Showing papers by "Eoin L. Brodie published in 2010"
TL;DR: Insight is provided into the CF airway microbiota, including initial diversification events in younger patients and establishment of specialized communities of pathogens associated with poor pulmonary function in older patient populations.
Abstract: Bacterial communities in the airways of cystic fibrosis (CF) patients are, as in other ecological niches, influenced by autogenic and allogenic factors. However, our understanding of microbial colonization in younger versus older CF airways and the association with pulmonary function is rudimentary at best. Using a phylogenetic microarray, we examine the airway microbiota in age stratified CF patients ranging from neonates (9 months) to adults (72 years). From a cohort of clinically stable patients, we demonstrate that older CF patients who exhibit poorer pulmonary function possess more uneven, phylogenetically-clustered airway communities, compared to younger patients. Using longitudinal samples collected form a subset of these patients a pattern of initial bacterial community diversification was observed in younger patients compared with a progressive loss of diversity over time in older patients. We describe in detail the distinct bacterial community profiles associated with young and old CF patients with a particular focus on the differences between respective “early” and “late” colonizing organisms. Finally we assess the influence of Cystic Fibrosis Transmembrane Regulator (CFTR) mutation on bacterial abundance and identify genotype-specific communities involving members of the Pseudomonadaceae, Xanthomonadaceae, Moraxellaceae and Enterobacteriaceae amongst others. Data presented here provides insights into the CF airway microbiota, including initial diversification events in younger patients and establishment of specialized communities of pathogens associated with poor pulmonary function in older patient populations.
418 citations
TL;DR: In this article, a foregut microbiome dataset was constructed using 16S rRNA gene sequences obtained from oral, esophageal, and gastric microbiomes produced by Sanger sequencing.
Abstract: AIM: To design and validate broad-range 16S rRNA primers for use in high throughput sequencing to clas-sify bacteria isolated from the human foregut microbi-ome. METHODS: A foregut microbiome dataset was con-structed using 16S rRNA gene sequences obtained from oral, esophageal, and gastric microbiomes produced by Sanger sequencing in previous studies represented by 219 bacterial species. Candidate primers evaluated were from the European rRNA database. To assess the effect of sequence length on accuracy of classification, 16S rRNA genes of various lengths were created by trimming the full length sequences. Sequences spanning various hypervariable regions were selected to simulate the amplicons that would be obtained using possible primer pairs. The sequences were compared with full length 16S rRNA genes for accuracy in taxonomic classification using online software at the Ribosomal Database Project (RDP). The universality of the primer set was evaluated using the RDP 16S rRNA database which is comprised of 433 306 16S rRNA genes, represented by 36 phyla.
350 citations
TL;DR: The microbiota of the nostril and oropharynx show distinct phylum-level distribution patterns, supporting niche-specific colonization at discrete anatomical sites, and an inverse correlation existed between the Firmicutes family Staphylococcaceae and Actinobacteria families, suggesting potential antagonism between these groups.
Abstract: The nose and throat are important sites of pathogen colonization, yet the microbiota of both is relatively unexplored by culture-independent approaches. We examined the bacterial microbiota of the nostril and posterior wall of the oropharynx from seven healthy adults using two culture-independent methods, a 16S rRNA gene microarray (PhyloChip) and 16S rRNA gene clone libraries. While the bacterial microbiota of the oropharynx was richer than that of the nostril, the oropharyngeal microbiota varied less among participants than did nostril microbiota. A few phyla accounted for the majority of the bacteria detected at each site: Firmicutes and Actinobacteria in the nostril and Firmicutes , Proteobacteria , and Bacteroidetes in the oropharynx. Compared to culture-independent surveys of microbiota from other body sites, the microbiota of the nostril and oropharynx show distinct phylum-level distribution patterns, supporting niche-specific colonization at discrete anatomical sites. In the nostril, the distribution of Actinobacteria and Firmicutes was reminiscent of that of skin, though Proteobacteria were much less prevalent. The distribution of Firmicutes , Proteobacteria , and Bacteroidetes in the oropharynx was most similar to that in saliva, with more Proteobacteria than in the distal esophagus or mouth. While Firmicutes were prevalent at both sites, distinct families within this phylum dominated numerically in each. At both sites there was an inverse correlation between the prevalences of Firmicutes and another phylum: in the oropharynx, Firmicutes and Proteobacteria , and in the nostril, Firmicutes and Actinobacteria . In the nostril, this inverse correlation existed between the Firmicutes family Staphylococcaceae and Actinobacteria families, suggesting potential antagonism between these groups. IMPORTANCE The human nose and throat, though connected, contain distinct niches that are important sites of colonization by pathogenic bacteria. For many of these pathogens, colonization increases the risk of infection. Most research on the microbiota of nose and throat habitats has focused on carriage of one or a few pathogens. We hypothesized that increased knowledge of the composition of the complex bacterial communities in which these pathogens reside would provide new insights into why some individuals become colonized with pathogens, while others do not. Indeed, in the nostril microbiota of participants, there was an inverse correlation between the prevalences of the Staphylococcaceae family ( Firmicutes ), whose members include important pathogens, and the Corynebacteriaceae and Propionibacteriaceae families (both Actinobacteria ), whose members are more commonly benign commensals. An improved understanding of competitive bacterial colonization will increase our ability to define predispositions to pathogen carriage at these sites and the subsequent risk of infection.
285 citations
TL;DR: This survey of intragenomic diversity of 16S rRNA genes provides strong evidence supporting the theory of ribosomal constraint.
Abstract: Analysis of intragenomic variation of 16S rRNA genes is a unique approach to examining the concept of ribosomal constraints on rRNA genes; the degree of variation is an important parameter to consider for estimation of the diversity of a complex microbiome in the recently initiated Human Microbiome Project (http://nihroadmap.nih.gov/hmp). The current GenBank database has a collection of 883 prokaryotic genomes representing 568 unique species, of which 425 species contained 2 to 15 copies of 16S rRNA genes per genome (2.22 ± 0.81). Sequence diversity among the 16S rRNA genes in a genome was found in 235 species (from 0.06% to 20.38%; 0.55% ± 1.46%). Compared with the 16S rRNA-based threshold for operational definition of species (1 to 1.3% diversity), the diversity was borderline (between 1% and 1.3%) in 10 species and >1.3% in 14 species. The diversified 16S rRNA genes in Haloarcula marismortui (diversity, 5.63%) and Thermoanaerobacter tengcongensis (6.70%) were highly conserved at the 2° structure level, while the diversified gene in B. afzelii (20.38%) appears to be a pseudogene. The diversified genes in the remaining 21 species were also conserved, except for a truncated 16S rRNA gene in “Candidatus Protochlamydia amoebophila.” Thus, this survey of intragenomic diversity of 16S rRNA genes provides strong evidence supporting the theory of ribosomal constraint. Taxonomic classification using the 16S rRNA-based operational threshold could misclassify a number of species into more than one species, leading to an overestimation of the diversity of a complex microbiome. This phenomenon is especially seen in 7 bacterial species associated with the human microbiome or diseases.
265 citations
TL;DR: Detailed assessment of the COPD airway microbiota using high-throughput, culture-independent methods may prove key to understanding the relationships between airway bacterial colonization, acute exacerbation, and clinical outcomes in this and other chronic inflammatory airway diseases.
Abstract: Acute exacerbations of chronic obstructive pulmonary disease (COPD) are a major source of morbidity and contribute significantly to healthcare costs. Although bacterial infections are implicated in nearly 50% of exacerbations, only a handful of pathogens have been consistently identified in COPD airways, primarily by culture-based methods, and the bacterial microbiota in acute exacerbations remains largely uncharacterized. The aim of this study was to comprehensively profile airway bacterial communities using a culture-independent microarray, the 16S rRNA PhyloChip, of a cohort of COPD patients requiring ventilatory support and antibiotic therapy for exacerbation-related respiratory failure. PhyloChip analysis revealed the presence of over 1,200 bacterial taxa representing 140 distinct families, many previously undetected in airway diseases; bacterial community composition was strongly influenced by the duration of intubation. A core community of 75 taxa was detected in all patients, many of which are known pathogens. Bacterial community diversity in COPD airways is substantially greater than previously recognized and includes a number of potential pathogens detected in the setting of antibiotic exposure. Comprehensive assessment of the COPD airway microbiota using high-throughput, culture-independent methods may prove key to understanding the relationships between airway bacterial colonization, acute exacerbation, and clinical outcomes in this and other chronic inflammatory airway diseases.
234 citations
TL;DR: In this paper, the authors found correlations between bacterial community profiles and clinical disease markers in respiratory tracts of 45 children with cystic fibrosis and found that bacterial community complexity was inversely correlated with patient age, presence of Pseudomonas aeruginosa and antibiotic exposure, and was related to CF genotype.
Abstract: Summary Polymicrobial bronchopulmonary infections in cystic fibrosis (CF) cause progressive lung damage and death. Although the arrival of Pseudomonas aeruginosa often heralds a more rapid rate of pulmonary decline, there is significant inter-individual variation in the rate of decline, the causes of which remain poorly understood. By coupling culture-independent methods with ecological analyses, we discovered correlations between bacterial community profiles and clinical disease markers in respiratory tracts of 45 children with CF. Bacterial community complexity was inversely correlated with patient age, presence of P. aeruginosa and antibiotic exposure, and was related to CF genotype. Strikingly, bacterial communities lacking P. aeruginosa were much more similar to each other than were those containing P. aeruginosa, regardless of antibiotic exposure. This sug
225 citations
TL;DR: Pet-ownership is associated with increased house dust bacterial diversity and fewer fungal species, suggesting a potentially microbial-based mechanism for this protective effect.
Abstract: Pet-ownership, which has been shown to be protective against allergic disease development, is associated with increased house dust bacterial diversity and fewer fungal species, suggesting a potentially microbial-based mechanism for this protective effect.
205 citations
TL;DR: To the authors' knowledge, this SDS-TCA approach enables the deepest proteome characterizations of microbes in soil to date, without significant biases in protein size, localization, or functional category compared to pure cultures.
Abstract: We present a novel direct protocol for deep proteome characterization of microorganisms in soil. The method employs thermally assisted detergent-based cellular lysis (SDS) of soil samples, followed by TCA precipitation for proteome extraction/cleanup prior to liquid chromatography-mass spectrometric characterization. This approach was developed and optimized using different soils inoculated with genome-sequenced bacteria (Gram-negative Pseudomonas putida or Gram-positive Arthrobacter chlorophenolicus). Direct soil protein extraction was compared to protein extraction from cells isolated from the soil matrix prior to lysis (indirect method). Each approach resulted in identification of greater than 500 unique proteins, with a wide range in molecular mass and functional categories. To our knowledge, this SDS-TCA approach enables the deepest proteome characterizations of microbes in soil to date, without significant biases in protein size, localization, or functional category compared to pure cultures. This protocol should provide a powerful tool for ecological studies of soil microbial communities.
182 citations
TL;DR: It is hypothesize that a key mechanism for the protective effect of LGG supplementation on subsequent development of allergic disease is through promotion of a stable, even, and functionally redundant infant gastrointestinal community.
Abstract: Colonization of the infant gut by microorganisms over the first year of life is crucial for development of a balanced immune response. Early alterations in the gastrointestinal microbiota of neonates has been linked with subsequent development of asthma and atopy in older children. Here we describe high-resolution culture-independent analysis of stool samples from 6-month old infants fed daily supplements of Lactobacillus casei subsp. Rhamnosus (LGG) or placebo in a double-blind, randomized Trial of Infant Probiotic Supplementation (TIPS). Bacterial community composition was examined using a high-density microarray, the 16S rRNA PhyloChip, and the microbial assemblages of infants with either high or low LGG abundance were compared. Communities with high abundance of LGG exhibited promotion of phylogenetically clustered taxa including a number of other known probiotic species, and were significantly more even in their distribution of community members. Ecologically, these aspects are characteristic of communities that are more resistant to perturbation and outgrowth of pathogens. PhyloChip analysis also permitted identification of taxa negatively correlated with LGG abundance that have previously been associated with atopy, as well as those positively correlated that may prove useful alternative targets for investigation as alternative probiotic species. From these findings we hypothesize that a key mechanism for the protective effect of LGG supplementation on subsequent development of allergic disease is through promotion of a stable, even, and functionally redundant infant gastrointestinal community.
128 citations
TL;DR: Clear patterns of microbial secondary succession related to soil age, pH and phosphate status are observed, as exemplified by the overrepresentation of Verrucomicrobia, Acidobacteria, Gemmatimonadetes, and α-, δ- and ɛ-Proteobacteria at late successional stages.
Abstract: Although secondary succession has been studied extensively, we have little knowledge of the succession of soil-borne microbial communities. In this study, we therefore examined the structures of the microbial communities across two separate chronosequences of chalk grasslands in Limburg, the Netherlands, which are at different stages of secondary succession after being abandoned for between 17 and 466 years. Arable fields were also included in the investigation as non-abandoned references. Changes in the soil-borne microbial communities, as determined by phylogenetic microarray and quantitative PCR methodologies, were correlated with the prevailing environmental conditions related to vegetation and soil biochemistry. We observed clear patterns of microbial secondary succession related to soil age, pH and phosphate status, as exemplified by the overrepresentation of Verrucomicrobia, Acidobacteria, Gemmatimonadetes, and a-, d- and eProteobacteria at late successional stages. Moreover, effects of secondary succession versus changes in soil pH could be resolved, with pH significantly altering the trajectory of microbial succession.
77 citations
TL;DR: This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds, and comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health.
Abstract: Background
Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring.
TL;DR: The results suggest that Cr(VI) reduction by strain RCH2 under either aerobic or denitrifying conditions is primarily cometabolic in the sense that the physiological electron acceptor (oxygen or nitrate) appears to be required.
Abstract: Cr(VI) is a widespread groundwater contaminant that is a potent toxin, mutagen, and carcinogen. In situ reductive immobilization is a favored approach for Cr(VI) bioremediation, and Cr(VI) reduction has been reported in a variety of aerobic, facultative, and anaerobic bacteria, including a number of pseudomonads. However, studies comparing Cr(VI) reduction under aerobic and denitrifying conditions in the same organism are not available. We have conducted studies with strain RCH2, a bacterium similar to Pseudomonas stutzeri that we isolated from a Cr-contaminated aquifer. Cell suspension studies with lactate demonstrated that Cr(VI) reduction could occur under either denitrifying or aerobic conditions (at comparable specific rates) and that reduction was at least 20-fold more rapid when the terminal electron acceptor (i.e., nitrate or O(2)) was present. Our results suggest that Cr(VI) reduction by strain RCH2 under either aerobic or denitrifying conditions is primarily cometabolic in the sense that the physiological electron acceptor (oxygen or nitrate) appears to be required. Under both aerobic and denitrifying conditions, the gene(s) associated with chromate reduction are not inducible by Cr. Continuous culture (chemostat) studies showed strong correlations (r(2) values >0.93) between nitrate reduction rate and the transcript copy number of either nirS (cytochrome cd(1) nitrite reductase) or narG (nitrate reductase α subunit). As our studies indicate that anaerobic Cr(VI) reduction by this pseudomonad requires active denitrification and that denitrification and chromate reduction rates are highly correlated (r(2) > 0.99), monitoring expression of such denitrification genes in biostimulated aquifers could provide valuable proxy information for in situ chromate reduction by similar bacteria even if the specific genes involved in chromate reduction have not been identified. We also report incomplete removal of reduced Cr from solution and on artifacts in the widely used diphenylcarbazide assay for Cr(VI), most notably, its complete inactivation in the presence of millimolar nitrite.
TL;DR: An integrated workflow for metabolite identification using uniform stable isotope labeling is presented and a number of metabolites absent not only from the reconstructed draft metabolic network of Synechococcus sp.
Abstract: Metabolite profiling using mass spectrometry provides an attractive approach for the interrogation of cellular metabolic capabilities. Untargeted metabolite profiling has the potential to identify numerous novel metabolites; however, de novo identification of metabolites from spectral features remains a challenge. Here we present an integrated workflow for metabolite identification using uniform stable isotope labeling. Metabolite profiling of cell and growth media extracts of unlabeled control, 15N, and 13C-labeled cultures of the cyanobacterium, Synechococcus sp. PCC 7002 was performed using normal phase liquid chromatography coupled to mass spectrometry (LC−MS). Visualization of three-way comparisons of raw data sets highlighted characteristic labeling patterns for metabolites of biological origin allowing exhaustive identification of corresponding spectral features. Additionally, unambiguous assignment of chemical formulas was greatly facilitated by the use of stable isotope labeling. Chemical formula...
TL;DR: The overall community structure of the crop of the hoatzin changes with age in a complex manner, probably responding to new niches made available through dietary changes related to the transition from dependent to independent feeding.
Abstract: The hoatzin (Opisthocomus hoazin) is a South American strict folivorous bird, with a crop microbial ecosystem that ferments dietary plants. Chicks progressively become independent from the adultfed regurgitated crop liquids, and we hypothesized that the crop bacterial ecosystem develops through ecological succession mechanisms, as they grow into adults. The aim of this work was to compare the crop bacterial community in hoatzins from three age groups: newly hatched chicks, juveniles and adults by sequencing 16S rRNA genes and using the G2 PhyloChip. Cloning yielded a total of 2123 nearly full-length sequences binned into 294 operational taxonomic units (OTUs) (with o97% homology) belonging to 7 phyla, with 91% of novel OTUs. The microarray identified a diverse bacterial community dominated by Firmicutes and Bacteroidetes, with B1400 taxa grouped in 40 phyla that included those detected by cloning. In comparison with the adult, the hoatzin chick crop had a greater abundance of Flavobacteriaceae, Clostridiaceae and Lachnospiraceae but lacked phyla DSS1, Deferribacteres and Termite group 1, which were mostly present in adults. The overall community structure of the crop of the hoatzin changes with age in a complex manner, probably responding to new niches made available through dietary changes related to the transition from dependent to independent feeding.
Patent•
25 Jun 2010TL;DR: In this article, methods and systems for designing and using organism-specific and/or operational taxon unit (OTU)-specific probes for detecting, identifying and quantitating a plurality of biomolecules or rnicrorganisms in a sample based on the hybridization or binding of target molecules in the sample with the probes.
Abstract: Disclosed are methods and systems for designing and using organism-specific and/or operational taxon unit (OTU)-specific probes for detecting, identifying and quantitating a plurality of biomolecules or rnicrorganisms in a sample based on the hybridization or binding of target molecules in the sample with the probes. The disclosure further provides methods of selecting an oligonucleotide probe specific for a node on a clustering tree, and methods of selecting organism-specific or OTU-specific oligonucleotide probes for use in accurately detecting a plurality of organisms in a sample with high confidence. Further, the disclosure provides methods and systems to detect the presence of a rare OTU in a sample.
TL;DR: Incubation experiments with (13)C-labeled TCE introduced into microcosms containing basalt and groundwater from the aquifer confirm that TCE co-metabolism is possible and indicate that electron donor amendment designed to stimulate reductive dechlorination of TCE may also stimulate co-METabolism of T CE.
Abstract: For more than 10 years, electron donor has been injected into the Snake River aquifer beneath the Test Area North site of the Idaho National Laboratory for the purpose of stimulating microbial redu...
TL;DR: In this paper, new techniques such as the PhyloChip and pyrosequencing might help to see beyond the familiar fields, into areas that could help to forge a new understanding of the ecology of fungal entomopathogens.
Abstract: Entomopathogens are important natural enemies of many insect and mite species and as such have been recognised as providing an important ecosystem service. Indeed, fungal entomopathogens have been widely investigated as biological control agents of pest insects in attempts to improve the sustainability of crop protection. However, even though our understanding of the ecology of fungal entomopathogens has vastly increased since the early 1800s, we still require in-depth ecological research that can expand our scientific horizons in a manner that facilitates widespread adoption of these organisms as efficient biological control agents. Fungal entomopathogens have evolved some intricate interactions with arthropods, plants and other microorganisms. The full importance and complexity of these relationships is only just becoming apparent. It is important to shift our thinking from conventional biological control, to an understanding of an as yet unknown “deep space”. The use of molecular techniques and phylogenetic analyses have helped us move in this direction, and have provided important insights on fungal relationships. Nevertheless, new techniques such as the PhyloChip and pyrosequencing might help us see beyond the familiar fields, into areas that could help us forge a new understanding of the ecology of fungal entomopathogens.
TL;DR: A significant association between the foregut microbiome and GERD sequence, if demonstrated, will be the first step for eventually testing whether an abnormal microbiome is required for the development of the sequence of phenotypic changes toward EA.
Abstract: Esophageal adenocarcinoma (EA), the type of cancer linked to heartburn due to gastroesophageal reflux diseases (GERD), has increased six fold in the past 30 years. This cannot currently be explained by the usual environmental or by host genetic factors. EA is the end result of a sequence of GERD-related diseases, preceded by reflux esophagitis (RE) and Barrett’s esophagus (BE). Preliminary studies by Pei and colleagues at NYU on elderly male veterans identified two types of microbiotas in the esophagus. Patients who carry the type II microbiota are >15 fold likely to have esophagitis and BE than those harboring the type I microbiota. In a small scale study, we also found that 3 of 3 cases of EA harbored the type II biota. The findings have opened a new approach to understanding the recent surge in the incidence of EA.Our long-term goal is to identify the cause of GERD sequence. The hypothesis to be tested is that changes in the foregut microbiome are associated with EA and its precursors, RE and BE in GERD sequence. We will conduct a case control study to demonstrate the microbiome disease association in every stage of GERD sequence, as well as analyze the trend in changes in the microbiome along disease progression toward EA, by two specific aims. Aim 1 is to conduct a comprehensive population survey of the foregut microbiome and demonstrate its association with GERD sequence. Furthermore, spatial relationship between the esophageal microbiota and upstream (mouth) and downstream (stomach) foregut microbiotas as well as temporal stability of the microbiome-disease association will also be examined. Aim 2 is to define the distal esophageal metagenome and demonstrate its association with GERD sequence. Detailed analyses will include pathway-disease and gene-disease associations. Archaea, fungi and viruses, if identified, also will be correlated with the diseases. A significant association between the foregut microbiome and GERD sequence, if demonstrated, will be the first step for eventually testing whether an abnormal microbiome is required for the development of the sequence of phenotypic changes toward EA. If EA and its precursors represent a microecological disease, treating the cause of GERD might become possible, for example, by normalizing the microbiota through use of antibiotics, probiotics, or prebiotics. Causative therapy of GERD could prevent its progression and reverse the current trend of increasing incidence of EA.
01 May 2010
TL;DR: The Chip-SIP approach is employing the combination of high-density phylogenetic microarrays and stable isotope probing to determine which taxa incorporate carbon from which substrates to gain a better understanding of organic matter processing in these coastal environments.
Abstract: A fundamental goal in microbial ecology is to understand the biogeochemical role of individual microbial taxa in their natural habitat. This rather simple concept is in actuality a complex problem because 1) most microbes remain uncultivated and 2) the majority of microbial communities are very diverse. The former makes the direct testing of isolated strains for biogeochemical activity a limited approach. The latter impacts culture-independent methods like metagenomics as many biogeochemical processes cannot be directly inferred from sequence data alone, even when assembly of complete genomes is possible. Our approach to this problem (Chip-SIP) involves the combination of high-density phylogenetic microarrays (“chips”) and stable isotope probing (SIP) to directly link identity and function. Microbial communities are incubated in the presence of stable isotope-enriched substrate(s), RNA is extracted and hybridized onto a microarray synthesized on a conductive surface (a glass slide coated with Indium Tin Oxide). The array is subsequently imaged using high resolution secondary ion mass spectrometry (SIMS) with a Cameca NanoSIMS 50 to detect isotopic enrichment. We have successfully validated this approach utilizing RNA from a single pure culture with varying degrees of isotopic enrichment using two different substrates (N-labeled ammonium and C-labeled glucose). We show that isotopic enrichment of individual probe spots as detected by nanoSIMS is positively correlated with fluorescence as detected by a traditional microarray scanner. This allows the relationship between hybridization efficiency and relative isotopic enrichment to be determined. Further, we have successfully detected N enrichment in an estuarine bacterial community following incubation with N-NH4, demonstrating the utility of the method in mixed natural communities. Current efforts are aimed at elucidating the major players in the incorporation of organic carbon in estuarine microbial communities. It is currently unknown if members of heterotrophic communities in these eutrophic systems are generalists or instead specialize in the incorporation of specific substrates such as amino acids, starch, and fatty acids. We are employing the Chip-SIP approach to determine which taxa incorporate carbon from which substrates to gain a better understanding of organic matter processing in these coastal environments. 426 doi:10.1017/S1431927610061519 Microsc. Microanal. 16 (Suppl 2), 2010 © Microscopy Society of America 2010