Search

Coral diseases impact reefs globally. Although we continue to describe diseases, little is known about the etiology or progression of even the most common cases. To examine a spectrum of coral health and determine factors of disease progression we examined Orbicella faveolata exhibiting signs of Yellow Band Disease (YBD), a widespread condition in the Caribbean. We used a novel combined approach to assess three members of the coral holobiont: the coral-host, associated Symbiodinium algae, and bacteria. We profiled three conditions: (1) healthy-appearing colonies (HH), (2) healthy-appearing tissue on diseased colonies (HD), and (3) diseased lesion (DD). Restriction fragment length polymorphism analysis revealed health state-specific diversity in Symbiodinium clade associations. 16S ribosomal RNA gene microarrays (PhyloChips) and O. faveolata complimentary DNA microarrays revealed the bacterial community structure and host transcriptional response, respectively. A distinct bacterial community structure marked each health state. Diseased samples were associated with two to three times more bacterial diversity. HD samples had the highest bacterial richness, which included components associated with HH and DD, as well as additional unique families. The host transcriptome under YBD revealed a reduced cellular expression of defense- and metabolism-related processes, while the neighboring HD condition exhibited an intermediate expression profile. Although HD tissue appeared visibly healthy, the microbial communities and gene expression profiles were distinct. HD should be regarded as an additional (intermediate) state of disease, which is important for understanding the progression of YBD.

ObjectiveThe human intestine harbors trillions of commensal microbes that live in homeostasis with the host immune system. Changes in the composition and complexity of gut microbial communities are seen in inflammatory bowel disease (IBD), indicating disruption in host-microbe interactions. Multiple factors including diet and inflammatory conditions alter the microbial complexity. The goal of this study was to develop an optimized methodology for fecal sample processing and to detect changes in the gut microbiota of patients with Crohn's disease receiving specialized diets.DesignFecal samples were obtained from patients with Crohn's disease in a pilot diet crossover trial comparing the effects of a specific carbohydrate diet (SCD) versus a low residue diet (LRD) on the composition and complexity of the gut microbiota and resolution of IBD symptoms. The gut microbiota composition was assessed using a high-density DNA microarray PhyloChip.ResultsDNA extraction from fecal samples using a column based method provided consistent results. The complexity of the gut microbiome was lower in IBD patients compared to healthy controls. An increased abundance of Bacteroides fragilis (B. fragilis) was observed in fecal samples from IBD positive patients. The temporal response of gut microbiome to the SCD resulted in an increased microbial diversity while the LRD diet was associated with reduced diversity of the microbial communities.ConclusionChanges in the composition and complexity of the gut microbiome were identified in response to specialized carbohydrate diet. The SCD was associated with restructuring of the gut microbial communities.

Producing cellulosic biofuels from plant material has recently emerged as a key US Department of Energy goal. For this technology to be commercially viable on a large scale, it is critical to make production cost efficient by streamlining both the deconstruction of lignocellulosic biomass and fuel production. Many natural ecosystems efficiently degrade lignocellulosic biomass and harbor enzymes that, when identified, could be used to increase the efficiency of commercial biomass deconstruction. However, ecosystems most likely to yield relevant enzymes, such as tropical rain forest soil in Puerto Rico, are often too complex for enzyme discovery using current metagenomic sequencing technologies. One potential strategy to overcome this problem is to selectively cultivate the microbial communities from these complex ecosystems on biomass under defined conditions, generating less complex biomass-degrading microbial populations. To test this premise, we cultivated microbes from Puerto Rican soil or green waste compost under precisely defined conditions in the presence dried ground switchgrass (Panicum virgatum L.) or lignin, respectively, as the sole carbon source. Phylogenetic profiling of the two feedstock-adapted communities using SSU rRNA gene amplicon pyrosequencing or phylogenetic microarray analysis revealed that the adapted communities were significantly simplified compared to the natural communities from which they were derived. Several members of the lignin-adapted and switchgrass-adapted consortia are related to organisms previously characterized as biomass degraders, while others were from less well-characterized phyla. The decrease in complexity of these communities make them good candidates for metagenomic sequencing and will likely enable the reconstruction of a greater number of full-length genes, leading to the discovery of novel lignocellulose-degrading enzymes adapted to feedstocks and conditions of interest.

The spread of disease by enteric pathogens associated with fecal contamination is a major concern for the management of urban watersheds. So far, the relative contribution of natural and anthropogenic sources to fecal pollution in managed tropical watersheds remains poorly evaluated. In this study, the microbiomes of water samples collected from managed watersheds in Singapore were elicited using the PhyloChip, a dense 16S rRNA gene-based DNA microarray, and fecal impairment was inferred using a machine-learning classification algorithm (SourceTracker). The predicted contribution of wildlife fecal sources to environmental samples was generally negligible (< 0.01 ± 0.01), indicating a low likelihood of fecal impairment from natural sources. However, sewage showed considerably higher contribution (0.09 ± 0.05) to microbial communities in a subset of watershed samples from canals and rivers, suggesting persistent impairment of certain areas by anthropogenic activity although being managed. Interestingly, the contribution of sewage microbial communities showed decreasing trends from canals/rivers to the connected reservoirs, indicating meaningful auto-mitigation of fecal pollution in canals and rivers. Notably, exclusion of locally derived fecal samples and source categories from the training data set impaired the predictive performance of the classification algorithm despite a high degree of similarity in the phylogenetic composition of microbiomes in biologically similar but geographically distinct sources. [Display omitted] • Inclusion of geographically relevant source samples improved category predictions. • A representative background source category improved SourceTracker reliability. • Contributions of human-related sources correlated with Bacteroides HF183 abundance. • Canals showed greater contributions from human-related fecal sources than reservoirs. [ABSTRACT FROM AUTHOR]

With growing interest in the role of microbiomes, and symbionts in particular, the aim of this study was to determine the diversity of the bacterial endophyte population within Miscanthus and to ascertain the extent of vertical transmission via the seed. A great diversity of endophytic bacteria was found in all parts of the mature plant (rhizome, root, stem and leaf), and in seedlings grown from sterilized seed grown in sterile conditions. A total of three phyla and five families of bacteria were identified as cultures compared to 19 phyla and 85 families using 16S rDNA amplification and sequencing. Not all cultured bacteria could be identified by 16S rDNA, implying that the true diversity is even greater. More bacterial diversity was identified in sterile-grown seedlings than in all parts of the mature plant combined, 17 and 13 phyla, respectively, with 11 in common. Five phyla were present in all plant samples examined. Vertical transmission via the seed may therefore be a major source of endophytes in Miscanthus, presumably supplemented by ingress of soil bacteria as the plant grows. Bacteria identified from the mature plant were predominantly similar to known bacterial sequences in GenBank, but a small number from the stem and many from the seed were novel, potentially adapted to an in planta life cycle. Endophytic bacteria were found to form spores and other dense structures, and this provides a mechanism for long-term survival and seed transmission. The staining of germinating seeds identified bacteria at the root tip of the emerging radicle. We propose that seed transmission of bacterial endophytes requires adaptation of both plant and microbes, plays a role in germination and has evolutionary significance and implications for future plant breeding approaches, in Miscanthus and more widely. [ABSTRACT FROM AUTHOR]

Aims Huanglongbing ( HLB)-affected citrus often display zinc deficiency symptoms. In this study, supplemental zinc was applied to citrus to determine its effect on Candidatus Liberibacter asiaticus (Las) titre, HLB symptoms, and leaf microbiome. Methods and Results HLB-affected citrus were treated with various amounts of zinc. The treatments promoted Las growth and affected microbiomes in citrus leaves. Phylochip™-based results indicated that 5475 of over 50 000 known Operational Taxonomic Units ( OTUs) in 52 phyla were detected in the midribs of HLB-affected citrus, of which Proteobacteria was the most abundant, followed by Firmicutes and Actinobacteria. In comparison, the microbiomes of zinc-treated diseased plants had overall more OTUs with higher amounts of Proteobacteria, but decreased percentages of Firmicutes and Actinobacteria. In addition, more OTUs of siderophore-producing bacteria were present. Only zinc-sensitive Staphylococcaceae had higher OTU's in the diseased plants without zinc treatments. Conclusions Although HLB-affected citrus appear zinc deficient, zinc amendments increased the pathogen levels and shifted the microbiome. Significance and Impact of the Study HLB is currently the most devastating disease of citrus worldwide. Zinc is often applied to HLB-affected citrus due to zinc deficiency symptoms. This study provided new insights into the potential effects of zinc on HLB and the microbial ecology of citrus. [ABSTRACT FROM AUTHOR]

In estuarine ecosystems, metallic and organic contaminants are mainly associated with fine grain sediments which settle on mudflats. Over time, the layers of sediment accumulate and are then transformed by diagenetic processes mainly controlled by microbial activity, recording the history of the estuary's chemical contamination. In an environment of this specific type, we investigated the evolution of the chemical contamination and the structure of both total and active microbial communities, based on PhyloChip analysis of a 4.6-m core corresponding to a 40-year sedimentary record. While the archaeal abundance remained constant along the core, a decrease by one order of magnitude in the bacterial abundance was observed with depth. Both total and active microbial communities were dominated by Proteobacteria, Actinobacteria, and Firmicutes in all sediment samples. Among Proteobacteria, alpha- Proteobacteria dominated both total (from 37 to 60 %) and metabolically active (from 19.7 to 34.6 %) communities, including the Rhizobiales, Rhodobacter, Caulobacterales, and Sphingomonadales orders. Co-inertia analysis revealed a relationship between polycyclic aromatic hydrocarbons, zinc and some polychlorobiphenyls concentrations, and the structure of total and active microbial communities in the oldest and most contaminated sediments (from 1970 to 1975), suggesting that long-term exposure to chemicals shaped the structure of the microbial community. [ABSTRACT FROM AUTHOR]

Copyright of Implant Dentistry is the property of Lippincott Williams & Wilkins and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Aims The aim of the study was to develop a microarray dedicated to comprehensive analysis of the diverse rumen bacteria. Methods and Results All the 16S r RNA gene ( rrs) sequences of rumen origin were retrieved from the RDP database, and operational taxonomic units (OTUs) were calculated at 97% sequence similarity. A total of 1666 OTU-specific probes were designed and synthesized on microarray slides (referred to as RumenBactArray) in a 6 × 5 k format with each probe being represented in triplicate. The specificity, sensitivity and linear range of detection were determined using pools of rrs clones of known sequences. The RumenBactArray detected as few as approx. 106 copies of a target and had a linear detection range of >4 orders of magnitude. The utility of the RumenBactArray was tested using fractionated rumen samples obtained from sheep fed two different diets. More than 300 different OTUs were detected across the four fractionated samples, and differences in bacterial communities were found between the two diets. Conclusions This is the first phylochip dedicated to analysis of ruminal bacteria, and it enables comprehensive and semiquantitative analysis of ruminal bacteria. Significance and Impact of the Study RumenBactArray can be a robust tool to comparatively analyse ruminal bacteria needed in nutritional studies of ruminant animals. [ABSTRACT FROM AUTHOR]

A fundamental knowledge of microbial community structure in petroleum reservoirs can improve predictive modeling of these environments. We used hydrocarbon profiles, stable isotopes, and high-density DNA microarray analysis to characterize microbial communities in produced water from four Alaskan North Slope hydrocarbon reservoirs. Produced fluids from Schrader Bluff (24-27°C), Kuparuk (47-70°C), Sag River (80°C), and Ivishak (80-83°C) reservoirs were collected, with paired soured/non-soured wells sampled from Kuparuk and Ivishak. Chemical and stable isotope data suggested Schrader Bluff had substantial biogenic methane, whereas methane was mostly thermogenic in deeper reservoirs. Acetoclastic methanogens (Methanosaeta) were most prominent in Schrader Bluff samples, and the combined δD and δ13C values of methane also indicated acetoclastic methanogenesis could be a primary route for biogenic methane. Conversely, hydrogenotrophic methanogens (e.g., Methanobacteriaceae) and sulfide-producing Archaeoglobus and Thermococcus were more prominent in Kuparuk samples. Sulfide-producing microbes were detected in all reservoirs, uncoupled from souring status (e.g., the non-soured Kuparuk samples had higher relative abundances of many sulfate-reducers compared to the soured sample, suggesting sulfate-reducers may be living fermentatively/syntrophically when sulfate is limited). Sulfate abundance via long-term seawater injection resulted in greater relative abundances of Desulfonauticus, Desulfomicrobium, and Desulfuromonas in the soured Ivishak well compared to the non-soured well. In the non-soured Ivishak sample, several taxa affiliated with Thermoanaerobacter and Halomonas predominated. Archaea were not detected in the deepest reservoirs. Functional group taxa differed in relative abundance among reservoirs, likely reflecting differing thermal and/or geochemical influences. [ABSTRACT FROM AUTHOR]

Harmful algal blooms (HAB) occur worldwide and cause health problems and economic damage to fisheries and tourism. Monitoring for toxic algae is therefore essential but is based primarily on light microscopy, which is time consuming and can be limited by insufficient morphological characters such that more time is needed to examine critical features with electron microscopy. Monitoring with molecular tools is done in only a few places world-wide. EU FP7 MIDTAL (Microarray Detection of Toxic Algae) used SSU and LSU rRNA genes as targets on microarrays to identify toxic species. In order to comply with current monitoring requirements to report cell numbers as the relevant threshold measurement to trigger closure of fisheries, it was necessary to calibrate our microarray to convert the hybridisation signal obtained to cell numbers. Calibration curves for two species of Pseudo-nitzschia for use with the MIDTAL microarray are presented to obtain cell numbers following hybridisation. It complements work presented by Barra et al. (2012b. Environ. Sci. Pollut. Res. doi: 10.1007/s11356-012-1330-1v) for two other Pseudo-nitzschia spp., Dittami and Edvardsen (2012a. J. Phycol. 48, 1050) for Pseudochatonella, Blanco et al. (2013. Harmful Algae 24, 80) for Heterosigma, McCoy et al. (2013. FEMS. doi: 10.1111/1574-6941.12277) for Prymnesium spp., Karlodinium veneficum, and cf. Chatonella spp. and Taylor et al. (2014. Harmful Algae, in press) for Alexandrium. [ABSTRACT FROM AUTHOR]

The dinoflagellate genus Alexandrium contains several toxin producing species and strains, which can cause major economic losses to the shell fish industry. It is therefore important to be able to detect these toxin producers and also distinguish toxic strains from some of the morphologically identical non-toxic strains. To facilitate this DNA probes to be used in a microarray format were designed in silico or developed from existing published probes. These probes targeted either the 18S or 28S ribosomal ribonucleic acid (rRNA) gene in Alexandrium tamarense Group I, Group III and Group IV, Alexandrium ostenfeldii and Alexandrium minutum. Three strains of A. tamarense Group I, A. tamarense Group III, A. minutum and two strains of A. ostenfeldii were grown at optimal conditions and transferred into new environmental conditions changing either the light intensity, salinity, temperature or nutrient concentrations, to check if any of these environmental conditions induced changes in the cellular ribonucleic acid (RNA) concentration or growth rate. The aim of this experiment was the calibration of several species-specific probes for the quantification of the toxic Alexandrium strains. Growth rates were highly variable but only elevated or lowered salinity significantly lowered growth rate for A. tamarense Group I and Group III; differences in RNA content were not significant for the majority of the treatments. Only light intensity seemed to affect significantly the RNA content in A. tamarense Group I and Group III, but this was still within the same range as for the other treatments meaning that a back calibration from RNA to cell numbers was possible. The designed probes allow the production of quantitative information for Alexandrium species for the microarray chip. [ABSTRACT FROM AUTHOR]

Wastewater treatment plants use a variety of bioreactor types and configurations to remove organic matter and nutrients. Little is known regarding the effects of different configurations and within-plant immigration on microbial community dynamics. Previously, we found that the structure of ammonia-oxidizing bacterial (AOB) communities in a full-scale dispersed growth activated sludge bioreactor correlated strongly with levels of NO entering the reactor from an upstream trickling filter. Here, to further examine this puzzling association, we profile within-plant microbial biogeography (spatial variation) and test the hypothesis that substantial microbial immigration occurs along a transect (raw influent, trickling filter biofilm, trickling filter effluent, and activated sludge) at the same full-scale wastewater treatment plant. AOB amoA gene abundance increased >30-fold between influent and trickling filter effluent concomitant with NO production, indicating unexpected growth and activity of AOB within the trickling filter. Nitrosomonas europaea was the dominant AOB phylotype in trickling filter biofilm and effluent, while a distinct ' Nitrosomonas-like' lineage dominated in activated sludge. Prior time series indicated that this ' Nitrosomonas-like' lineage was dominant when NO levels in the trickling filter effluent (i.e., activated sludge influent) were low, while N. europaea became dominant in the activated sludge when NO levels were high. This is consistent with the hypothesis that NO production may cooccur with biofilm sloughing, releasing N. europaea from the trickling filter into the activated sludge bioreactor. Phylogenetic microarray (PhyloChip) analyses revealed significant spatial variation in taxonomic diversity, including a large excess of methanogens in the trickling filter relative to activated sludge and attenuation of Enterobacteriaceae across the transect, and demonstrated transport of a highly diverse microbial community via the trickling filter effluent to the activated sludge bioreactor. Our results provide compelling evidence that substantial immigration between coupled process units occurs and may exert significant influence over microbial community dynamics within staged bioreactors. [ABSTRACT FROM AUTHOR]

Phytoplankton community analysis is important with respect to natural or human-induced changes in the marine environment. Because of the efforts involved and the limitations of traditional methods, molecular sensing approaches are becoming more popular. Among others, microarray techniques targeting ribosomal 18S sequences have been successfully applied for phytoplankton investigation. In this contribution, we compared the results of two microarray methods targeting 18S rDNA and 18S rRNA with the results obtained from microscopy, HPLC and flow cytometry. On a qualitative basis, the microarrays showed similar or potentially better performance than the non-molecular methods. Quantitatively, our data suggest that microarray signals obtained from 18S rDNA provide relatively rough estimates of phytoplankton abundance. In contrast, when targeting 18S rRNA instead, a robust linear relationship (r² = 0.68) between molecular sensing signal and microscopic cell counts could be demonstrated using a probe specific to the genus Pseudo-nitzschia as an example. Thus, for both qualitative and quantitative purposes, microarray techniques can be valuable additions to traditional methods for phytoplankton analysis. Routine monitoring approaches in particular could benefit from advantages like reduced effort, higher taxonomic resolution and a potential for automation. [ABSTRACT FROM AUTHOR]

Wastewater treatment plants (WWTPs) are major collection pools of antibiotics of which low concentrations may induce antibiotic resistance in their microbial communities and pose threat to human health. However, information is still limited on the microbial community alteration in WWTPs upon exposure to low-dose antibiotics due to absence of negative control systems without input of resistant bacteria and resistance genes. Here we report the impact of trace erythromycin (ERY) and dehydrated erythromycin (ERY-HO) on microbial community dynamics in three long-term (1 year) running sequencing batch reactors (SBRs), R1 (ERY-HO), R2 (ERY), and negative control R3. The PhyloChip microarray analysis showed that ERY-HO and ERY significantly altered their microbial communities based on bacterial richness (e.g., 825 operational taxonomic units (OTUs) in R1, 699 OTUs in R2, and 920 OTUs in R3) and population abundance (15 and 48 subfamilies with >80 % abundance decrease in R1 and R2, respectively). ERY-HO and ERY have broad but distinct antimicrobial spectrums. For example, bacteria of all the major phyla (i.e., Proteobacteria, Actinobacteria, Bacteroidetes, and Chloroflexi) present in SBRs were severely inhibited by ERY-HO and ERY, but bacteria of Acidobacteria, Chlorobi, Firmicutes, Nitrospira and OP10 phyla were only inhibited by ERY. Very limited bacterial groups showed antibiotic resistance to ERY-HO or ERY through forming biofilms (e.g., Zoogloea) or synthesizing resistant proteins (e.g., Thauera, Candidatus Accumulibacter, Candidatus Competibacter, and Dechloromonas) in the SBRs. Inhibition was observed to be the main effect of ERY-HO and ERY on microbial communities in the reactors. The results would broaden our knowledge of effects of low-dose antibiotics on microbial communities in WWTPs. [ABSTRACT FROM AUTHOR]

Abstract: Molecular microbial community analyses provide information on thousands of microorganisms simultaneously, and integrate biotic and abiotic perturbations caused by fecal contamination entering water bodies. A few studies have explored community methods as emerging approaches for microbial source tracking (MST), however, an evaluation of the current state of this approach is lacking. Here, we utilized three types of community-based methods with 64 blind, single- or dual-source, challenge samples generated from 12 sources, including: humans (feces), sewage, septage, dogs, pigs, deer, horses, cows, chickens, gulls, pigeons, and geese. Each source was a composite from multiple donors from four representative geographical regions in California. Methods evaluated included terminal restriction fragment polymorphism (TRFLP), phylogenetic microarray (PhyloChip), and next generation (Illumina) sequencing. These methods correctly identified dominant (or sole) sources in over 90% of the challenge samples, and exhibited excellent specificity regardless of source, rarely detecting a source that was not present in the challenge sample. Sensitivity, however, varied with source and community analysis method. All three methods distinguished septage from human feces and sewage, and identified deer and horse with 100% sensitivity and 100% specificity. Method performance improved if the composition of blind dual-source reference samples were defined by DNA contribution of each single source within the mixture, instead of by Enterococcus colony forming units. Data analysis approach also influenced method performance, indicating the need to standardize data interpretation. Overall, results of this study indicate that community analysis methods hold great promise as they may be used to identify any source, and they are particularly useful for sources that currently do not have, and may never have, a source-specific single marker gene. [Copyright &y& Elsevier]

Abstract: The biogeochemical processes that occur in marine sediments on continental margins are complex; however, from one perspective they can be considered with respect to three geochemical zones based on the presence and form of methane: sulfate–methane transition (SMTZ), gas hydrate stability zone (GHSZ), and free gas zone (FGZ). These geochemical zones may harbor distinct microbial communities that are important in biogeochemical carbon cycles. The objective of this study was to describe the microbial communities in sediments from the SMTZ, GHSZ, and FGZ using molecular ecology methods (i.e. PhyloChip microarray analysis and terminal restriction fragment length polymorphism (T-RFLP)) and examining the results in the context of non-biological parameters in the sediments. Non-metric multidimensional scaling and multi-response permutation procedures were used to determine whether microbial community compositions were significantly different in the three geochemical zones and to correlate samples with abiotic characteristics of the sediments. This analysis indicated that microbial communities from all three zones were distinct from one another and that variables such as sulfate concentration, hydrate saturation of the nearest gas hydrate layer, and depth (or unmeasured variables associated with depth e.g. temperature, pressure) were correlated to differences between the three zones. The archaeal anaerobic methanotrophs typically attributed to performing anaerobic oxidation of methane were not detected in the SMTZ; however, the marine benthic group-B, which is often found in SMTZ, was detected. Within the GHSZ, samples that were typically closer to layers that contained higher hydrate saturation had indicator sequences related to Vibrio-type taxa. These results suggest that the biogeographic patterns of microbial communities in marine sediments are distinct based on geochemical zones defined by methane. [Copyright &y& Elsevier]

Tibetan lakes represent a unique microbial environment and are a good ecosystem to investigate the microbial diversity of high mountain lakes and their relationship with environmental factors. The diversity and community structure of bacterioplankton in Tibetan lakes was determined using DNA fingerprinting analysis, high-density 16S rRNA gene microarray (PhyloChip) analysis, and extensive clone library analysis of bacterial 16S rRNA genes. A previously unseen high microbial diversity (1732 operational taxonomic units based on PhyloChip data) and numerous novel bacterial 16S rRNA gene sequences were observed. Abundant SAR11-like sequences retrieved from saline Lake Qinghai demonstrated a unique SAR11 phylogenetic sister clade related to the freshwater LD12 clade. Water chemistry (e.g. salinity) and altitude played important roles in the selection of bacterial taxa (both presence and relative abundance) in Tibetan lakes. The ubiquity and uniqueness of bacterial taxa, as well as the correlation between environmental factors and bacterial taxa, was observed to vary gradually with different phylogenetic levels. Our study suggested high microbial cosmopolitanism and high endemicity observed at higher and lower phylogenetic levels, respectively. [ABSTRACT FROM AUTHOR]

A microarray for the detection of toxic algal species was developed in the European Union 7th Framework project MIDTAL. We initially tested all available fluorescence in situ hybridisation probes for toxic algae, which are normally designed to a length of 18 nt, and found that in most cases the signal was rather weak or all probes designed from the second half of the molecule were inaccessible in a microarray format because of secondary structure of the ribosomal RNA molecule We modified the length of the probes, the fragmentation of the rRNA, the stringency of the washing buffers and the length of the spacer molecules linking the probes to the glass surface of the microarray. Because of the secondary structure of the rRNA molecule, regions of the molecule can be difficult to access by the probes. Each of these modifications has improved probe accessibility and probe specificity to reduce false positives. [ABSTRACT FROM AUTHOR]

Highlights: [•] Two anaerobic microbial consortia were established to depolymerize lignin. [•] The consortia could produce biomethane during lignin depolymerization. [•] The consortia could increase the hydrolytic efficiency of lignocellulosic biomass (e.g. OPEFB). [ABSTRACT FROM AUTHOR]

Background: The gut microbiome, a dynamic bacterial community that interacts with the host, is integral to human health because it regulates energy metabolism and immune functions. The gut microbiome may also play a role in risks from environmental toxicants. Objectives: We investigated the effects of polychlorinated biphenyls (PCBs) and exercise on the composition and structure of the gut microbiome in mice. Methods: After mice exercised voluntarily for 5 weeks, they were treated by oral gavage with a mixture of environmentally relevant PCB congeners (PCB153, PCB138, and PCB180; total PCB dose, 150 µmol/kg) for 2 days. We then assessed the microbiome by determination of 16S rRNA using microarray analysis. Results: Oral exposure to PCBs significantly altered the abundance of the gut microbiome in mice primarily by decreasing the levels of Proteobacteria. The activity level of the mice correlated with a substantial shift in abundance, biodiversity, and composition of the microbiome. Importantly, exercise attenuated PCB-induced changes in the gut microbiome. Conclusions: Our results show that oral exposure to PCBs can induce substantial changes in the gut microbiome, which may then influence their systemic toxicity. These changes can be attenuated by behavioral factors, such as voluntary exercise. [ABSTRACT FROM AUTHOR]

Abstract: Globally, tussock-based grasslands are being modified to increase productive capacity. The impacts of cultivation and over-sowing with exotic grass and legumes on soil microbiology were assessed at four sites in New Zealand which differed in soil type, climate and vegetation. Primary alteration of the soil physicochemical status occurred with land use change. This was driven by addition of mineral fertiliser and alteration of pH. Genes associated with several biogeochemical cycles (GeoChip data) were impacted by land-use but not sampling location. A number of functional gene families associated with biogeochemical cycling of C, N and S were present in greater relative abundance in the undisturbed soils. Similarly, soil bacterial (PhyloChip) and fungal (TRFLP) communities were strongly influenced by land-use change, but unaffected by sampling location. Alteration of land-use increased the relative abundance of Firmicutes, Actinobacteria and OD1 phyla, but many of the less-common phyla, such as Verrucomicrobia and Dictyoglomi decreased in abundance; these phyla may be important in internal soil nutrient cycling processes. This work provides evidence that tussock grassland soils are strongly dependent on microbially-mediated nutrient cycling, and these processes are highly-sensitive to exogenous nutrient inputs and/or alteration of pH. De-coupling of processes following addition of fertilisers or removal of organic matter (grazing) may make these improved grassland systems more susceptible to nutrient leakage. This has important implications for environmental quality. [Copyright &y& Elsevier]

Abstract: Soil microbial diversity is vast, and we lack even basic understanding of how this diversity is distributed ecologically. Using pyrosequencing and microarray methods, we quantified the structure of bacterial communities in two contrasting soils underlying Bornean rain forest (clay and sandy loam) that differ markedly in soil properties, aboveground tree flora, and leaf litter decomposition rates. We found significant soil-related taxonomic and phylogenetic differences between communities that, due to their proximity, are independent of climate. Bacterial communities showed distinct compositional and taxon-abundance distributions that were significantly correlated with the structure of the overlying tree community. Richness of bacteria was greater in the more resource-rich clay soil. Phylogenetic community analyses suggested that environmental filtering may be an important mechanism of community assembly in clay, compared to niche-competition in sandy loam. The Acidobacteria were the most abundant group in clay, but the Proteobacteria dominated in sandy loam. Of the ten most abundant classes, the Actinobacteria, Betaproteobacteria, Clostridia, Bacilli, and Gammaproteobacteria were more abundant in sandy loam than clay. Our study, which is the first to quantify edaphic variation in bacterial communities using high-throughput methods in soils underlying one of the most tree species rich forests on Earth, indicates an important role of plant–soil feedbacks linking the community structure of the trees and the underlying soil microbiome. We suggest the biochemical composition of carbon and nutrient resources in plant litter and soil pH and oxygen availability as important determinants of the distribution of bacterial diversity. [Copyright &y& Elsevier]

The bacterial community structure of a chromium water bath, a chromium drainage waste system, a chromium pretreatment tank, and a trivalent chromium precipitation tank from the Hellenic Aerospace Industry S.A. was assessed using 16S rRNA libraries and a high-density DNA microarray (PhyloChip). 16S rRNA libraries revealed a bacterial diversity consisting of 14 distinct operational taxonomic units belonging to five bacterial phyla: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, and Bacteroidetes. However, employing a novel microarray-based approach (PhyloChip), a high bacterial diversity consisting of 30 different phyla was revealed, with representatives of 181 different families. This made it possible to identify a core set of genera present in all wastewater treatment stages examined, consisting of members of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria, and Bacteroidetes. In the chromium pretreatment tank, where the concentration of Cr(VI) is high (2.3 mg/l), we identified the presence of Pseudomonadales, Actinomycetales, and Enterobacteriales in abundance. In the chromium precipitation tank, where the concentration of Cr(III) is high, the dominant bacteria consortia were replaced by members of Rhodocyclales and Chloroflexi. The bacterial community structure changed significantly with changes in the chromium concentration. This in-depth analysis should prove useful for the design and development of improved bioremediation strategies. [ABSTRACT FROM AUTHOR]

Background & Aims: The intestinal microbiomes of healthy children and pediatric patients with irritable bowel syndrome (IBS) are not well defined. Studies in adults have indicated that the gastrointestinal microbiota could be involved in IBS. Methods: We analyzed 71 samples from 22 children with IBS (pediatric Rome III criteria) and 22 healthy children, ages 7–12 years, by 16S ribosomal RNA gene sequencing, with an average of 54,287 reads/stool sample (average 454 read length = 503 bases). Data were analyzed using phylogenetic-based clustering (Unifrac), or an operational taxonomic unit (OTU) approach using a supervised machine learning tool (randomForest). Most samples were also hybridized to a microarray that can detect 8741 bacterial taxa (16S rRNA PhyloChip). Results: Microbiomes associated with pediatric IBS were characterized by a significantly greater percentage of the class γ-proteobacteria (0.07% vs 0.89% of total bacteria, respectively; P < .05); 1 prominent component of this group was Haemophilus parainfluenzae. Differences highlighted by 454 sequencing were confirmed by high-resolution PhyloChip analysis. Using supervised learning techniques, we were able to classify different subtypes of IBS with a success rate of 98.5%, using limited sets of discriminant bacterial species. A novel Ruminococcus-like microbe was associated with IBS, indicating the potential utility of microbe discovery for gastrointestinal disorders. A greater frequency of pain correlated with an increased abundance of several bacterial taxa from the genus Alistipes. Conclusions: Using16S metagenomics by PhyloChip DNA hybridization and deep 454 pyrosequencing, we associated specific microbiome signatures with pediatric IBS. These findings indicate the important association between gastrointestinal microbes and IBS in children; these approaches might be used in diagnosis of functional bowel disorders in pediatric patients. [ABSTRACT FROM AUTHOR]

Information concerning the bacterial and archaeal communities present on calcite speleothems in carbonate caves is of interest because the activity of these microbes has been implicated as a potential biogenic component in the formation of secondary mineral deposits. In addition, these speleothems may harbor unique, previously unidentified microbes. The current study presents a comparative analysis of the superficial bacterial and archaeal community structure of multiple stalactites from two different cave formations located in close proximity to each other in a nonhuman-impacted area of Kartchner Caverns, Arizona, USA. PCR-denaturing gradient gel electrophoresis analysis (PCR-DGGE) revealed that microbial communities sampled from stalactites of a single speleothem are more similar to each other than to the communities sampled from stalactites of an adjacent speleothem, suggesting that both bacterial and archaeal communities are speleothem-specific. SR-XRD analysis confirmed that both speleothems sampled were primarily calcite, but subtle differences were detected in the elemental composition profiles obtained from ICP-MS analysis indicating that substrate geochemistry was also speleothem-specific. PhyloChip analysis of composite samples from both speleothems revealed a broad diversity of phyla represented in the bacterial communities, while bacterial and archaeal bands sequenced from the DGGE profiles confirmed the presence of unique phylotypes not closely related (< 96% similarity) to any sequences deposited in the GenBank database. [ABSTRACT FROM AUTHOR]

Irritable bowel syndrome (IBS) is a chronic, episodic gastrointestinal disorder that is prevalent in a significant fraction of western human populations; and changes in the microbiota of the large bowel have been implicated in the pathology of the disease. Using a novel comprehensive, high-density DNA microarray (PhyloChip) we performed a phylogenetic analysis of the microbial community of the large bowel in a rat model in which intracolonic acetic acid in neonates was used to induce long lasting colonic hypersensitivity and decreased stool water content and frequency, representing the equivalent of human constipation-predominant IBS. Our results revealed a significantly increased compositional difference in the microbial communities in rats with neonatal irritation as compared with controls. Even more striking was the dramatic change in the ratio of Firmicutes relative to Bacteroidetes, where neonatally irritated rats were enriched more with Bacteroidetes and also contained a different composition of species within this phylum. Our study also revealed differences at the level of bacterial families and species. The PhyloChip is a useful and convenient method to study enteric microflora. Further, this rat model system may be a useful experimental platform to study the causes and consequences of changes in microbial community composition associated with IBS. [ABSTRACT FROM AUTHOR]

Abstract: Sludge reduction is one of the major challenges in biological wastewater treatment. One approach is to increase the sludge degradation yield together with the biodegradation kinetics. Among the various sludge pretreatment strategies proposed, thermal pretreatment at around 65 °C was described as promising. The enhancement in the biodegradation activity due to the selection of thermophilic hydrolytic bacteria was proposed, but further experiments are needed to demonstrate the specific role of these bacteria. In this study, concentrated activated sludge grown at 20 °C was subjected to thermal treatment at 65 °C for different periods. The originality of the work relied on a polyphasic approach based on the correlation between kinetics (chemical oxygen demand, COD; mixed liquor suspended solids, MLSS), bacterial activity (respirometry) and bacterial community structure (phylochip monitoring) in order to characterize the mechanisms involved in the thermal reduction of sludge. The bacterial activity in the aeration basin decreased to a very low level when recycling sludge was treated at 65 °C from 13 to 60 h, but then, started to increase after 60 h. In parallel to these fluctuations in activity, a drastic shift occurred in the bacterial community structure with the selection of thermophilic bacteria (mainly related to genera Paenibacillus and Bacillus), which are known for their specific hydrolases. [ABSTRACT FROM AUTHOR]

Microbial fuel cells (MFCs) have applications other than electricity production, including the capacity to power desirable reactions in the cathode chamber. However, current knowledge of the microbial ecology and physiology of biocathodes is minimal, and as a result more research dedicated to understanding the microbial communities active in cathode biofilms is required. Here we characterize the microbiology of denitrifying bacterial communities stimulated by reducing equivalents generated from the anodic oxidation of acetate. We analyzed biofilms isolated from two types of cathodic denitrification systems: (1) a loop format where the effluent from the carbon oxidation step in the anode is subjected to a nitrifying reactor which is fed to the cathode chamber and (2) an alternative non-loop format where anodic and cathodic feed streams are separated. The results of our study indicate the superior performance of the loop reactor in terms of enhanced current production and nitrate removal rates. We hypothesized that phylogenetic or structural features of the microbial communities could explain the increased performance of the loop reactor. We used PhyloChip with 16S rRNA (cDNA) and fluorescent in situ hybridization to characterize the active bacterial communities. Our study results reveal a greater richness, as well as an increased phylogenetic diversity, active in denitrifying biofilms than was previously identified in cathodic systems. Specifically, we identified Proteobacteria, Firmicutes and Chloroflexi members that were dominant in denitrifying cathodes. In addition, our study results indicate that it is the structural component, in terms of bacterial richness and evenness, rather than the phylogenetic affiliation of dominant bacteria, that best corresponds to cathode performance. [ABSTRACT FROM AUTHOR]

Abstract: The arrival of chemicals in a soil or groundwater ecosystem could upset the natural balance of the microbial community. Since soil microorganisms are the first to be exposed to the chemicals released into the soil environment, we evaluated the use of a phylogenetic microarray as a bio-indicator of community perturbations due to the exposure to trichloroethylene (TCE). The phylogenetic microarray, which measures the presence of different members of the soil community, was used to evaluate unpolluted soils exposed to TCE as well as to samples from historically TCE polluted sites. We were able to determine an apparent threshold at which the microbial community structure was significantly affected (about 1ppm). In addition, the members of the microbial community most affected were identified. This approach could be useful for assessing environmental impact of chemicals on the biosphere as well as important members of the microbial community involved in TCE degradation. [Copyright &y& Elsevier]

Abstract: We designed an oligonucleotide microarray using probe sequences based upon a phylogenetic analysis of 16S rRNA genes recovered from members of the bacterial division Acidobacteria. A total of 42,194 oligonucleotide probes targeting members of the Acidobacteria division at multiple phylogenetic levels were included on a high-density microarray. Positive control hybridizations revealed a linear relationship between hybridization signal and template concentration, and a substantial decrease in non-specific hybridization was achieved through the addition of 2.5 M betaine to the hybridization buffer. A mean hybridization signal value was calculated for each Acidobacteria lineage, with the resultant lineage-specific hybridization data revealing strong predictive value for the positive control hybridizations. The Acidobacteria phylochip was then used to evaluate Acidobacteria rRNA genes from a Wisconsin soil and within a soil clay fraction. The Acidobacteria hybridization profile revealed the predominance of Acidobacteria subdivisions four and six, and also suggested a decrease in the abundance of subdivision six relative to subdivision four in the soil clay fraction. The change in relative abundance of these subdivisions in a soil clay fraction was supported by data from quantitative PCR. These results support the utility of a phylogenetic microarray in revealing changes in microbial population-level distributions in a complex soil microbial assemblage. [Copyright &y& Elsevier]

Extensive physiological analyses of different microbial community members in many samples are difficult because of the restricted number of target populations that can be investigated in reasonable time by standard substrate-mediated isotope-labeling techniques. The diversity and ecophysiology of Rhodocyclales in activated sludge from a full-scale wastewater treatment plant were analyzed following a holistic strategy based on the isotope array approach, which allows for a parallel functional probing of different phylogenetic groups. Initial diagnostic microarray, comparative 16S rRNA gene sequence, and quantitative fluorescence in situ hybridization surveys indicated the presence of a diverse community, consisting of an estimated number of 27 operational taxonomic units that grouped in at least seven main Rhodocyclales lineages. Substrate utilization profiles of probe-defined populations were determined by radioactive isotope array analysis and microautoradiography-fluorescence in situ hybridization of activated sludge samples that were briefly exposed to different substrates under oxic and anoxic, nitrate-reducing conditions. Most detected Rhodocyclales groups were actively involved in nitrogen transformation, but varied in their consumption of propionate, butyrate, or toluene, and thus in their ability to use different carbon sources in activated sludge. This indicates that the functional redundancy of nitrate reduction and the functional versatility of substrate usage are important factors governing niche overlap and differentiation of diverse Rhodocyclales members in this activated sludge. [ABSTRACT FROM AUTHOR]

Increasing evidence confirms the crucial role bacteria and archaea play within the coral holobiont, that is, the coral host and its associated microbial community. The bacterial component constitutes a community of high diversity, which appears to change in structure in response to disease events. In this study, we highlight the limitation of 16S rRNA gene (16S rDNA) clone library sequencing as the sole method to comprehensively describe coral-associated communities. This limitation was addressed by combining a high-density 16S rRNA gene microarray with, clone library sequencing as a novel approach to study bacterial communities in healthy versus diseased corals. We determined an increase in diversity as well as a significant shift in community structure in Montastraea faveolata colonies displaying phenotypic signs of White Plague Disease type II (WPD-II). An accumulation of species that belong to families that include known coral pathogens (Alteromonadaceae, Vibrionaceae), bacteria previously isolated from diseased, stressed or injured marine invertebrates (for example, Rhodobacteraceae), and other species (for example, Campylobacteraceae) was observed. Some of these species were also present in healthy tissue samples, but the putative primary pathogen, Aurantimonas corallicida, was not detected in any sample by either method. Although an ecological succession of bacteria during disease progression after causation by a primary agent represents a possible explanation for our observations, we also discuss the possibility that a disease of yet to be determined etiology may have affected M. faveolata colonies and resulted in (or be a result of) an increase in opportunistic pathogens.The ISME Journal (2009) 3, 512–521; doi:10.1038/ismej.2008.131; published online 8 January 2009 [ABSTRACT FROM AUTHOR]

Roots moving through soil induce physical and chemical changes that differentiate rhizosphere from bulk soil, and the effects of these changes on soil microorganisms have long been a topic of interest. The use of a high-density 16S rRNA microarray (PhyloChip) for bacterial and archaeal community analysis has allowed definition of the populations that respond to the root within the complex grassland soil community; this research accompanies compositional changes reported earlier, including increases in chitinase- and protease-specific activity, cell numbers and quorum sensing signal. PhyloChip results showed a significant change compared with bulk soil in relative abundance for 7% of the total rhizosphere microbial community (147 of 1917 taxa); the 7% response value was confirmed by16S rRNA terminal restriction fragment length polymorphism analysis. This PhyloChip-defined dynamic subset was comprised of taxa in 17 of the 44 phyla detected in all soil samples. Expected rhizosphere-competent phyla, such as Proteobacteria and Firmicutes, were well represented, as were less-well-documented rhizosphere colonizers including Actinobacteria, Verrucomicrobia and Nitrospira. Richness of Bacteroidetes and Actinobacteria decreased in soil near the root tip compared with bulk soil, but then increased in older root zones. Quantitative PCR revealed rhizosphere abundance of β-Proteobacteria and Actinobacteria at about 108 copies of 16S rRNA genes per g soil, with Nitrospira having about 105 copies per g soil. This report demonstrates that changes in a relatively small subset of the soil microbial community are sufficient to produce substantial changes in functions observed earlier in progressively more mature rhizosphere zones.The ISME Journal (2009) 3, 168–178; doi:10.1038/ismej.2008.103; published online 13 November 2008 [ABSTRACT FROM AUTHOR]

Abstract: A combination of culture-dependent and independent approaches was employed to identify the microbial community structure in a Greek solar saltern. A total of 219 and 132 isolates belonging, respectively, to Bacteria and Archaea, were recovered. All bacterial isolates were phylogenetically related to 43 members of Actinobacteria, Firmicutes and γ-Proteobacteria. The archaeal isolates were placed within the Halobacteriaceae. At least four groups of isolates represented novel species among the Bacteria. High bacterial diversity, consisting of 417 subfamilies, was revealed using a high-density oligonucleotide microarray (PhyloChip). At the four stages of saltern operation analyzed, the archaeal community consisted of both Crenarchaeota and Euryarchaeota, except for the sediment where Crenarchaeota were not detected. The bacterial community in sediment consisted mainly of γ-Proteobacteria and Actinobacteria, while, in hypersaline water, it was restricted to a few representatives of Bacteria. Members of α-Proteobacteria were the main constituents in saturated brine and crude salt, followed by γ-Proteobacteria, Actinobacteria and Firmicutes. A large Bacteroidetes and Verrucomicrobia diversity was identified in saturated brine, while δ-Proteobacteria and Cloroflexi were abundant in crude salt. Significant changes in the microbial community structure were detected during a short time period, denoting a rapidly adaptive dynamic ecosystem and viable diversity. Prokaryotic members reported for the first time in solar salterns were identified. [Copyright &y& Elsevier]

In the past decade, molecular probe-based methods have proved successful in improving both the efficiency and accuracy of the identification of microorganisms, especially those that are devoid of distinct morphological features. However until recently, these methods had the major drawback of being limited to the identification of only one or just a few species at a time. With the use of DNA microarrays, it is possible to identify large numbers of taxa on a single-glass slide, the so-called phylochip. There are numerous microarray protocols in the literature. These protocols share the same principles, but vary in details, e.g. labelling approach or detergent concentration in the washing buffer. In this study, we show that even small variations in hybridization protocols can have a strong impact on the outcome of the microarray hybridization. An optimized protocol for species identification on phylochips is presented. The optimized protocol is the result of a joined effort of three laboratories to develop phylochips for microbial species identification. [ABSTRACT FROM AUTHOR]

Contents Summary 719 I. Introduction 720 II. General methodology 721 III. Methodological considerations 722 IV. Application of microarrays in the soil environment 726 V. Conclusions 731 Acknowledgements 732 References 732 Soil microbial communities are responsible for important physiological and metabolic processes. In the last decade soil microorganisms have been frequently analysed by cultivation-independent techniques because only a minority of the natural microbial communities are accessible by cultivation. Cultivation-independent community analyses have revolutionized our understanding of soil microbial diversity and population dynamics. Nevertheless, many methods are still laborious and time-consuming, and high-throughput methods have to be applied in order to understand population shifts at a finer level and to be better able to link microbial diversity with ecosystems functioning. Microbial diagnostic microarrays (MDMs) represent a powerful tool for the parallel, high-throughput identification of many microorganisms. Three categories of MDMs have been defined based on the nature of the probe and target molecules used: phylogenetic oligonucleotide microarrays with short oligonucleotides against a phylogenetic marker gene; functional gene arrays containing probes targeting genes encoding specific functions; and community genome arrays employing whole genomes as probes. In this review, important methodological developments relevant to the application of the different types of diagnostic microarrays in soil ecology will be addressed and new approaches, needs and future directions will be identified, which might lead to a better insight into the functional activities of soil microbial communities. [ABSTRACT FROM AUTHOR]

Pharmaceutical active compounds (PhACs) are molecules used for the treatment of physiological disorders that can generate environmental imbalances when discharged into wastewater. In this work, the use of Penicillium oxalicum XD-3.1 as bioremediation tool for the elimination of PhACs in non-sterile real hospital wastewater in batch bench scale bioreactor and its impact on microbial community was evaluated. A quantitative analysis using UHPLC-QToF was performed under three different conditions to determine the elimination of the different (PhACs) by this ascomycetes fungus. On the other hand, the changes on microbial community over time were analysed using Illumina MiSeq sequencing platform and a phylogenetic microarray (PhyloChip). P. oxalicum XD-3.1 was able to reduce the concentration of the majority of the analysed PhACs in 24 h such as ketoprofen, naproxen and paracetamol. Moreover, P. oxalicum inhibited the native fungal populations present in the wastewater, including opportunistic human pathogens such as Mycosphaerella and Drechslera, as well as some bacterial human pathogens belonging to Clostridiaceae and Brucellaceae families. However, important degraders such as Pseudomonadaceae bacteria groups remained in the system, indicating a possible natural consortium formation between fungi and bacteria. These results indicate the possibility to use this system for the removal of PhACs in real applications. Image 1 • P. oxalicum XD-3.1 was used as bioaugmented treatment in a fluidised batch bioreactor. • The fungus removed diclofenac, paracetamol and ketoprofen in 24 h. • Fungal populations related with human diseases decreased after bioaugmentation. • Bacterial biodiversity decreased during the treatment. • PhyloChip showed an accurate technology to detect rare populations. [ABSTRACT FROM AUTHOR]

• The European Project μAqua (FP7-KBBE-2010-4, 265409) was conceived as a project to make novel tools for the early and sensitive detection of freshwater-borne pathogens and cyanobacterial toxins. • The novel tools developed in μAqua were a phylochip (microarray), which identifies the presence of freshwater pathogenic targets using RNA barcodes and a RT-PCR microarray to amplify the mRNA captured by the barcodes for genes involved in cyanobacterial toxin synthesis. • We present results for three sites in along the Mediterranean coast of south-east France ranging from fresh to brackish to full strength seawater to test the applicability of the probes across the marine/freshwater boundary and infer the distribution of these pathogens across these boundaries. • The results for the cyanobacteria and Protozoa are reported here. • As freshwaters flow into marine systems, these pathogens and their toxins flow into a different environmental habitat. • Nevertheless these pathogens and toxins can still cause health problems in the marine environment and this paper shows the application of a phylochip across these different habitats. Monitoring drinking water quality is an important public health issue and pathogenic organisms present a particularly serious health hazard in freshwater bodies. However, many pathogenic bacteria, including cyanobacteria, and pathogenic protozoa can be swept into coastal lagoons and into near-shore marine environments where they continue to grow and pose a health threat to marine mammals and invertebrates. In this study, we tested the suitability of a phylochip (microarray for species detection) developed for freshwater pathogenic organisms to be applied to samples taken across a marine/freshwater interface at monthly intervals for two years. Toxic cyanobacteria and pathogenic protozoa were more numerous in a coastal lagoon than at the freshwater or marine site, indicating that this microarray can be used to detect the presence of these pathogens across a marine/freshwater interface and thus the potential for toxicity to occur within the entire watershed. [ABSTRACT FROM AUTHOR]