to study the cycling of resistant DOM that is preserved at centennial timescales and could represent a mechanism of carbon sequestration (humic-like fraction) and the decaying DOM injected into the dark global ocean, where it decreases at centennial timescales (tyrosine-like fraction).

Relationships Between Dissolved Organic Matter Composition and Photochemistry in Lakes of Diverse Trophic Status.

PubMed

Maizel, Andrew C; Li, Jing; Remucal, Christina K

2017-09-05

The North Temperate Lakes Long-Term Ecological Research site includes seven lakes in northern Wisconsin that vary in hydrology, trophic status, and landscape position. We examine the molecular composition of dissolved organic matter (DOM) within these lakes using Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) and quantify DOM photochemical activity using probe compounds. Correlations between the relative intensity of individual molecular formulas and reactive species production demonstrate the influence of DOM composition on photochemistry. For example, highly aromatic, tannin-like formulas correlate positively with triplet formation rates, but negatively with triplet quantum yields, as waters enriched in highly aromatic formulas exhibit much higher rates of light absorption, but only slightly higher rates of triplet production. While commonly utilized optical properties also correlate with DOM composition, the ability of FT-ICR MS to characterize DOM subpopulations provides unique insight into the mechanisms through which DOM source and environmental processing determine composition and photochemical activity.

Interaction Between Domperidone and Ketoconazole: Toward Prediction of Consequent QTc Prolongation Using Purely In Vitro Information

PubMed Central

Mishra, H; Polak, S; Jamei, M; Rostami-Hodjegan, A

2014-01-01

We aimed to investigate the application of combined mechanistic pharmacokinetic (PK) and pharmacodynamic (PD) modeling and simulation in predicting the domperidone (DOM) triggered pseudo-electrocardiogram modification in the presence of a CYP3A inhibitor, ketoconazole (KETO), using in vitro–in vivo extrapolation. In vitro metabolic and inhibitory data were incorporated into physiologically based pharmacokinetic (PBPK) models within Simcyp to simulate time course of plasma DOM and KETO concentrations when administered alone or in combination with KETO (DOM+KETO). Simulated DOM concentrations in plasma were used to predict changes in gender-specific QTcF (Fridericia correction) intervals within the Cardiac Safety Simulator platform taking into consideration DOM, KETO, and DOM+KETO triggered inhibition of multiple ionic currents in population. Combination of in vitro–in vivo extrapolation, PBPK, and systems pharmacology of electric currents in the heart was able to predict the direction and magnitude of PK and PD changes under coadministration of the two drugs although some disparities were detected. PMID:25116274

Colored dissolved organic matter in shallow estuaries: relationships between carbon sources and light attenuation

NASA Astrophysics Data System (ADS)

Oestreich, W. K.; Ganju, N. K.; Pohlman, J. W.; Suttles, S. E.

2016-02-01

Light availability is of primary importance to the ecological function of shallow estuaries. For example, benthic primary production by submerged aquatic vegetation is contingent upon light penetration to the seabed. A major component that attenuates light in estuaries is colored dissolved organic matter (CDOM). CDOM is often measured via a proxy, fluorescing dissolved organic matter (fDOM), due to the ease of in situ fDOM sensor measurements. Fluorescence must be converted to CDOM absorbance for use in light attenuation calculations. However, this CDOM-fDOM relationship varies among and within estuaries. We quantified the variability in this relationship within three estuaries along the mid-Atlantic margin of the eastern United States: West Falmouth Harbor (MA), Barnegat Bay (NJ), and Chincoteague Bay (MD/VA). Land use surrounding these estuaries ranges from urban to developed, with varying sources of nutrients and organic matter. Measurements of fDOM (excitation and emission wavelengths of 365 nm (±5 nm) and 460 nm (±40 nm), respectively) and CDOM absorbance were taken along a terrestrial-to-marine gradient in all three estuaries. The ratio of the absorption coefficient at 340 nm (m-1) to fDOM (QSU) was higher in West Falmouth Harbor (1.22) than in Barnegat Bay (0.22) and Chincoteague Bay (0.17). The CDOM : fDOM absorption ratio was variable between sites within West Falmouth Harbor and Barnegat Bay, but consistent between sites within Chincoteague Bay. Stable carbon isotope analysis for constraining the source of dissolved organic matter (DOM) in West Falmouth Harbor and Barnegat Bay yielded δ13C values ranging from -19.7 to -26.1 ‰ and -20.8 to -26.7 ‰, respectively. Concentration and stable carbon isotope mixing models of DOC (dissolved organic carbon) indicate a contribution of 13C-enriched DOC in the estuaries. The most likely source of 13C-enriched DOC for the systems we investigated is Spartina cordgrass. Comparison of DOC source to CDOM : fDOM absorption ratios at each site demonstrates the relationship between source and optical properties. Samples with 13C-enriched carbon isotope values, indicating a greater contribution from marsh organic material, had higher CDOM : fDOM absorption ratios than samples with greater contribution from terrestrial organic material. Applying a uniform CDOM : fDOM absorption ratio and spectral slope within a given estuary yields errors in modeled light attenuation ranging from 11 to 33 % depending on estuary. The application of a uniform absorption ratio across all estuaries doubles this error. This study demonstrates that light attenuation coefficients for CDOM based on continuous fDOM records are highly dependent on the source of DOM present in the estuary. Thus, light attenuation models for estuaries would be improved by quantification of CDOM absorption and DOM source identification.

High field NMR Spectroscopy and FTICR Mass Spectrometry: Powerful Discovery Tools for the Characterization of Marine Dissolved Organic Matter

NASA Astrophysics Data System (ADS)

Hertkorn, N.; Harir, M.; Koch, B. P.; Michalke, B.; Grill, P.; Schmitt-Kopplin, P.

2012-04-01

High-field NMR and FTMS of SPE-derived marine dissolved organic matter (SPE-DOM) from the South Atlantic Ocean provided molecular level information of complex unknowns with unprecedented coverage of carbon and resolution. SPE-DOM represented major oceanic regimes of general significance: 5 m (near surface photic zone), 48 m (fluorescence maximum), 200 m (upper mesopelagic zone) and 5446 m (30 m above ground). 1H NMR spectra showed rather smooth bulk NMR envelopes with a few percent of visibly resolved signatures. 1H NMR spectra of SPE-DOM indicated considerable variance in abundance for all major chemical environments. Two-dimensional NMR spectra of SPE-DOM displayed exceptional resolution. JRES (sensitive but limited resolution), COSY (highly resolved) and HMBC NMR (informative but limited S/N ratio) spectra depicted resolved molecular signatures in excess of a certain minimum abundance. COSY cross peaks were most diverse for sample FMAX and conformed to >1,500 molecules present. Classical methyl groups terminating aliphatic chains represented only ~ 15 % of total methyl in all marine DOM investigated; 2 % of methyl was bound to olefinic carbon. Methyl ethers were abundant in surface marine DOM, and the chemical diversity of carbohydrates was larger than that of freshwater and soil DOM. TOCSY and HSQC cross peaks enabled unprecedented depiction of sp2-hybridized carbon chemical environments in marine SPE-DOM with discrimination of isolated and conjugated olefins as well as ?,?-unsaturated double bonds. Olefinic protons were more abundant than aromatic protons; relative HSQC cross peak integrals indicated more abundant olefinic carbon than aromatic carbon in all marine DOM as well. Furan, pyrrol and thiophene derivatives were marginal. Benzene derivatives and phenols as well as six-membered nitrogen heterocycles were prominent. Various key polycyclic aromatic hydrocarbon substructures suggested the presence of thermogenic organic matter (TMOC) in marine DOM at all water depths. Eventually, olefinic unsaturation in marine DOM will be more directly traceable to ultimate biogenic precursors than aromatic unsaturation. The conformity of key NMR signatures suggests the presence of a numerous set of identical molecules throughout the entire ocean column even if the investigated water masses belonged to different oceanic regimes and currents. High field (12 T) negative electrospray ionization FTICR mass spectra showed abundant CHO, CHNO, CHOS and CHNOS molecular series with slightly increasing numbers of mass peaks and average mass from surface to bottom SPE-DOM. The proportion of CHO and CHNO molecular series increased from surface to depth whereas CHOS and especially CHNOS molecular series markedly declined. The exhaustive characterization of complex unknowns in marine DOM will enable a meaningful assessment of individual marine biogeosignatures which carry the holistic memory of the oceanic water masses.

Construction of a menu-based system

NASA Technical Reports Server (NTRS)

Noonan, R. E.; Collins, W. R.

1985-01-01

The development of the user interface to a software code management system is discussed. The user interface was specified using a grammar and implemented using a LR parser generator. This was found to be an effective method for the rapid prototyping of a menu based system.

Identifying the null subject: evidence from event-related brain potentials.

PubMed

Demestre, J; Meltzer, S; García-Albea, J E; Vigil, A

1999-05-01

Event-related brain potentials (ERPs) were recorded during spoken language comprehension to study the on-line effects of gender agreement violations in controlled infinitival complements. Spanish sentences were constructed in which the complement clause contained a predicate adjective marked for syntactic gender. By manipulating the gender of the antecedent (i.e., the controller) of the implicit subject while holding constant the gender of the adjective, pairs of grammatical and ungrammatical sentences were created. The detection of such a gender agreement violation would indicate that the parser had established the coreference relation between the null subject and its antecedent. The results showed a complex biphasic ERP (i.e., an early negativity with prominence at anterior and central sites, followed by a centroparietal positivity) in the violating condition as compared to the non-violating conditions. The brain reacts to NP-adjective gender agreement violations within a few hundred milliseconds of their occurrence. The data imply that the parser has properly coindexed the null subject of an infinitive clause with its antecedent.

Seeing the light: Applications of in situ optical measurements for understanding DOM dynamics in river systems (Invited)

NASA Astrophysics Data System (ADS)

Pellerin, B. A.; Bergamaschi, B. A.; Downing, B. D.; Saraceno, J.; Fleck, J.; Shanley, J. B.; Aiken, G.; Boss, E.; Fujii, R.

2009-12-01

A critical challenge for understanding the sources, character and cycling of dissolved organic matter (DOM) is making measurements at the time scales in which changes occur in aquatic systems. Traditional approaches for data collection (daily to monthly discrete sampling) are often limited by analytical and field costs, site access and logistical challenges, particularly for long-term sampling at a large number of sites. The ability to make optical measurements of DOM in situ has been known for more than 50 years, but much of the work on in situ DOM absorbance and fluorescence using commercially-available instruments has taken place in the last few years. Here we present several recent examples that highlight the application of in situ measurements for understanding DOM dynamics in riverine systems at intervals of minutes to hours. Examples illustrate the utility of in situ optical sensors for studies of DOM over short-duration events of days to weeks (diurnal cycles, tidal cycles, storm events and snowmelt periods) as well as longer-term continuous monitoring for months to years. We also highlight the application of in situ optical DOM measurements as proxies for constituents that are significantly more difficult and expensive to measure at high frequencies (e.g. methylmercury, trihalomethanes). Relatively simple DOM absorbance and fluorescence measurements made in situ could be incorporated into short and long-term ecological research and monitoring programs, resulting in advanced understanding of organic matter sources, character and cycling in riverine systems.

Microbial Community Response to Terrestrially Derived Dissolved Organic Matter in the Coastal Arctic

PubMed Central

Sipler, Rachel E.; Kellogg, Colleen T. E.; Connelly, Tara L.; Roberts, Quinn N.; Yager, Patricia L.; Bronk, Deborah A.

2017-01-01

Warming at nearly twice the global rate, higher than average air temperatures are the new ‘normal’ for Arctic ecosystems. This rise in temperature has triggered hydrological and geochemical changes that increasingly release carbon-rich water into the coastal ocean via increased riverine discharge, coastal erosion, and the thawing of the semi-permanent permafrost ubiquitous in the region. To determine the biogeochemical impacts of terrestrially derived dissolved organic matter (tDOM) on marine ecosystems we compared the nutrient stocks and bacterial communities present under ice-covered and ice-free conditions, assessed the lability of Arctic tDOM to coastal microbial communities from the Chukchi Sea, and identified bacterial taxa that respond to rapid increases in tDOM. Once thought to be predominantly refractory, we found that ∼7% of dissolved organic carbon and ∼38% of dissolved organic nitrogen from tDOM was bioavailable to receiving marine microbial communities on short 4 – 6 day time scales. The addition of tDOM shifted bacterial community structure toward more copiotrophic taxa and away from more oligotrophic taxa. Although no single order was found to respond universally (positively or negatively) to the tDOM addition, this study identified 20 indicator species as possible sentinels for increased tDOM. These data suggest the true ecological impact of tDOM will be widespread across many bacterial taxa and that shifts in coastal microbial community composition should be anticipated. PMID:28649233

Characterisation of dissolved organic matter in stormwater using high-performance size exclusion chromatography.

PubMed

Huang, Huiping; Chow, Christopher W K; Jin, Bo

2016-04-01

Understanding the complexity of dissolved organic matter (DOM) in stormwater has drawn a lot of interest, since DOM from stormwater causes not only environmental impacts, but also worsens downstream aquatic quality associated with water supply and treatability. This study introduced and employed high-performance size exclusion chromatography (HPSEC) coupled with an ultraviolet-visible (UV-vis) diode array detector to assess changes in stormwater-associated DOM characteristics. Stormwater DOM was also analysed in relation to storm event characteristics, water quality and spectroscopic analysis. Statistical tools were used to determine the correlations within DOM and water quality measurements. Results showed that dissolved organic carbon (DOC) and UV absorbance at 254 nm (UV254) as conventional DOM parameters were found to be correlated well to the changes in stormwater quality during each of the three storm events studied. Both detector wavelengths (210 and 254 nm) and their ratio (A210/A254) were found to provide additional information on the physiochemical properties of stormwater-associated DOM. This study indicated that A210/A254 is an important parameter which could be used to estimate the DOM proportions of functional groups and conjugated carbon species. This study provided also an understanding of stormwater quality constituents through assessing variability and sensitivity for various parameters, and the additional information of rainfall characteristics on runoff quality data for a better understanding of parameter correlations and influences. Copyright © 2015. Published by Elsevier B.V.

Methylmercury photodegradation in surface water of the Florida Everglades: importance of dissolved organic matter-methylmercury complexation.

PubMed

Tai, Chao; Li, Yanbin; Yin, Yongguang; Scinto, Leonard J; Jiang, Guibin; Cai, Yong

2014-07-01

Photodegradation is the major pathway of methylmercury (MeHg) degradation in many surface waters. However, the mechanism of MeHg photodegradation is still not completely understood. Dissolved organic matter (DOM) is expected to play a critical role in MeHg photodegradation. By using several techniques, including N2/O2 purging and the addition of stable isotope (Me(201)Hg), scavengers, competing ligands, and a singlet oxygen ((1)O2) generator, the role played by MeHg-DOM complexation in MeHg photodegradation of Everglades surface water was investigated. DOM appeared to be involved in MeHg photodegradation via the formation MeHg-DOM complexes based on three findings: (1) MeHg was quickly photodegraded in solutions containing DOM extracts; (2) degradation of MeHg did not occur in deionized water; and (3) addition of competing complexation reagents (dithiothreitol-DTT) dramatically prohibited the photodegradation of MeHg in Everglades water. Further experiments indicated that free radicals/reactive oxygen species, including hydroxyl radical (·OH), (1)O2, triplet excited state of DOM ((3)DOM*), and hydrated electron (e(-)aq), played a minor role in MeHg photodegradation in Everglades water, based on the results of scavenger addition, (1)O2 generator addition and N2/O2 purging. A pathway, involving direct photodegradation of MeHg-DOM complexes via intramolecular electron transfer, is proposed as the dominant mechanism for MeHg photodegradation in Everglades water.

A targeted genetic modifier screen links the SWI2/SNF2 protein domino to growth and autophagy genes in Drosophila melanogaster.

PubMed

Kwon, Matt Hyoung; Callaway, Heather; Zhong, Jim; Yedvobnick, Barry

2013-05-20

Targeted genetic studies can facilitate phenotypic analyses and provide important insights into development and other complex processes. The SWI2/SNF2 DNA-dependent ATPase Domino (Dom) of Drosophila melanogaster, a component of the Tip60 acetyltransferase complex, has been associated with a wide spectrum of cellular processes at multiple developmental stages. These include hematopoiesis, cell proliferation, homeotic gene regulation, histone exchange during DNA repair, and Notch signaling. To explore the wider gene network associated with Dom action, we used RNAi directed against domino (dom) to mediate loss-of-function at the wing margin, a tissue that is readily scored for phenotypic changes. Dom RNAi driven through GAL4-UAS elicited dominant wing nicking that responded phenotypically to the dose of dom and other loci known to function with dom. We screened for phenotypic modifiers of this wing phenotype among 2500 transpositions of the EP P element and found both enhancers and suppressors. Several classes of modifier were obtained, including those encoding transcription factors, RNA regulatory proteins, and factors that regulate cell growth, proliferation and autophagy, a lysosomal degradation pathway that affects cell growth under conditions of starvation and stress. Our analysis is consistent with prior studies, suggesting that Dom acts pleiotropically as a positive effector of Notch signaling and a repressor of proliferation. This genetic system should facilitate screens for additional loci associated with Dom function, and complement biochemical approaches to their regulatory activity.

Unveiling the transformation and bioavailability of dissolved organic matter in contrasting hydrothermal vents using fluorescence EEM-PARAFAC.

PubMed

Yang, Liyang; Zhuang, Wan-E; Chen, Chen-Tung Arthur; Wang, Bing-Jye; Kuo, Fu-Wen

2017-03-15

The submarine hydrothermal systems are extreme environments where active cycling of dissolved organic matter (DOM) may occur. However, little is known about the optical properties and bioavailability of hydrothermal DOM, which could provide valuable insights into its transformation processes and biogeochemical reactivity. The quantity, quality, and bioavailability of DOM were investigated for four very different hydrothermal vents east of Taiwan, using dissolved organic carbon (DOC), absorption spectroscopy, and fluorescence excitation-emission matrices-parallel factor analysis (EEM-PARAFAC). The DOC and absorption coefficient a 280 were both lower in the two hydrothermal vents off the Orchid Island and on the Green Island than in the surrounding seawater and the two vents off the Kueishantao Island, indicating effective removals of DOM in the former two hydrothermal systems owing to possible adsorption/co-precipitation and thermal degradation respectively. The four hydrothermal DOM showed notable differences in the absorption spectral slope S 275-295 , humification index HIX, biological index BIX, EEM spectra, and the relative distributions of seven PARAFAC components. The results demonstrated a high diversity of chemical composition and transformation history of DOM under contrasting hydrothermal conditions. The little change in the hydrothermal DOC after 28-day microbial incubations indicated a low bioavailability of the bulk DOM, and different PARAFAC components showed contrasting bioavailability. The results have profound implications for understanding the biogeochemical cycling and environmental effects of hydrothermal DOM in the marine environments. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Optical, Chemical, and Molecular Dissolved Organic Matter Succession Along a Boreal Soil-Stream-River Continuum

NASA Astrophysics Data System (ADS)

Hutchins, Ryan H. S.; Aukes, Pieter; Schiff, Sherry L.; Dittmar, Thorsten; Prairie, Yves T.; del Giorgio, Paul A.

2017-11-01

Soils export large amounts of organic matter to rivers, and there are still major uncertainties concerning the composition and reactivity of this material and its fate within the fluvial network. Here we reconstructed the pattern of movement and processing of dissolved organic matter (DOM) along a soil-stream-river continuum under summer baseflow conditions in a boreal region of Québec (Canada), using a combination of fluorescence spectra, size exclusion chromatography and ultrahigh resolution mass spectrometry. Our results show that there is a clear sequence of selective DOM degradation along the soil-stream-river continuum, which results in pronounced compositional shifts downstream. The soil-stream interface was a hot spot of DOM degradation, where biopolymers and low molecular weight (LMW) compounds were selectively removed. In contrast, processing in the stream channel was dominated by the degradation of humic-like aromatic DOM, likely driven by photolysis, with little further degradation of either biopolymers or LMW compounds. Overall, there was a high degree of coherence between the patterns observed in DOM chemical composition, optical properties, and molecular profiles, and none of these approaches pointed to measurable production of new DOM components, suggesting that the DOM pools removed during transit were likely mineralized to CO2. Our first order estimates suggest that rates of soil-derived DOM mineralization could potentially sustain over half of the measured CO2 emissions from this stream network, with mineralization of biopolymers and humic substances contributing roughly equally to these fluvial emissions.

Interaction of bisphenol A with dissolved organic matter in extractive and adsorptive removal processes.

PubMed

Zhu, Fei-Die; Choo, Kwang-Ho; Chang, Hyun-Shik; Lee, Byunghwan

2012-05-01

The fate of endocrine disrupting chemicals (EDCs) in natural and engineered systems is complicated due to their interactions with various water constituents. This study investigated the interaction of bisphenol A (BPA) with dissolved organic matter (DOM) and colloids present in surface water and secondary effluent as well as its adsorptive removal by powdered activated carbons. The solid phase micro-extraction (SPME) method followed by thermal desorption and gas chromatography-mass spectrometry (GC-MS) was utilized for determining the distribution of BPA molecules in water. The BPA removal by SPME decreased with the increased DOM content, where the formation of BPA-DOM complexes in an aqueous matrix was responsible for the reduced extraction of BPA. Colloidal particles in water samples sorbed BPA leading to the marked reduction of liquid phase BPA. BPA-DOM complexes had a negative impact on the adsorptive removal of BPA by powered activated carbons. The complex formation was characterized based on Fourier transform infrared (FTIR) and ultraviolet-visible (UV-Vis) spectroscopy, along with the calculation of molecular interactions between BPA and functional groups in DOM. It was found that the hydrogen bonding between DOM and BPA would be preferred over aromatic interactions. A pseudo-equilibrium molecular coordination model for the complexation between a BPA molecule and a hydroxyl group of the DOM was developed, which enabled estimation of the maximum sorption site and complex formation constant as well as prediction of organic complexes at various DOM levels. Copyright © 2012 Elsevier Ltd. All rights reserved.

Dissolved organic matter kinetically controls mercury bioavailability to bacteria.

PubMed

Chiasson-Gould, Sophie A; Blais, Jules M; Poulain, Alexandre J

2014-03-18

Predicting the bioavailability of inorganic mercury (Hg) to bacteria that produce the potent bioaccumulative neurotoxin monomethylmercury remains one of the greatest challenges in predicting the environmental fate and transport of Hg. Dissolved organic matter (DOM) affects mercury methylation due to its influence on cell physiology (as a potential nutrient) and its influence on Hg(II) speciation in solution (as a complexing agent), therefore controlling Hg bioavailability. We assessed the role of DOM on Hg(II) bioavailability to a gram-negative bacterium bioreporter under oxic pseudo- and nonequilibrium conditions, using defined media and field samples spanning a wide range of DOM levels. Our results showed that Hg(II) was considerably more bioavailable under nonequilibrium conditions than when DOM was absent or when Hg(II) and DOM had reached pseudoequilibrium (24 h) prior to cell exposure. Under these enhanced uptake conditions, Hg(II) bioavailability followed a bell shaped curve as DOM concentrations increased, both for defined media and natural water samples, consistent with bioaccumulation results in a companion paper (this issue) observed for amphipods. Experiments also suggest that DOM may not only provide shuttle molecules facilitating Hg uptake, but also alter cell wall properties to facilitate the first steps toward Hg(II) internalization. We propose the existence of a short-lived yet critical time window (<24 h) during which DOM facilitates the entry of newly deposited Hg(II) into aquatic food webs, suggesting that the bulk of mercury incorporation in aquatic food webs would occur within hours following its deposition from the atmosphere.

Dissolved organic matter effects on the performance of a barrier to polycyclic aromatic hydrocarbon transport by groundwater

NASA Astrophysics Data System (ADS)

Moon, Jung-Won; Goltz, Mark N.; Ahn, Kyu-Hong; Park, Jae-Woo

2003-02-01

In order to contain the movement of organic contaminants in groundwater, a subsurface sorption barrier consisting of sand or clay minerals coated with a cationic surfactant has been proposed. The effectiveness of such a sorption barrier might be affected by the presence of dissolved organic matter (DOM) in the groundwater. To study the impact of DOM on barrier performance, a series of batch experiments were performed by measuring naphthalene and phenanthrene sorption onto sand coated with cetylpyridinium chloride (CPC) and bentonite coated with hexadecyltrimethylammonium bromide (HDTMA) in the presence of various concentrations of DOM. The overall soil-water distribution coefficient ( K*) of naphthalene and phenanthrene onto CPC-coated sand decreased with increasing DOM concentration, whereas the K* of the compounds onto HDTMA-coated bentonite slightly increased with increasing DOM concentration. To describe the overall distribution of polycyclic aromatic hydrocarbons (PAHs) in the systems, a competitive multiphase sorption (CMS) model was developed and compared with an overall mechanistic sorption (OMS) model. The modeling studies showed that while the OMS model did not explain the CPC-coated sand experimental results, a model that included competitive sorption between DOM and PAH did. The experimental results and the modeling study indicated that there was no apparent competition between DOM and PAH in the HDTMA-coated bentonite system, and indicated that in groundwater systems with high DOM, a barrier using HDTMA-coated bentonite might be more effective.

THE INFLUENCE OF DOM CHARACTER ON OZONE DECOMPOSITION RATES AND RCT

EPA Science Inventory

The effects of DOM character on ozonation of natural waters and solutions of DOM isolates were investigated. Batch kinetic investigations measured O3 decomposition rate constants and Rct values. Rct describes the ratio of ?OH concentration to O3 concentration, and thus provides...

Delayed onset muscle soreness : treatment strategies and performance factors.

PubMed

Cheung, Karoline; Hume, Patria; Maxwell, Linda

2003-01-01

Delayed onset muscle soreness (DOMS) is a familiar experience for the elite or novice athlete. Symptoms can range from muscle tenderness to severe debilitating pain. The mechanisms, treatment strategies, and impact on athletic performance remain uncertain, despite the high incidence of DOMS. DOMS is most prevalent at the beginning of the sporting season when athletes are returning to training following a period of reduced activity. DOMS is also common when athletes are first introduced to certain types of activities regardless of the time of year. Eccentric activities induce micro-injury at a greater frequency and severity than other types of muscle actions. The intensity and duration of exercise are also important factors in DOMS onset. Up to six hypothesised theories have been proposed for the mechanism of DOMS, namely: lactic acid, muscle spasm, connective tissue damage, muscle damage, inflammation and the enzyme efflux theories. However, an integration of two or more theories is likely to explain muscle soreness. DOMS can affect athletic performance by causing a reduction in joint range of motion, shock attenuation and peak torque. Alterations in muscle sequencing and recruitment patterns may also occur, causing unaccustomed stress to be placed on muscle ligaments and tendons. These compensatory mechanisms may increase the risk of further injury if a premature return to sport is attempted.A number of treatment strategies have been introduced to help alleviate the severity of DOMS and to restore the maximal function of the muscles as rapidly as possible. Nonsteroidal anti-inflammatory drugs have demonstrated dosage-dependent effects that may also be influenced by the time of administration. Similarly, massage has shown varying results that may be attributed to the time of massage application and the type of massage technique used. Cryotherapy, stretching, homeopathy, ultrasound and electrical current modalities have demonstrated no effect on the alleviation of muscle soreness or other DOMS symptoms. Exercise is the most effective means of alleviating pain during DOMS, however the analgesic effect is also temporary. Athletes who must train on a daily basis should be encouraged to reduce the intensity and duration of exercise for 1-2 days following intense DOMS-inducing exercise. Alternatively, exercises targeting less affected body parts should be encouraged in order to allow the most affected muscle groups to recover. Eccentric exercises or novel activities should be introduced progressively over a period of 1 or 2 weeks at the beginning of, or during, the sporting season in order to reduce the level of physical impairment and/or training disruption. There are still many unanswered questions relating to DOMS, and many potential areas for future research.

High field NMR spectroscopy and FTICR mass spectrometry: powerful discovery tools for the molecular level characterization of marine dissolved organic matter from the South Atlantic Ocean

NASA Astrophysics Data System (ADS)

Hertkorn, N.; Harir, M.; Koch, B. P.; Michalke, B.; Grill, P.; Schmitt-Kopplin, P.

2012-01-01

Non target high resolution organic structural spectroscopy of marine dissolved organic matter (DOM) isolated on 27 November 2008 by means of solid phase extraction (SPE) from four different depths in the South Atlantic Ocean off the Angola coast (3.1° E; -17.7° S; Angola basin) provided molecular level information of complex unknowns with unprecedented coverage and resolution. The sampling was intended to represent major characteristic oceanic regimes of general significance: 5 m (FISH; near surface photic zone), 48 m (FMAX; fluorescence maximum), 200 m (upper mesopelagic zone) and 5446 m (30 m above ground). 800 MHz proton (1H) nuclear magnetic resonance (NMR) 1H NMR, spectra were least affected by fast and differential transverse NMR relaxation and produced at first similar looking, rather smooth bulk NMR envelopes reflecting intrinsic averaging from massive signal overlap. Visibly resolved NMR signatures were most abundant in surface DOM but contributed at most a few percent to the total 1H NMR integral and were mainly limited to unsaturated and singly oxygenated carbon chemical environments. The relative abundance and variance of resolved signatures between samples was maximal in the aromatic region; in particular, the aromatic resolved NMR signature of the deep ocean sample at 5446 m was considerably different from that of all other samples. When scaled to equal total NMR integral, 1H NMR spectra of the four marine DOM samples revealed considerable variance in abundance for all major chemical environments across the entire range of chemical shift. Abundance of singly oxygenated CH units and acetate derivatives declined from surface to depth whereas aliphatics and carboxyl-rich alicyclic molecules (CRAM) derived molecules increased in abundance. Surface DOM contained a remarkably lesser abundance of methyl esters than all other marine DOM, likely a consequence of photodegradation from direct exposure to sunlight. All DOM showed similar overall 13C NMR resonance envelopes typical of an intricate mixture of natural organic matter with noticeable peaks of anomerics and C-aromatics carbon whereas oxygenated aromatics and ketones were of too low abundance to result in noticeable humps at the S/N ratio provided. Integration according to major substructure regimes revealed continual increase of carboxylic acids and ketones from surface to deep marine DOM, reflecting a progressive oxygenation of marine DOM, with concomitant decline of carbohydrate-related substructures. Isolation of marine DOM by means of SPE likely discriminated against carbohydrates but produced materials with beneficial NMR relaxation properties: a substantial fraction of dissolved organic molecules present allowed the acquisition of two-dimensional NMR spectra with exceptional resolution. JRES, COSY and HMBC NMR spectra were capable to depict resolved molecular signatures of compounds exceeding a certain minimum abundance. Here, JRES spectra suffered from limited resolution whereas HMBC spectra were constrained because of limited S/N ratio. Hence, COSY NMR spectra appeared best suited to depict organic complexity in marine DOM. The intensity and number of COSY cross peaks was found maximal for sample FMAX and conformed to about 1500 molecules recognizable in variable abundance. Surface DOM (FISH) produced a slightly (~25%) lesser number of cross peaks with remarkable positional accordance to FMAX (~80% conforming COSY cross peaks were found in FISH and FMAX). With increasing water depth, progressive attenuation of COSY cross peaks was caused by fast transverse NMR relaxation of yet unknown origin. However, most of the faint COSY cross peak positions of deep water DOM conformed to those observed in the surface DOM, suggesting the presence of a numerous set of identical molecules throughout the entire ocean column even if the investigated water masses belonged to different oceanic regimes and currents. Aliphatic chemical environments of methylene (CH2) and methyl (CH3) in marine DOM were nicely discriminated in DEPT HSQC NMR spectra. Classical methyl groups terminating aliphatic chains represented only ~15% of total methyl in all marine DOM investigated. Chemical shift anisotropy from carbonyl derivatives (i.e. most likely carboxylic acids) displaced aliphatic methyl 1H NMR resonances up to δH ~1.6 ppm, indicative of alicyclic geometry which furnishes more numerous short range connectivities for any given atom pairs. A noticeable fraction of methyl (~2%) was bound to olefinic carbon. The comparatively large abundance of methyl ethers in surface marine DOM contrasted with DOM of freshwater and soil origin. The chemical diversity of carbohydrates as indicated by H2CO-groups (δC ~ 62 ± 2 ppm) and anomerics (δC ~ 102 ± 7 ppm) exceeded that of freshwater and soil DOM considerably. HSQC NMR spectra were best suited to identify chemical environments of methin carbon (CH) and enabled discrimination of olefinic and aromatic cross peaks (δC > 110 ppm) and those of doubly oxygenated carbon (δC < 110 ppm). The abundance of olefinic protons exceeded that of aromatic protons; comparison of relative HSQC cross peak integrals indicated larger abundance of olefinic carbon than aromatic carbon in all marine DOM as well. A considerable fraction of olefins seemed isolated and likely sterically constrained as judged from small nJHH couplings associated with those olefins. High S/N ratio and fair resolution of TOCSY and HSQC cross peaks enabled unprecedented depiction of sp2-hybridized carbon chemical environments in marine DOM with discrimination of isolated and conjugated olefins as well as α, β-unsaturated double bonds. However, contributions from five-membered heterocycles (furan, pyrrol and thiophene derivatives) even if very unlikely from given elemental C/N and C/S ratios and upfield proton NMR chemical shift (δH < 6.5 ppm) could not yet been ruled out entirely. In addition to classical aromatic DOM, like benzene derivatives and phenols, six-membered nitrogen heterocycles were found prominent contributors to the downfield region of proton chemical shift (δH > 8 ppm). Specifically, a rather confined HSQC cross peak at δH/δC = 8.2/164 ppm indicated a limited set of nitrogen heterocycles with several nitrogen atoms in analogy to RNA derivatives present in all four marine DOM. Appreciable amounts of extended HSQC and TOCSY cross peaks derived from various key polycyclic aromatic hydrocarbon substructures suggested the presence of previously proposed but NMR invisible thermogenic organic matter (TMOC) in marine DOM at all water depths. Eventually, olefinic unsaturation in marine DOM will be more directly traceable to ultimate biogenic precursors than aromatic unsaturation of which a substantial fraction originates from an aged material which from the beginning was subjected to complex and less specific biogeochemical reactions like thermal decomposition. The variance in molecular mass as indicated from Fourier transform ion cyclotron resonance (FTICR) mass spectra was limited and could not satisfactorily explain the observed disparity in NMR transverse relaxation of the four marine DOM samples. Likewise, the presence of metal ions in isolated marine DOM remained near constant or declined from surface to depth for important paramagnetic ions like Mn, Cr, Fe, Co, Ni and Cu. Iron in particular, a strong complexing paramagnetic ion, was found most abundant by a considerable margin in surface (FISH) marine DOM for which well resolved COSY cross peaks were observed. Hence, facile relationships between metal content of isolated DOM (which does not reflect authentic marine DOM metal content) and transverse NMR relaxation were not observed. High field (12 T) negative electrospray ionization FTICR mass spectra showed at first view rather conforming mass spectra for all four DOM samples with abundant CHO, CHNO, CHOS and CHNOS molecular series with slightly increasing numbers of mass peaks from surface to bottom DOM and similar fractions (~50%) of assigned molecular compositions throughout all DOM samples. The average mass increased from surface to bottom DOM by about 10 Dalton. The limited variance of FTICR mass spectra probably resulted from a rather inherent conformity of marine DOM at the mandatory level of intrinsic averaging provided by FTICR mass spectrometry, when many isomers unavoidably project on single nominal mass peaks. In addition, averaging from ion suppression added to the accordance observed. The proportion of CHO and CHNO molecular series increased from surface to depth whereas CHOS and especially CHNOS molecular series markedly declined. The abundance of certain aromatic CHOS compounds declined with water depth. For future studies, COSY NMR spectra appear best suited to assess organic molecular complexity of marine DOM and to define individual DOM molecules of yet unknown structure and function. Non-target organic structural spectroscopy at the level demonstrated here covered nearly all carbon present in marine DOM. The exhaustive characterization of complex unknowns in marine DOM will reveal a meaningful assessment of individual marine biogeosignatures which carry the holistic memory of the oceanic water masses (Koch et al., 2011).

Characterization and treatment of dissolved organic matter from oilfield produced waters.

PubMed

Wang, Xiaojing; Goual, Lamia; Colberg, Patricia J S

2012-05-30

Dissolved organic matter (DOM) has been studied intensively in streams, lakes and oceans due to its role in the global carbon cycle and because it is a precursor of carcinogenic disinfection by-products in drinking water; however, relatively little research has been conducted on DOM in oilfield produced waters. In this study, recovery of DOM from two oilfield produced waters was relatively low (~34%), possibly due to the presence of high concentrations of volatile organic compounds (VOCs). A van Krevelen diagram of the extracted DOM suggested the presence of high concentrations of lipids, lignin, and proteins, but low concentrations of condensed hydrocarbons. Most of the compounds in the oilfield DOM contained sulfur in their structures. Fourier transform infrared (FTIR) spectra indicated the presence of methyl groups, amides, carboxylic acids, and aromatic compounds, which is in agreement with results of Fourier transform ion cyclotron resonance (FT-ICR) analysis. Qualitatively, DOM in oilfield produced waters is similar to that reported in oceans and freshwater, except that it contains much more sulfur and is less aromatic. Treatment studies conducted in a fluidized bed reactor suggested that volatilization of organics may be a more important mechanism of DOM removal than microbial degradation. Copyright © 2012 Elsevier B.V. All rights reserved.

Changes in Dissolved Organic Matter Composition and Disinfection Byproduct Precursors in Advanced Drinking Water Treatment Processes.

PubMed

Phungsai, Phanwatt; Kurisu, Futoshi; Kasuga, Ikuro; Furumai, Hiroaki

2018-03-20

Molecular changes in dissolved organic matter (DOM) from treatment processes at two drinking water treatment plants in Japan were investigated using unknown screening analysis by Orbitrap mass spectrometry. DOM formulas with carbon, hydrogen and oxygen (CHO-DOM) were the most abundant class in water samples, and over half of them were commonly found at both plants. Among the treatment processes, ozonation induced the most drastic changes to DOM. Mass peak intensities of less saturated CHO-DOM (positive (oxygen subtracted double bond equivalent per carbon (DBE-O)/C)) decreased by ozonation, while more saturated oxidation byproducts (negative (DBE-O)/C) increased and new oxidation byproducts (OBPs) were detected. By Kendrick mass analysis, ozone reactions preferred less saturated CHO-DOM in the same alkylation families and produced more saturated alkylation families of OBPs. Following ozonation, biological activated carbon filtration effectively removed <300 Da CHO-DOM, including OBPs. Following chlorination, over 50 chlorinated formulas of disinfection byproducts (DBPs) were found in chlorinated water samples where at least half were unknown. Putative precursors of these DBPs were determined based on electrophilic substitutions and addition reactions. Ozonation demonstrated better decomposition of addition reaction-type precursors than electrophilic substitution-type precursors; over half of both precursor types decreased during biological activated carbon filtration.

Diversity of bacterial communities and dissolved organic matter in a temperate estuary.

PubMed

Osterholz, Helena; Kirchman, David L; Niggemann, Jutta; Dittmar, Thorsten

2018-06-14

Relationships between bacterial community and dissolved organic matter (DOM) include microbial uptake, transformation and secretion, all of which influence DOM composition. In this study, we explore diversity and similarity metrics of dissolved organic molecules (Fourier-transform ion cyclotron resonance mass spectrometry) and bacterial communities (tag-sequencing of 16S rRNA genes) along the salinity gradient of the Delaware Estuary (USA). We found that even though mixing, discharge and seasonal changes explained most of the variation in DOM and bacterial communities, there was still a relationship, albeit weak, between the composition of DOM and bacterial communities in the estuary. Overall, many DOM molecular formulas (MFs) and bacterial operational taxonomic units (OTUs) reoccurred over years and seasons while the frequency of MF-OTU correlations varied. Diversity based on MFs and OTUs was significantly correlated, decreasing towards the open ocean. However, while the diversity of bacterial OTUs dropped markedly with low salinity, MF diversity decreased strongly only at high salinities. We hypothesize that the different turnover times of DOM and bacteria lead to different abundance distributions of OTUs and MFs. A significant portion of the detected DOM is of a more refractory nature with lifetimes largely exceeding the mixing time of the estuary, while bacterial community turnover times in the Delaware Estuary are estimated at several days.

Induced structural changes of humic acid by exposure of polystyrene microplastics: A spectroscopic insight.

PubMed

Chen, Wei; Ouyang, Zhen-Yu; Qian, Chen; Yu, Han-Qing

2018-02-01

The occurrence of microplastics (MPs) as emerging contaminants in the environment may cause changes in water or sediment characteristics, and further affect their biogeochemical cycles. Thus, insights into the interactions between dissolved organic matter (DOM) and MPs are essential for the assessment of environmental impacts of MPs in ecosystems. Integrating spectroscopic methods with chemometric analyses, this work explored the chemical and microstructural changes of DOM-MP complex to reveal the mechanism of DOM-MP interaction at a molecular level. MPs were found to interact with the aromatic structure of DOM via π-π conjugation, then be entrapped in the DOM polymers by the carboxyl groups and C=O bonds, constituting a highly conjugated co-polymer with increased electron density. This induced the fluorescence intensity increase in DOM. The interaction affinity of DOM-MP was highly dependent on the MP size and solution pH. This work offers a new insight into the impact of MP discharge on environment and may provide an analytical framework for evaluating MP hetero-aggregation and the roles of MPs in the transportation of other contaminants. Furthermore, the integrated methods used in this work exhibit potential applications in exploring the fragmentation processes of MPs and formation of secondary MPs under natural conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Characterizing Dissolved Organic Matter (DOM) Isolated From Specific Allochthonous and Autochthonous Sources in a North-Temperate Stream Ecosystem

NASA Astrophysics Data System (ADS)

Wong, J. C.; Williams, D.

2009-05-01

Detrital energy in temperate headwater streams is mainly derived from the annual input of leaf litter from the surrounding landscape. Presumably, its decomposition and other sources of autochthonous organic matter will change dissolved organic carbon (DOC) concentrations and dissolved organic matter (DOM) quality. To investigate this, DOM was leached from two allochthonous sources: white birch (Betula papyrifera) and white cedar (Thuja occidentalis); and one autochthonous source, streambed biofilm, for a period of 7 days on 3 separate occasions in fall 2007. As a second treatment, microorganisms from the water column were filtered out. Deciduous leaf litter was responsible for high, short-term increases to DOC concentrations whereas the amounts leached from conifer needles were relatively constant in each month. Using UV spectroscopy, changes to DOM characteristics like aromaticity, spectral slopes, and molecular weight were mainly determined by source and indicated a preferential use of the labile DOM pool by the microorganisms. Excitation-emission matrices (EEMs) collected using fluorescence spectroscopy suggested that cedar litter was an important source of protein-like fluorescence and that the nature of the fluorescing DOM components changed in the presence of microorganisms. This study demonstrates that simultaneous examination of DOC concentrations and DOM quality will allow a better understanding of the carbon dynamics that connect terrestrial with aquatic ecosystems.

Geochemistry of Dissolved Organic Matter in a Spatially Highly Resolved Groundwater Petroleum Hydrocarbon Plume Cross-Section.

PubMed

Dvorski, Sabine E-M; Gonsior, Michael; Hertkorn, Norbert; Uhl, Jenny; Müller, Hubert; Griebler, Christian; Schmitt-Kopplin, Philippe

2016-06-07

At numerous groundwater sites worldwide, natural dissolved organic matter (DOM) is quantitatively complemented with petroleum hydrocarbons. To date, research has been focused almost exclusively on the contaminants, but detailed insights of the interaction of contaminant biodegradation, dominant redox processes, and interactions with natural DOM are missing. This study linked on-site high resolution spatial sampling of groundwater with high resolution molecular characterization of DOM and its relation to groundwater geochemistry across a petroleum hydrocarbon plume cross-section. Electrospray- and atmospheric pressure photoionization (ESI, APPI) ultrahigh resolution mass spectrometry (FT-ICR-MS) revealed a strong interaction between DOM and reactive sulfur species linked to microbial sulfate reduction, i.e., the key redox process involved in contaminant biodegradation. Excitation emission matrix (EEM) fluorescence spectroscopy in combination with Parallel Factor Analysis (PARAFAC) modeling attributed DOM samples to specific contamination traits. Nuclear magnetic resonance (NMR) spectroscopy evaluated the aromatic compounds and their degradation products in samples influenced by the petroleum contamination and its biodegradation. Our orthogonal high resolution analytical approach enabled a comprehensive molecular level understanding of the DOM with respect to in situ petroleum hydrocarbon biodegradation and microbial sulfate reduction. The role of natural DOM as potential cosubstrate and detoxification reactant may improve future bioremediation strategies.

Land-based salmon aquacultures change the quality and bacterial degradation of riverine dissolved organic matter

PubMed Central

Kamjunke, Norbert; Nimptsch, Jorge; Harir, Mourad; Herzsprung, Peter; Schmitt-Kopplin, Philippe; Neu, Thomas R.; Graeber, Daniel; Osorio, Sebastian; Valenzuela, Jose; Carlos Reyes, Juan; Woelfl, Stefan; Hertkorn, Norbert

2017-01-01

Aquacultures are of great economic importance worldwide but pollute pristine headwater streams, lakes, and estuaries. However, there are no in-depth studies of the consequences of aquacultures on dissolved organic matter (DOM) composition and structure. We performed a detailed molecular level characterization of aquaculture DOM quality and its bacterial degradation using four salmon aquacultures in Chile. Fluorescence measurements, ultrahigh-resolution mass spectrometry, and nuclear magnetic resonance spectroscopy of the DOM revealed specific and extensive molecular alterations caused by aquacultures. Aquacultures released large quantities of readily bioavailable metabolites (primarily carbohydrates and peptides/proteins, and lipids), causing the organic matter downstream of all the investigated aquacultures to deviate strongly from the highly processed, polydisperse and molecularly heterogeneous DOM found in pristine rivers. However, the upstream individual catchment DOM signatures remained distinguishable at the downstream sites. The benthic algal biovolume decreased and the bacterial biovolume and production increased downstream of the aquacultures, shifting stream ecosystems to a more heterotrophic state and thus impairing the ecosystem health. The bacterial DOM degradation rates explain the attenuation of aquaculture DOM within the subsequent stream reaches. This knowledge may aid the development of improved waste processing facilities and may help to define emission thresholds to protect sensitive stream ecosystems. PMID:28256613

High Resolution Seamless Dom Generation Over CHANG'E-5 Landing Area Using Lroc Nac Images

NASA Astrophysics Data System (ADS)

Di, K.; Jia, M.; Xin, X.; Liu, B.; Liu, Z.; Peng, M.; Yue, Z.

2018-04-01

Chang'e-5, China's first sample return lunar mission, will be launched in 2019, and the planned landing area is near Mons Rümker in Oceanus Procellarum. High-resolution and high-precision mapping of the landing area is of great importance for supporting scientific analysis and safe landing. This paper proposes a systematic method for large area seamless digital orthophoto map (DOM) generation, and presents the mapping result of Chang'e-5 landing area using over 700 LROC NAC images. The developed method mainly consists of two stages of data processing: stage 1 includes subarea block adjustment with rational function model (RFM) and seamless subarea DOM generation; stage 2 includes whole area adjustment through registration of the subarea DOMs with thin plate spline model and seamless DOM mosaicking. The resultant seamless DOM coves a large area (20° longitude × 4° latitude) and is tied to the widely used reference DEM - SLDEM2015. As a result, the RMS errors of the tie points are all around half pixel in image space, indicating a high internal precision; the RMS errors of the control points are about one grid cell size of SLDEM2015, indicating that the resultant DOM is tied to SLDEM2015 well.

An Extraction Method of an Informative DOM Node from a Web Page by Using Layout Information

NASA Astrophysics Data System (ADS)

Tsuruta, Masanobu; Masuyama, Shigeru

We propose an informative DOM node extraction method from a Web page for preprocessing of Web content mining. Our proposed method LM uses layout data of DOM nodes generated by a generic Web browser, and the learning set consists of hundreds of Web pages and the annotations of informative DOM nodes of those Web pages. Our method does not require large scale crawling of the whole Web site to which the target Web page belongs. We design LM so that it uses the information of the learning set more efficiently in comparison to the existing method that uses the same learning set. By experiments, we evaluate the methods obtained by combining one that consists of the method for extracting the informative DOM node both the proposed method and the existing methods, and the existing noise elimination methods: Heur removes advertisements and link-lists by some heuristics and CE removes the DOM nodes existing in the Web pages in the same Web site to which the target Web page belongs. Experimental results show that 1) LM outperforms other methods for extracting the informative DOM node, 2) the combination method (LM, {CE(10), Heur}) based on LM (precision: 0.755, recall: 0.826, F-measure: 0.746) outperforms other combination methods.

Dissolved Organic Matter Quality in a Shallow Aquifer of Bangladesh: Implications for Arsenic Mobility.

PubMed

Mladenov, Natalie; Zheng, Yan; Simone, Bailey; Bilinski, Theresa M; McKnight, Diane M; Nemergut, Diana; Radloff, Kathleen A; Rahman, M Moshiur; Ahmed, Kazi Matin

2015-09-15

In some high arsenic (As) groundwater systems, correlations are observed between dissolved organic matter (DOM) and As concentrations, but in other systems, such relationships are absent. The role of labile DOM as the main driver of microbial reductive dissolution is not sufficient to explain the variation in DOM-As relationships. Other processes that may also influence As mobility include complexation of As by dissolved humic substances, and competitive sorption and electron shuttling reactions mediated by humics. To evaluate such humic DOM influences, we characterized the optical properties of filtered surface water (n = 10) and groundwater (n = 24) samples spanning an age gradient in Araihazar, Bangladesh. Further, we analyzed large volume fulvic acid (FA) isolates (n = 6) for optical properties, C and N content, and (13)C NMR spectroscopic distribution. Old groundwater (>30 years old) contained primarily sediment-derived DOM and had significantly higher (p < 0.001) dissolved As concentration than groundwater that was younger than 5 years old. Younger groundwater had DOM spectroscopic signatures similar to surface water DOM and characteristic of a sewage pollution influence. Associations between dissolved As, iron (Fe), and FA concentration and fluorescence properties of isolated FA in this field study suggest that aromatic, terrestrially derived FAs promote As-Fe-FA complexation reactions that may enhance As mobility.

Molecular Fractionation of Dissolved Organic Matter in a Shallow Subterranean Estuary: The Role of the Iron Curtain

PubMed Central

2016-01-01

Iron that precipitates under aerobic conditions in natural aquatic systems scavenges dissolved organic matter (DOM) from solution. Subterranean estuaries (STEs) are of major importance for land–ocean biogeochemical fluxes. Their specific redox boundaries, coined the “iron curtain” due to the abundance of precipitated iron(III) (oxy)hydroxides, are hot spots for the removal and redissolution of iron, associated nutrients, and DOM. We used ultra-high-resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry to molecularly characterize the iron-coagulating fractions of 32 groundwater and seawater DOM samples along a salinity gradient from a shallow STE on Spiekeroog Island, North Sea, Germany, and linked our findings to trace metal and nutrient concentrations. We found systematic iron coagulation of large (>450 Da), oxygen-rich, and highly aromatic DOM molecules of terrestrial origin. The extent of coagulation increased with growing terrestrial influence along the salinity gradient. Our study is the first to show that the iron curtain may be capable of retaining terrigenous DOM fractions in marine sediments. We hypothesize that the iron curtain serves as an inorganic modulator for the supply of DOM from groundwaters to the sea, and that the STE has the potential to act as a temporal storage or even sink for terrigenous aromatic DOM compounds. PMID:27976873

Land-based salmon aquacultures change the quality and bacterial degradation of riverine dissolved organic matter

NASA Astrophysics Data System (ADS)

Kamjunke, Norbert; Nimptsch, Jorge; Harir, Mourad; Herzsprung, Peter; Schmitt-Kopplin, Philippe; Neu, Thomas R.; Graeber, Daniel; Osorio, Sebastian; Valenzuela, Jose; Carlos Reyes, Juan; Woelfl, Stefan; Hertkorn, Norbert

2017-03-01

Aquacultures are of great economic importance worldwide but pollute pristine headwater streams, lakes, and estuaries. However, there are no in-depth studies of the consequences of aquacultures on dissolved organic matter (DOM) composition and structure. We performed a detailed molecular level characterization of aquaculture DOM quality and its bacterial degradation using four salmon aquacultures in Chile. Fluorescence measurements, ultrahigh-resolution mass spectrometry, and nuclear magnetic resonance spectroscopy of the DOM revealed specific and extensive molecular alterations caused by aquacultures. Aquacultures released large quantities of readily bioavailable metabolites (primarily carbohydrates and peptides/proteins, and lipids), causing the organic matter downstream of all the investigated aquacultures to deviate strongly from the highly processed, polydisperse and molecularly heterogeneous DOM found in pristine rivers. However, the upstream individual catchment DOM signatures remained distinguishable at the downstream sites. The benthic algal biovolume decreased and the bacterial biovolume and production increased downstream of the aquacultures, shifting stream ecosystems to a more heterotrophic state and thus impairing the ecosystem health. The bacterial DOM degradation rates explain the attenuation of aquaculture DOM within the subsequent stream reaches. This knowledge may aid the development of improved waste processing facilities and may help to define emission thresholds to protect sensitive stream ecosystems.

High Pressure Size Exclusion Chromatography (HPSEC) Determination of Dissolved Organic Matter Molecular Weight Revisited: Accounting for Changes in Stationary Phases, Analytical Standards, and Isolation Methods.

PubMed

McAdams, Brandon C; Aiken, George R; McKnight, Diane M; Arnold, William A; Chin, Yu-Ping

2018-01-16

We reassessed the molecular weight of dissolved organic matter (DOM) determined by high pressure size exclusion chromatography (HPSEC) using measurements made with different columns and various generations of polystyrenesulfonate (PSS) molecular weight standards. Molecular weight measurements made with a newer generation HPSEC column and PSS standards from more recent lots are roughly 200 to 400 Da lower than initial measurements made in the early 1990s. These updated numbers match DOM molecular weights measured by colligative methods and fall within a range of values calculated from hydroxyl radical kinetics. These changes suggest improved accuracy of HPSEC molecular weight measurements that we attribute to improved accuracy of PSS standards and changes in the column packing. We also isolated DOM from wetlands in the Prairie Pothole Region (PPR) using XAD-8, a cation exchange resin, and PPL, a styrene-divinylbenzene media, and observed little difference in molecular weight and specific UV absorbance at 280 nm (SUVA 280 ) between the two solid phase extraction resins, suggesting they capture similar DOM moieties. PPR DOM also showed lower SUVA 280 at similar weights compared to DOM isolates from a global range of environments, which we attribute to oxidized sulfur in PPR DOM that would increase molecular weight without affecting SUVA 280 .

Multimedia CALLware: The Developer's Responsibility.

ERIC Educational Resources Information Center

Dodigovic, Marina

The early computer-assisted-language-learning (CALL) programs were silent and mostly limited to screen or printer supported written text as the prevailing communication resource. The advent of powerful graphics, sound and video combined with AI-based parsers and sound recognition devices gradually turned the computer into a rather anthropomorphic…

Mention Detection: Heuristics for the OntoNotes Annotations

DTIC Science & Technology

2011-01-01

Mention Detection: Heuristics for the OntoNotes annotations Jonathan K. Kummerfeld, Mohit Bansal, David Burkett and Dan Klein Computer Science...considered the provided parses and parses produced by the Berke - ley parser (Petrov et al., 2006) trained on the pro- vided training data. We added a

Bioavailability of riverine dissolved organic matter in three Baltic Sea estuaries and the effect of catchment land use

NASA Astrophysics Data System (ADS)

Asmala, E.; Autio, R.; Kaartokallio, H.; Pitkänen, L.; Stedmon, C. A.; Thomas, D. N.

2013-11-01

The microbial degradation of dissolved organic carbon and nitrogen (DOC, DON) was studied in three Finnish boreal estuaries with contrasting land use patterns (Kiiminkijoki - natural forest and peatland; Kyrönjoki - agricultural; Karjaanjoki - mixed/urban). Bioassays of 12-18 d long durations were used in 3 seasons at in situ temperatures. Besides the bulk parameters, a suite of dissolved organic matter (DOM) quality parameters were also investigated, including colored DOM (CDOM), fluorescent DOM and the molecular weight of DOM. Bioavailable DOC and DON pools varied significantly between the estuaries, from 7.9 to 10.6% and from 5.5 to 21.9%, respectively. DOM originating from the catchment dominated by natural forests and peatlands (Kiiminkijoki) had the lowest DOC and DON degradation rates, as well as the lowest proportions of biodegradable DOC and DON. A greater proportion of agricultural land in the catchment increased the bioavailability of DON, but not the bioavailability of DOC (Kyrönjoki). Additionally, DOM quality varied significantly between the estuaries, and DOM originating from the agricultural Kyrönjoki catchment sustained higher DOC and DON degradation rates and higher bacterial growth efficiency (BGE) compared to those of the natural forest and peat dominated Kiiminkijoki catchment. The quality of DOM, indicated by differences in CDOM, fluorescent DOM and molecular weight, varied between estuaries with differing land use and was concluded to be major driver of BGE of these systems and thereafter to the microbial CO2 fluxes from the estuaries. The differences in BGE resulted in a 5-fold difference in the calculated daily bacterial CO2 emissions between the study's estuaries due to bacterial activity, ranging from 40 kg C d-1 in the Karjaanjoki estuary to 200 kg C d-1 in the Kyrönjoki estuary. Lower DOC:DON ratios, smaller molecular weight and higher CDOM absorption spectral slope values of DOM resulted in higher proportion of the initial DOC and DON being transferred to microbial growth and therefore to the pelagic food web. The pristine, peatland and forest-dominated Kiiminkijoki catchment had the lowest BGE, and therefore proportionally highest CO2 fluxes.

Similarities and differences in dissolved organic matter response in two headwater streams under contrasted hydro-climatic regimes

NASA Astrophysics Data System (ADS)

Butturini, Andrea; Guarch, Alba; Battin, Tom

2017-04-01

Dissolved organic matter (DOM) concentration and properties in headwater streams are strongly shaped by hydrology. Besides the direct relationship with storms and high flows, seasonal variability of base flow also influences DOM variability. This study focuses on identifying the singularities and similarities in DOM - discharge relationships between an intermittent Mediterranean stream (Fuirosos) and a perennial Alpine stream (Oberer Seebach). Oberer Seebach had a higher discharge mean, but Fuirosos had a higher variability in flow and in magnitude of storm events. During three years we performed an intensive sampling that allows us to satisfactorily capture abrupt and extreme storms. We analysed dissolved organic carbon concentration (DOC) and optical properties of DOM and we calculated the specific ultraviolet absorbance (SUVA), the spectral slopes ratio (SR), the fluorescence index (FI), the biological index (BIX) and the humification index (HIX). DOM in Fuirosos was significantly more concentrated than in Oberer Seebach, and more terrigenous (lower FI), more degraded (lower BIX), more aromatic (higher SUVA) and more humificated (higher HIX). Most of the DOM properties showed a clear relationship with discharge and the sign of the global response was identical in both streams. However, discharge was a more robust predictor of DOM variability in Oberer Seebach than in Fuirosos. In fact, low flow and rewetting periods in Fuirosos introduced considerable dispersion in the relationship. During snowmelt in Oberer Seebach the sensitivity to discharge also decreased (DOC and BIX) or disappeared (SR, FI and HIX). The magnitude of the storm events (DQ) in Fuirosos significantly drove the changes in DOC, FI, BIX and SUVA. This suggests that the flushing/dilution patterns were essentially associated to the occurrence of storm episodes in Fuirosos. In contrast, in Oberer Seebach all DOM qualitative properties were unrelated to DQ and it significantly explained only the change in DOC. While the storms were behind the DOC oscillations, DOM quality change in Oberer Seebach was more coupled to basal flow conditions. Finally, the biogeochemical analysis of two hydrologically different headwaters motivates to speculate about the impact of the hydrological regime alteration forced by atmospheric drivers on DOM quantity and properties.

Short-term degradation of terrestrial DOM in the coastal ocean: Implications for nutrient subsidies and marine microbial community structure

NASA Astrophysics Data System (ADS)

Oliver, A. A.; Tank, S. E.; Kellogg, C.

2015-12-01

The export of riverine dissolved organic matter (DOM) to the coastal ocean provides an important link between terrestrial and aquatic ecosystems. The coastal temperate rainforests of British Columbia contain extensive freshwater networks that export significant amounts of water and DOM to the ocean, representing significant cross-system hydrologic and biogeochemical linkages. To better understand the importance of these linkages and implications for ecosystem structure and function, we used an experimental approach to investigate the role of microbial and photodegradation transformations of DOM exported from small coastal catchments to the marine environment. At two time periods (August 2014, March 2015), stream water from the outlets of two coastal watersheds was filtered (<0.2 μm), and treated with microbial inoculums from across a salinity gradient (i.e., freshwater, estuarine, and marine). Treatments were incubated in the ocean under light and dark conditions for 8 days. At 0, 3 and 8 days, samples were analyzed for DOC, TDN, DIN, and DON. Changes in DOM composition were determined with optical characterization techniques such as absorbance (SUVA, S, Sr) and fluorescence (EEM). Microbial community response was measured using cell counts and DNA/RNA amplicon sequencing to determine changes in bacterial abundance and community composition. General patterns indicated that microbial communities from the high salinity treatment (i.e. most marine) were the most effective at utilizing freshwater DOM, especially under light conditions. In some treatments, DOM appeared as a potential source of inorganic nitrogen with corresponding shifts in microbial community composition. Incubations using inoculum from low and mid salinity levels demonstrated smaller changes, indicating that DOM exported from these streams may not be extensively utilized until exposed to higher salinity environments further from stream outlets. These results suggest a role for terrestrial sourced-DOM as a subsidy for microbial communities within the near shore marine environment, and emphasize that changes in DOM exports due to land development or climate change may have implications for coastal food web processes and biogeochemical cycling.

Environmental drivers of dissolved organic matter molecular composition in the Delaware Estuary

NASA Astrophysics Data System (ADS)

Osterholz, Helena; Kirchman, David L.; Niggemann, Jutta; Dittmar, Thorsten

2016-11-01

Estuaries as connectors of freshwater and marine aquatic systems are hotspots of biogeochemical element cycling. In one of the best studied temperate estuaries, the Delaware Estuary (USA), we investigated the variability of dissolved organic matter (DOM) over five sampling cruises along the salinity gradient in August and November of 3 consecutive years. Dissolved organic carbon (DOC) concentrations were more variable in the upper reaches of the estuary (245±49 µmol L-1) than at the mouth of the estuary (129±14 µmol L-1). Bulk DOC decreased conservatively along the transect in November but was non-conservative with increased DOC concentrations mid-estuary in August. Detailed analysis of the solid-phase extractable DOM pool via ultrahigh resolution mass spectrometry (Fourier-transform ion cyclotron resonance mass spectrometry, FT-ICR-MS) revealed compositional differences at the molecular level that were not reflected in changes in concentration. Besides the mixing of terrestrial and marine endmember signatures, river discharge levels and biological activity were found to impact DOM molecular composition. DOM composition changed less between August and November than along the salinity gradient. Relative contributions of presumed photolabile DOM compounds did not reveal non-conservative behavior indicative of photochemical processing; suggesting that on the timescales of estuarine mixing photochemical removal of molecules plays a minor role in the turbid Delaware Bay. Overall, a large portion of molecular formulae overlapped between sampling campaigns and persisted during estuarine passage. Extending the analysis to the structural level via the fragmentation of molecular masses in the FT-ICR-MS cell, we found that the relative abundance of isomers along the salinity gradient did not change, indicating a high structural similarity of aquatic DOM independent of the origin. These results point towards a recalcitrant character of the DOM supplied by the Delaware River. We demonstrate that in addition to bulk DOC quantification, detailed information on molecular composition is essential for constraining sources of DOM and to identify the processes that impact estuarine DOM, thereby controlling amount and composition of DOM eventually discharged to the ocean through estuaries.

Enhanced catalytic performance for methane combustion of 3DOM CoFe2O4 by co-loading MnOx and Pd-Pt alloy nanoparticles

NASA Astrophysics Data System (ADS)

Li, Xiangyu; Liu, Yuxi; Deng, Jiguang; Xie, Shaohua; Zhao, Xingtian; Zhang, Yang; Zhang, Kunfeng; Arandiyan, Hamidreza; Guo, Guangsheng; Dai, Hongxing

2017-05-01

Three-dimensionally ordered macroporous (3DOM) CoFe2O4, zMnOx/3DOM CoFe2O4 (z = 4.99-12.30 wt%), and yPd-Pt/6.70 wt% MnOx/3DOM CoFe2O4 (y = 0.44-1.81 wt%; Pd/Pt molar ratio = 2.1-2.2) have been prepared using the polymethyl methacrylate microspheres-templating, incipient wetness impregnation, and bubble-assisted polyvinyl alcohol-protected reduction strategies, respectively. All of the samples were characterized by means of various techniques. Catalytic performance of the samples was measured for methane combustion. It is shown that the as-prepared samples exhibited a high-quality 3DOM structure (103 ± 20 nm in pore size) and a surface area of 19-28 m2/g, and the noble metal or alloy nanoparticles (NPs) with a size of 2.2-3.0 nm were uniformly dispersed on the macropore wall surface of 3DOM CoFe2O4. The loading of MnOx on CoFe2O4 gave rise to a slight increase in activity, however, the dispersion of Pd-Pt NPs on 6.70MnOx/3DOM CoFe2O4 significantly enhanced the catalytic performance, with the 1.81Pd2.1Pt/6.70MnOx/3DOM CoFe2O4 sample showing the highest activity (T10% = 255 °C, T50% = 301 °C, and T90% = 372 °C at a space velocity of 20,000 mL/(g h)). We believe that the excellent catalytic activity of 1.81Pd2.1Pt/6.70MnOx/3DOM CoFe2O4 was related to its well-dispersed Pd-Pt alloy NPs, high adsorbed oxygen species concentration, good low-temperature reducibility, and strong interaction between MnOx or Pd-Pt NPs and 3DOM CoFe2O4.

The Influence of Water Circulation on Dissolved Organic Matter Dynamics in Bald Head Creek

NASA Astrophysics Data System (ADS)

Lebrasse, M. C.; Osburn, C. L.; Bohnenstiehl, D. R.; He, R.

2016-12-01

Dissolved organic matter (DOM) plays an important role in biogeochemical cycles in estuaries such as tidal creeks draining coastal wetlands such as salt marshes. However, significant knowledge gaps remain regarding the quantity and quality of the DOM that tidally exchanges between salt marshes and their adjacent estuaries. Tidal movements play a central role in lateral exchanges of materials and bidirectional flow results in the mixing of DOM from marsh plants and estuarine DOM. The aim of this study was to better understand the role of water circulation on the distribution and quality of DOM in Bald Head Creek, a tributary to the Cape Fear River estuary in eastern North Carolina. Dissolved organic carbon (DOC) concentration, stable carbon isotopes, and chromophoric DOM (CDOM) absorbance at 254 nm (a254) were used to distinguish between DOM quantity and quality at three locations along the creek: Site 3 (upstream), Site 2 (middle stream), and Site 1 (near the creek mouth). Samples were collected over four tidal cycles between March-August 2016 and compared to time series data collected approximately weekly from 2014-2016. DOM characteristics differed substantially over the tidal cycle. Higher CDOM and DOC concentration were observed at low tide than at high tide at all three sites, suggesting greater export of carbon from the marsh into the creek as the tides recede. Analysis of CDOM quality based on specific UV absorbance at 254 nm (SUVA254) and spectral slope ratio (SR) showed that the marsh end-member (Site 3) source of DOM had greater aromaticity and higher molecular weight. Site 1 showed greater variability over the tidal cycle most likely due to a greater tidal influence, being closer to the mouth. Additionally, an unmanned surface vehicle (USV) and a hydrodynamic model were used to map water circulation and DOC concentration along the creek to compute exchanges with the adjacent estuary. Results suggest that estuarine OM dynamics are strongly controlled by the circulation of water, especially for tidal creeks where tidal pumping can dominate lateral fluxes of DOM to adjacent waters.

Temperature and chemical composition controls on sorption of DOC to iron hydroxides under dynamic flow conditions

NASA Astrophysics Data System (ADS)

Daugherty, E.; Lobo, G.; Pallud, C. E.; Borch, T.

2017-12-01

Mineral-organic associations contribute substantially to the long-term preservation of soil organic matter (SOM) and carbon sequestration. Iron-organic associations are especially important because iron (hydr)oxide minerals and surface coatings are prevalent and effective sorbents of SOM. While mineral-organic associations, and iron-organic associations in particular have been studied extensively, it remains unclear how the abiotic interactions between these soil components will be affected by shifting climate. Will DOM adsorption increase or decrease with rising temperature? Does the adsorption response to temperature depend on the type of DOM? To answer these questions, we investigated the impacts of temperature (7, 25, and 45˚C) and dissolved organic matter (DOM) type on DOM sorption to ferrihydrite-coated sand in a fixed bed column at neutral pH. Breakthrough curves of the standard humic substances at 25˚C indicated that humic acids were in general retained less than fulvic acids. Response to temperature varied from no effect to a marked increase in the quantity adsorbed. Modeling of DOM breakthrough curves using the advection-diffusion equation with a linear adsorption isotherm showed that the equilibrium distribution coefficient increased over time, with retardation factors increasing 4 to 10 times for every simulation. This suggests that the DOM adsorbed to the ferrihydrite-coated sand acts as a sorbent that is 4 to 10 times more powerful than the coated sand alone. Differences in breakthrough due to DOM type and temperature became less pronounced at slower flow rates, and breakthrough occurred at nearly half as many pore volumes at a flow rate of 0.01 mL min-1 vs. 0.05 mL min-1. These results suggest DOM adsorption was diffusion controlled at low flow rates and kinetically controlled at high flow rates, which may explain the increased temperature sensitivity at high flow rates. Analyses to determine adsorptive fractionation are ongoing, but preliminary data suggest that aromatic moieties may be selectively retained during initial contact between DOM and ferrihydrite. Our results suggest that water flow rate is likely to play an important role in determining the relative effects of temperature on DOM sorption to iron minerals.

Non-riverine pathways of terrigenous carbon to the ocean

NASA Astrophysics Data System (ADS)

Dittmar, T.

2007-12-01

The extent and nature of non-riverine fluxes of carbon from land to ocean are poorly understood. Tidal pumping from highly productive coastal environments, atmospheric deposition and submarine groundwater discharge can be significant transport mechanisms for carbon to the ocean. Evidence is mounting that tidally-induced porewater fluxes ("outwelling") of dissolved organic matter (DOM) from mangroves and salt marshes alone may be similar in magnitude as the global riverine flux of DOM. Tidal pumping of dissolved inorganic carbon (DIC) might exceed organic carbon fluxes by far, but the existing knowledge on DIC outwelling is too scarce for a first global estimate. Results from two case studies on the biogeochemistry of DOM outwelling are presented, from the mangroves in Northern Brazil and the salt marshes in the Northern Gulf of Mexico. Ongoing research in the Northern Gulf of Mexico indicates that outwelling and groundwater inputs probably exceed riverine DOM fluxes in this region. Similar observations were made in Northern Brazil. There, the fate of mangrove-derived DOM could be traced from its source in the mangrove sediments to the outer North Brazil shelf by using a combination of isotopic and molecular approaches. Reversed-phase liquid chromatography / mass spectrometry (LC/MS) provided a multifaceted array of information that mirrors the molecular complexity of DOM. Statistical analyses on these data revealed significant differences between mangrove and open-ocean DOM which successively disappeared by irradiating the samples with natural sunlight. Nuclear magnetic resonance analyses yielded concurrent results. Ultrahigh-resolution Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) is the only technique capable of resolving and identifying individual elemental compositions in these complex mixtures. We applied this technique for characterizing mangrove-derived DOM and to assess the molecular changes that occur in the initial stages of outwelling. The different approaches concordantly show the presence of photodegraded mangrove DOM on the North Brazil shelf. During transport offshore, sunlight efficiently destroyed aromatic molecules, removing about one third of mangrove-derived DOM. The remainder was refractory and may thus be distributed over the oceans.

Removal of inorganic mercury and methylmercury from surface waters following coagulation of dissolved organic matter with metal-based salts

USGS Publications Warehouse

Henneberry, Y.K.; Kraus, T.E.C.; Fleck, J.A.; Krabbenhoft, D.P.; Bachand, P.M.; Horwath, W.R.

2011-01-01

The presence of inorganic mercury (IHg) and methylmercury (MeHg) in surface waters is a health concern worldwide. This study assessed the removal potential use of metal-based coagulants as a means to remove both dissolved IHg and MeHg from natural waters and provides information regarding the importance of Hg associations with the dissolved organic matter (DOM) fraction and metal hydroxides. Previous research indicated coagulants were not effective at removing Hg from solution; however these studies used high concentrations of Hg and did not reflect naturally occurring concentrations of Hg. In this study, water collected from an agricultural drain in the Sacramento-San Joaquin Delta was filtered to isolate the dissolved organic matter (DOM) fraction. The DOM was then treated with a range of coagulant doses to determine the efficacy of removing all forms of Hg from solution. Three industrial-grade coagulants were tested: ferric chloride, ferric sulfate, and polyaluminum chloride. Coagulation removed up to 85% of DOM from solution. In the absence of DOM, all three coagulants released IHg into solution, however in the presence of DOM the coagulants removed up to 97% of IHg and 80% of MeHg. Results suggest that the removal of Hg is mediated by DOM-coagulant interactions. There was a preferential association of IHg with the more aromatic, higher molecular weight fraction of DOM but no such relationship was found for MeHg. This study offers new fundamental insights regarding large-scale removal of Hg at environmentally relevant regarding large-scale removal of Hg at environmentally relevant concentrations.

Tracing the origin of dissolved organic matter (DOM) in subterranean estuaries using colored DOM and amino acids

NASA Astrophysics Data System (ADS)

Kim, T.; Kwon, E.; Kim, G.

2011-12-01

In order to determine the origin of dissolved organic matter (DOM) in the subterranean estuary (STE), the mixing zone of fresh terrestrial groundwater and recirculating seawater in a coastal permeable aquifer, we conducted water sampling from two STEs with different geological settings: (1) Jeju Island beaches (Hwasun and Samyang), which are composed of volcanic rocks and sandy sediments, and (2) Hampyeong beach, which is located in a large intertidal, sandy flat zone. The distributions of salinity, total hydrolysable amino acids (THAA), dissolved organic carbon (DOC), and colored DOM (CDOM) were measured for groundwater samples in these STEs. In the Hwasun STE, the humic-like peak decreases with increasing salinity, whereas the protein-like peak does not show a clear relationship with salinity. In contrast, in the Samyang STE, both humic-like peak and protein-like peak increase with increasing salinity. These contrasting results indicate that DOM in the Hwasun STE originates mainly from terrestrial inputs, while that in the Samyang STE originates mainly from biological and/or microbial activities. In the Hampyeong STE, we observed good correlations among the biodegradation index, alanine D/L ratios, THAA concentrations, DOC, and CDOM index (both humic-like and protein-like). Together with their geographical distribution patterns, these correlations indicate that DOM in the Hampyeong STE is mainly derived from marine sediments in the course of seawater recirculation. Our study shows that CDOM and amino acids are excellent tracers of DOM in the STE where DOM is derived from diverse sources.

Interactions between copper(II) and DOM in the urban stormwater runoff: modeling and characterizations.

PubMed

Zhao, Chen; Wang, Chong-Chen; Li, Jun-Qi; Wang, Peng; Ou, Jia-Qi; Cui, Jing-Rui

2018-01-01

Dissolved organic matter (DOM) can strongly interact with both organic and inorganic contaminants to influence their transportation, transformation, bioavailability, toxicity and even their ultimate fate. Within this work, DOM was extracted from urban stormwater runoff samples collected from a regular sampling site of a typical residential area in Beijing, China. Copper(II) ions were selected as model to investigate the interactions between DOM and typical heavy metals. Both ultraviolet (UV) absorbance and fluorescence titration methods were introduced to determine the complex capacities (C L ) and conditional stability constants (log K M ) of bonding between DOM and copper (II) ions, which revealed that the values of C L were 85.62 and 87.23 μmol mg -1 and the log K M values were 5.37 and 5.48, respectively. The results suggested the successful complexation between DOM and copper(II) ions. Furthermore, morphology of the DOM binding to copper(II) ions was confirmed by both energy-dispersive X-ray spectroscopy (EDX) and X-ray photoelectron spectroscopy (XPS), which can facilitate to clarify the corresponding mechanism. The Cu 2p 3/2 peak at 933.7 eV and the characteristic shake-up peaks of Cu-O were found in the XPS spectra, implying that copper(II) ions might coordinate with hydroxyl (aliphatic or phenolic) or carboxyl groups. With these profitable results, it can be concluded that DOM in urban stormwater runoff has a strong binding affinity with copper(II) ions, which may further lead to potentially significant influence on their migration and transformation.

Hydrologic control of dissolved organic matter concentration and quality in a semiarid artificially drained agricultural catchment

NASA Astrophysics Data System (ADS)

Bellmore, Rebecca A.; Harrison, John A.; Needoba, Joseph A.; Brooks, Erin S.; Kent Keller, C.

2015-10-01

Agricultural practices have altered watershed-scale dissolved organic matter (DOM) dynamics, including in-stream concentration, biodegradability, and total catchment export. However, mechanisms responsible for these changes are not clear, and field-scale processes are rarely directly linked to the magnitude and quality of DOM that is transported to surface water. In a small (12 ha) agricultural catchment in eastern Washington State, we tested the hypothesis that hydrologic connectivity in a catchment is the dominant control over the concentration and quality of DOM exported to surface water via artificial subsurface drainage. Concentrations of dissolved organic carbon (DOC) and humic-like components of DOM decreased while the Fluorescence Index and Freshness Index increased with depth through the soil profile. In drain discharge, these characteristics were significantly correlated with drain flow across seasons and years, with drain DOM resembling deep sources during low-flow and shallow sources during high flow, suggesting that DOM from shallow sources bypasses removal processes when hydrologic connectivity in the catchment is greatest. Assuming changes in streamflow projected for the Palouse River (which contains the study catchment) under the A1B climate scenario (rapid growth, dependence on fossil fuel, and renewable energy sources) apply to the study catchment, we project greater interannual variability in annual DOC export in the future, with significant increases in the driest years. This study highlights the variability in DOM inputs from agricultural soil to surface water on daily to interannual time scales, pointing to the need for a more nuanced understanding of agricultural impacts on DOM dynamics in surface water.

Dissolved organic matter composition of Arctic rivers: Linking permafrost and parent material to riverine carbon

USGS Publications Warehouse

O’Donnell, Jonathan A.; Aiken, George R.; Swanson, David K.; Santosh, Panda; Butler, Kenna D.; Baltensperger, Andrew P.

2016-01-01

Recent climate change in the Arctic is driving permafrost thaw, which has important implications for regional hydrology and global carbon dynamics. Permafrost is an important control on groundwater dynamics and the amount and chemical composition of dissolved organic matter (DOM) transported by high-latitude rivers. The consequences of permafrost thaw for riverine DOM dynamics will likely vary across space and time, due in part to spatial variation in ecosystem properties in Arctic watersheds. Here we examined watershed controls on DOM composition in 69 streams and rivers draining heterogeneous landscapes across a broad region of Arctic Alaska. We characterized DOM using bulk dissolved organic carbon (DOC) concentration, optical properties, and chemical fractionation and classified watersheds based on permafrost characteristics (mapping of parent material and ground ice content, modeling of thermal state) and ecotypes. Parent material and ground ice content significantly affected the amount and composition of DOM. DOC concentrations were higher in watersheds underlain by fine-grained loess compared to watersheds underlain by coarse-grained sand or shallow bedrock. DOC concentration was also higher in rivers draining ice-rich landscapes compared to rivers draining ice-poor landscapes. Similarly, specific ultraviolet absorbance (SUVA254, an index of DOM aromaticity) values were highest in watersheds underlain by fine-grained deposits or ice-rich permafrost. We also observed differences in hydrophobic organic acids, hydrophilic compounds, and DOM fluorescence across watersheds. Both DOC concentration and SUVA254 were negatively correlated with watershed active layer thickness, as determined by high-resolution permafrost modeling. Together, these findings highlight how spatial variations in permafrost physical and thermal properties can influence riverine DOM.

Colored dissolved organic matter in shallow estuaries: relationships between carbon sources and light attenuation

USGS Publications Warehouse

Oestreich, W.K.; Ganju, Neil K.; Pohlman, John; Suttles, Steven E.

2016-01-01

Light availability is of primary importance to the ecological function of shallow estuaries. For example, benthic primary production by submerged aquatic vegetation is contingent upon light penetration to the seabed. A major component that attenuates light in estuaries is colored dissolved organic matter (CDOM). CDOM is often measured via a proxy, fluorescing dissolved organic matter (fDOM), due to the ease of in situ fDOM sensor measurements. Fluorescence must be converted to CDOM absorbance for use in light attenuation calculations. However, this CDOM–fDOM relationship varies among and within estuaries. We quantified the variability in this relationship within three estuaries along the mid-Atlantic margin of the eastern United States: West Falmouth Harbor (MA), Barnegat Bay (NJ), and Chincoteague Bay (MD/VA). Land use surrounding these estuaries ranges from urban to developed, with varying sources of nutrients and organic matter. Measurements of fDOM (excitation and emission wavelengths of 365 nm (±5 nm) and 460 nm (±40 nm), respectively) and CDOM absorbance were taken along a terrestrial-to-marine gradient in all three estuaries. The ratio of the absorption coefficient at 340 nm (m−1) to fDOM (QSU) was higher in West Falmouth Harbor (1.22) than in Barnegat Bay (0.22) and Chincoteague Bay (0.17). The CDOM : fDOM absorption ratio was variable between sites within West Falmouth Harbor and Barnegat Bay, but consistent between sites within Chincoteague Bay. Stable carbon isotope analysis for constraining the source of dissolved organic matter (DOM) in West Falmouth Harbor and Barnegat Bay yielded δ13C values ranging from −19.7 to −26.1 ‰ and −20.8 to −26.7 ‰, respectively. Concentration and stable carbon isotope mixing models of DOC (dissolved organic carbon) indicate a contribution of 13C-enriched DOC in the estuaries. The most likely source of 13C-enriched DOC for the systems we investigated is Spartina cordgrass. Comparison of DOC source to CDOM : fDOM absorption ratios at each site demonstrates the relationship between source and optical properties. Samples with 13C-enriched carbon isotope values, indicating a greater contribution from marsh organic material, had higher CDOM : fDOM absorption ratios than samples with greater contribution from terrestrial organic material. Applying a uniform CDOM : fDOM absorption ratio and spectral slope within a given estuary yields errors in modeled light attenuation ranging from 11 to 33 % depending on estuary. The application of a uniform absorption ratio across all estuaries doubles this error. This study demonstrates that light attenuation coefficients for CDOM based on continuous fDOM records are highly dependent on the source of DOM present in the estuary. Thus, light attenuation models for estuaries would be improved by quantification of CDOM absorption and DOM source identification.

Chemical compositions of dissolved organic matter from various sources as characterized by solid-state NMR

USDA-ARS?s Scientific Manuscript database

Dissolved organic matter (DOM) in surface waters plays an important role in biogeochemical and ecological processes. This study used solid-state NMR techniques to explore the molecular signatures of riverine DOM in relation to its point and nonpoint sources. DOM samples were isolated from (1) two st...

MEETING IN PHILADELPHIA: NUTRIENT CONCENTRATIONS IN FLOWING WATERS OF THE SOUTH FORK BROAD RIVER, GEORGIA WATERSHED

EPA Science Inventory

The objective of this poster is by comparing nutrient and DOM concentrations in small and large streams, we hope to better understand: (1) watershed controls on stream nutrient and DOM concentrations; and (2) the variability of nutrient and DOM concentrations within a river netwo...

Transformations of dissolved organic matter in a landfill leachate--a size exclusion chromatography/mass spectrometric approach.

PubMed

Persson, Linn; Alsberg, Tomas; Ledin, Anna; Odham, Göran

2006-08-01

The aim of the present study was to search for qualitative changes in the landfill leachate DOM along a groundwater gradient. The study was focused on DOM characteristics of importance for its interaction with pollutants, such as molecular weight distribution and aromaticity. It was concluded that the leachate DOM underwent substantial qualitative changes along the investigated gradient at the Vejen landfill, Denmark. The molecular weight decreased, the polydispersity increased, and the aromaticity varied with the lowest values found in the middle of the gradient. The high aromaticity in the end of the gradient may explain the higher DOM binding capacity towards hydrophobic compounds seen earlier in these samples. The relative abundance of ions with mass to charge ratio (m/z) of 600-1200 seemed to be very stable along the gradient, indicating that the observed qualitative changes of the DOM is mostly attributed to changes in the m/z 100-600 range. The DOM seemed to become more similar to fulvic acids present in uncontaminated groundwater with respect to molecular weight and polydispersity along the gradient.

Using latent effects to determine the ecological importance of dissolved organic matter to marine invertebrates.

PubMed

Wendt, Dean E; Johnson, Collin H

2006-10-01

The uptake and utilization of dissolved organic matter (DOM) by marine invertebrates is a field that has received significant attention over the past 100 years. Although it is well established that DOM is taken up by marine invertebrates, the extent to which it contributes to an animal's survival, growth, and reproduction (that is, the ecological benefits) remains largely unknown. Previous work seeking to demonstrate the putative ecological benefits of DOM uptake have examined them within a single life stage of an animal. Moreover, most of the benefits are demonstrated through indirect approaches by examining (1) mass balance, or (2) making comparisons of oxyenthalpic conversions of transport rates to metabolic rate as judged by oxygen consumption. We suggest that directly examining delayed metamorphosis or the latent effects associated with nutritional stress of larvae is a better model for investigating the ecological importance of DOM to marine invertebrates. We also provide direct evidence that availability of DOM enhances survival and growth of the bryozoan Bugula neritina. That DOM offsets latent effects in B. neritina suggests that the underlying mechanisms are at least in part energetic.

Dissolved organic matter in the Florida everglades: Implications for ecosystem restoration

USGS Publications Warehouse

Aiken, G.R.; Gilmour, C.C.; Krabbenhoft, D.P.; Orem, W.

2011-01-01

Dissolved organic matter (DOM) in the Florida Everglades controls a number of environmental processes important for ecosystem function including the absorption of light, mineral dissolution/precipitation, transport of hydrophobic compounds (e.g., pesticides), and the transport and reactivity of metals, such as mercury. Proposed attempts to return the Everglades to more natural flow conditions will result in changes to the present transport of DOM from the Everglades Agricultural Area and the northern conservation areas to Florida Bay. In part, the restoration plan calls for increasing water flow throughout the Everglades by removing some of the manmade barriers to flow in place today. The land- and water-use practices associated with the plan will likely result in changes in the quality, quantity, and reactivity of DOM throughout the greater Everglades ecosystem. The authors discuss the factors controlling DOM concentrations and chemistry, present distribution of DOM throughout the Everglades, the potential effects of DOM on key water-quality issues, and the potential utility of dissolved organic matter as an indicator of success of restoration efforts. Copyright ?? 2011 Taylor & Francis Group, LLC.

Operationalizing Dynamic Ocean Management (DOM): Understanding the Incentive Structure, Policy and Regulatory Context for DOM in Practice

NASA Astrophysics Data System (ADS)

Lewison, R. L.; Saumweber, W. J.; Erickson, A.; Martone, R. G.

2016-12-01

Dynamic ocean management, or management that uses near real-time data to guide the spatial distribution of commercial activities, is an emerging approach to balance ocean resource use and conservation. Employing a wide range of data types, dynamic ocean management in a fisheries context can be used to meet multiple objectives - managing target quota, bycatch reduction, and reducing interactions with species of conservation concern. There is a growing list of DOM applications currently in practice in fisheries around the world, yet the approach is new enough that both fishers and fisheries managers are unclear how DOM can be applied to their fishery. Here, we use the experience from dynamic ocean management applications that are currently in practice to address the commonly asked question "How can dynamic management approaches be implemented in a traditionally managed fishery?". Combining knowledge from the DOM participants with a review of regulatory frameworks and incentive structures, stakeholder participation, and technological requirements of DOM in practice, we identify ingredients that have supported successful implementation of this new management approach.

[Are antioxidant supplements effective in reducing delayed onset muscle soreness? A systematic review].

PubMed

Candia-Luján, Ramón; De Paz Fernández, José Antonio; Costa Moreira, Osvaldo

2014-10-05

In recent years, antioxidant supplements have become popular to counter the effects of free radicals and muscle damage symptoms, including delayed onset muscle soreness (DOMS). To conduct a systematic review in different databases to determine the effects of antioxidant supplements on DOMS. We conducted a search in databases; Cochrane, Pubmed, Scopus and SportDiscus and Web of Science (WOS). The words and acronyms used were; Delayed onset muscle soreness, exercise induced muscle damage, DOMS, EIMD, antioxidant and oxidative stress. 54 articles were identified of which 48 were retreived, all in English, 17 related to vitamin C and E, supplements polyphenolic correspond to fourteen, eleven other antioxidant supplements and six to commercial supplements, all of them used to diminish the DOMS and other variables. Both vitamins and commercial supplements have low effectiveness in reducing DOMS, while polyphenols and other antioxidant supplements show moderate to good effectiveness in combating DOMS. However, most of the studies have effectiveness in reducing other symptoms of muscle damage besides helping in the post-exercise recovery. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Molecular characterization of dissolved organic matter during the Arctic spring melt period

NASA Astrophysics Data System (ADS)

Gueguen, C.; Mangal, V.; Shi, Y. X.

2016-02-01

The application of high resolution electrospray ionization mass spectrometry has advanced our understanding of dissolved organic matter (DOM) at molecular level. The arctic spring melt period has been largely undersampled owing to logistical and safety issues, yet this period is extremely important to the overall flux of DOM and related contaminants including metals from high latitude rivers. In this study, we present high resolution molecular composition of 35 DOM samples collected in the Churchill River (Manitoba) during the 2015 spring melt period. As spring melt progresses, a significant change in the two most dominant carbon pools, protein and lignin, was observed. For example, the relative abundance of proteins detected in the river DOM samples increased from 19 to 44% during the spring flush, likely reflecting a change in DOM source. Similar patterns were found using fluorescence spectroscopy.

Characterising Event-Based DOM Inputs to an Urban Watershed

NASA Astrophysics Data System (ADS)

Croghan, D.; Bradley, C.; Hannah, D. M.; Van Loon, A.; Sadler, J. P.

2017-12-01

Dissolved Organic Matter (DOM) composition in urban streams is dominated by terrestrial inputs after rainfall events. Urban streams have particularly strong terrestrial-riverine connections due to direct input from terrestrial drainage systems. Event driven DOM inputs can have substantial adverse effects on water quality. Despite this, DOM from important catchment sources such as road drains and Combined Sewage Overflows (CSO's) remains poorly characterised within urban watersheds. We studied DOM sources within an urbanised, headwater watershed in Birmingham, UK. Samples from terrestrial sources (roads, roofs and a CSO), were collected manually after the onset of rainfall events of varying magnitude, and again within 24-hrs of the event ending. Terrestrial samples were analysed for fluorescence, absorbance and Dissolved Organic Carbon (DOC) concentration. Fluorescence and absorbance indices were calculated, and Parallel Factor Analysis (PARAFAC) was undertaken to aid sample characterization. Substantial differences in fluorescence, absorbance, and DOC were observed between source types. PARAFAC-derived components linked to organic pollutants were generally highest within road derived samples, whilst humic-like components tended to be highest within roof samples. Samples taken from the CSO generally contained low fluorescence, however this likely represents a dilution effect. Variation within source groups was particularly high, and local land use seemed to be the driving factor for road and roof drain DOM character and DOC quantity. Furthermore, high variation in fluorescence, absorbance and DOC was apparent between all sources depending on event type. Drier antecedent conditions in particular were linked to greater presence of terrestrially-derived components and higher DOC content. Our study indicates that high variations in DOM character occur between source types, and over small spatial scales. Road drains located on main roads appear to contain the poorest quality DOM of the sources studied due to the presence of hydrocarbons. In order to prevent storm-derived DOM degradation of water quality of urban streams, greater knowledge of links between these drainage sources, and their pathways to streams is required.

Influences of the alternation of wet-dry periods on the variability of chromophoric dissolved organic matter in the water level fluctuation zone of the Three Gorges Reservoir area, China.

PubMed

Jiang, Tao; Wang, Dingyong; Wei, Shiqiang; Yan, Jinlong; Liang, Jian; Chen, Xueshuang; Liu, Jiang; Wang, Qilei; Lu, Song; Gao, Jie; Li, Lulu; Guo, Nian; Zhao, Zheng

2018-04-26

Dissolved organic matter (DOM) is a crucial driver of various biogeochemical processes in aquatic systems. Thus, many lakes and streams have been investigated in the past several decades. However, fewer studies have sought to understand the changes in DOM characteristics in the waters of the Three Gorges Reservoir (TGR) areas, which are the largest artificial reservoir areas in the world. Thus, a field investigation of dissolved organic carbon (DOC) concentrations and of chromophoric dissolved organic matter (CDOM) properties was conducted from 2013 to 2015 to track the spatial-temporal variability of DOM properties in the TGR areas. The results showed that the alternations of wet and dry periods due to hydrological management have a substantial effect on the quantity and quality of aquatic DOM in TGR areas. Increases in DOC concentrations in the wet period show an apparent "dilution effect" that decreases CDOM compounds with relatively lower aromaticity (i.e., SUVA 254 ) and molecular weight (i.e., S R ). In contrast to the obvious temporal variations of DOM, significant spatial variability was not observed in this study. Additionally, DOM showed more terrigenous characteristics in the dry period but weak terrigenous characteristics in the wet period. Furthermore, the positive correlation between SUVA 254 and CDOM suggests that the aromatic component controls the CDOM dynamics in TGR areas. The first attempt to investigate the DOM dynamics in TGR areas since the Three Gorges Dam was conducted in 2012, and the unique patterns of spatial-temporal variations in DOM that are highlighted in this study might provide a new insight for understanding the role of DOM in the fates of contaminants and may help in the further management of flow loads and water quality in the TGR area. Copyright © 2018 Elsevier B.V. All rights reserved.

Biochemical Composition of Dissolved Organic Matter Released During Experimental Diatom Blooms

NASA Technical Reports Server (NTRS)

Mannino, Antonio; Harvey, H. Rodger

2002-01-01

An axenic culture of Skeletonema costatum was grown to late-log phase to examine the molecular weight distribution and the biochemical composition of high molecular weight dissolved organic matter released in the absence of actively growing bacteria. A second culture was grown in a 5 m(exp 3) mesocosm and placed in darkness for a period of 51 days to examine the impact of phytoplankton bloom dynamics and microbial decomposition on dissolved (DOM) and particulate organic matter (POM) composition. DOM was separated using tangential-flow ultrafiltration into three nominal size fractions: LDOM (less than 1 kDa DOM), HDOM (1-30 kDa) and VHDOM (30 kDa-0.2 micron) and characterized. Both axenic and mesocosm diatom blooms released 28-33% of net primary production as dissolved organic carbon (DOC). In the axenic culture, HDOM and LDOM each comprised about half of the diatom-released DOC with less than l% as VHDOM. Diatoms from both experiments released carbohydrate-rich high molecular weight DOM. Much of the axenic diatom-released high molecular weight DOC could be chemically characterized (61% of HDOM and 78% of VHDOM) with carbohydrates as the primary component (45% of HDOM and 55% of VHDOM). Substantial amounts of hydrolyzable amino acids (16% of HDOM and 22% of VHDOM) and small amounts of lipids (less than 1%) were also released. Proportions of recognizable biochemical components in DOM produced in the mesocosm bloom were lower compared to the axenic culture. The presence of bacterial fatty acids and peptidoglycan-derived D-amino acids within high molecular weight fractions from the mesocosm bloom revealed that bacteria contributed a variety of macromolecules to DOM during the growth and decay of the diatom bloom. Release of significant amounts of DOC by diatoms demonstrates that DOM excretion is an important component of phytoplankton primary production. Similarities in high molecular weight DOM composition in marine waters and diatom cultures highlight the importance of phytoplankton to DOM composition in the ocean.

Characterization and copper binding of humic and nonhumic organic matter isolated from the South Platte River: Evidence for the presence of nitrogenous binding site

USGS Publications Warehouse

Croue, J.-P.; Benedetti, M.F.; Violleau, D.; Leenheer, J.A.

2003-01-01

Humic substances typically constitute 40-60% of the dissolved organic matter (DOM) in surface waters. However, little information is available regarding the metal binding properties of the nonhumic hydrophilic portion of the DOM. In this study, humic and nonhumic DOM samples were isolated from the South Platte River (Colorado, DOC = 2.6 mg??L-1, SUVA254 = 2.4 L/mg??m) using a two-column array of XAD-8 and XAD-4 resins. The three major isolated fractions of DOM, which accounted for 57% of the bulk DOM, were characterized using a variety of analytical tools. Proton and copper binding properties were studied for each fraction. The main objective of this work was to compare the structural and chemical characteristics of the isolated fractions and test models describing DOM reactivity toward metal ions. The characterization work showed significant structural differences between the three isolated fractions of DOM. The hydrophobic acid fraction (i.e., humic substances isolated from the XAD-8 resin) gave the largest C/H, C/O, and C/N ratios and aromatic carbon content among the three isolated fractions. The transphilic acid (TPHA) fraction ("transphilic" meaning fraction of intermediate polarity isolated from the XAD-4 resin) was found to incorporate the highest proportion of polysaccharides, whereas the transphilic neutral (TPHN) fraction was almost entirely proteinaceous. The gradual increase of the charge with pH for the three DOM fractions is most likely caused by a large distribution of proton affinity constants for the carboxylic groups, as well as a second type of group more generally considered to be phenolic. In the case of the DOM fraction enriched in proteinaceous material (i.e., TPHN fraction), the results showed that the amino groups are reponsible for the charge reversal. For low copper concentrations, nitrogen-containing functional groups similar to those of amino acids are likely to be involved in complexation, in agreement with previously published data.

Grammar as a Programming Language. Artificial Intelligence Memo 391.

ERIC Educational Resources Information Center

Rowe, Neil

Student projects that involve writing generative grammars in the computer language, "LOGO," are described in this paper, which presents a grammar-running control structure that allows students to modify and improve the grammar interpreter itself while learning how a simple kind of computer parser works. Included are procedures for…

The Effect of Syntactic Constraints on the Processing of Backwards Anaphora

ERIC Educational Resources Information Center

Kazanina, Nina; Lau, Ellen F.; Lieberman, Moti; Yoshida, Masaya; Phillips, Colin

2007-01-01

This article presents three studies that investigate when syntactic constraints become available during the processing of long-distance backwards pronominal dependencies ("backwards anaphora" or "cataphora"). Earlier work demonstrated that in such structures the parser initiates an active search for an antecedent for a pronoun, leading to gender…

A natural language interface to databases

NASA Technical Reports Server (NTRS)

Ford, D. R.

1988-01-01

The development of a Natural Language Interface which is semantic-based and uses Conceptual Dependency representation is presented. The system was developed using Lisp and currently runs on a Symbolics Lisp machine. A key point is that the parser handles morphological analysis, which expands its capabilities of understanding more words.

Brain Responses to Filled Gaps

ERIC Educational Resources Information Center

Hestvik, Arild; Maxfield, Nathan; Schwartz, Richard G.; Shafer, Valerie

2007-01-01

An unresolved issue in the study of sentence comprehension is whether the process of gap-filling is mediated by the construction of empty categories (traces), or whether the parser relates fillers directly to the associated verb's argument structure. We conducted an event-related potentials (ERP) study that used the violation paradigm to examine…

Robo-Sensei's NLP-Based Error Detection and Feedback Generation

ERIC Educational Resources Information Center

Nagata, Noriko

2009-01-01

This paper presents a new version of Robo-Sensei's NLP (Natural Language Processing) system which updates the version currently available as the software package "ROBO-SENSEI: Personal Japanese Tutor" (Nagata, 2004). Robo-Sensei's NLP system includes a lexicon, a morphological generator, a word segmentor, a morphological parser, a syntactic…

High pressure size exclusion chromatography (HPSEC) determination of dissolved organic matter molecular weight revisited: Accounting for changes in stationary phases, analytical standards, and isolation methods

USGS Publications Warehouse

McAdams, Brandon C.; Aiken, George R.; McKnight, Diane M.; Arnold, William A.; Chin, Yu-Ping

2018-01-01

We reassessed the molecular weight of dissolved organic matter (DOM) determined by high pressure size exclusion chromatography (HPSEC) using measurements made with different columns and various generations of polystyrenesulfonate (PSS) molecular weight standards. Molecular weight measurements made with a newer generation HPSEC column and PSS standards from more recent lots are roughly 200 to 400 Da lower than initial measurements made in the early 1990s. These updated numbers match DOM molecular weights measured by colligative methods and fall within a range of values calculated from hydroxyl radical kinetics. These changes suggest improved accuracy of HPSEC molecular weight measurements that we attribute to improved accuracy of PSS standards and changes in the column packing. We also isolated DOM from wetlands in the Prairie Pothole Region (PPR) using XAD-8, a cation exchange resin, and PPL, a styrene-divinylbenzene media, and observed little difference in molecular weight and specific UV absorbance at 280 nm (SUVA280) between the two solid phase extraction resins, suggesting they capture similar DOM moieties. PPR DOM also showed lower SUVA280 at similar weights compared to DOM isolates from a global range of environments, which we attribute to oxidized sulfur in PPR DOM that would increase molecular weight without affecting SUVA280.

Influence of dissolved organic matter on the complexation of mercury under sulfidic conditions.

PubMed

Miller, Carrie L; Mason, Robert P; Gilmour, Cynthia C; Heyes, Andrew

2007-04-01

The complexation of Hg under sulfidic conditions influences its bioavailability for microbial methylation. Neutral dissolved Hg-sulfide complexes are readily available to Hg-methylating bacteria in culture, and thermodynamic models predict that inorganic Hg-sulfide complexes dominate dissolved Hg speciation under natural sulfidic conditions. However, these models have not been validated in the field. To examine the complexation of Hg in natural sulfidic waters, octanol/water partitioning methods were modified for use under environmentally relevant conditions, and a centrifuge ultrafiltration technique was developed. These techniques demonstrated much lower concentrations of dissolved Hg-sulfide complexes than predicted. Furthermore, the study revealed an interaction between Hg, dissolved organic matter (DOM), and sulfide that is not captured by current thermodynamic models. Whereas Hg forms strong complexes with DOM under oxic conditions, these complexes had not been expected to form in the presence of sulfide because of the stronger affinity of Hg for sulfide relative to its affinity for DOM. The observed interaction between Hg and DOM in the presence of sulfide likely involves the formation of a DOM-Hg-sulfide complex or results from the hydrophobic partitioning of neutral Hg-sulfide complexes into the higher-molecular-weight DOM. An understanding of the mechanism of this interaction and determination of complexation coefficients for the Hg-sulfide-DOM complex are needed to adequately assess how our new finding affects Hg bioavailability, sorption, and flux.

Metal complexation properties of freshwater dissolved organic matter are explained by its aromaticity and by anthropogenic ligands.

PubMed

Baken, Stijn; Degryse, Fien; Verheyen, Liesbeth; Merckx, Roel; Smolders, Erik

2011-04-01

Dissolved organic matter (DOM) in surface waters affects the fate and environmental effects of trace metals. We measured variability in the Cd, Cu, Ni, and Zn affinity of 23 DOM samples isolated by reverse osmosis from freshwaters in natural, agricultural, and urban areas. Affinities at uniform pH and ionic composition were assayed at low, environmentally relevant free Cd, Cu, Ni, and Zn activities. The C-normalized metal binding of DOM varied 4-fold (Cu) or about 10-fold (Cd, Ni, Zn) among samples. The dissolved organic carbon concentration ranged only 9-fold in the waters, illustrating that DOM quality is an equally important parameter for metal complexation as DOM quantity. The UV-absorbance of DOM explained metal affinity only for waters receiving few urban inputs, indicating that in those waters, aromatic humic substances are the dominant metal chelators. Larger metal affinities were found for DOM from waters with urban inputs. Aminopolycarboxylate ligands (mainly EDTA) were detected at concentrations up to 0.14 μM and partly explained the larger metal affinity. Nickel concentrations in these surface waters are strongly related to EDTA concentrations (R2=0.96) and this is underpinned by speciation calculations. It is concluded that metal complexation in waters with anthropogenic discharges is larger than that estimated with models that only take into account binding on humic substances.

Associations Between the Molecular and Optical Properties of Dissolved Organic Matter in the Florida Everglades, a Model Coastal Wetland System

PubMed Central

Wagner, Sasha; Jaffé, Rudolf; Cawley, Kaelin; Dittmar, Thorsten; Stubbins, Aron

2015-01-01

Optical properties are easy-to-measure proxies for dissolved organic matter (DOM) composition, source, and reactivity. However, the molecular signature of DOM associated with such optical parameters remains poorly defined. The Florida coastal Everglades is a subtropical wetland with diverse vegetation (e.g., sawgrass prairies, mangrove forests, seagrass meadows) and DOM sources (e.g., terrestrial, microbial, and marine). As such, the Everglades is an excellent model system from which to draw samples of diverse origin and composition to allow classically-defined optical properties to be linked to molecular properties of the DOM pool. We characterized a suite of seasonally- and spatially-collected DOM samples using optical measurements (EEM-PARAFAC, SUVA254, S275−295, S350−400, SR, FI, freshness index, and HIX) and ultrahigh resolution mass spectrometry (FTICR-MS). Spearman's rank correlations between FTICR-MS signal intensities of individual molecular formulae and optical properties determined which molecular formulae were associated with each PARAFAC component and optical index. The molecular families that tracked with the optical indices were generally in agreement with conventional biogeochemical interpretations. Therefore, although they represent only a small portion of the bulk DOM pool, absorbance, and fluorescence measurements appear to be appropriate proxies for the aquatic cycling of both optically-active and associated optically-inactive DOM in coastal wetlands. PMID:26636070

Size and resin fractionations of dissolved organic matter and trihalomethane precursors from four typical source waters in China.

PubMed

Wei, Qunshan; Wang, Dongsheng; Wei, Qia; Qiao, Chunguang; Shi, Baoyou; Tang, Hongxiao

2008-06-01

Dissolved organic matter (DOM) and its potential to form disinfection by-products (DBPs) during drinking water treatment raise challenges to water quality control. Understanding both chemical and physical characteristics of DOM in source waters is key to better water treatment. In this study, the DOM from four typical source waters in China was fractionated by XAD resin adsorption (RA) and ultrafiltration (UF) techniques. The trihalomethane formation potential (THMFP) of all fractions in the DOM were investigated to reveal the major THM precursors. The fraction distributions of DOM could be related to their geographical origins in a certain extent. The dominant chemical fraction as THM precursors in the DOM from south waters (East-Lake reservoir in Shenzhen and Peal rivers in Guangzhou) was hydrophobic acid (HoA). The size fraction with molecular weight (MW) <1 kDa in both south waters had the highest THMFP. The results of cluster analysis showed that the parameters of fractions including DOC percentage (DOC%), UV254%, SUVA254 (specific UV254 absorbance) and THMFP were better for representing the differences of DOM from the studied waters than specific THMFP (STHMFP). The weak correlation between SUVA254 and STHMFP for either size or XAD fractions suggests that whether SUVA254 can be used as an indicator for the reactivity of THM formation is highly dependent on the nature of organic matter.

Influence of rice straw-derived dissolved organic matter on lactic acid fermentation by Rhizopus oryzae.

PubMed

Chen, Xingxuan; Wang, Xiahui; Xue, Yiyun; Zhang, Tian-Ao; Li, Yuhao; Hu, Jiajun; Tsang, Yiu Fai; Zhang, Hongsheng; Gao, Min-Tian

2018-06-01

Rice straw can be used as carbon sources for lactic acid fermentation. However, only a small amount of lactic acid is produced even though Rhizopus oryzae can consume glucose in rice straw-derived hydrolysates. This study correlated the inhibitory effect of rice straw with rice straw-derived dissolved organic matter (DOM). Lactic acid fermentations with and without DOM were conducted to investigate the effect of DOM on lactic acid fermentation by R. oryzae. Fermentation using control medium with DOM showed a similar trend to fermentation with rice straw-derived hydrolysates, showing that DOM contained the major inhibitor of rice straw. DOM assay indicated that it mainly consisted of polyphenols and polysaccharides. The addition of polyphenols and polysaccharides derived from rice straw confirmed that lactic acid fermentation was promoted by polysaccharides and significantly inhibited by polyphenols. The removal of polyphenols also improved lactic acid production. However, the loss of polysaccharides during the removal of polyphenols resulted in low glucose consumption. This study is the first to investigate the effects of rice straw-derived DOM on lactic acid fermentation by R. oryzae. The results may provide a theoretical basis for identifying inhibitors and promoters associated with lactic acid fermentation and for establishing suitable pretreatment methods. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

A Comparison between Chocolate Milk and a Raw Milk Honey Solution’s Influence on Delayed Onset of Muscle Soreness

PubMed Central

Hatchett, Andrew; Berry, Christopher; Oliva, Claudia; Wiley, Douglas; St. Hilaire, Jacob; LaRochelle, Alex

2016-01-01

This investigation sought to examine the effect that a chocolate milk solution (CMS) and a raw milk solution (RMS) had on lower extremity induced delayed onset of muscle soreness (DOMS). Twenty trained male participants completed a set of questionnaires, prior to completing a lower extremity DOMS protocol, to determine the level of discomfort and functional limitations. Once the DOMS protocol was completed, participants were randomly assigned to either the CM or RM group. Once assigned, participants ingested 240 mL of the respective solution and completed the same set of questionnaires immediately post, 24-, 48- and 72-h post DOMS protocol. Additionally, for 10 days post-ingestion participants were contacted to learn if any negative effects were experienced as a result of ingesting either solution. Both groups reported an increase in lower extremity discomfort at each data collection interval post-DOMS protocol (post, 24-, 48- and 72-h). Participants assigned to the RM group reported high discomfort post and a relative decline in discomfort from immediately post-DOMS protocol to 72-h post. The RMS group reported substantially less discomfort at 72-h when compared to the CMS group. Ingestion of a raw milk solution immediately post strength exercise can substantially reduce the level of self-reported discomfort associated with DOMS. PMID:29910267

Release and microbial degradation of dissolved organic matter (DOM) from the macroalgae Ulva prolifera.

PubMed

Zhang, Tao; Wang, Xuchen

2017-12-15

Release and microbial degradation of dissolved organic matter (DOM) and chromophoric dissolved organic matter (CDOM) from the macroalgae Ulva prolifera were studied in laboratory incubation experiments. The release of DOM and CDOM from Ulva prolifera was a rapid process, and hydrolysis played an important role in the initial leaching of the organic compounds from the algae. Bacterial activity enhanced the release of DOM and CDOM during degradation of the algae and utilization of the released organic compounds. It is calculated that 43±2% of the C and 63±3% of the N from Ulva prolifera's biomass were released during the 20-day incubation, and 65±3% of the released C and 87±4% of the released N were utilized by bacteria. In comparison, only 18±1% of the algae's C and 17±1% of its N were released when bacterial activities were inhibited. The fluorescence characteristics of the CDOM indicate that protein-like DOM was the major organic component released from Ulva prolifera that was highly labile and biodegradable. Bacteria played an important role in regulating the chemical composition and fluorescence characteristics of the DOM. Our study suggests that the release of DOM from Ulva prolifera provides not only major sources of organic C and N, but also important food sources to microbial communities in coastal waters. Copyright © 2017 Elsevier Ltd. All rights reserved.

Importance of lateral flux and its percolation depth on organic carbon export in Arctic tundra soil: Implications from a soil leaching experiment

NASA Astrophysics Data System (ADS)

Zhang, Xiaowen; Hutchings, Jack A.; Bianchi, Thomas S.; Liu, Yina; Arellano, Ana R.; Schuur, Edward A. G.

2017-04-01

Temperature rise in the Arctic is causing deepening of active layers and resulting in the mobilization of deep permafrost dissolved organic matter (DOM). However, the mechanisms of DOM mobilization from Arctic soils, especially upper soil horizons which are drained most frequently through a year, are poorly understood. Here we conducted a short-term leaching experiment on surface and deep organic active layer soils, from the Yukon River basin, to examine the effects of DOM transport on bulk and molecular characteristics. Our data showed a net release of DOM from surface soils equal to an average of 5% of soil carbon. Conversely, deep soils percolated with surface leachates retained up to 27% of bulk DOM while releasing fluorescent components (up to 107%), indicating selective release of aromatic components (e.g., lignin and tannin), while retaining nonchromophoric components, as supported by spectrofluorometric and ultrahigh-resolution mass spectroscopic techniques. Our findings highlight the importance of the lateral flux of DOM on ecosystem carbon balance as well as processing of DOM transport through organic active layer soils en route to rivers and streams. This work also suggests the potential role of leachate export as an important mechanism of C losses from Arctic soils, in comparison with the more traditional pathway from soil to atmosphere in a warming Arctic.

Implementation of the NAS Parallel Benchmarks in Java

NASA Technical Reports Server (NTRS)

Frumkin, Michael A.; Schultz, Matthew; Jin, Haoqiang; Yan, Jerry; Biegel, Bryan (Technical Monitor)

2002-01-01

Several features make Java an attractive choice for High Performance Computing (HPC). In order to gauge the applicability of Java to Computational Fluid Dynamics (CFD), we have implemented the NAS (NASA Advanced Supercomputing) Parallel Benchmarks in Java. The performance and scalability of the benchmarks point out the areas where improvement in Java compiler technology and in Java thread implementation would position Java closer to Fortran in the competition for CFD applications.

Performance and Scalability of the NAS Parallel Benchmarks in Java

NASA Technical Reports Server (NTRS)

Frumkin, Michael A.; Schultz, Matthew; Jin, Haoqiang; Yan, Jerry; Biegel, Bryan A. (Technical Monitor)

2002-01-01

Several features make Java an attractive choice for scientific applications. In order to gauge the applicability of Java to Computational Fluid Dynamics (CFD), we have implemented the NAS (NASA Advanced Supercomputing) Parallel Benchmarks in Java. The performance and scalability of the benchmarks point out the areas where improvement in Java compiler technology and in Java thread implementation would position Java closer to Fortran in the competition for scientific applications.

Implementation of BT, SP, LU, and FT of NAS Parallel Benchmarks in Java

NASA Technical Reports Server (NTRS)

Schultz, Matthew; Frumkin, Michael; Jin, Hao-Qiang; Yan, Jerry

2000-01-01

A number of Java features make it an attractive but a debatable choice for High Performance Computing. We have implemented benchmarks working on single structured grid BT,SP,LU and FT in Java. The performance and scalability of the Java code shows that a significant improvement in Java compiler technology and in Java thread implementation are necessary for Java to compete with Fortran in HPC applications.

Variation of organic matter quantity and quality in streams at Critical Zone Observatory watersheds

Treesearch

Matthew P. Miller; Elizabeth W. Boyer; Diane M. McKnight; Michael G. Brown; Rachel S. Gabor; Carolyn Hunsaker; Lidiia Iavorivska; Shreeram Inamdar; Dale W. Johnson; Louis A. Kaplan; Henry Lin; William H. McDowell; Julia N. Perdrial

2016-01-01

The quantity and chemical composition of dissolved organic matter (DOM) in surface waters influence ecosystem processes and anthropogenic use of freshwater. However, despite the importance of understanding spatial and temporal patterns in DOM, measures of DOM quality are not routinely included as part of large-scale ecosystem monitoring programs and variations in...

DOMstudio: an integrated workflow for Digital Outcrop Model reconstruction and interpretation

NASA Astrophysics Data System (ADS)

Bistacchi, Andrea

2015-04-01

Different Remote Sensing technologies, including photogrammetry and LIDAR, allow collecting 3D dataset that can be used to create 3D digital representations of outcrop surfaces, called Digital Outcrop Models (DOM), or sometimes Virtual Outcrop Models (VOM). Irrespective of the Remote Sensing technique used, DOMs can be represented either by photorealistic point clouds (PC-DOM) or textured surfaces (TS-DOM). The first are datasets composed of millions of points with XYZ coordinates and RGB colour, whilst the latter are triangulated surfaces onto which images of the outcrop have been mapped or "textured" (applying a tech-nology originally developed for movies and videogames). Here we present a workflow that allows exploiting in an integrated and efficient, yet flexible way, both kinds of dataset: PC-DOMs and TS-DOMs. The workflow is composed of three main steps: (1) data collection and processing, (2) interpretation, and (3) modelling. Data collection can be performed with photogrammetry, LIDAR, or other techniques. The quality of photogrammetric datasets obtained with Structure From Motion (SFM) techniques has shown a tremendous improvement over the past few years, and this is becoming the more effective way to collect DOM datasets. The main advantages of photogrammetry over LIDAR are represented by the very simple and lightweight field equipment (a digital camera), and by the arbitrary spatial resolution, that can be increased simply getting closer to the out-crop or by using a different lens. It must be noted that concerns about the precision of close-range photogrammetric surveys, that were justified in the past, are no more a problem if modern software and acquisition schemas are applied. In any case, LIDAR is a well-tested technology and it is still very common. Irrespective of the data collection technology, the output will be a photorealistic point cloud and a collection of oriented photos, plus additional imagery in special projects (e.g. infrared images). This dataset can be used as-is (PC-DOM), or a 3D triangulated surface can be interpolated from the point cloud, and images can be used to associate a texture to this surface (TS-DOM). In the DOMstudio workflow we use both PC-DOMs and TS-DOMs. Particularly, the latter are obtained projecting the original images onto the triangulated surface, without any downsampling, thus retaining the original resolution and quality of images collected in the field. In the DOMstudio interpretation step, PC-DOM is considered the best option for fracture analysis in outcrops where facets corresponding to fractures are present. This allows obtaining orientation statistics (e.g. stereoplots, Fisher statistics, etc.) directly from a point cloud where, for each point, the unit vector normal to the outcrop surface has been calculated. A recent development in this kind of processing is represented by the possibility to automatically select (segment) subset point clouds representing single fracture surfaces, which can be used for studies on fracture length, spacing, etc., allowing to obtain parameters like the frequency-length distribution, P21, etc. PC-DOM interpretation can be combined or complemented, depending on the outcrop morphology, with an interpretation carried out on a TS-DOM in terms of traces, which are the linear intersection of "geological" surfaces (fractures, faults, bedding, etc.) with the outcrop surface. This kind of interpretation is very well suited for outcrops with smooth surfaces, and can be performed either by manual picking, or by applying image analysis techniques on the images associated with the DOM. In this case, a huge mass of data, with very high resolution, can be collected very effectively. If we consider applications like lithological or mineral map-ping, TS-DOM datasets are the only suitable support. Finally, the DOMstudio workflow produces output in formats that are compatible with all common geomodelling packages (e.g. Gocad/Skua, Petrel, Move), allowing to directly use the quantitative data collected on DOMs to generate and calibrate geological, structural, or geostatistical models. I will present examples of applications including hydrocarbon reservoir analogue studies, studies on fault zone architecture, lithological mapping on sedimentary and metamorphic rocks, and studies on the surface of planets and small bodies in the Solar System.

Effects of redox conditions on the adsorption of dissolved organic matter to soil minerals and differently aged paddy soils

NASA Astrophysics Data System (ADS)

Sauerwein, Meike; Hanke, Alexander; Kaiser, Klaus; Kalbitz, Karsten

2010-05-01

Effects of redox conditions on the adsorption of dissolved organic matter to soil minerals and differently aged paddy soils Meike Sauerwein1, Alexander Hanke2, Klaus Kaiser3, Karsten Kalbitz2 1) Dept. of Soil Ecology, Bayreuth Centre of Ecology and Environmental Research (BayCEER), University of Bayreuth, 95440 Bayreuth, Germany, meike.sauerwein@gmail.com 2) Institute of ecosystem dynamics and biodiversity, University of Amsterdam, 1018 WV, Netherlands, a.hanke@uva.nl, k.kalbitz@uva.nl 3) Soil Sciences, Martin Luther University Halle, 06099 Halle, Germany, klaus.kaiser@landw.uni-halle.de Current knowledge on dissolved organic matter (DOM) in soils is based mainly on observations and experiments in aerobic environments. Adsorption to soil minerals is an important mechanism of DOM retention and stabilization against microbial decay under oxic conditions. Under anoxic conditions where hydrous iron oxides, the potential main adsorbents of DOM, possibly dissolve, the importance of adsorption seems questionable. Therefore, we studied the adsorption of DOM to selected soil minerals and to mineral soils under oxic and anoxic conditions. In detail, we tested the following hypotheses: 1. Minerals and soils adsorb less DOM under anoxic conditions than under oxic ones. 2. The reduced adsorption under anoxic conditions is result of the smaller adsorption to hydrous Fe oxides whereas adsorption to clay minerals and Al hydroxides is not sensitive to changes in redox conditions 3. DOM adsorption will increase with the number of redox cycles, thus time of soil formation, due to increasing contents of poorly crystalline Fe oxides. This will, however, cause a stronger sensitivity to redox changes as poor crystalline Fe oxides are more reactive. 4. Aromatic compounds, being preferentially adsorbed under oxic conditions, will be less strongly adsorbed under anoxic conditions. We chose paddy soils as models because their periodically and regular exposure to changing redox cycles, with anoxic conditions during the rice growing period and oxic conditions during harvest and growth of other crops. Soils of a unique chronosequence of paddy soils (50, 300, 700 and 2000 years) in China were studied in direct comparison to non-paddy soils of the same age. In additions, selected soil minerals (goethite, ferrihydrite, amorphous Al hydroxide, hydrobiotite, nontronite and ripodolite), differing in their response to changes in redox conditions, were studied in order to indentify those mineral constituents responsible for redox-induced changes in DOM adsorption to the test soils. The DOM for the adsorption was extracted from composted rice straw as a surrogate for DOM percolating in paddy soils. Batch adsorption experiments were carried out with DOM pre-incubated to give oxic and anoxic conditions and maintaining these redox conditions during the whole procedure. The redox potential resulting from anoxic pre-incubation was about 100 mV, thus in the range of Fe reduction. Besides of dissolved organic carbon (DOC), we determined changes in the composition of DOM by the specific UV absorbance. We also analyzed main cations, anions and redox-sensitive elements to give a comprehensive picture of the effects of changing redox conditions on the dynamics of organic C, N, P, S, Fe and Al. First results indicated indeed less adsorption of DOM to Fe oxides under anoxic than under oxic conditions, with a more pronounced effect for ferrihydrite than for goethite. Maximum adsorption of DOM was more than 50% larger under oxic than under anoxic conditions. The effect was less pronounced but still detectable for clay minerals such as hydrobiotite, nontronite, and ripodolite. The specific UV absorbance of DOM contact with minerals was 20-50% stronger under anoxic than under oxic conditions. These changes in DOM composition indicated that preferential adsorption of aromatic compounds might be limited to aerated soils. We conclude that adsorption, although less strong than under oxic conditions, is an important mechanism of DOM retention also under anoxic conditions. Decreasing amounts of adsorbed DOM and changes in its composition might result in a less effective sorptive stabilization against microbial decay under anoxic than under oxic conditions.

Bioavailability of riverine dissolved organic matter in three Baltic Sea estuaries and the effect of catchment land-use

NASA Astrophysics Data System (ADS)

Asmala, E.; Autio, R.; Kaartokallio, H.; Pitkänen, L.; Stedmon, C. A.; Thomas, D. N.

2013-06-01

The microbial degradation of dissolved organic carbon and nitrogen (DOC, DON) was studied in three boreal estuaries with contrasting land use patterns (Kiiminkijoki - natural forest and peatland; Kyrönjoki - agricultural; Karjaanjoki - mixed/urban). Bioassays conducted for 12-18 days were used in 3 seasons at in situ temperatures. Besides the bulk parameters, a suite of dissolved organic matter (DOM) quality parameters were investigated, including colored DOM (CDOM), fluorescent DOM and the molecular weight of DOM. Bioavailable DOC and DON pools varied significantly between the estuaries, from 7.9% in Kiiminkijoki to 10.6% in Karjaanjoki and from 5.5% in Kiiminkijoki to 21.9% in Kyrönjoki, respectively. DOM originating from catchment dominated by natural forests and peatlands had the lowest DOC and DON degradation rates, as well as the lowest proportions of biodegradable DOC and DON. A greater proportion of agricultural land in the catchment increased the bioavailability of DON, but not the bioavailability of DOC. Also DOM quality varied significantly between the estuaries, and DOM originating from the agricultural Kyrönjoki catchment sustained higher DOC and DON degradation rates and higher bacterial growth efficiency (BGE) compared to those of the natural forest and peat dominated Kiiminkijoki catchment. The quality of DOM, indicated by differences in CDOM, fluorescent DOM and molecular weight, varied between estuaries with differing land use and was concluded to be major driver of BGE of these systems and thereafter to the microbial CO2 fluxes from the estuaries. The differences in BGE resulted in a 5-fold differences in the calculated daily bacterial CO2-emissions between the study estuaries due to bacterial activity, ranging from 40 kg C d-1 in Karjaanjoki estuary to 200 kg C d-1 in Kyrönjoki estuary. Two of the study systems (Karjaanjoki, mixed land use; Kyrönjoki, intensive agriculture) in which the DOM pool had lower DOC : DON ratio, smaller molecular weight and higher CDOM absorption spectral slope values resulted in higher proportion of the initial DOC and DON being transferred to microbial growth and therefore to the pelagic food web. The pristine, peatland and forest-dominated Kiiminkijoki catchment had the lowest BGE, and therefore proportionally highest CO2 fluxes. The slope coefficient S275-295 was a good proxy of molecular weight across estuaries and seasons, and also for different diagenetic stages of DOM during biological degradation.

Molecular Characterization and Reactivity of Dissolved Organic Matter by High Resolution Nanospray Ionization Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS)

NASA Astrophysics Data System (ADS)

Sleighter, R. L.; Hatcher, S. A.; Hatcher, P. G.

2006-12-01

The ultrahigh resolving power of FTICR-MS allows for the intense characterization of dissolved organic matter (DOM). DOM is the largest reactive component of the global carbon cycle, and an improved understanding of its composition is necessary to determine the transport and eventual fate of pollutants. The seasonal and spatial variations in DOM composition are investigated by taking surface water samples from five different sampling sites, four times a year. Water sampling begins at the Dismal Swamp in North Carolina, continues north up the Elizabeth River to the Chesapeake Bay, and concludes approximately ten miles off the coast in the Atlantic Ocean. DOM was extracted from the water samples using C18 extraction disks and were prepared in 50:50 methanol:water. Ammonium hydroxide was added prior to nanospray in order to solubilize the DOM as well as to increase the ionization efficiency. The samples were continuously infused into the Apollo II ion source with an Advion TriVersa NanoMate system of a Bruker 12 Tesla Apex QE FTICR-MS with resolving powers exceeding 400,000. All samples were analyzed in negative ion mode and were externally and internally calibrated prior to data analysis. Our DOM mass spectra consist of a multitude of peaks spanning the range of 200-850 m/z. Complexity is apparent from the detection of up to 20 peaks per nominal mass at nearly every mass throughout that range. A molecular formula calculator generated molecular formula matches from which van Krevelen plots were constructed for characterization purposes. A wide range of molecules were observed each containing oxygen, sulfur and nitrogen functional groups. We utilize the van Krevelen diagram to assist in clustering the molecules according to their functional group compositions. To test the hypothesis that formation of adducts to DOM serve to protect peptides from bacterial degradation, microcosm experiments were performed with a small isotopically enriched peptide, GGGR. This peptide was predicted to covalently bond to DOM via a Michael addition reaction or Schiff base formation. Following the incubation of GGGR with DOM, adduct formation was examined by FTICR-MS. Covalent binding of GGGR to DOM is a process that may reduce the bioavailability and degradation of proteins in the environment and could potentially lead to their preservation on longer time scales. FTICR-MS is clearly a powerful technique used to examine the complex composition of DOM and allow for advancements in the areas of aquatic and analytical chemistry.

Trace metal mobilization by organic soil amendments: insights gained from analyses of solid and solution phase complexation of cadmium, nickel and zinc.

PubMed

Welikala, Dharshika; Hucker, Cameron; Hartland, Adam; Robinson, Brett H; Lehto, Niklas J

2018-05-01

The accumulation of Cd in soils worldwide has increased the demand for methods to reduce the metal's plant bioavailability. Organic matter rich soil amendments have been shown to be effective in achieving this. However, it is not known how long these amendments can retain the Cd, and whether dissolved organic matter (DOM) released from them can enhance the metal's mobility in the environment. In this study we sought to test the Cd binding capacity of various organic soil amendments, and evaluate differences in characteristics of the DOM released to see if they can explain the lability of the Cd-DOM complexes. We collected ten organic soil amendments from around New Zealand: five different composts, biosolids from two sources, two types of peat and spent coffee grounds. We characterised the amendments' elemental composition and their ability to bind the Cd. We then selected two composts and two peats for further tests, where we measured the sorption of Ni or Zn by the amendments. We analysed the quality of the extracted DOM from the four amendments using 3D Excitation Emission Matrix analysis, and tested the lability of the metal-DOM complexes using an adapted diffusive gradients in thin-films (DGT) method. We found that composts bound the most Cd and that the emergent Cd-DOM complexes were less labile than those from the peats. Ni-DOM complexes were the least labile. The aromaticity of the extracted DOM appears to be an important factor in determining the lability of Ni complexes, but less so for Zn and Cd. Copyright © 2018 Elsevier Ltd. All rights reserved.

Comprehensive structure-selective characterization of dissolved organic matter by reducing molecular complexity and increasing analytical dimensions.

PubMed

Li, Yan; Harir, Mourad; Lucio, Marianna; Gonsior, Michael; Koch, Boris P; Schmitt-Kopplin, Philippe; Hertkorn, Norbert

2016-12-01

Deciphering the molecular codes of dissolved organic matter (DOM) improves our understanding of its role in the global element cycles and its active involvement in ecosystem services. This study demonstrates comprehensive characterization of DOM by an initial polarity-based stepwise solid phase extraction (SPE) with single methanol elution of the cartridges, but separate collection of equal aliquots of eluate. The reduction of molecular complexity in the individual DOM fractions attenuates intermolecular interactions and substantially increases the disposable resolution of any structure selective characterization. Suwannee River DOM (SR DOM) was used to collect five distinct SPE fractions with overall 91% DOC recovery. Optical spectroscopy (UV and fluorescence spectroscopy), high-field Fourier transform ion cyclotron mass spectrometry (FTICR MS) and nuclear magnetic resonance (NMR) spectroscopy showed analogous hierarchical clustering among the five eluates corroborating the robustness of this approach. Two abundant moderately hydrophobic fractions contained most of the SR DOM compounds, with substantial proportions of aliphatics, carboxylic-rich alicyclic molecules, carbohydrates and aromatics. A minor early eluting hydrophilic fraction was highly aliphatic and presented a large diversity of alicyclic carboxylic acids, whereas the two late eluting, minor hydrophobic fractions appeared as a largely defunctionalized mixture of aliphatic molecules. Comparative mass analysis showed that fractionation of SR DOM was governed by multiple molecular interactions depending on O/C ratio, molecular weight and aromaticity. The traditional optical indices SUVA 254 and fluorescence index (FI) indicated the relative aromaticity in agreement with FTICR mass and NMR spectra; the classical fluorescent peaks A and C were observed in all four latter eluates. This versatile approach can be easily expanded to preparative scale under field conditions, and transferred to different DOM sources and SPE conditions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biogeochemical Processes That Produce Dissolved Organic Matter From Wheat Straw

USGS Publications Warehouse

Wershaw, Robert L.; Rutherford, David W.; Leenheer, Jerry A.; Kennedy, Kay R.; Cox, Larry G.; Koci, Donald R.

2003-01-01

The chemical reactions that lead to the formation of dissolved organic matter (DOM) in natural waters are poorly understood. Studies on the formation of DOM generally are complicated because almost all DOM isolates have been derived from mixtures of plant species composed of a wide variety of different types of precursor compounds for DOM formation. This report describes a study of DOM derived mainly from bales of wheat straw that had been left in a field for several years. During this period of time, black water from the decomposing wheat straw accumulated in pools in the field. The nuclear magnetic resonance and infrared spectra of the black water DOM indicate that it is composed almost entirely of lignin and carbohydrate polymeric units. Analysis by high-performance size-exclusion chromatography with multi-angle laser-light scattering detection indicates that the number average molecular weight of the DOM is 124,000 daltons. The results presented in this report indicate that the black water DOM is composed of hemicellulose chains cross-linked to lignin oligomers. These types of structures have been shown to exist in the hemicellulose matrix of plant cell walls. The cross-linked lignin-hemicellulose complexes apparently were released from partially degraded wheat-straw cell walls with little alteration. In solution in the black water, these lignin-hemicellulose polymers fold into compact globular particles in which the nonpolar parts of the polymer form the interiors of the particles and the polar groups are on the exterior surfaces of the particles. The tightly folded, compact conformation of these particles probably renders them relatively resistant to microbial degradation. This should be especially the case for the aromatic lignin structures that will be buried in the interiors of the particles.

High Frequency Monitoring of the Quantity and Quality of Dissolved Organic Matter Flux Between Salt Marshes and Plum Island Sound, MA

NASA Astrophysics Data System (ADS)

Zhao, Y.; Raymond, P.

2012-12-01

Salt marshes are highly productive continental margin ecosystems, due to abundant solar radiation, water, and nutrients provided by tidal water. The unique bi-directional water movement introduced by tidal effect has a major impact on the formation and productivity of salt marsh and the material exchange between salt marsh and adjacent estuary. As a major term in carbon, energy, and nutrient budget for aquatic ecosystem, dissolved organic matter (DOM) has broad impact on food webs, carbon cycle, and nutrient retention/release. The frequency and period of DOM measurement is greatly increased by the use of reagent-free, low-cost, and reliable measurement with fluorescent and UV sensors measuring the chromophoric fraction of total DOM. Although fluorescent sensors can only measure concentration, UV absorbance in a wide spectral range (200nm-380nm) could potentially provide information on DOM composition. With the help of accurate direct real time water flux measurement and lab analysis of lability, DON, and 3D excitation emission matrix spectroscopy (EEMs), a database of DOM quantity and quality exchanged between several comparative salt marshes and Plum Island Sound, MA could be established to study the dynamics of DOM behavior in the salt marsh-estuary system. Understanding DOM source and fate is very important for evaluating the role of salt marsh in the carbon cycle and food web in coastal and global scale because coastal carbon cycling represents up to 21% of the ocean's primary production (Jahnke 2008). In addition, the approaches outlined in this proposal have broad applicability to study DOM quantity and quality in the material exchange theme between systems.

[Spectral characteristics of dissolved organic matter released during the metabolic process of small medusa].

PubMed

Guo, Dong-Hui; Yi, Yue-Yuan; Zhao, Lei; Guo, Wei-Dong

2012-06-01

The metabolic processes of jellyfish can produce dissolved organic matter (DOM) which will influence the functioning of the aquatic ecosystems, yet the optical properties of DOM released by jellyfish are unknown. Here we report the absorption and fluorescence properties of DOM released by a medusa species Black fordia virginica during a 24 h incubation experiment. Compared with the control group, an obvious increase in the concentrations of dissolved organic carbon (DOC), absorption coefficient (a280) and total dissolved nitrogen (TDN) was observed in incubation group. This clearly demonstrated the release of DOM, chromophoric DOM (CDOM) and dissolved nutrients by B. virginica which feed on enough of Artemia sp. before the experiment. The increase in spectral slope ratio (SR) and decrease in humification index (HIX) indicated that the released DOM was less-humified and had relatively lower molecular weight. Parallel factor analysis (PARAFAC) decomposed the fluorescence matrices of DOM into three humic-like components (C1-C3) and one protein-like component (C4). The Fmax of two components (C2: < 250, 295/386 nm; C4: 275/334 nm) with the emission wavelength < 400 nm increased significantly during the metabolic process of B. virginica. However, the Fmax of the other two components with the emission wavelength > 400 nm showed little changes. Thus, we suggested a zooplankton index (ZIX) to trace and characterize the DOM excreted by metabolic activity of zooplankton, which is calculated as the ratio of the sum of Fmax of all fluorescence components with the emission wavelength < 400 nm to the sum of Fmax of the other components with the emission wavelength > 400 nm.

Diel fluctuations in natural organic matter quality in an oligotrophic cave system

NASA Astrophysics Data System (ADS)

Brown, T.; Engel, A. S.; Pfiffner, S. M.

2016-12-01

Transformations of natural organic matter (NOM) and effects of photochemical degradation on dissolved organic matter (DOM) quality in recharge can be readily studied in cave systems with hydrologic connections between the surface and subsurface. Specifically, diel controls on photodegradation, fresh NOM production, and microbial C cycling were examined from recharge to resurgence of an oligotrophic cave stream in Kentucky. We used NOM isolation and spectroscopic analysis to concentrate and characterize DOM, and lipid profiling to evaluate microbial community structure. A hydrophilic fraction of DOM was isolated from bulk waters in the field using diethylaminoethyl (DEAE) weak anion exchange column chromatography, and isolates were characterized with FTIR spectroscopy to identify differences in macromolecular structure between surface and subsurface (downstream) DOM. Lipids from colloidal NOM (retained on 0.2 µm filter) and stream sediments were extracted using a modified Bligh Dyer method, segregated into classes, and converted to fatty acid methyl esters (FAME) for quantification and identification by GC-MS. During a late summer, low flow, 24-hour sampling event, the quality of surface water DOM recharged at night was 40% richer in aliphatic esters, 30% richer in phenols and alkanes, and elevated in polysaccharides compared with DOM recharged during daylight. IR absorptivity in nocturnal DOM isolates was an order of magnitude lower in the cave stream, with recalcitrant DOM interpreted from bands of aliphatic esters, alkanes, and organo-silicates. Phospholipid fatty acid (PLFA) profiles indicated that the abundance of polyunsaturated PLFA associated with algae, fungi, and higher plants decreased along the flowpath. Cave microbes exhibited elevated trans:cis ratios relative to surface communities, and the ratio increased at night. This suggested that downstream microbial communities existed in a state of reduced activity without inputs of photosynthates at night.

Impact of dissolved organic matter on the photolysis of the ionizable antibiotic norfloxacin.

PubMed

Liang, Chen; Zhao, Huimin; Deng, Minjie; Quan, Xie; Chen, Shuo; Wang, Hua

2015-01-01

Norfloxacin (NOR), an ionizable antibiotic frequently used in the aquaculture industry, has aroused public concern due to its persistence, bacterial resistance, and environmental ubiquity. Therefore, we investigated the photolysis of different species of NOR and the impact of a ubiquitous component of natural water - dissolved organic matter (DOM), which has a special photochemical activity and normally acts as a sensitizer or inhibiter in the photolysis of diverse organics; furthermore, scavenging experiments combined with electron paramagnetic resonance (EPR) were performed to evaluate the transformation of NOR in water. The results demonstated that NOR underwent direct photolysis and self-sensitized photolysis via hydroxyl radical (OH) and singlet oxygen ((1)O2) based on the scavenging experiments. In addition, DOM was found to influence the photolysis of different NOR species, and its impact was related to the concentration of DOM and type of NOR species. Photolysis of cationic NOR was photosensitized by DOM at low concentration, while zwitterionic and anionic NOR were photoinhibited by DOM, where quenching of OH predominated according to EPR experiments, accompanied by possible participation of excited triplet-state NOR and (1)O2. Photo-intermediate identification of different NOR species in solutions with/without DOM indicated that NOR underwent different photodegradation pathways including dechlorination, cleavage of the piperazine side chain and photooxidation, and DOM had little impact on the distribution but influenced the concentration evolution of photolysis intermediates. The results implied that for accurate ecological risk assessment of emerging ionizable pollutants, the impact of DOM on the environmental photochemical behavior of all dissociated species should not be ignored. Copyright © 2014. Published by Elsevier B.V.

Soreness-related changes in three-dimensional running biomechanics following eccentric knee extensor exercise.

PubMed

Paquette, Max R; Peel, Shelby A; Schilling, Brian K; Melcher, Dan A; Bloomer, Richard J

2017-06-01

Runners often experience delayed onset muscle soreness (DOMS), especially of the knee extensors, following prolonged running. Sagittal knee joint biomechanics are altered in the presence of knee extensor DOMS but it is unclear how muscle soreness affects lower limb biomechanics in other planes of motion. The purpose of this study was to assess the effects of knee extensor DOMS on three-dimensional (3D) lower limb biomechanics during running. Thirty-three healthy men (25.8 ± 6.8 years; 84.1 ± 9.2 kg; 1.77 ± 0.07 m) completed an isolated eccentric knee extensor damaging protocol to elicit DOMS. Biomechanics of over-ground running at a set speed of 3.35 m s -1 ±5% were measured before eccentric exercise (baseline) and, 24 h and 48 h following exercise in the presence of knee extensor DOMS. Knee flexion ROM was reduced at 48 h (P = 0.01; d = 0.26), and peak knee extensor moment was reduced at 24 h (P = 0.001; d = 0.49) and 48 h (P < 0.001; d = 0.68) compared to baseline. Frontal and transverse plane biomechanics were unaffected by the presence of DOMS (P > 0.05). Peak positive ankle and knee joint powers and, peak negative knee joint power were all reduced from baseline to 24 h and 48 h (P < 0.05). These findings suggest that knee extensor DOMS greatly influences sagittal knee joint angular kinetics and, reduces sagittal power production at the ankle joint. However, knee extensor DOMS does not affect frontal and transverse plane lower limb joint biomechanics during running.

Shifts in the Source and Composition of Dissolved Organic Matter in Southwest Greenland Lakes Along a Regional Hydro-climatic Gradient

NASA Astrophysics Data System (ADS)

Osburn, Christopher L.; Anderson, Nicholas J.; Stedmon, Colin A.; Giles, Madeline E.; Whiteford, Erika J.; McGenity, Terry J.; Dumbrell, Alex J.; Underwood, Graham J. C.

2017-12-01

Dissolved organic matter (DOM) concentration and quality were examined from Arctic lakes located in three clusters across south-west (SW) Greenland, covering the regional climatic gradient: cool, wet coastal zone; dry inland interior; and cool, dry ice-marginal areas. We hypothesized that differences in mean annual precipitation between sites would result in a reduced hydrological connectivity between lakes and their catchments and that this concentrates degraded DOM. The DOM in the inland lake group was characterized by a lower aromaticity and molecular weight, a low soil-like fluorescence, and carbon stable isotope (δ13C-DOC) values enriched by 2‰ relative to the coastal group. DOC-specific absorbance (SUVA254) and DOC-specific soil-like fluorescence (SUVFC1) revealed seasonal and climatic gradients across which DOM exhibited a dynamic we term "pulse-process": Pulses of DOM exported from soils to lakes during snow and ice melt were followed by pulses of autochthonous DOM inputs (possibly from macrophytes), and their subsequent photochemical and microbial processing. These effects regulated the dynamics of DOM in the inland lakes and suggested that if circumpolar lakes currently situated in cool wetter climatic regimes with strong hydrological connectivity have reduced connectivity under a drier future climate, they may evolve toward an end-point of large stocks of highly degraded DOC, equivalent to the inland lakes in the present study. The regional climatic gradient across SW Greenland and its influence on DOM properties in these lakes provide a model of possible future changes to lake C cycling in high-latitude systems where climatic changes are most pronounced.

Production and transformation of dissolved neutral sugars and amino acids by bacteria in seawater

NASA Astrophysics Data System (ADS)

Jørgensen, L.; Lechtenfeld, O. J.; Benner, R.; Middelboe, M.; Stedmon, C. A.

2014-10-01

Dissolved organic matter (DOM) in the ocean consists of a heterogeneous mixture of molecules, most of which are of unknown origin. Neutral sugars and amino acids are among the few recognizable biomolecules in DOM, and the molecular composition of these biomolecules is shaped primarily by biological production and degradation processes. This study provides insight into the bioavailability of biomolecules as well as the chemical composition of DOM produced by bacteria. The molecular compositions of combined neutral sugars and amino acids were investigated in DOM produced by bacteria and in DOM remaining after 32 days of bacterial degradation. Results from bioassay incubations with natural seawater (sampled from water masses originating from the surface waters of the Arctic Ocean and the North Atlantic Ocean) and artificial seawater indicate that the molecular compositions following bacterial degradation are not strongly influenced by the initial substrate or bacterial community. The molecular composition of neutral sugars released by bacteria was characterized by a high glucose content (47 mol %) and heterogeneous contributions from other neutral sugars (3-14 mol %). DOM remaining after bacterial degradation was characterized by a high galactose content (33 mol %), followed by glucose (22 mol %) and the remaining neutral sugars (7-11 mol %). The ratio of D-amino acids to L-amino acids increased during the experiments as a response to bacterial degradation, and after 32 days, the D/L ratios of aspartic acid, glutamic acid, serine and alanine reached around 0.79, 0.32, 0.30 and 0.51 in all treatments, respectively. The striking similarity in neutral sugar and amino acid compositions between natural (representing marine semi-labile and refractory DOM) and artificial (representing bacterially produced DOM) seawater samples, suggests that microbes transform bioavailable neutral sugars and amino acids into a common, more persistent form.

Fractionation and characterization of dissolved organic matter (DOM) in refinery wastewater by revised phase retention and ion-exchange adsorption solid phase extraction followed by ESI FT-ICR MS.

PubMed

Fang, Zhi; He, Chen; Li, Yongyong; Chung, Keng H; Xu, Chunming; Shi, Quan

2017-01-01

Although the progress of high resolution mass spectrometry in the past decade has enabled the molecular characterization of dissolved organic matter (DOM) in water as a whole, fractionation of DOM is necessary for a comprehensive characterization due to its super-complex nature. Here we proposed a method for the fractionation of DOM in a wastewater based on solubility and acidic-basic properties. Solid phase extraction (SPE) cartridges with reversed phase retention and ion-exchange adsorption capacities, namely MAX and MCX, were used in succession to fractionate a petroleum refinery wastewater into four fractions: hydrophobic acid (HOA), hydrophobic neutral (HON), hydrophobic base (HOB), and hydrophilic substance (HIS) fractions. According to the total organic carbon (TOC) analysis, 72.6% (in term of TOC) of DOM was extracted in hydrophobic fractions, in which HON was the most abundant. Hydrophobic extracts were characterized by negative and positive ion electrospray (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), respectively. Compounds with multiple oxygen atoms were predominant in the HOA, which were responded strongly in the negative ESI MS. Nitrogen containing compounds were the major detected species by positive ion ESI in all hydrophobic fractions. The molecular composition of the DOM were discussed based on the FT-ICR MS results. The fractionation provided salt free samples which enables the direct analysis of the fractions by ESI and a deep insight into the molecular composition of DOM in the wastewater. The method is potential for routine evaluation of DOM in industry wastewaters, as well as environmental water samples. Copyright © 2016. Published by Elsevier B.V.

Molecular Alteration of Marine Dissolved Organic Matter under Experimental Hydrothermal Conditions

NASA Astrophysics Data System (ADS)

Hawkes, J. A.; Hansen, C. T.; Goldhammer, T.; Bach, W.; Dittmar, T.

2016-02-01

Marine dissolved organic matter (DOM) is a large (660 Pg) pool of reduced carbon that is subject to thermal alteration in hydrothermal systems and sedimentary basins. In natural hydrothermal systems, DOM is almost completely removed, but the mechanism, kinetics and temperature dependence of this removal have not been studied to date. We investigated molecular-level changes to DOM that was solid-phase extracted (SPE-DOM) from the deep ocean of the North Pacific Ocean. This complex molecular mixture was experimentally exposed to temperatures between 100-380 °C over the course of two weeks in artificial seawater, and was then characterized on a molecular level via ultrahigh-resolution mass spectrometry (FTICRMS & Orbitrap). Almost 93% of SPE-DOM was removed by the treatment at 380 °C, and this removal was accompanied by a consistent pattern of SPE-DOM alteration across the temperatures studied, which can likely be extrapolated down to temperatures around 68 °C. Higher molecular weight and more oxygen rich compounds were preferentially degraded, suggesting that decarboxylation and dehydration of carboxylic acid and alcohol groups are the most rapid degradation mechanisms. Nitrogen containing compounds followed the same overall trends as those containing just C, H and O up to 300 °C. Above this temperature, the most highly degraded samples contained very little of the original character of marine DOM, instead being mainly composed of very low intensity N- and S- containing molecules with a high H:C ratio (>1.5). Our experiments were conducted without a sedimentary or mineral phase, and demonstrate that profound molecular alteration and almost complete removal of marine SPE-DOM requires nothing more than heating in a seawater matrix.

Molecular characterization of dissolved organic matter in contrasted freshwater environments by electrospray ionization mass spectrometry and EEM-PARAFAC

NASA Astrophysics Data System (ADS)

Parot, Jérémie; Parlanti, Edith; Guéguen, Céline

2015-04-01

Dissolved organic matter (DOM) is a key parameter in the fate, transport and mobility of inorganic and organic pollutants in natural waters. Excitation emission matrix (EEM) spectra coupled to parallel factor analysis (PARAFAC) provide insights on the main fluorescent DOM constituents. However, the molecular structures associated with PARAFAC DOM remain poorly understood. In this study, DOM from rivers, marshes and algal culture was characterized by EEM-PARAFAC and electrospray ionization Fourier transform mass spectrometry (ESI-FT-MS, Orbitrap Q Exactive). The high resolution of the Orbitrap (i.e. 140,000) allowed us to separate unique molecular species from the complex DOM mixtures. The majority of chemical species were found within the mass to charge ratio (m/z) 200 to 400. Weighted averages of neutral mass were 271.254, 236.480, 213.992Da for river, marsh and algal-derived DOM, respectively, congruent with previous studies. The assigned formula were dominated by CHO in humic-rich river waters whereas N- and S-containing compounds were predominant in marsh and algal samples. Marsh consisted of N and S-containing compounds, which were presumed to be linear alkylbenzene sulfonates. And the double bond equivalent (DBE) was higher in the marsh and in comparison was lower in the algal culture. Kendrick masses, used to identify homologous compounds differing only by a number of base units in high resolution mass spectra, and Van Krevelen diagrams, plot of molar ratio of hydrogen to carbon (H/C) versus oxygen to carbon (O/C), will be discussed in relation to PARAFAC components to further discriminate freshwater systems based on the origin and maturity of DOM. Together, these results showed that ESI-FT-MS has a great potential to distinguish freshwater DOM at the molecular level without any fractionation.

Transport of dissolved organic matter in Boom Clay: Size effects

NASA Astrophysics Data System (ADS)

Durce, D.; Aertsens, M.; Jacques, D.; Maes, N.; Van Gompel, M.

2018-01-01

A coupled experimental-modelling approach was developed to evaluate the effects of molecular weight (MW) of dissolved organic matter (DOM) on its transport through intact Boom Clay (BC) samples. Natural DOM was sampled in-situ in the BC layer. Transport was investigated with percolation experiments on 1.5 cm BC samples by measuring the outflow MW distribution (MWD) by size exclusion chromatography (SEC). A one-dimensional reactive transport model was developed to account for retardation, diffusion and entrapment (attachment and/or straining) of DOM. These parameters were determined along the MWD by implementing a discretisation of DOM into several MW points and modelling the breakthrough of each point. The pore throat diameter of BC was determined as 6.6-7.6 nm. Below this critical size, transport of DOM is MW dependent and two major types of transport were identified. Below MW of 2 kDa, DOM was neither strongly trapped nor strongly retarded. This fraction had an averaged capacity factor of 1.19 ± 0.24 and an apparent dispersion coefficient ranging from 7.5 × 10- 11 to 1.7 × 10- 11 m2/s with increasing MW. DOM with MW > 2 kDa was affected by both retardation and straining that increased significantly with increasing MW while apparent dispersion coefficients decreased. Values ranging from 1.36 to 19.6 were determined for the capacity factor and 3.2 × 10- 11 to 1.0 × 10- 11 m2/s for the apparent dispersion coefficient for species with 2.2 kDa < MW < 9.3 kDa. Straining resulted in an immobilisation of in average 49 ± 6% of the injected 9.3 kDa species. Our findings show that an accurate description of DOM transport requires the consideration of the size effects.

Effect of catchment land use and soil type on the concentration, quality, and bacterial degradation of riverine dissolved organic matter.

PubMed

Autio, Iida; Soinne, Helena; Helin, Janne; Asmala, Eero; Hoikkala, Laura

2016-04-01

We studied the effects of catchment characteristics (soil type and land use) on the concentration and quality of dissolved organic matter (DOM) in river water and on the bacterial degradation of terrestrial DOM. The share of organic soil was the strongest predictor of high concentrations of dissolved organic carbon, nitrogen, and phosphorus (DOC, DON, and DOP, respectively), and was linked to DOM quality. Soil type was more important than land use in determining the concentration and quality of riverine DOM. On average, 5-9 % of the DOC and 45 % of the DON were degraded by the bacterial communities within 2-3 months. Simultaneously, the proportion of humic-like compounds in the DOM pool increased. Bioavailable DON accounted for approximately one-third of the total bioavailable dissolved nitrogen, and thus, terrestrial DON can markedly contribute to the coastal plankton dynamics and support the heterotrophic food web.

Characterization of DOM adsorption of CNTs by using excitation-emission matrix fluorescence spectroscopy and multiway analysis.

PubMed

Peng, Mingguo; Li, Huajie; Li, Dongdong; Du, Erdeng; Li, Zhihong

2017-06-01

Carbon nanotubes (CNTs) were utilized to adsorb DOM in micro-polluted water. The characteristics of DOM adsorption on CNTs were investigated based on UV 254 , TOC, and fluorescence spectrum measurements. Based on PARAFAC (parallel factor) analysis, four fluorescent components were extracted, including one protein-like component (C4) and three humic acid-like components (C1, C2, and C3). The adsorption isotherms, kinetics, and thermodynamics of DOM adsorption on CNTs were further investigated. A Freundlich isotherm model fit the adsorption data well with high values of correlation. As a type of macro-porous and meso-porous adsorbent, CNTs preferably adsorb humic acid-like substances rather than protein-like substances. The increasing temperature will speed up the adsorption process. The self-organizing map (SOM) analysis further explains the fluorescent properties of water samples. The results provide a new insight into the adsorption behaviour of DOM fluorescent components on CNTs.

Implementation of NAS Parallel Benchmarks in Java

NASA Technical Reports Server (NTRS)

Frumkin, Michael; Schultz, Matthew; Jin, Hao-Qiang; Yan, Jerry

2000-01-01

A number of features make Java an attractive but a debatable choice for High Performance Computing (HPC). In order to gauge the applicability of Java to the Computational Fluid Dynamics (CFD) we have implemented NAS Parallel Benchmarks in Java. The performance and scalability of the benchmarks point out the areas where improvement in Java compiler technology and in Java thread implementation would move Java closer to Fortran in the competition for CFD applications.

Effects of watershed history on dissolved organic matter characteristics in headwater streams

Treesearch

Youhei Yamashita; Brian D. Kloeppel; Jennifer Knoepp; Gregory L. Zausen; Rudolf Jaffe'

2011-01-01

Dissolved organic matter (DOM) is recognized as a major component in the global carbon cycle and is an important driver in aquatic ecosystem function. Climate, land use, and forest cover changes all impact stream DOM and alter biogeochemical cycles in terrestrial environments. We determined the temporal variation in DOM quantity and quality in headwater streams at a...

Uptake of allochthonous dissolved organic matter from soil and salmon in coastal temperate rainforest streams

Treesearch

Jason B. Fellman; Eran Hood; Richard T. Edwards; Jeremy B. Jones

2009-01-01

Dissolved organic matter (DOM) is an important component of aquatic food webs. We compare the uptake kinetics for NH4-N and different fractions of DOM during soil and salmon leachate additions by evaluating the uptake of organic forms of carbon (DOC) and nitrogen (DON), and proteinaceous DOM, as measured by parallel factor (PARAFAC) modeling of...

Dissolved Organic Matter (DOM) Export from Watersheds to Coastal Oceans

NASA Astrophysics Data System (ADS)

Chen, R. F.; Gardner, G. B.; Peri, F.

2016-02-01

Dissolved organic matter (DOM) from terrestrial plants and soils is transported by surface waters and groundwaters to coastal ocean waters. Along the way, photochemical and biological degradation can remove DOM, and in situ processes such as phytoplankton leaching and sediment sources can add to the DOM in the river water. Wetlands, especially coastal wetlands can add significant amounts of DOM that is carried by rivers and is exported through estuaries to coastal systems. We will present observational data from a variety of coastal systems (San Francisco Bay, Boston Harbor, Chesapeake Bay, Hudson River, the Mississippi River, and a small salt marsh in the Gulf of Mexico). High resolution measurements of chromophoric dissolved organic matter (CDOM) can be correlated with dissolved organic carbon (DOC) so can be used to estimate DOC in specific systems and seasons. Gradients in CDOM/DOC combined with water fluxes can be used to estimate DOC fluxes from a variety of coastal watersheds to coastal systems. Influences of land use, system size, residence time, DOM quality, and photochemical and biological degradation will be discussed. The significance of coastal wetlands in the land-to-ocean export of DOC will be emphasized.

Changes of Photochemical Properties of Dissolved Organic Matter During a Hydrological Year

NASA Astrophysics Data System (ADS)

Porcal, P.; Dillon, P. J.

2009-05-01

The fate of dissolved organic matter (DOM) in lakes and streams is significantly affected by photochemical transformation of DOM. A series of laboratory photochemical experiments has been conducted to describe long term changes in photochemical properties of DOM. The stream samples used in this study originated from three different watersheds in Dorset area (Ontario, Canada), the first watershed has predominantly coniferous cove, the second one is dominated by maple and birch, and a large wetland dominates to the third one. The first order kinetic constant rate was used as a suitable characteristic of photochemical properties of DOM. The higher rates were observed in samples from watershed dominated by coniferous forest while the lower rates were determined in deciduous forest. Kinetic rates from all three watersheds showed sinusoidal pattern during the hydrological year. The rates increased steadily during autumn and winter and decreased during spring and summer. The highest values were observed during the spring melt events when the fresh DOM was flushed out from terrestrial sources. The minimum rate constants were in summer when the discharge was lower. The photochemical properties of DOM changes during the hydrological year and correspond to the seasonal cycles of terrestrial organic matter.

Bioavailability of Dissolved Organic Carbon and Nitrogen From Tropical Montane Rainforest Streams Across a Geologic age Gradient

NASA Astrophysics Data System (ADS)

Wiegner, T. N.

2005-05-01

Dissolved organic matter (DOM) is metabolically important in streams. Its bioavailability is influenced by organic matter sources to streams and inorganic nutrient availability. As forest canopies and soils develop over time, organic matter inputs to streams should switch from algal to watershed sources. Across this succession gradient, nutrient limitation should also change. This study examines how chemical composition and bioavailability of DOM from tropical montane rainforest streams on Hawaii change across a geologic age gradient from 4 ky to 150 ky. Dissolved organic C (DOC) and N (DON) concentrations, chemical characteristics, and bioavailability varied with site age. With increasing stream age, DOC and DON concentrations, DOM aromaticity, and the C:N of the stream DOM increased. Changes in stream DOM chemistry and inorganic nutrient availability affected DOM bioavailability. Fifty percent of the DOC from the 4 ky site was bioavailable, where little to none was bioavailable from the older streams. Inorganic nutrient availability did not affect DOC bioavailability. In contrast, DON bioavailability was similar (12%) across sites and was affected by inorganic nutrient availability. This study demonstrates that the chemistry and metabolism of streams draining forests change with ecosystem age and development.

Effect of dissolved organic matter (DOM) of contrasting origins on Cu and Pb speciation and toxicity to Paracentrotus lividus larvae.

PubMed

Sánchez-Marín, Paula; Santos-Echeandía, Juan; Nieto-Cid, Mar; Alvarez-Salgado, Xosé Antón; Beiras, Ricardo

2010-01-31

Water samples of contrasting origin, including natural seawater, two sediment elutriates and sewage-influenced seawater, were collected and obtained to examine the effect of the dissolved organic matter (DOM) present on metal bioavailability. The carbon content (DOC) and the optical properties (absorbance and fluorescence) of the coloured DOM fraction (CDOM) of these materials were determined. Cu and Pb complexation properties were measured by anodic stripping voltammetry (ASV) and the effect of DOM on Cu and Pb bioavailability was studied by means of the Paracentrotus lividus embryo-larval bioassay. Sediment elutriates and sewage-influenced water (1) were enriched 1.4-1.7 times in DOC; (2) absorbed and reemitted more light; and (3) presented higher Cu complexation capacities (L(Cu)) than the natural seawater used for their preparation. L(Cu) varied from 0.08 microM in natural seawater to 0.3 and 0.5 microM in sediment elutriates and sewage-influenced water, respectively. Differences in DOC, CDOM and Cu complexation capacities were reflected in Cu toxicity. DOM enriched samples presented a Cu EC(50) of 0.64 microM, significantly higher than the Cu EC(50) of natural and artificial seawater, which was 0.38 microM. The protecting effect of DOM on Cu toxicity greatly disappeared when the samples were irradiated with high intensity UV-light. Cu toxicity could be successfully predicted considering ASV-labile Cu concentrations in the samples. Pb complexation by DOM was only detected in the DOM-enriched samples and caused little effect on Pb EC(50). This effect was contrary for both elutriates: one elutriate reduced Pb toxicity in comparison with the control artificial seawater, while the other increased it. UV irradiation of the samples caused a marked increase in Pb toxicity, which correlated with the remaining DOC concentration. DOM parameters were related to Cu speciation and toxicity: good correlations were found between DOC and Cu EC(50), while L(Cu) correlated better with the fluorescence of marine humic substances. The present results stress the importance of characterizing not only the amount but also the quality of seawater DOM to better predict ecological effects from total metal concentration data. Copyright (c) 2009 Elsevier B.V. All rights reserved.

Controls on dissolved organic matter (DOM) degradation in a headwater stream: the influence of photochemical and hydrological conditions in determining light-limitation or substrate-limitation of photo-degradation

NASA Astrophysics Data System (ADS)

Cory, R. M.; Harrold, K. H.; Neilson, B. T.; Kling, G. W.

2015-07-01

We investigated how absorption of sunlight by chromophoric dissolved organic matter (CDOM) controls the degradation and export of DOM from Imnavait Creek, a beaded stream in the Alaskan Arctic. We measured concentrations of dissolved organic carbon (DOC), as well as concentrations and characteristics of CDOM and fluorescent dissolved organic matter (FDOM), during ice-free periods of 2011-2012 in the pools of Imnavait Creek and in soil waters draining to the creek. Spatial and temporal patterns in CDOM and FDOM in Imnavait Creek were analyzed in conjunction with measures of DOM degradation by sunlight and bacteria and assessments of hydrologic residence times and in situ UV exposure. CDOM was the dominant light attenuating constituent in the UV and visible portion of the solar spectrum, with high attenuation coefficients ranging from 86 ± 12 m-1 at 305 nm to 3 ± 1 m-1 in the photosynthetically active region (PAR). High rates of light absorption and thus light attenuation by CDOM contributed to thermal stratification in the majority of pools in Imnavait Creek under low-flow conditions. In turn, thermal stratification increased the residence time of water and DOM, and resulted in a separation of water masses distinguished by contrasting UV exposure (i.e., UV attenuation by CDOM with depth resulted in bottom waters receiving less UV than surface waters). When the pools in Imnavait Creek were stratified, DOM in the pool bottom water closely resembled soil water DOM in character, while the concentration and character of DOM in surface water was reproduced by experimental photo-degradation of bottom water. These results, in combination with water column rates of DOM degradation by sunlight and bacteria, suggest that photo-degradation is the dominant process controlling DOM fate and export in Imnavait Creek. A conceptual model is presented showing how CDOM amount and lability interact with incident UV light and water residence time to determine whether photo-degradation is "light-limited" or "substrate-limited". We suggest that degradation, and thus export, of DOM in CDOM-rich streams or ponds similar to Imnavait is typically light-limited under most flow conditions.

Characterization of dissolved organic matter in drinking water sources impacted by multiple tributaries.

PubMed

Rosario-Ortiz, Fernando L; Snyder, Shane A; Suffet, I H

2007-10-01

The characterization of dissolved organic matter (DOM) in drinking water sources is important as this material contributes to the formation of disinfection by-products (DBPs) and affects how water treatment unit operations are optimized. Drinking water utilities often draw water from sources impacted by multiple tributaries, with possible shifts in DOM concentrations and reactivity over time, depending on specific environmental conditions. In this study, results are presented on the characterization of DOM under varying ambient conditions from the four main tributaries of Lake Mead, a large reservoir in the southwest United States. The tributaries include the Las Vegas Wash (LVW), Muddy River (MR), Virgin River (VR) and the upper Colorado River (UCR). One additional sample was collected at the outflow of the reservoir (lower Colorado River (LCR)). The DOM was characterized by both bulk parameters (specific ultraviolet absorbance (SUVA)) and specific physicochemical properties, i.e. size, polarity and fluorescence. The analyses were performed emphasizing limited changes in its natural configuration by eliminating analytical preparation steps, excluding sample filtration (0.45 microm filter). Results indicate that each tributary had a different molecular weight distribution, as well as fluorescence properties, which helped in the identification of the relative source of DOM (allochthonous versus autochthonous). The largest apparent molecular weight distribution was observed for DOM samples collected at the MR site, which is fed mostly by groundwater seepage. The smallest apparent molecular weight was observed for DOM collected at the LCR site, suggesting that retention in the reservoir resulted in a decrease in molecular weight as a probable result of photo oxidation and microbial processes. Fluorescence analysis aided the differentiation of DOM by clearly identifying waters that were affected by microbial activity (LVW, UCR, and LCR), either by wastewater influence or by autochthonous processes, versus limited microbial influence (MR and VR). Polarity analysis revealed clear differences in the hydrophobic/hydrophilic nature between waters, including temporal differences within individual waters at a particular site. The DOM from the LVW and VR sites had higher hydrophobic character, as measured by retention onto non-polar sorbents. Additionally, the DOM collected at the LCR had the least hydrophobic character. This type of analysis would be beneficial to utilities who want to better understand and manage their source waters, especially in the evaluation of temporal variation within a watershed.

The molecular characteristics of pyrogenic organic materials and their aqueous leachates

NASA Astrophysics Data System (ADS)

Wozniak, A. S.; Hatcher, P.; Mitra, S.; Bostick, K. W.; Zimmerman, A. R.

2016-12-01

Pyrogenic organic matter (Py-OM), or black carbon, is known to impact soil chemistry, pollutant transport, regional and global carbon cycling, and climate. Py-OM is incorporated into soils via atmospheric deposition (e.g., from biomass, fossil fuel combustion) or direct applications by humans (e.g., biochars applied for agricultural production). Due to its presumed refractory and immobile nature, soil Py-OM is thought to be efficiently buried, sequestering atmospheric CO2. However, tracers of dissolved Py-OM (Py-DOM) have been detected in appreciable quantities in riverine, estuarine, and oceanic waters suggesting that Py-OM is more mobile in the environment than expected. The molecular characteristics of Py-OM are likely to be a controlling factor in the quantities and impacts of Py-DOM released to aqueous systems. Yet, little is known about the detailed molecular composition of these materials, let alone how those molecular characteristics vary with combustion conditions or are altered by environmental processes. Here, we examine oak and grass Py-OM (combusted over a range of temperatures), natural Py-OM (chars aged in the environment for variable lengths of time), and their Py-DOM leachates via nuclear magnetic resonance spectroscopy (NMR) and Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). Multi-CP 13C NMR analyses of Py-OM materials and 1H NMR analyses of corresponding Py-DOM leachates reveal that Py-OM combustion temperature, environmental exposure, and molecular characteristics are reflected in Py-DOM quantities and characteristics. The relative amounts of aromatic C in Py-OM 1) decreases with environmental exposure, the relative oxygen-content in both Py-OM and Py-DOM, and the amount of Py-DOC released per g of Py-OC but 2) is positively correlated with combustion temperature and the relative contributions of acetate and aliphatic hydrogens (CH2) in Py-DOM. Preliminary FTICR-MS analyses show Py-DOM produced from oak at 400 °C to have lost carbohydrate-like compounds found in 250 °C Py-DOM and to contain an abundance of oxygenated aromatic compounds. Oak combusted at 650 °C produces Py-DOM characterized by high H/C, low O/C compounds. The results from this work will improve our understanding of Py-OM transport within and between terrestrial and aqueous systems.

Glucuronidation of deoxynivalenol (DON) by different animal species: identification of iso-DON glucuronides and iso-deepoxy-DON glucuronides as novel DON metabolites in pigs, rats, mice, and cows.

PubMed

Schwartz-Zimmermann, Heidi E; Hametner, Christian; Nagl, Veronika; Fiby, Iris; Macheiner, Lukas; Winkler, Janine; Dänicke, Sven; Clark, Erica; Pestka, James J; Berthiller, Franz

2017-12-01

The Fusarium mycotoxin deoxynivalenol (DON) is a frequent contaminant of cereal-based food and feed. Mammals metabolize DON by conjugation to glucuronic acid (GlcAc), the extent and regioselectivity of which is species-dependent. So far, only DON-3-glucuronide (DON-3-GlcAc) and DON-15-GlcAc have been unequivocally identified as mammalian DON glucuronides, and DON-7-GlcAc has been proposed as further DON metabolite. In the present work, qualitative HPLC-MS/MS analysis of urine samples of animals treated with DON (rats: 2 mg/kg bw, single bolus, gavage; mice: 1 mg/kg bw, single i.p. injection; pigs: 74 µg/kg bw, single bolus, gavage; cows: 5.2 mg DON/kg dry mass, oral for 13 weeks) revealed additional DON and deepoxy-DON (DOM) glucuronides. To elucidate their structures, DON and DOM were incubated with human (HLM) and rat liver microsomes (RLM). Besides the expected DON/DOM-3- and 15-GlcAc, minor amounts of four DON- and four DOM glucuronides were formed. Isolation and enzymatic hydrolysis of four of these compounds yielded iso-DON and iso-DOM, the identities of which were eventually confirmed by NMR. Incubation of iso-DON and iso-DOM with RLM and HLM yielded two main glucuronides for each parent compound, which were isolated and identified as iso-DON/DOM-3-GlcAc and iso-DON/DOM-8-GlcAc by NMR. Iso-DON-3-GlcAc, most likely misidentified as DON-7-GlcAc in the literature, proved to be a major DON metabolite in rats and a minor metabolite in pigs. In addition, iso-DON-8-GlcAc turned out to be one of the major DON metabolites in mice. DOM-3-GlcAc was the dominant DON metabolite in urine of cows and an important DON metabolite in rat urine. Iso-DOM-3-GlcAc was detected in urine of DON-treated rats and cows. Finally, DON-8,15-hemiketal-8-glucuronide, a previously described by-product of DON-3-GlcAc production by RLM, was identified in urine of DON-exposed mice and rats. The discovery of several novel DON-derived glucuronides in animal urine requires adaptation of the currently used methods for DON-biomarker analysis.

Importance of lateral flux and its percolation depth on organic carbon export in Arctic tundra soil: Implications from a soil leaching experiment: Changes of OC in Arctic Soil Leachate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xiaowen; Hutchings, Jack A.; Bianchi, Thomas S.

Temperature rise in the Arctic is causing deepening of active layers and resulting in the mobilization of deep permafrost dissolved organic matter (DOM). However, the mechanisms of DOM mobilization from Arctic soils, especially upper soil horizons which are drained most frequently through a year, are poorly understood. Here, we conducted a short-term leaching experiment on surface and deep organic active layer soils, from the Yukon River basin, to examine the effects of DOM transport on bulk and molecular characteristics. Our data showed a net release of DOM from surface soils equal to an average of 5% of soil carbon. Conversely,more » deep soils percolated with surface leachates retained up to 27% of bulk DOM-while releasing fluorescent components (up to 107%), indicating selective release of aromatic components (e.g. lignin, tannin), while retaining non-chromophoric components, as supported by spectrofluorometric and ultra high resolution mass spectroscopic techniques. Our findings highlight the importance of the lateral flux of DOM on ecosystem carbon balance as well as processing of DOM transport through organic active layer soils en route to rivers and streams. This work also suggests the potential role of leachate export as an important mechanism of C losses from Arctic soils, in comparison with the more traditional pathway from soil to atmosphere in a warming Arctic.« less

Linking groundwater dissolved organic matter to sedimentary organic matter from a fluvio-lacustrine aquifer at Jianghan Plain, China by EEM-PARAFAC and hydrochemical analyses.

PubMed

Huang, Shuang-bing; Wang, Yan-xin; Ma, Teng; Tong, Lei; Wang, Yan-yan; Liu, Chang-rong; Zhao, Long

2015-10-01

The sources of dissolved organic matter (DOM) in groundwater are important to groundwater chemistry and quality. This study examined similarities in the nature of DOM and investigated the link between groundwater DOM (GDOM) and sedimentary organic matter (SOM) from a lacustrine-alluvial aquifer at Jianghan Plain. Sediment, groundwater and surface water samples were employed for SOM extraction, optical and/or chemical characterization, and subsequent fluorescence excitation-emission matrix (EEM) and parallel factor analyses (PARAFAC). Spectroscopic properties of bulk DOM pools showed that indices indicative of GDOM (e.g., biological source properties, humification level, aromaticity and molecule mobility) varied within the ranges of those of two extracted end-members of SOM: humic-like materials and microbe-associated materials. The coexistence of PARAFAC compositions and the sustaining internal relationship between GDOM and extracted SOM indicate a similar source. The results from principal component analyses with selected spectroscopic indices showed that GDOM exhibited a transition trend regarding its nature: from refractory high-humification DOM to intermediate humification DOM and then to microbe-associated DOM, with decreasing molecular weight. Correlations of spectroscopic indices with physicochemical parameters of the groundwater suggested that GDOM was released from SOM and was modified by microbial diagenetic processes. The current study demonstrated the associations of GDOM with SOM from a spectroscopic viewpoint and provided new evidence supporting SOM as the source of GDOM. Copyright © 2015 Elsevier B.V. All rights reserved.

Predicting Reactive Intermediate Quantum Yields from Dissolved Organic Matter Photolysis Using Optical Properties and Antioxidant Capacity.

PubMed

Mckay, Garrett; Huang, Wenxi; Romera-Castillo, Cristina; Crouch, Jenna E; Rosario-Ortiz, Fernando L; Jaffé, Rudolf

2017-05-16

The antioxidant capacity and formation of photochemically produced reactive intermediates (RI) was studied for water samples collected from the Florida Everglades with different spatial (marsh versus estuarine) and temporal (wet versus dry season) characteristics. Measured RI included triplet excited states of dissolved organic matter ( 3 DOM*), singlet oxygen ( 1 O 2 ), and the hydroxyl radical ( • OH). Single and multiple linear regression modeling were performed using a broad range of extrinsic (to predict RI formation rates, R RI ) and intrinsic (to predict RI quantum yields, Φ RI ) parameters. Multiple linear regression models consistently led to better predictions of R RI and Φ RI for our data set but poor prediction of Φ RI for a previously published data set,1 probably because the predictors are intercorrelated (Pearson's r > 0.5). Single linear regression models were built with data compiled from previously published studies (n ≈ 120) in which E2:E3, S, and Φ RI values were measured, which revealed a high degree of similarity between RI-optical property relationships across DOM samples of diverse sources. This study reveals that • OH formation is, in general, decoupled from 3 DOM* and 1 O 2 formation, providing supporting evidence that 3 DOM* is not a • OH precursor. Finally, Φ RI for 1 O 2 and 3 DOM* correlated negatively with antioxidant activity (a surrogate for electron donating capacity) for the collected samples, which is consistent with intramolecular oxidation of DOM moieties by 3 DOM*.

Spatial and seasonal variations in the composition of dissolved organic matter in a tropical catchment: the Lower Kinabatangan River, Sabah, Malaysia.

PubMed

Harun, Sahana; Baker, Andy; Bradley, Chris; Pinay, Gilles

2016-01-01

Dissolved organic matter (DOM) was characterised in water samples sampled in the Lower Kinabatangan River Catchment, Sabah, Malaysia between October 2009 and May 2010. This study aims at: (i) distinguishing between the quality of DOM in waters draining palm oil plantations (OP), secondary forests (SF) and coastal swamps (CS) and, (ii) identifying the seasonal variability of DOM quantity and quality. Surface waters were sampled during fieldwork campaigns that spanned the wet and dry seasons. DOM was characterised optically by using the fluorescence Excitation Emission Matrix (EEM), the absorption coefficient at 340 nm and the spectral slope coefficient (S). Parallel Factor Analysis (PARAFAC) was undertaken to assess the DOM composition from EEM spectra and five terrestrial derived components were identified: (C1, C2, C3, C4 and C5). Components C1 and C4 contributed the most to DOM fluorescence in all study areas during both the wet and dry seasons. The results suggest that component C4 could be a significant (and common) PARAFAC signal found in similar catchments. Peak M (C2 and C3) was dominant in all samples collected during wet and dry seasons, which could be anthropogenic in origin given the active land use change in the study area. In conclusion, there were significant seasonal and spatial variations in DOM which demonstrated the effects of land use cover and precipitation amounts in the Kinabatangan catchment.

DOE Office of Scientific and Technical Information (OSTI.GOV)

von Laszewski, G.; Gawor, J.; Lane, P.

In this paper we report on the features of the Java Commodity Grid Kit (Java CoG Kit). The Java CoG Kit provides middleware for accessing Grid functionality from the Java framework. Java CoG Kit middleware is general enough to design a variety of advanced Grid applications with quite different user requirements. Access to the Grid is established via Globus Toolkit protocols, allowing the Java CoG Kit to also communicate with the services distributed as part of the C Globus Toolkit reference implementation. Thus, the Java CoG Kit provides Grid developers with the ability to utilize the Grid, as well asmore » numerous additional libraries and frameworks developed by the Java community to enable network, Internet, enterprise and peer-to-peer computing. A variety of projects have successfully used the client libraries of the Java CoG Kit to access Grids driven by the C Globus Toolkit software. In this paper we also report on the efforts to develop serverside Java CoG Kit components. As part of this research we have implemented a prototype pure Java resource management system that enables one to run Grid jobs on platforms on which a Java virtual machine is supported, including Windows NT machines.« less

Rapid development of entity-based data models for bioinformatics with persistence object-oriented design and structured interfaces.

PubMed

Ezra Tsur, Elishai

2017-01-01

Databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and context-dependent interconnections between data entities. These challenges drove the development of unified data interfaces and specialized databases. The curation of specialized databases is an ever-growing challenge due to the introduction of new data sources and the emergence of new relational connections between established datasets. Here, an open-source framework for the curation of specialized databases is proposed. The framework supports user-designed models of data encapsulation, objects persistency and structured interfaces to local and external data sources such as MalaCards, Biomodels and the National Centre for Biotechnology Information (NCBI) databases. The proposed framework was implemented using Java as the development environment, EclipseLink as the data persistency agent and Apache Derby as the database manager. Syntactic analysis was based on J3D, jsoup, Apache Commons and w3c.dom open libraries. Finally, a construction of a specialized database for aneurysms associated vascular diseases is demonstrated. This database contains 3-dimensional geometries of aneurysms, patient's clinical information, articles, biological models, related diseases and our recently published model of aneurysms' risk of rapture. Framework is available in: http://nbel-lab.com.

The Effect of Semantic Transparency on the Processing of Morphologically Derived Words: Evidence from Decision Latencies and Event-Related Potentials

ERIC Educational Resources Information Center

Jared, Debra; Jouravlev, Olessia; Joanisse, Marc F.

2017-01-01

Decomposition theories of morphological processing in visual word recognition posit an early morpho-orthographic parser that is blind to semantic information, whereas parallel distributed processing (PDP) theories assume that the transparency of orthographic-semantic relationships influences processing from the beginning. To test these…

Disfluencies along the Garden Path: Brain Electrophysiological Evidence of Disrupted Sentence Processing

ERIC Educational Resources Information Center

Maxfield, Nathan D.; Lyon, Justine M.; Silliman, Elaine R.

2009-01-01

Bailey and Ferreira (2003) hypothesized and reported behavioral evidence that disfluencies (filled and silent pauses) undesirably affect sentence processing when they appear before disambiguating verbs in Garden Path (GP) sentences. Disfluencies here cause the parser to "linger" on, and apparently accept as correct, an erroneous parse. Critically,…

Intelligent interfaces for expert systems

NASA Technical Reports Server (NTRS)

Villarreal, James A.; Wang, Lui

1988-01-01

Vital to the success of an expert system is an interface to the user which performs intelligently. A generic intelligent interface is being developed for expert systems. This intelligent interface was developed around the in-house developed Expert System for the Flight Analysis System (ESFAS). The Flight Analysis System (FAS) is comprised of 84 configuration controlled FORTRAN subroutines that are used in the preflight analysis of the space shuttle. In order to use FAS proficiently, a person must be knowledgeable in the areas of flight mechanics, the procedures involved in deploying a certain payload, and an overall understanding of the FAS. ESFAS, still in its developmental stage, is taking into account much of this knowledge. The generic intelligent interface involves the integration of a speech recognizer and synthesizer, a preparser, and a natural language parser to ESFAS. The speech recognizer being used is capable of recognizing 1000 words of connected speech. The natural language parser is a commercial software package which uses caseframe instantiation in processing the streams of words from the speech recognizer or the keyboard. The systems configuration is described along with capabilities and drawbacks.

Two models of minimalist, incremental syntactic analysis.

PubMed

Stabler, Edward P

2013-07-01

Minimalist grammars (MGs) and multiple context-free grammars (MCFGs) are weakly equivalent in the sense that they define the same languages, a large mildly context-sensitive class that properly includes context-free languages. But in addition, for each MG, there is an MCFG which is strongly equivalent in the sense that it defines the same language with isomorphic derivations. However, the structure-building rules of MGs but not MCFGs are defined in a way that generalizes across categories. Consequently, MGs can be exponentially more succinct than their MCFG equivalents, and this difference shows in parsing models too. An incremental, top-down beam parser for MGs is defined here, sound and complete for all MGs, and hence also capable of parsing all MCFG languages. But since the parser represents its grammar transparently, the relative succinctness of MGs is again evident. Although the determinants of MG structure are narrowly and discretely defined, probabilistic influences from a much broader domain can influence even the earliest analytic steps, allowing frequency and context effects to come early and from almost anywhere, as expected in incremental models. Copyright © 2013 Cognitive Science Society, Inc.

Evaluation of forest disturbance legacy effects on dissolved organic matter characteristics in streams at the Hubbard Brook Experimental Forest, New Hampshire

Treesearch

Kaelin M. Cawley; John Campbell; Melissa Zwilling; Rudolf. Jaffé

2014-01-01

Dissolved organic matter (DOM) source and composition are critical drivers of its reactivity, impact microbial food webs and influence ecosystem functions. It is believed that DOM composition and abundance represent an integrated signal derived from the surrounding watershed. Recent studies have shown that land-use may have a long-term effect on DOM composition....

The effect of freezing and drying on leaching of DOM from above ground vascular plant material from the Alaskan Arctic

NASA Astrophysics Data System (ADS)

Khosh, M. S.; McClelland, J. W.

2014-12-01

Our understanding of the seasonal dynamics of fluvial dissolved organic matter (DOM) concentrations and fluxes in Arctic catchments has increased substantially during recent years, especially during the spring, which historically has been an under-sampled time period. While a number of studies have observed peaks in both DOM concentrations and fluxes during the spring snowmelt, our knowledge of the mechanisms that control these observations are still lacking. During the initial snowmelt period, frozen ground and the snow matrix act to constrain melt-water to the soil surface. We hypothesize that restriction of flow during this time facilitates leaching of DOM from senescent above ground vegetation and detritus contributing to the high DOM concentrations observed during the spring melt. This study focuses on the effect of freezing and drying on the leaching of dissolved organic carbon and nitrogen (DOC and DON) from above ground vascular plant material. Specifically, we examined the treatment effects of freezing, drying, and freeze-drying on three genera of common Alaskan Arctic vascular plants; Eriophorum (spp.), Carex (spp.), and Salix (spp.). Frozen and freeze-dried plant material released more DOC over the experimental 96 hour leaching period compared to plant material that was only dried. Qualitatively, these patterns were similar among the different plant types, while quantitatively Salix leached more DOC than either Eriophorum or Carex in all treatments. Similar patterns were also seen for DON between the different treatments and among the different plant types. Compositionally, DOM that was leached from frozen and freeze-dried material had higher C:N ratios than material that was only dried. Comparatively, DOM leached from Salix had much higher C:N ratios than either Eriophorum or Carex. During the first 24 hours of leaching, C:N ratios tended to increase followed by a subsequent leveling or decrease, suggesting that the composition of leached DOM varied during the 96 hour time period. Our findings suggest that the seasonal timing of freezing and drying conditions experienced by senesced plant material during the late summer, fall, and winter may impact DOM leaching dynamics on that same plant material the following spring during snowmelt.

Wet-dry cycles impact DOM retention in subsurface soils

NASA Astrophysics Data System (ADS)

Olshansky, Yaniv; Root, Robert A.; Chorover, Jon

2018-02-01

Transport and reactivity of carbon in the critical zone are highly controlled by reactions of dissolved organic matter (DOM) with subsurface soils, including adsorption, transformation and exchange. These reactions are dependent on frequent wet-dry cycles common to the unsaturated zone, particularly in semi-arid regions. To test for an effect of wet-dry cycles on DOM interaction and stabilization in subsoils, samples were collected from subsurface (Bw) horizons of an Entisol and an Alfisol from the Catalina-Jemez Critical Zone Observatory and sequentially reacted (four batch steps) with DOM extracted from the corresponding soil litter layers. Between each reaction step, soils either were allowed to air dry (wet-dry treatment) before introduction of the following DOM solution or were maintained under constant wetness (continually wet treatment). Microbial degradation was the dominant mechanism of DOM loss from solution for the Entisol subsoil, which had higher initial organic C content, whereas sorptive retention predominated in the lower C Alfisol subsoil. For a given soil, bulk dissolved organic C losses from solution were similar across treatments. However, a combination of Fourier transform infrared (FTIR) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopic analyses revealed that wet-dry treatments enhanced the interactions between carboxyl functional groups and soil particle surfaces. Scanning transmission X-ray microscopy (STXM) data suggested that cation bridging by Ca2+ was the primary mechanism for carboxyl association with soil surfaces. STXM data also showed that spatial fractionation of adsorbed OM on soil organo-mineral surfaces was diminished relative to what might be inferred from previously published observations pertaining to DOM fractionation on reaction with specimen mineral phases. This study provides direct evidence of the role of wet-dry cycles in affecting sorption reactions of DOM to a complex soil matrix. In the soil environment, where wet-dry cycles occur at different frequencies from site to site and along the soil profile, different interactions between DOM and soil surfaces are expected and need to be considered for the overall assessment of carbon dynamics.

A critical evaluation of an asymmetrical flow field-flow fractionation system for colloidal size characterization of natural organic matter.

PubMed

Zhou, Zhengzhen; Guo, Laodong

2015-06-19

Colloidal retention characteristics, recovery and size distribution of model macromolecules and natural dissolved organic matter (DOM) were systematically examined using an asymmetrical flow field-flow fractionation (AFlFFF) system under various membrane size cutoffs and carrier solutions. Polystyrene sulfonate (PSS) standards with known molecular weights (MW) were used to determine their permeation and recovery rates by membranes with different nominal MW cutoffs (NMWCO) within the AFlFFF system. Based on a ≥90% recovery rate for PSS standards by the AFlFFF system, the actual NMWCOs were determined to be 1.9 kDa for the 0.3 kDa membrane, 2.7 kDa for the 1 kDa membrane, and 33 kDa for the 10 kDa membrane, respectively. After membrane calibration, natural DOM samples were analyzed with the AFlFFF system to determine their colloidal size distribution and the influence from membrane NMWCOs and carrier solutions. Size partitioning of DOM samples showed a predominant colloidal size fraction in the <5 nm or <10 kDa size range, consistent with the size characteristics of humic substances as the main terrestrial DOM component. Recovery of DOM by the AFlFFF system, as determined by UV-absorbance at 254 nm, decreased significantly with increasing membrane NMWCO, from 45% by the 0.3 kDa membrane to 2-3% by the 10 kDa membrane. Since natural DOM is mostly composed of lower MW substances (<10 kDa) and the actual membrane cutoffs are normally larger than their manufacturer ratings, a 0.3 kDa membrane (with an actual NMWCO of 1.9 kDa) is highly recommended for colloidal size characterization of natural DOM. Among the three carrier solutions, borate buffer seemed to provide the highest recovery and optimal separation of DOM. Rigorous calibration with macromolecular standards and optimization of system conditions are a prerequisite for quantifying colloidal size distribution using the flow field-flow fractionation technique. In addition, the coupling of AFlFFF with fluorescence EEMs could provide new insights into DOM heterogeneity in different colloidal size fractions. Copyright © 2015 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

von Laszewski, G.; Foster, I.; Gawor, J.

In this paper we report on the features of the Java Commodity Grid Kit. The Java CoG Kit provides middleware for accessing Grid functionality from the Java framework. Java CoG Kit middleware is general enough to design a variety of advanced Grid applications with quite different user requirements. Access to the Grid is established via Globus protocols, allowing the Java CoG Kit to communicate also with the C Globus reference implementation. Thus, the Java CoG Kit provides Grid developers with the ability to utilize the Grid, as well as numerous additional libraries and frameworks developed by the Java community tomore » enable network, Internet, enterprise, and peer-to peer computing. A variety of projects have successfully used the client libraries of the Java CoG Kit to access Grids driven by the C Globus software. In this paper we also report on the efforts to develop server side Java CoG Kit components. As part of this research we have implemented a prototype pure Java resource management system that enables one to run Globus jobs on platforms on which a Java virtual machine is supported, including Windows NT machines.« less

Optical properties and bioavailability of dissolved organic matter along a flow-path continuum from soil pore waters to the Kolyma River mainstem, East Siberia

NASA Astrophysics Data System (ADS)

Frey, Karen E.; Sobczak, William V.; Mann, Paul J.; Holmes, Robert M.

2016-04-01

The Kolyma River in northeast Siberia is among the six largest Arctic rivers and drains a region underlain by vast deposits of Holocene-aged peat and Pleistocene-aged loess known as yedoma, most of which is currently stored in ice-rich permafrost throughout the region. These peat and yedoma deposits are important sources of dissolved organic matter (DOM) to inland waters that in turn play a significant role in the transport and ultimate remineralization of organic carbon to CO2 and CH4 along the terrestrial flow-path continuum. The turnover and fate of terrigenous DOM during offshore transport largely depends upon the composition and amount of carbon released to inland and coastal waters. Here, we measured the ultraviolet-visible optical properties of chromophoric DOM (CDOM) from a geographically extensive collection of waters spanning soil pore waters, streams, rivers, and the Kolyma River mainstem throughout a ˜ 250 km transect of the northern Kolyma River basin. During the period of study, CDOM absorption coefficients were found to be robust proxies for the concentration of DOM, whereas additional CDOM parameters such as spectral slopes (S) were found to be useful indicators of DOM quality along the flow path. In particular, the spectral slope ratio (SR) of CDOM demonstrated statistically significant differences between all four water types and tracked changes in the concentration of bioavailable DOC, suggesting that this parameter may be suitable for clearly discriminating shifts in organic matter characteristics among water types along the full flow-path continuum across this landscape. However, despite our observations of downstream shifts in DOM composition, we found a relatively constant proportion of DOC that was bioavailable ( ˜ 3-6 % of total DOC) regardless of relative water residence time along the flow path. This may be a consequence of two potential scenarios allowing for continual processing of organic material within the system, namely (a) aquatic microorganisms are acclimating to a downstream shift in DOM composition and/or (b) photodegradation is continually generating labile DOM for continued microbial processing of DOM along the flow-path continuum. Without such processes, we would otherwise expect to see a declining fraction of bioavailable DOC downstream with increasing residence time of water in the system. With ongoing and future permafrost degradation, peat and yedoma deposits throughout the northeast Siberian region will become more hydrologically active, providing greater amounts of DOM to fluvial networks and ultimately to the Arctic Ocean. The ability to rapidly and comprehensively monitor shifts in the quantity and quality of DOM across the landscape is therefore critical for understanding potential future feedbacks within the Arctic carbon cycle.

The influence of natural dissolved organic matter on herbicide toxicity to marine microalgae is species-dependent.

PubMed

Coquillé, Nathalie; Ménard, Dominique; Rouxel, Julien; Dupraz, Valentin; Éon, Mélissa; Pardon, Patrick; Budzinski, Hélène; Morin, Soizic; Parlanti, Édith; Stachowski-Haberkorn, Sabine

2018-05-01

Microalgae, which are the foundation of aquatic food webs, may be the indirect target of herbicides used for agricultural and urban applications. Microalgae also interact with other compounds from their environment, such as natural dissolved organic matter (DOM), which can itself interact with herbicides. This study aimed to evaluate the influence of natural DOM on the toxicity of three herbicides (diuron, irgarol and S-metolachlor), singly and in ternary mixtures, to two marine microalgae, Chaetoceros calcitrans and Tetraselmis suecica, in monospecific, non-axenic cultures. Effects on growth, photosynthetic efficiency (Ф' M ) and relative lipid content were evaluated. The chemical environment (herbicide and nutrient concentrations, dissolved organic carbon and DOM optical properties) was also monitored to assess any changes during the experiments. The results show that, without DOM, the highest irgarol concentration (I0.5: 0.5 mg.L -1 ) and the strongest mixture (M2: irgarol 0.5 μg.L -1  + diuron 0.5 μg.L -1  + S-metolachlor 5.0 μg.L -1 ) significantly decreased all parameters for both species. Similar impacts were induced by I0.5 and M2 in C. calcitrans (around -56% for growth, -50% for relative lipid content and -28% for Ф' M ), but a significantly higher toxicity of M2 was observed in T. suecica (-56% and -62% with I0.5 and M2 for growth, respectively), suggesting a possible interaction between molecules. With DOM added to the culture media, a significant inhibition of these three parameters was also observed with I0.5 and M2 for both species. Furthermore, DOM modulated herbicide toxicity, which was decreased for C. calcitrans (-51% growth at I0.5 and M2) and increased for T. suecica (-64% and -75% growth at I0.5 and M2, respectively). In addition to the direct and/or indirect (via their associated bacteria) use of molecules present in natural DOM, the characterization of the chemical environment showed that the toxic effects observed on microalgae were accompanied by modifications of DOM composition and the quantity of dissolved organic carbon excreted and/or secreted by microorganisms. This toxicity modulation in presence of DOM could be explained by (i) the modification of herbicide bioavailability, (ii) a difference in cell wall composition between the two species, and/or (iii) a higher detoxification capacity of C. calcitrans by the use of molecules contained in DOM. This study therefore demonstrated, for the first time, the major modulating role of natural DOM on the toxicity of herbicides to marine microalgae. Copyright © 2018 Elsevier B.V. All rights reserved.

JavaGenes and Condor: Cycle-Scavenging Genetic Algorithms

NASA Technical Reports Server (NTRS)

Globus, Al; Langhirt, Eric; Livny, Miron; Ramamurthy, Ravishankar; Soloman, Marvin; Traugott, Steve

2000-01-01

A genetic algorithm code, JavaGenes, was written in Java and used to evolve pharmaceutical drug molecules and digital circuits. JavaGenes was run under the Condor cycle-scavenging batch system managing 100-170 desktop SGI workstations. Genetic algorithms mimic biological evolution by evolving solutions to problems using crossover and mutation. While most genetic algorithms evolve strings or trees, JavaGenes evolves graphs representing (currently) molecules and circuits. Java was chosen as the implementation language because the genetic algorithm requires random splitting and recombining of graphs, a complex data structure manipulation with ample opportunities for memory leaks, loose pointers, out-of-bound indices, and other hard to find bugs. Java garbage-collection memory management, lack of pointer arithmetic, and array-bounds index checking prevents these bugs from occurring, substantially reducing development time. While a run-time performance penalty must be paid, the only unacceptable performance we encountered was using standard Java serialization to checkpoint and restart the code. This was fixed by a two-day implementation of custom checkpointing. JavaGenes is minimally integrated with Condor; in other words, JavaGenes must do its own checkpointing and I/O redirection. A prototype Java-aware version of Condor was developed using standard Java serialization for checkpointing. For the prototype to be useful, standard Java serialization must be significantly optimized. JavaGenes is approximately 8700 lines of code and a few thousand JavaGenes jobs have been run. Most jobs ran for a few days. Results include proof that genetic algorithms can evolve directed and undirected graphs, development of a novel crossover operator for graphs, a paper in the journal Nanotechnology, and another paper in preparation.

Does post-exercise massage treatment reduce delayed onset muscle soreness? A systematic review

PubMed Central

Ernst, E.

1998-01-01

BACKGROUND: Delayed onset muscle soreness (DOMS) is a frequent problem after unaccustomed exercise. No universally accepted treatment exists. Massage therapy is often recommended for this condition but uncertainty exists about its effectiveness. AIM: To determine whether post-exercise massage alleviates the symptoms of DOMS after a bout of strenuous exercise. METHOD: Various computerised literature searches were carried out and located seven controlled trials. RESULTS: Most of the trials were burdened with serious methodological flaws, and their results are far from uniform. However, most suggest that post-exercise massage may alleviate symptoms of DOMS. CONCLUSIONS: Massage therapy may be a promising treatment for DOMS. Definitive studies are warranted. 


 PMID:9773168

Deciphering ocean carbon in a changing world

PubMed Central

Moran, Mary Ann; Stubbins, Aron; Fatland, Rob; Aluwihare, Lihini I.; Buchan, Alison; Crump, Byron C.; Dorrestein, Pieter C.; Dyhrman, Sonya T.; Hess, Nancy J.; Howe, Bill; Longnecker, Krista; Medeiros, Patricia M.; Obernosterer, Ingrid; Repeta, Daniel J.; Waldbauer, Jacob R.

2016-01-01

Dissolved organic matter (DOM) in the oceans is one of the largest pools of reduced carbon on Earth, comparable in size to the atmospheric CO2 reservoir. A vast number of compounds are present in DOM, and they play important roles in all major element cycles, contribute to the storage of atmospheric CO2 in the ocean, support marine ecosystems, and facilitate interactions between organisms. At the heart of the DOM cycle lie molecular-level relationships between the individual compounds in DOM and the members of the ocean microbiome that produce and consume them. In the past, these connections have eluded clear definition because of the sheer numerical complexity of both DOM molecules and microorganisms. Emerging tools in analytical chemistry, microbiology, and informatics are breaking down the barriers to a fuller appreciation of these connections. Here we highlight questions being addressed using recent methodological and technological developments in those fields and consider how these advances are transforming our understanding of some of the most important reactions of the marine carbon cycle. PMID:26951682

Deciphering ocean carbon in a changing world.

PubMed

Moran, Mary Ann; Kujawinski, Elizabeth B; Stubbins, Aron; Fatland, Rob; Aluwihare, Lihini I; Buchan, Alison; Crump, Byron C; Dorrestein, Pieter C; Dyhrman, Sonya T; Hess, Nancy J; Howe, Bill; Longnecker, Krista; Medeiros, Patricia M; Niggemann, Jutta; Obernosterer, Ingrid; Repeta, Daniel J; Waldbauer, Jacob R

2016-03-22

Dissolved organic matter (DOM) in the oceans is one of the largest pools of reduced carbon on Earth, comparable in size to the atmospheric CO2 reservoir. A vast number of compounds are present in DOM, and they play important roles in all major element cycles, contribute to the storage of atmospheric CO2 in the ocean, support marine ecosystems, and facilitate interactions between organisms. At the heart of the DOM cycle lie molecular-level relationships between the individual compounds in DOM and the members of the ocean microbiome that produce and consume them. In the past, these connections have eluded clear definition because of the sheer numerical complexity of both DOM molecules and microorganisms. Emerging tools in analytical chemistry, microbiology, and informatics are breaking down the barriers to a fuller appreciation of these connections. Here we highlight questions being addressed using recent methodological and technological developments in those fields and consider how these advances are transforming our understanding of some of the most important reactions of the marine carbon cycle.

The IceCube data acquisition system: Signal capture, digitization, and timestamping

NASA Astrophysics Data System (ADS)

Abbasi, R.; Ackermann, M.; Adams, J.; Ahlers, M.; Ahrens, J.; Andeen, K.; Auffenberg, J.; Bai, X.; Baker, M.; Barwick, S. W.; Bay, R.; Bazo Alba, J. L.; Beattie, K.; Becka, T.; Becker, J. K.; Becker, K.-H.; Berghaus, P.; Berley, D.; Bernardini, E.; Bertrand, D.; Besson, D. Z.; Bingham, B.; Blaufuss, E.; Boersma, D. J.; Bohm, C.; Bolmont, J.; Böser, S.; Botner, O.; Braun, J.; Breeder, D.; Burgess, T.; Carithers, W.; Castermans, T.; Chen, H.; Chirkin, D.; Christy, B.; Clem, J.; Cowen, D. F.; D'Agostino, M. V.; Danninger, M.; Davour, A.; Day, C. T.; Depaepe, O.; De Clercq, C.; Demirörs, L.; Descamps, F.; Desiati, P.; de Vries-Uiterweerd, G.; DeYoung, T.; Diaz-Velez, J. C.; Dreyer, J.; Dumm, J. P.; Duvoort, M. R.; Edwards, W. R.; Ehrlich, R.; Eisch, J.; Ellsworth, R. W.; Engdegård, O.; Euler, S.; Evenson, P. A.; Fadiran, O.; Fazely, A. R.; Feusels, T.; Filimonov, K.; Finley, C.; Foerster, M. M.; Fox, B. D.; Franckowiak, A.; Franke, R.; Gaisser, T. K.; Gallagher, J.; Ganugapati, R.; Gerhardt, L.; Gladstone, L.; Glowacki, D.; Goldschmidt, A.; Goodman, J. A.; Gozzini, R.; Grant, D.; Griesel, T.; Groß, A.; Grullon, S.; Gunasingha, R. M.; Gurtner, M.; Ha, C.; Hallgren, A.; Halzen, F.; Han, K.; Hanson, K.; Hardtke, R.; Hasegawa, Y.; Haugen, J.; Hays, D.; Heise, J.; Helbing, K.; Hellwig, M.; Herquet, P.; Hickford, S.; Hill, G. C.; Hodges, J.; Hoffman, K. D.; Hoshina, K.; Hubert, D.; Huelsnitz, W.; Hughey, B.; Hülß, J.-P.; Hulth, P. O.; Hultqvist, K.; Hussain, S.; Imlay, R. L.; Inaba, M.; Ishihara, A.; Jacobsen, J.; Japaridze, G. S.; Johansson, H.; Jones, A.; Joseph, J. M.; Kampert, K.-H.; Kappes, A.; Karg, T.; Karle, A.; Kawai, H.; Kelley, J. L.; Kiryluk, J.; Kislat, F.; Klein, S. R.; Kleinfelder, S.; Klepser, S.; Kohnen, G.; Kolanoski, H.; Köpke, L.; Kowalski, M.; Kowarik, T.; Krasberg, M.; Kuehn, K.; Kujawski, E.; Kuwabara, T.; Labare, M.; Laihem, K.; Landsman, H.; Lauer, R.; Laundrie, A.; Leich, H.; Leier, D.; Lewis, C.; Lucke, A.; Ludvig, J.; Lundberg, J.; Lünemann, J.; Madsen, J.; Maruyama, R.; Mase, K.; Matis, H. S.; McParland, C. P.; Meagher, K.; Meli, A.; Merck, M.; Messarius, T.; Mészáros, P.; Minor, R. H.; Miyamoto, H.; Mohr, A.; Mokhtarani, A.; Montaruli, T.; Morse, R.; Movit, S. M.; Münich, K.; Muratas, A.; Nahnhauer, R.; Nam, J. W.; Nießen, P.; Nygren, D. R.; Odrowski, S.; Olivas, A.; Olivo, M.; Ono, M.; Panknin, S.; Patton, S.; Pérez de los Heros, C.; Petrovic, J.; Piegsa, A.; Pieloth, D.; Pohl, A. C.; Porrata, R.; Potthoff, N.; Pretz, J.; Price, P. B.; Przybylski, G. T.; Rawlins, K.; Razzaque, S.; Redl, P.; Resconi, E.; Rhode, W.; Ribordy, M.; Rizzo, A.; Robbins, W. J.; Rodrigues, J. P.; Roth, P.; Rothmaier, F.; Rott, C.; Roucelle, C.; Rutledge, D.; Ryckbosch, D.; Sander, H.-G.; Sarkar, S.; Satalecka, K.; Sandstrom, P.; Schlenstedt, S.; Schmidt, T.; Schneider, D.; Schulz, O.; Seckel, D.; Semburg, B.; Seo, S. H.; Sestayo, Y.; Seunarine, S.; Silvestri, A.; Smith, A. J.; Song, C.; Sopher, J. E.; Spiczak, G. M.; Spiering, C.; Stanev, T.; Stezelberger, T.; Stokstad, R. G.; Stoufer, M. C.; Stoyanov, S.; Strahler, E. A.; Straszheim, T.; Sulanke, K.-H.; Sullivan, G. W.; Swillens, Q.; Taboada, I.; Tarasova, O.; Tepe, A.; Ter-Antonyan, S.; Tilav, S.; Tluczykont, M.; Toale, P. A.; Tosi, D.; Turčan, D.; van Eijndhoven, N.; Vandenbroucke, J.; Van Overloop, A.; Viscomi, V.; Vogt, C.; Voigt, B.; Vu, C. Q.; Wahl, D.; Walck, C.; Waldenmaier, T.; Waldmann, H.; Walter, M.; Wendt, C.; Westerhof, S.; Whitehorn, N.; Wharton, D.; Wiebusch, C. H.; Wiedemann, C.; Wikström, G.; Williams, D. R.; Wischnewski, R.; Wissing, H.; Woschnagg, K.; Xu, X. W.; Yodh, G.; Yoshida, S.; IceCube Collaboration

2009-04-01

IceCube is a km-scale neutrino observatory under construction at the South Pole with sensors both in the deep ice (InIce) and on the surface (IceTop). The sensors, called Digital Optical Modules (DOMs), detect, digitize and timestamp the signals from optical Cherenkov-radiation photons. The DOM Main Board (MB) data acquisition subsystem is connected to the central DAQ in the IceCube Laboratory (ICL) by a single twisted copper wire-pair and transmits packetized data on demand. Time calibration is maintained throughout the array by regular transmission to the DOMs of precisely timed analog signals, synchronized to a central GPS-disciplined clock. The design goals and consequent features, functional capabilities, and initial performance of the DOM MB, and the operation of a combined array of DOMs as a system, are described here. Experience with the first InIce strings and the IceTop stations indicates that the system design and performance goals have been achieved.

Airlift Operation Modeling Using Discrete Event Simulation (DES)

DTIC Science & Technology

2009-12-01

Java ......................................................................................................20 2. Simkit...JRE Java Runtime Environment JVM Java Virtual Machine lbs Pounds LAM Load Allocation Mode LRM Landing Spot Reassignment Mode LEGO Listener Event...SOFTWARE DEVELOPMENT ENVIRONMENT The following are the software tools and development environment used for constructing the models. 1. Java Java

Highly Sensitive and Selective Ethanol Sensor Fabricated with In-Doped 3DOM ZnO.

PubMed

Wang, Zhihua; Tian, Ziwei; Han, Dongmei; Gu, Fubo

2016-03-02

ZnO is an important n-type semiconductor sensing material. Currently, much attention has been attracted to finding an effective method to prepare ZnO nanomaterials with high sensing sensitivity and excellent selectivity. A three-dimensionally ordered macroporous (3DOM) ZnO nanostructure with a large surface area is beneficial to gas and electron transfer, which can enhance the gas sensitivity of ZnO. Indium (In) doping is an effective way to improve the sensing properties of ZnO. In this paper, In-doped 3DOM ZnO with enhanced sensitivity and selectivity has been synthesized by using a colloidal crystal templating method. The 3DOM ZnO with 5 at. % of In-doping exhibits the highest sensitivity (∼88) to 100 ppm ethanol at 250 °C, which is approximately 3 times higher than that of pure 3DOM ZnO. The huge improvement to the sensitivity to ethanol was attributed to the increase in the surface area and the electron carrier concentration. The doping by In introduces more electrons into the matrix, which is helpful for increasing the amount of adsorbed oxygen, leading to high sensitivity. The In-doped 3DOM ZnO is a promising material for a new type of ethanol sensor.

Microscale characterization of dissolved organic matter production and uptake in marine microbial mat communities

NASA Technical Reports Server (NTRS)

Paerl, H. W.; Bebout, B. M.; Joye, S. B.; Des Marais, D. J.

1993-01-01

Intertidal marine microbial mats exhibited biologically mediated uptake of low molecular weight dissolved organic matter (DOM), including D-glucose, acetate, and an L-amino acid mixture at trace concentrations. Uptake of all compounds occurred in darkness, but was frequently enhanced under natural illumination. The photosystem 2 inhibitor, 3-(3,4-dichlorophenyl)-1,1-dimethyl urea (DCMU) generally failed to inhibit light-stimulated DOM uptake. Occasionally, light plus DCMU-amended treatments led to uptake rates higher than light-incubated samples, possibly due to phototrophic bacteria present in subsurface anoxic layers. Uptake was similar with either 3H- or 14C-labeled substrates, indicating that recycling of labeled CO2 via photosynthetic fixation was not interfering with measurements of light-stimulated DOM uptake. Microautoradiographs showed a variety of pigmented and nonpigmented bacteria and, to a lesser extent, cyanobacteria and eucaryotic microalgae involved in light-mediated DOM uptake. Light-stimulated DOM uptake was often observed in bacteria associated with sheaths and mucilage surrounding filamentous cyanobacteria, revealing a close association of organisms taking up DOM with photoautotrophic members of the mat community. The capacity for dark- and light-mediated heterotrophy, coupled to efficient retention of fixed carbon in the mat community, may help optimize net production and accretion of mats, even in oligotrophic waters.

Detection and structural identification of dissolved organic matter in Antarctic glacial ice at natural abundance by SPR-W5-WATERGATE 1H NMR spectroscopy.

PubMed

Pautler, Brent G; Simpson, André J; Simpson, Myrna J; Tseng, Li-Hong; Spraul, Manfred; Dubnick, Ashley; Sharp, Martin J; Fitzsimons, Sean J

2011-06-01

Dissolved organic matter (DOM) is ubiquitous in aquatic ecosystems and is derived from various inputs that control its turnover. Glaciers and ice sheets are the second largest water reservoir in the global hydrologic cycle, but little is known about glacial DOM composition or contributions to biogeochemical cycling. Here we employ SPR-W5-WATERGATE (1)H NMR spectroscopy to elucidate and quantify the chemical structures of DOM constituents in Antarctic glacial ice as they exist in their natural state (average DOC of 8 mg/L) without isolation or preconcentration. This Antarctic glacial DOM is predominantly composed of a mixture of small recognizable molecules differing from DOM in marine, lacustrine, and other terrestrial environments. The major constituents detected in three distinct types of glacial ice include lactic and formic acid, free amino acids, and a mixture of simple sugars and amino sugars with concentrations that vary between ice types. The detection of free amino acid and amino sugar monomer components of peptidoglycan within the ice suggests that Antarctic glacial DOM likely originates from in situ microbial activity. As these constituents are normally considered to be biologically labile (fast cycling) in nonglacial environments, accelerated glacier melt and runoff may result in a flux of nutrients into adjacent ecosystems.

Nature and chlorine reactivity of organic constituents from reclaimed water in groundwater, Los Angeles County, California

USGS Publications Warehouse

Leenheer, J.A.; Rostad, C.E.; Barber, L.B.; Schroeder, R.A.; Anders, R.; Davisson, M.L.

2001-01-01

The nature and chlorine reactivity of organic constituents in reclaimed water (tertiary-treated municipal wastewater) before, during, and after recharge into groundwater at the Montebello Forebay in Los Angeles County, CA, was the focus of this study. Dissolved organic matter (DOM) in reclaimed water from this site is primarily a mixture of aromatic sulfonates from anionic surfactant degradation, N-acetyl amino sugars and proteins from bacterial activity, and natural fulvic acid, whereas DOM from native groundwaters in the aquifer to which reclaimed water was recharged consists of natural fulvic acids. The hydrophilic neutral N-acetyl amino sugars that constitute 40% of the DOM in reclaimed water are removed during the first 3 m of vertical infiltration in the recharge basin. Groundwater age dating with 3H and 3He isotopes, and determinations of organic and inorganic C isotopes, enabled clear differentiation of recent recharged water from older native groundwater. Phenol structures in natural fulvic acids in DOM isolated from groundwater produced significant trihalomethanes (THM) and total organic halogen (TOX) yields upon chlorination, and these structures also were responsible for the enhanced SUVA and specific fluorescence characteristics relative to DOM in reclaimed water. Aromatic sulfonates and fulvic acids in reclaimed water DOM produced minimal THM and TOX yields.

Bacterial Degradation of Phosphonates Bound to High-Molecular-Weight Dissolved Organic Matter Produces Methane and Other Hydrocarbons

NASA Astrophysics Data System (ADS)

Sosa, O.; Ferron Smith, S.; Karl, D. M.; DeLong, E.; Repeta, D.

2016-02-01

The biological degradation of dissolved organic matter (DOM) plays important roles in the carbon cycle and energy balance of the ocean. Yet, the biochemical pathways that drive DOM turnover remain to be fully characterized. In this study, we tested the ability of two open ocean bacterial isolates (a Pseudomonas stutzeri strain (Gammaproteobacteria) and a Sulfitobacter isolate (Alphaproteobacteria)) to degrade DOM phosphonates. Each isolate encoded a complete phosphonate degradation pathway in its genome, and each was able to degrade simple alkyl-phosphonates like methyl phosphonate, releasing methane (or other short chain hydrocarbon gases) as a result. We found that cultures incubated in the presence of HMW DOM polysaccharides also produced methane and other trace gases under aerobic conditions. To demonstrate that phosphonates were the source of these gases, we constructed a P. stutzeri mutant disabled in the phosphonate degradation pathway. Unlike the wild type, the mutant strain was deficient in the production of methane and other gases from HMW DOM-associated phosphonates. These observations support the hypothesis that DOM-bound methyl phosphonates may be a significant source of methane in the water column, and that bacterial degradation of these compounds likely contribute to the subsurface methane maxima observed throughout the world's oceans.

Impacts of aeration management and polylactic acid addition on dissolved organic matter characteristics in intensified aquaponic systems.

PubMed

Wu, Haiming; Zou, Yina; Lv, Jialong; Hu, Zhen

2018-08-01

Aquaponics as a potential alternative for conventional aquaculture industry has increasingly attracted worldwide attention in recent years. However, the sustainable application of aquaponics is facing a growing challenge. In particular, there is a pressing need to better understand and control the accumulation of dissolved organic matter (DOM) in aquaponics with the aim of optimizing nitrogen utilization efficiency. This study was aiming for assessing the characteristics of DOM in the culture water and the relationship with the nitrogen transformations in different intensified aquaponic systems with hydroponic aeration supplement and polylactic acid (PLA) addition. Two enhancing attempts altered the quantity of DOM in aquaponic systems significantly with a varying DOM content of 21.98-45.65 mg/L. The DOM could be represented by four identified fluorescence components including three humic -like materials (83-86%) and one tryptophan-like substance (14-17%). The fluorescence intensities of humic acid-like components were decreased significantly after the application of intensifying strategies, which indicating that two enhancing attempts possibly affected humic acid-like fluorescence. Variation of optical indices also suggested the reductions of water DOM which could be impacted by the enhancing nitrogen treatment processes. These findings will benefit the potential applications and sustainable operation of these strategies in aquaponics. Copyright © 2018 Elsevier Ltd. All rights reserved.

ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes

PubMed Central

Bhasi, Ashwini; Philip, Philge; Manikandan, Vinu; Senapathy, Periannan

2009-01-01

We have developed ExDom, a unique database for the comparative analysis of the exon–intron structures of 96 680 protein domains from seven eukaryotic organisms (Homo sapiens, Mus musculus, Bos taurus, Rattus norvegicus, Danio rerio, Gallus gallus and Arabidopsis thaliana). ExDom provides integrated access to exon-domain data through a sophisticated web interface which has the following analytical capabilities: (i) intergenomic and intragenomic comparative analysis of exon–intron structure of domains; (ii) color-coded graphical display of the domain architecture of proteins correlated with their corresponding exon-intron structures; (iii) graphical analysis of multiple sequence alignments of amino acid and coding nucleotide sequences of homologous protein domains from seven organisms; (iv) comparative graphical display of exon distributions within the tertiary structures of protein domains; and (v) visualization of exon–intron structures of alternative transcripts of a gene correlated to variations in the domain architecture of corresponding protein isoforms. These novel analytical features are highly suited for detailed investigations on the exon–intron structure of domains and make ExDom a powerful tool for exploring several key questions concerning the function, origin and evolution of genes and proteins. ExDom database is freely accessible at: http://66.170.16.154/ExDom/. PMID:18984624

Influence of dissolved organic matter on photogenerated reactive oxygen species and metal-oxide nanoparticle toxicity.

PubMed

Li, Yang; Niu, Junfeng; Shang, Enxiang; Crittenden, John Charles

2016-07-01

The effect of humic acid (HA) or fulvic acid (FA) on reactive oxygen species (ROS) generation by six metal-oxide nanoparticles (NPs) and their toxicities toward Escherichia coli was investigated under UV irradiation. Dissolved organic matter (DOM) decreased OH generation by TiO2, ZnO, and Fe2O3, with FA inhibiting OH generation more than HA. The generated OH in NPs/DOM mixtures was higher than the measured concentrations because DOM consumes OH faster than its molecular probe. None of NPs/FA mixtures produced O2(-). The generated O2(-) concentrations in NPs/HA mixtures (except Fe2O3/HA) were higher than the sum of O2(-) concentrations that produced as NPs and HA were presented by themselves. Synergistic O2(-) generation in NPs/HA mixtures resulted from O2 reduction by electron transferred from photoionized HA to NPs. DOM increased (1)O2 generation by TiO2, CuO, CeO2, and SiO2, and FA promoted (1)O2 generation more than HA. Enhanced (1)O2 generation resulted from DOM sensitization of NPs. HA did not increase (1)O2 generation by ZnO and Fe2O3 primarily because released ions quenched (1)O2 precursor ((3)HA*). Linear correlation was developed between total ROS concentrations generated by NPs/DOM mixtures and bacterial survival rates (R(2) ≥ 0.80). The results implied the necessity of considering DOM when investigating the photoreactivity of NPs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of short-term warming and nitrogen addition on the quantity and quality of dissolved organic matter in a subtropical Cunninghamia lanceolata plantation.

PubMed

Yuan, Xiaochun; Si, Youtao; Lin, Weisheng; Yang, Jingqing; Wang, Zheng; Zhang, Qiufang; Qian, Wei; Chen, Yuehmin; Yang, Yusheng

2018-01-01

Increasing temperature and nitrogen (N) deposition are two large-scale changes projected to occur over the coming decades. The effects of these changes on dissolved organic matter (DOM) are largely unknown. This study aimed to assess the effects of warming and N addition on the quantity and quality of DOM from a subtropical Cunninghamia lanceolata plantation. Between 2014 and 2016, soil solutions were collected from 0-15, 15-30, and 30-60 cm depths by using a negative pressure sampling method. The quantity and quality of DOM were measured under six different treatments. The spectra showed that the DOM of the forest soil solution mainly consisted of aromatic protein-like components, microbial degradation products, and negligible amounts of humic-like substances. Warming, N addition, and warming + N addition significantly inhibited the concentration of dissolved organic carbon (DOC) in the surface (0-15 cm) soil solution. Our results suggested that warming reduced the amount of DOM originating from microbes. The decrease in protein and carboxylic acid contents was mostly attributed to the reduction of DOC following N addition. The warming + N addition treatment showed an interactive effect rather than an additive effect. Thus, short-term warming and warming + N addition decreased the quantity of DOM and facilitated the migration of nutrients to deeper soils. Further, N addition increased the complexity of the DOM structure. Hence, the loss of soil nutrients and the rational application of N need to be considered in order to prevent the accumulation of N compounds in soil.

Dynamics of dissolved organic matter during four storm events in two forest streams: source, export, and implications for harmful disinfection byproduct formation.

PubMed

Yang, Liyang; Hur, Jin; Lee, Sonmin; Chang, Soon-Woong; Shin, Hyun-Sang

2015-06-01

Dynamics of river dissolved organic matter (DOM) during storm events have profound influences on the downstream aquatic ecosystem and drinking water safety. This study investigated temporal variations in DOM during four storm events in two forest headwater streams (the EH and JH brooks, South Korea) and the impacts on the disinfection byproducts (DBPs) formation potential. The within-event variations of most DOM quantity parameters were similar to the flow rate in the EH but not in the larger JH brook. The dissolved organic carbon (DOC) showed clockwise and counterclockwise hysteresis with the flow rate in the EH and JH brooks, respectively, indicating the importance of both flow path and DOM source pool size in determining the effects of storm events. The stream DOM became less aromatic/humified from the first to the last event in both brooks, probably due to the increasing fresh plant pool and the decreasing leaf litter pool during the course of rainy season. The DOC export during each event increased 1.3-2.7- and 1.1-7.0-fold by stormflows in the EH and JH brooks, respectively. The leaf litter and soil together was the major DOM source, particularly during early events. The enhanced DOM export probably increases the risks of DBPs formation in disinfection, as indicated by a strong correlation observed between DOC and trihalomethanes formation potential (THMFP). High correlations between two humic-like fluorescent components and THMFP further suggested the potential of assessing THMFP with in situ fluorescence sensors during storms.

Molecular simulation of a model of dissolved organic matter.

PubMed

Sutton, Rebecca; Sposito, Garrison; Diallo, Mamadou S; Schulten, Hans-Rolf

2005-08-01

A series of atomistic simulations was performed to assess the ability of the Schulten dissolved organic matter (DOM) molecule, a well-established model humic molecule, to reproduce the physical and chemical behavior of natural humic substances. The unhydrated DOM molecule had a bulk density value appropriate to humic matter, but its Hildebrand solubility parameter was lower than the range of current experimental estimates. Under hydrated conditions, the DOM molecule went through conformational adjustments that resulted in disruption of intramolecular hydrogen bonds (H-bonds), although few water molecules penetrated the organic interior. The radius of gyration of the hydrated DOM molecule was similar to those measured for aquatic humic substances. To simulate humic materials under aqueous conditions with varying pH levels, carboxyl groups were deprotonated, and hydrated Na+ or Ca2+ were added to balance the resulting negative charge. Because of intrusion of the cation hydrates, the model metal-humic structures were more porous, had greater solvent-accessible surface areas, and formed more H-bonds with water than the protonated, hydrated DOM molecule. Relative to Na+, Ca2+ was both more strongly bound to carboxylate groups and more fully hydrated. This difference was attributed to the higher charge of the divalent cation. The Ca-DOM hydrate, however, featured fewer H-bonds than the Na-DOM hydrate, perhaps because of the reduced orientational freedom of organic moieties and water molecules imposed by Ca2+. The present work is, to our knowledge, the first rigorous computational exploration regarding the behavior of a model humic molecule under a range of physical conditions typical of soil and water systems.

Concentrations and distributions of metals associated with dissolved organic matter from the Suwannee River (GA, USA)

USGS Publications Warehouse

Kuhn, M. Keshia; Neubauer, Elisabeth; Hofmann, Thilo; von der Kammer, Frank; Aiken, George R.; Maurice, Patricia A.

2015-01-01

Concentrations and distributions of metals in Suwannee River (SR) raw filtered surface water (RFSW) and dissolved organic matter (DOM) processed by reverse osmosis (RO), XAD-8 resin (for humic and fulvic acids [FA]), and XAD-4 resin (for “transphilic” acids) were analyzed by asymmetrical flow field-flow fractionation (AsFlFFF). SR samples were compared with DOM samples from Nelson's Creek (NLC), a wetland-draining stream in northern Michigan; previous International Humic Substances Society (IHSS) FA and RO samples from the SR; and an XAD-8 sample from Lake Fryxell (LF), Antarctica. Despite application of cation exchange during sample processing, all XAD and RO samples contained substantial metal concentrations. AsFlFFF fractograms allowed metal distributions to be characterized as a function of DOM component molecular weight (MW). In SR RFSW, Fe, Al, and Cu were primarily associated with intermediate to higher than average MW DOM components. SR RO, XAD-8, and XAD-4 samples from May 2012 showed similar MW trends for Fe and Al but Cu tended to associate more with lower MW DOM. LF DOM had abundant Cu and Zn, perhaps due to amine groups that should be present due to its primarily algal origins. None of the fractograms showed obvious evidence for mineral nanoparticles, although some very small mineral nanoparticles might have been present at trace concentrations. This research suggests that AsFlFFF is important for understanding how metals are distributed in different DOM samples (including IHSS samples), which may be key to metal reactivity and bioavailability.

Hydrological and Biogeochemical Controls on Absorption and Fluorescence of Dissolved Organic Matter in the Northern South China Sea

NASA Astrophysics Data System (ADS)

Wang, Chao; Guo, Weidong; Li, Yan; Stubbins, Aron; Li, Yizhen; Song, Guodong; Wang, Lei; Cheng, Yuanyue

2017-12-01

The Kuroshio intrusion from the West Philippine Sea (WPS) and mesoscale eddies are important hydrological features in the northern South China Sea (SCS). In this study, absorption and fluorescence of dissolved organic matter (CDOM and FDOM) were determined to assess the impact of these hydrological features on DOM dynamics in the SCS. DOM in the upper 100 m of the northern SCS had higher absorption, fluorescence, and degree of humification than in the Kuroshio Current of the WPS. The results of an isopycnal mixing model showed that CDOM and humic-like FDOM inventories in the upper 100 m of the SCS were modulated by the Kuroshio intrusion. However, protein-like FDOM was influenced by in situ processes. This basic trend was modified by mesoscale eddies, three of which were encountered during the fieldwork (one warm eddy and two cold eddies). DOM optical properties inside the warm eddy resembled those of DOM in the WPS, indicating that warm eddies could derive from the Kuroshio Current through Luzon Strait. DOM at the center of cold eddies was enriched in humic-like fluorescence and had lower spectral slopes than in eddy-free waters, suggesting inputs of humic-rich DOM from upwelling and enhanced productivity inside the eddy. Excess CDOM and FDOM in northern SCS intermediate water led to export to the Pacific Ocean interior, potentially delivering refractory carbon to the deep ocean. This study demonstrated that DOM optical properties are promising tools to study active marginal sea-open ocean interactions.

Comparative study of dissolved organic matter generated from activated sludge during exposure to hypochlorite, hydrogen peroxide, acid and alkaline: Implications for on-line chemical cleaning of MBR.

PubMed

Cai, Weiwei; Liu, Yu

2018-02-01

Although on-line chemical cleaning has been extensively employed for maintaining the MBR permeability, little attention has been given to the negative impacts of such prevalent membrane cleaning practice. This study thus comparatively investigated the potential release of dissolved organic matter (DOM) from activated sludge upon the exposure to different kinds of frequently-used cleaning reagents, i.e. NaClO, H 2 O 2 , HCl and NaOH. It was found that NaClO at 50 and 80 mg L -1 triggered significant release of DOM, while NaOH strongly promoted soluble nitrogen release. However, the DOM generation induced by H 2 O 2 in the range of 0-80 mg L -1 was nearly negligible. The combined analysis by EEM-PARAFAC and LC-OCD-OND further revealed that NaClO-triggered DOM mainly originated from the breakdown of humic substances and other small humics with molecular weight (MW) less than 500 Da. In contrast, proteins and other biopolymers with higher MW highly contributed to DOM induced by NaOH. Most of DOM detected in this study belonged to low molecular weight (LMW) substances, which were not considered readily biodegradable or physically retainable by microfiltration membrane. It appears from this study that DOM generated from suspended activated sludge during membrane cleaning with different chemicals should be taken into serious consideration when water recycle and reuse are concerned. Copyright © 2017 Elsevier Ltd. All rights reserved.

Tracking the behavior of different size fractions of dissolved organic matter in a full-scale advanced drinking water treatment plant.

PubMed

Quang, Viet Ly; Choi, Ilhwan; Hur, Jin

2015-11-01

In this study, five different dissolved organic matter (DOM) fractions, defined based on a size exclusion chromatography with simultaneous detection of organic carbon (OCD) and ultraviolet (UVD), were quantitatively tracked with a treatment train of coagulation/flocculation-sand filtration-ozonation-granular activated carbon (GAC) filtration in a full-scale advanced drinking water treatment plant (DWTP). Five DOM samples including raw water were taken after each treatment process in the DWTP every month over the period of three years. A higher abundance of biopolymer (BP) fraction was found in the raw water during spring and winter than in the other seasons, suggesting an influence of algal bloom and/or meltwater on DOM composition. The greater extent of removal was observed upon the coagulation/flocculation for high-molecular-weight fractions including BP and humic substances (HS) and aromatic moieties, while lower sized fractions were preferentially removed by the GAC filtration. Ozone treatment produced the fraction of low-molecular-weight neutrals probably resulting from the breakdown of double-bonded carbon structures by ozone oxidation. Coagulation/flocculation was the only process that revealed significant effects of influent DOM composition on the treatment efficiency, as revealed by a high correlation between the DOM removal rate and the relative abundance of HS for the raw water. Our study demonstrated that SEC-OCD-UVD was successful in monitoring size-based DOM composition for the advanced DWTP, providing an insight into optimizing the treatment options and the operational conditions for the removal of particular fractions within the bulk DOM.

Photodegradation of Pyrogenic Dissolved Organic Matter (Biochar Leachates)

NASA Astrophysics Data System (ADS)

Bostick, K. W.; Zimmerman, A. R.; Hatcher, P.; Mitra, S.; Wozniak, A. S.

2017-12-01

A large portion of soil organic matter has been suggested to be pyrogenic (e.g., charred biomass or soot). While pyrogenic organic matter has been regarded as relatively stable in the environment, significant losses of pyrogenic organic carbon can occur via degradation and solubilization. Pyrogenic dissolved organic matter (py-DOM) could be an important intermediate in global C cycling, however its geochemical fate is still unknown. In the current study, the mineralization and transformation of py-DOM were explored through a series of photodegradation experiments. A biochar prepared by pyrolyzing oak wood at 400 °C was leached for a period of 48 hours. This leachate was exposed to light simulating the irradiance and spectra of natural sunlight from 295 to 365 nm. Photodegraded leachate was subsampled during a period of 20 days and analyzed for TOC, DIC and TN. Additionally, solid phase (PPL) extracts of leachate DOM were oxidized in hot nitric acid and analyzed via HPLC for benzenepolycarboxylic acids (BPCAs). In previous studies, the proportion of aromatically condensed py-DOM (as indicated carboxyl substitution in BPCA) in biochar leachates was found to increase with parent char pyrolysis temperature. Thus, to explore the influence of py-DOM type on photodegradation, losses of C, N, and condensed aromatic C were examined in leachates of an oak biochar thermal series (pyrolyzed at 400, 525, 650 °C). The resulting rates of photo-degradative losses in py-C and condensed aromatics in these leachates can be used to estimate the stability/longevity of py-DOM in aquatic systems, potential for py-DOM export from terrestrial systems, and negative effects to aquatic ecosystems.

Effects of short-term warming and nitrogen addition on the quantity and quality of dissolved organic matter in a subtropical Cunninghamia lanceolata plantation

PubMed Central

Yuan, Xiaochun; Si, Youtao; Lin, Weisheng; Yang, Jingqing; Wang, Zheng; Zhang, Qiufang; Qian, Wei; Yang, Yusheng

2018-01-01

Increasing temperature and nitrogen (N) deposition are two large-scale changes projected to occur over the coming decades. The effects of these changes on dissolved organic matter (DOM) are largely unknown. This study aimed to assess the effects of warming and N addition on the quantity and quality of DOM from a subtropical Cunninghamia lanceolata plantation. Between 2014 and 2016, soil solutions were collected from 0–15, 15–30, and 30–60 cm depths by using a negative pressure sampling method. The quantity and quality of DOM were measured under six different treatments. The spectra showed that the DOM of the forest soil solution mainly consisted of aromatic protein-like components, microbial degradation products, and negligible amounts of humic-like substances. Warming, N addition, and warming + N addition significantly inhibited the concentration of dissolved organic carbon (DOC) in the surface (0–15 cm) soil solution. Our results suggested that warming reduced the amount of DOM originating from microbes. The decrease in protein and carboxylic acid contents was mostly attributed to the reduction of DOC following N addition. The warming + N addition treatment showed an interactive effect rather than an additive effect. Thus, short-term warming and warming + N addition decreased the quantity of DOM and facilitated the migration of nutrients to deeper soils. Further, N addition increased the complexity of the DOM structure. Hence, the loss of soil nutrients and the rational application of N need to be considered in order to prevent the accumulation of N compounds in soil. PMID:29360853