Molecular and optical characterization of dissolved organic matter in the Central Arctic Ocean

Dissolved organic matter (DOM) in the ocean is a complex mixture of molecules derived from autochthonous (marine) or allochthonous (terrestrial) origins. DOM plays an important role in marine biogeochemical cycles by attenuating light available for primary production, serving as an energy and nutrient source for heterotrophic communities, regulating the ultraviolet and visible light absorption, undergoing photochemical processing, and acting as a trace metal ligand. DOM in the Central Arctic Ocean (CAO) is influenced by increased freshwater input and associated terrestrial materials in recent decades due to rapid climate change. The quantification of DOM sources (terrestrial versus marine) in the water column of the CAO is not well constrained. Few studies have systematically investigated the seasonality and spatial variability of DOM by combining optical and molecular-level analytical techniques in the CAO, especially during winter. State of the art chemical characterization of DOM is subject to major challenges: Solid phase extraction (SPE) that is often used to desalt and pre-concentrate marine DOM introduces chemical fractionation effects, which limits the comparability between analytical results for original samples and those carried out for SPE-DOM. There is no specific method to quantify fractionation effects, nor specific guidelines to avoid fractionation. Using mass spectrometry, quantitative DOM analyses is challenged by selective ionization of molecules and the large number of unresolved structural isomers that prevent classical external calibration. In the first part of this thesis, a method was developed to quantitatively track optical or chemical fractionation during SPE and investigate the potential mechanisms. We found a decrease in extraction efficiency of dissolved organic carbon (DOC), fluorescence and absorbance, and polar organic substances with increasing carbon loading on the SPE column. As the surface loading of the solid-phase increased, the dominant extraction mechanism shifted from PPL physisorption to increased DOM self-assembly, resulting in optical and chemical fractionation. The relative DOC loading (DOCload) was used to assess the carbon loading during SPE, and a double sigmoid model was applied to our online permeate fluorescence data as a function of DOCload, which allowed us to assess the degree of variability induced by DOCload. This finding has ample implications for the future processing and previous interpretation of chemical characteristics in SPE-DOM of aquatic organic matter. For the second part of the thesis, original water samples were acquired from the “Multidisciplinary Drifting Observatory for the Study of Arctic Climate” (MOSAiC) expedition. The water column samples covered a full year (2019 / 2020) and included the regions Amundsen Basin, western Nansen Basin and Yermak Plateau and Fram Strait. Samples were analyzed using optical spectroscopy to determine chromophoric DOM (CDOM) and fluorescent DOM (FDOM). In addition, a new method was applied that used Fourier transform ion cyclotron resonance mass spectrometry hyphenated to high performance liquid chromatography (LC-FTMS). The method allowed DOM analysis in original filtered water and thus avoided the chemical fractionation introduced by SPE. During the MOSAiC expedition, DOC concentrations and CDOM characteristics in the water column were primarily influenced by regional differences. These differences were largely dependent on terrestrially-derived DOM (tDOM) input by the transpolar drift (TPD) as indicative of average 136% and 45% higher aCDOM(350) and DOC concentration, respectively, in the Amundsen compared to the western Nansen Basin and Yermak Plateau, and slightly modified by seasonal changes. Despite the convenient identification of tDOM, optical spectroscopy was not suitable to quantify the contribution of tDOM to bulk DOC or to track sea ice derived DOM in the water column. In contrast, using LC-FTMS, we found quantitative linear correlation between the summed mass peak magnitudes for each sample (intsum) and DOC concentration. By combing LC-FTMS and source identification with optical parameters, we were able to quantify DOM sources (terrestrial versus marine) in the water column: 83% of the summed peak magnitude of all samples could be related to marine or terrestrial sources. tDOM contributed ∼17% (or 8 µmol kg-1) to deep DOC (~2000 m) in the CAO and was more refractory and had a higher state of unsaturation compared to marine DOM. The quantitative characterization of DOM in original seawater from different origin is a major step in the field of research. It provides a unique and new insight into the molecular changes in marine DOM composition and an improved understanding of the terrestrial DOM distribution in the CAO

Solid-Phase Extraction of Aquatic Organic Matter: Loading-Dependent Chemical Fractionation and Self-Assembly

Dissolved organic matter (DOM) is an important component in marine and freshwater environments and plays a fundamental role in global biogeochemical cycles. In the past, optical and molecular-level analytical techniques evolved and improved our mechanistic understanding about DOM fluxes. For most molecular chemical techniques, sample desalting and enrichment is a prerequisite. Solid-phase extraction has been widely applied for concentrating and desalting DOM. The major aim of this study was to constrain the influence of sorbent loading on the composition of DOM extracts. Here, we show that increased loading resulted in reduced extraction efficiencies of dissolved organic carbon (DOC), fluorescence and absorbance, and polar organic substances. Loading-dependent optical and chemical fractionation induced by the altered adsorption characteristics of the sorbent surface (styrene divinylbenzene polymer) and increased multilayer adsorption (DOM self-assembly) can fundamentally affect biogeochemical interpretations, such as the source of organic matter. Online fluorescence monitoring of the permeate flow allowed to empirically model the extraction process and to assess the degree of variability introduced by changing the sorbent loading in the extraction procedure. Our study emphasizes that it is crucial for sample comparison to keep the relative DOC loading (DOCload [wt %]) on the sorbent always similar to avoid chemical fractionation

International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database - the quality controlled standard tool for routine identification of human and animal pathogenic fungi

Human and animal fungal pathogens are a growing threat worldwide leading to emerging infections and creating new risks for established ones. There is a growing need for a rapid and accurate identification of pathogens to enable early diagnosis and targeted antifungal therapy. Morphological and biochemical identification methods are time-consuming and require trained experts. Alternatively, molecular methods, such as DNA barcoding, a powerful and easy tool for rapid monophasic identification, offer a practical approach for species identification and less demanding in terms of taxonomical expertise. However, its wide-spread use is still limited by a lack of quality-controlled reference databases and the evolving recognition and definition of new fungal species/complexes. An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database under the umbrella of the ISHAM working group on "DNA barcoding of human and animal pathogenic fungi." A new database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool at http://www.isham.org and http://its.mycologylab.org/ to rapidly and reliably identify most agents of mycoses, was established. The generated sequences included in the new database were used to evaluate the variation and overall utility of the ITS region for the identification of pathogenic fungi at intra-and interspecies level. The average intraspecies variation ranged from 0 to 2.25%. This highlighted selected pathogenic fungal species, such as the dermatophytes and emerging yeast, for which additional molecular methods/genetic markers are required for their reliable identification from clinical and veterinary specimens.This study was supported by an National Health and Medical Research Council of Australia (NH&MRC) grant [#APP1031952] to W Meyer, S Chen, V Robert, and D Ellis; CNPq [350338/2000-0] and FAPERJ [E-26/103.157/2011] grants to RM Zancope-Oliveira; CNPq [308011/2010-4] and FAPESP [2007/08575-1] Fundacao de Amparo Pesquisa do Estado de So Paulo (FAPESP) grants to AL Colombo; PEst-OE/BIA/UI4050/2014 from Fundacao para a Ciencia e Tecnologia (FCT) to C Pais; the Belgian Science Policy Office (Belspo) to BCCM/IHEM; the MEXBOL program of CONACyT-Mexico, [ref. number: 1228961 to ML Taylor and [122481] to C Toriello; the Institut Pasteur and Institut de Veil le Sanitaire to F Dromer and D Garcia-Hermoso; and the grants from the Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) and the Fundacao de Amparo a Pesquisa do Estado de Goias (FAPEG) to CM de Almeida Soares and JA Parente Rocha. I Arthur would like to thank G Cherian, A Higgins and the staff of the Molecular Diagnostics Laboratory, Division of Microbiology and Infectious Diseases, Path West, QEII Medial Centre. Dromer would like to thank for the technical help of the sequencing facility and specifically that of I, Diancourt, A-S Delannoy-Vieillard, J-M Thiberge (Genotyping of Pathogens and Public Health, Institut Pasteur). RM Zancope-Oliveira would like to thank the Genomic/DNA Sequencing Platform at Fundacao Oswaldo Cruz-PDTIS/FIOCRUZ [RPT01A], Brazil for the sequencing. B Robbertse and CL Schoch acknowledge support from the Intramural Research Program of the NIH, National Library of Medicine. T Sorrell's work is funded by the NH&MRC of Australia; she is a Sydney Medical School Foundation Fellow.info:eu-repo/semantics/publishedVersio

Molecular and optical characterization of dissolved organic matter in the Central Arctic Ocean

Dissolved organic matter (DOM) in the ocean is a complex mixture of molecules derived from autochthonous (marine) or allochthonous (terrestrial) origins. DOM plays an important role in marine biogeochemical cycles by attenuating light available for primary production, serving as an energy and nutrient source for heterotrophic communities, regulating the ultraviolet and visible light absorption, undergoing photochemical processing, and acting as a trace metal ligand. DOM in the Central Arctic Ocean (CAO) is influenced by increased freshwater input and associated terrestrial materials in recent decades due to rapid climate change. The quantification of DOM sources (terrestrial versus marine) in the water column of the CAO is not well constrained. Few studies have systematically investigated the seasonality and spatial variability of DOM by combining optical and molecular-level analytical techniques in the CAO, especially during winter. State of the art chemical characterization of DOM is subject to major challenges: Solid phase extraction (SPE) that is often used to desalt and pre-concentrate marine DOM introduces chemical fractionation effects, which limits the comparability between analytical results for original samples and those carried out for SPE-DOM. There is no specific method to quantify fractionation effects, nor specific guidelines to avoid fractionation. Using mass spectrometry, quantitative DOM analyses is challenged by selective ionization of molecules and the large number of unresolved structural isomers that prevent classical external calibration. In the first part of this thesis, a method was developed to quantitatively track optical or chemical fractionation during SPE and investigate the potential mechanisms. We found a decrease in extraction efficiency of dissolved organic carbon (DOC), fluorescence and absorbance, and polar organic substances with increasing carbon loading on the SPE column. As the surface loading of the solid-phase increased, the dominant extraction mechanism shifted from PPL physisorption to increased DOM self-assembly, resulting in optical and chemical fractionation. The relative DOC loading (DOCload) was used to assess the carbon loading during SPE, and a double sigmoid model was applied to our online permeate fluorescence data as a function of DOCload, which allowed us to assess the degree of variability induced by DOCload. This finding has ample implications for the future processing and previous interpretation of chemical characteristics in SPE-DOM of aquatic organic matter. For the second part of the thesis, original water samples were acquired from the “Multidisciplinary Drifting Observatory for the Study of Arctic Climate” (MOSAiC) expedition. The water column samples covered a full year (2019 / 2020) and included the regions Amundsen Basin, western Nansen Basin and Yermak Plateau and Fram Strait. Samples were analyzed using optical spectroscopy to determine chromophoric DOM (CDOM) and fluorescent DOM (FDOM). In addition, a new method was applied that used Fourier transform ion cyclotron resonance mass spectrometry hyphenated to high performance liquid chromatography (LC-FTMS). The method allowed DOM analysis in original filtered water and thus avoided the chemical fractionation introduced by SPE. During the MOSAiC expedition, DOC concentrations and CDOM characteristics in the water column were primarily influenced by regional differences. These differences were largely dependent on terrestrially-derived DOM (tDOM) input by the transpolar drift (TPD) as indicative of average 136% and 45% higher aCDOM(350) and DOC concentration, respectively, in the Amundsen compared to the western Nansen Basin and Yermak Plateau, and slightly modified by seasonal changes. Despite the convenient identification of tDOM, optical spectroscopy was not suitable to quantify the contribution of tDOM to bulk DOC or to track sea ice derived DOM in the water column. In contrast, using LC-FTMS, we found quantitative linear correlation between the summed mass peak magnitudes for each sample (intsum) and DOC concentration. By combing LC-FTMS and source identification with optical parameters, we were able to quantify DOM sources (terrestrial versus marine) in the water column: 83% of the summed peak magnitude of all samples could be related to marine or terrestrial sources. tDOM contributed ∼17% (or 8 µmol kg-1) to deep DOC (~2000 m) in the CAO and was more refractory and had a higher state of unsaturation compared to marine DOM. The quantitative characterization of DOM in original seawater from different origin is a major step in the field of research. It provides a unique and new insight into the molecular changes in marine DOM composition and an improved understanding of the terrestrial DOM distribution in the CAO

Evaluation of a Multiplex PCR-Based Reverse Line Blot-Hybridization Assay for Identification of Serotype and Surface Protein Antigens of Streptococcus agalactiae

A 33-primer multiplex PCR-based reverse line blot (mPCR/RLB) assay was developed to identify Streptococcus agalactiae serotypes and surface protein antigen genes simultaneously. It was evaluated by using 551 clinical isolates. The mPCR/RLB assay was more sensitive than conventional serotyping, especially for protein antigen typing, but otherwise the results correlated well

Simultaneous Detection of Nine Antibiotic Resistance-Related Genes in Streptococcus agalactiae Using Multiplex PCR and Reverse Line Blot Hybridization Assay

Streptococcus agalactiae (group B streptococcus [GBS]) is the leading cause of neonatal and maternal sepsis. Penicillin is recommended for intrapartum prophylaxis, but erythromycin or clindamycin is used for penicillin-allergic carriers. Antibiotic resistance (AR) has increased recently and needs to be monitored. We have developed a multiplex PCR-based reverse line blot (mPCR/RLB) hybridization assay to detect, simultaneously, seven genes encoding AR—erm(A/TR), erm(B), mef(A/E), tet(M), tet(O), aphA-3, and aad-6—and two AR-related genes, int-Tn and mreA. We tested 512 GBS isolates from Asia and Australasia and compared mPCR/RLB with antibiotic susceptibility phenotype or single-gene PCR. Phenotypic resistance to tetracycline was identified in 450 (88%) isolates, of which 442 had tet(M) (93%) and/or tet(O) (6%). Of 67 (13%) erythromycin-resistant isolates, 18 were susceptible to clindamycin, i.e., had the M phenotype, encoded by mef(A/E); 39 had constitutive (cMLS(B)) and 10 inducible clindamycin resistance, and of these, 34 contained erm(B) and 12 erm(A/TR). Of four additional isolates with mef(A/E), three contained erm(B) with cMLS(B) and one was erythromycin susceptible. Of 61 (12%) clindamycin-resistant isolates, 20 were susceptible to erythromycin and two had intermediate resistance. Based on sequencing, 21 of 22 isolates with mef had mef(E), and 8 of 353 with int-Tn had an atypical sequence. Several AR genes, erm(B), tet(O), aphA-3, aad-6, and mef(A/E), were significantly more common among Asian than Australasian isolates, and there were significant differences in distribution of AR genes between GBS serotypes. Our mPCR/RLB assay is simple, rapid, and suitable for surveillance of antibiotic resistance in GBS

Multiplex PCR-Based Reverse Line Blot Hybridization Assay To Identify 23 Streptococcus pneumoniae Polysaccharide Vaccine Serotypes

We developed a multiplex PCR-based reverse line blot assay to identify 23 pneumococcal serotypes represented in the polysaccharide vaccine, using 334 well-characterized isolates, representing all 90 serotypes, and 268 “unknowns.” The assay identified all target serotypes, but 11, which cross-react with 1 to 4 nonvaccine serotypes, could be distinguished using serotype-specific antisera

Influence of Disk Separation Distance on Accuracy of the Disk Approximation Test for Detection of Inducible Clindamycin Resistance in Staphylococcus spp.

We undertook this study to assess the accuracy of the clindamycin-erythromycin disk approximation test (D-test) for detection of inducible clindamycin resistance in Staphylococcus spp. One hundred sixty-three Staphylococcus aureus and 68 coagulase-negative Staphylococcus (CoNS) spp. which were erythromycin nonsusceptible but clindamycin susceptible were tested using the D-test performed at both 15-mm and 22-mm disk separations and compared with genotyping as the “gold standard.” The rate of inducible clindamycin resistance was 96.3% for S. aureus and 33.8% for CoNS spp. The sensitivities of the D-tests performed at 15 mm and 22 mm were 100% and 87.7%, respectively, and specificities were 100% for both. The use of 22-mm disk separation for the D-test to detect inducible clindamycin resistance results in an unacceptably high very major error rate (12.3%). All isolates with false-negative results harbored the ermA gene, and the majority were methicillin-resistant Staphylococcus aureus. False-negative results were associated with smaller clindamycin zone sizes and double-edged zones. We recommend using a disk separation distance of ≤15 mm. There is wide geographic variation in the rates of inducible clindamycin resistance, and each laboratory should determine the local rate before deciding whether to either perform the D-test routinely or else report that all erythromycin-resistant S. aureus isolates are also clindamycin resistant

Reverse Line Blot Hybridization Assay for Identification of Medically Important Fungi from Culture and Clinical Specimens▿

We evaluated a combined panfungal PCR-reverse line blot (RLB) hybridization assay based on internal transcribed spacer 1 (ITS1) and ITS2 region polymorphisms to identify 159 Candida, Cryptococcus neoformans, and Aspergillus isolates (22 species). Its utility to identify fungal pathogens directly from 27 clinical specimens was also determined. ITS sequence analysis was performed to resolve discrepant identifications or where no RLB result was obtained. Species-specific ITS2- and ITS1-based probes correctly identified 155 of 159 isolates (98%) and 149 (93.7%) isolates, respectively. All strains were unambiguously differentiated with the exception of cross-reactivity between the Candida norvegensis probe and Candida haemulonii DNA product. Species identification of the pathogen was made for all 21 specimens (sensitivity of 100%) where species-specific probes were included in the RLB; however, there was no ITS2 probe-based hybridization signal for two specimens. Results were concordant with the culture results for 18 (85.7%) specimens. The assay was able to provide species identification in the absence of a culture result (two specimens) and to detect mixed infection (one specimen). The results indicate that the RLB assay is capable of reliably detecting yeasts and Aspergillus spp. in clinical specimens and that the incorporation of both ITS1- and ITS2-targeted probes is required for optimal sensitivity. The test has potential utility in the early diagnosis of invasive fungal infection, since “fungal” DNA was detected in all 27 specimens. Prior to incorporation of probes to detect other fungal species, ITS sequencing may be performed to achieve species identification

Comparison of Single- and Multilocus Sequence Typing and Toxin Gene Profiling for Characterization of Methicillin-Resistant Staphylococcus aureus▿

We compared three novel methicillin-resistant Staphylococcus aureus (MRSA) genotyping methods with multilocus sequence typing (MLST) and spa typing to assess their utility for routine strain typing. The new methods were femA and nuc sequence typing and toxin gene profiling (TGP), using a multiplex-PCR-based reverse line blot assay to detect 13 pyrogenic superantigen and exfoliative toxin genes. Forty-two well-characterized MRSA strains, representing 15 MLSTs or 9 clonal clusters (CCs), were genotyped by all methods. Twenty-two spa, nine femA, and seven nuc sequence types were identified. The femA sequence types correlated exactly with CCs; nuc sequences types were less discriminatory but generally correlated well with femA types and CCs. Ten isolates contained none of 13 toxin genes; TGPs of the remainder comprised 1 to 5 toxin genes. The combination of spa typing and TGPs identified 26 genotypes among the 42 strains studied. A combination of two or three rapid, inexpensive genotyping methods could potentially provide rapid MRSA strain typing as well as useful information about clonal origin and virulence