Microbial Community Fingerprints Research Articles

Namib Desert edaphic bacterial, fungal and archaeal communities assemble through deterministic processes but are influenced by different abiotic parameters.

The central Namib Desert is hyperarid, where limited plant growth ensures that biogeochemical processes are largely driven by microbial populations. Recent research has shown that niche partitioning is critically involved in the assembly of Namib Desert edaphic communities. However, these studies have mainly focussed on the Domain Bacteria. Using microbial community fingerprinting, we compared the assembly of the bacterial, fungal and archaeal populations of microbial communities across nine soil niches from four Namib Desert soil habitats (riverbed, dune, gravel plain and salt pan). Permutational multivariate analysis of variance indicated that the nine soil niches presented significantly different physicochemistries (R 2 = 0.8306, P ≤ 0.0001) and that bacterial, fungal and archaeal populations were soil niche specific (R 2 ≥ 0.64, P ≤ 0.001). However, the abiotic drivers of community structure were Domain-specific (P < 0.05), with P, clay and sand fraction, and NH4 influencing bacterial, fungal and archaeal communities, respectively. Soil physicochemistry and soil niche explained over 50% of the variation in community structure, and communities displayed strong non-random patterns of co-occurrence. Taken together, these results demonstrate that in central Namib Desert soil microbial communities, assembly is principally driven by deterministic processes.

Investigation of the microbial communities colonizing prepainted steel used for roofing and walling.

Microbial colonization of prepainted steel, commonly used in roofing applications, impacts their aesthetics, durability, and functionality. Understanding the relevant organisms and the mechanisms by which colonization occurs would provide valuable information that can be subsequently used to design fouling prevention strategies. Here, next‐generation sequencing and microbial community finger printing (T‐RFLP) were used to study the community composition of microbes colonizing prepainted steel roofing materials at Burrawang, Australia and Kapar, Malaysia over a 52‐week period. Community diversity was low and was dominated by Bacillus spp., cyanobacteria, actinobacteria, Cladosporium sp., Epicoccum nigrum, and Teratosphaeriaceae sp. Cultivation‐based methods isolated approximately 20 different fungi and bacteria, some of which, such as E. nigrum and Cladosporium sp., were represented in the community sequence data. Fluorescence in situ hybridization imaging showed that fungi were the most dominant organisms present. Analysis of the sequence and T‐RFLP data indicated that the microbial communities differed significantly between locations and changed significantly over time. The study demonstrates the utility of molecular ecology tools to identify and characterize microbial communities associated with the fouling of painted steel surfaces and ultimately can enable the targeted development of control strategies based on the dominant species responsible for fouling.

Summer microbial community composition governed by upper-ocean stratification and nutrient availability in northern Marguerite Bay, Antarctica

The Western Antarctic Peninsula warmed significantly during the second half of the twentieth century, with a concurrent retreat of the majority of its glaciers, and marked changes in the sea-ice field. These changes may affect summertime upper-ocean stratification, and thereby the seasonal dynamics of phytoplankton and bacteria. In the present study, we examined coastal Antarctic microbial community dynamics by pigment analysis and applying molecular tools, and analysed various environmental parameters to identify the most important environmental drivers. Sampling focussed on the austral summer of 2009–2010 at the Rothera oceanographic and biological Time Series (RaTS) site in northern Marguerite bay, Antarctica.The Antarctic summer was characterized by a salinity decrease (measured at 15m depth) coinciding with increased meteoric water fraction. Maximum Chl-a values of 35µgl-1 were observed during midsummer and mainly comprised of diatoms. Microbial community fingerprinting revealed four distinct periods in phytoplankton succession during the summer while bacteria showed a delayed response to the phytoplankton community. Non-metric multidimensional scaling analyses showed that phytoplankton community dynamics were mainly directed by temperature, mixed layer depth and wind speed. Both high and low N/P ratios might have influenced phytoplankton biomass accumulation. The bacterioplankton community composition was mainly governed by Chl-a, suggesting a link to phytoplankton community changes. High-throughput 16S and 18S rRNA amplicon sequencing revealed stable eukaryotic and bacterial communities with regards to observed species, yet varying temporal relative contributions. Eukaryotic sequences were dominated by pennate diatoms in December followed by polar centric diatoms in January and February. Our results imply that the reduction of mixed layer depth during summer, caused by meltwater-related surface stratification, promotes a succession in diatoms rather than in nanophytoflagellates in northern Marguerite Bay, which may favour higher trophic levels.

Source tracking using microbial community fingerprints: Method comparison with hydrodynamic modelling

Urban estuaries around the world are experiencing contamination from diffuse and point sources, which increases risks to public health. To mitigate and manage risks posed by elevated levels of contamination in urban waterways, it is critical to identify the primary water sources of contamination within catchments. Source tracking using microbial community fingerprints is one tool that can be used to identify sources. However, results derived from this approach have not yet been evaluated using independent datasets. As such, the key objectives of this investigation were: (1) to identify the major sources of water responsible for bacterial loadings within an urban estuary using microbial source tracking (MST) using microbial communities; and (2) to evaluate this method using a 3-dimensional hydrodynamic model. The Yarra River estuary, which flows through the city of Melbourne in South-East Australia was the focus of this study. We found that the water sources contributing to the bacterial community in the Yarra River estuary varied temporally depending on the estuary's hydrodynamic conditions. The water source apportionment determined using microbial community MST correlated to those determined using a 3-dimensional hydrodynamic model of the transport and mixing of a tracer in the estuary. While there were some discrepancies between the two methods, this investigation demonstrated that MST using bacterial community fingerprints can identify the primary water sources of microorganisms in an estuarine environment. As such, with further optimization and improvements, microbial community MST has the potential to become a powerful tool that could be practically applied in the mitigation of contaminated aquatic systems.

Reflection on Molecular Approaches Influencing State-of-the-Art Bioremediation Design: Culturing to Microbial Community Fingerprinting to Omics.

Bioremediation is generally viewed as a cost effective and sustainable technology because it relies on microbes to transform pollutants into benign compounds. Advances in molecular biological analyses allow unprecedented microbial detection and are increasingly incorporated into bioremediation. Throughout history, state-of-the-art techniques have informed bioremediation strategies. However, the insights those techniques provided were not as in depth as those provided by recently developed omics tools. Advances in next generation sequencing (NGS) have now placed metagenomics and metatranscriptomics within reach of environmental engineers. As NGS costs decrease, metagenomics and metatranscriptomics have become increasingly feasible options to rapidly scan sites for specific degradative functions and identify microorganisms important in pollutant degradation. These omic techniques are capable of revolutionizing biological treatment in environmental engineering by allowing highly sensitive characterization of previously uncultured microorganisms. Omics enables the discovery of novel microorganisms for use in bioaugmentation and supports systematic optimization of biostimulation strategies. This review describes the omics journey from roots in biology and medicine to its current status in environmental engineering including potential future directions in commercial application.

Geomicrobiological Features of Ferruginous Sediments from Lake Towuti, Indonesia.

Lake Towuti is a tectonic basin, surrounded by ultramafic rocks. Lateritic soils form through weathering and deliver abundant iron (oxy)hydroxides but very little sulfate to the lake and its sediment. To characterize the sediment biogeochemistry, we collected cores at three sites with increasing water depth and decreasing bottom water oxygen concentrations. Microbial cell densities were highest at the shallow site—a feature we attribute to the availability of labile organic matter (OM) and the higher abundance of electron acceptors due to oxic bottom water conditions. At the two other sites, OM degradation and reduction processes below the oxycline led to partial electron acceptor depletion. Genetic information preserved in the sediment as extracellular DNA (eDNA) provided information on aerobic and anaerobic heterotrophs related to Nitrospirae, Chloroflexi, and Thermoplasmatales. These taxa apparently played a significant role in the degradation of sinking OM. However, eDNA concentrations rapidly decreased with core depth. Despite very low sulfate concentrations, sulfate-reducing bacteria were present and viable in sediments at all three sites, as confirmed by measurement of potential sulfate reduction rates. Microbial community fingerprinting supported the presence of taxa related to Deltaproteobacteria and Firmicutes with demonstrated capacity for iron and sulfate reduction. Concomitantly, sequences of Ruminococcaceae, Clostridiales, and Methanomicrobiales indicated potential for fermentative hydrogen and methane production. Such first insights into ferruginous sediments showed that microbial populations perform successive metabolisms related to sulfur, iron, and methane. In theory, iron reduction could reoxidize reduced sulfur compounds and desorb OM from iron minerals to allow remineralization to methane. Overall, we found that biogeochemical processes in the sediments can be linked to redox differences in the bottom waters of the three sites, like oxidant concentrations and the supply of labile OM. At the scale of the lacustrine record, our geomicrobiological study should provide a means to link the extant subsurface biosphere to past environments.

Effect of protein supplementation on ruminal parameters and microbial community fingerprint of Nellore steers fed tropical forages

In tropical regions, protein supplementation is a common practice in dairy and beef farming. However, the effect of highly degradable protein in ruminal fermentation and microbial community composition has not yet been investigated in a systematic manner. In this work, we aimed to investigate the impact of casein supplementation on volatile fatty acids (VFA) production, specific activity of deamination (SAD), ammonia concentration and bacterial and archaeal community composition. The experimental design was a 4×4 Latin square balanced for residual effects, with four animals (average initial weight of 280±10 kg) and four experimental periods, each with duration of 29 days. The diet comprised Tifton 85 (Cynodon sp.) hay with an average CP content of 9.8%, on a dry matter basis. Animals received basal forage (control) or infusions of pure casein (230 g) administered direct into the rumen, abomasum or divided (50 : 50 ratio) in the rumen/abomasum. There was no differences (P>0.05) in ruminal pH and microbial protein concentration between supplemented v. non-supplemented animals. However, in steers receiving ruminal infusion of casein the SAD and ruminal ammonia concentration increased 33% and 76%, respectively, compared with the control. The total concentration of VFA increased (P<0.05) in steers receiving rumen infusion of casein. SAD and the microbial protein concentration did not vary significantly among treatments during the feeding cycle, but mean SAD values were greater in steers supplemented in the rumen and rumen/abomasum. Ruminal ammonia concentration was positively correlated with SAD in animals receiving ruminal infusion of casein. Polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE) analysis revealed low similarity between treatments, animals and time of sample collection. Richness analysis and determination of the Shannon–Wiener index indicated no differences (P>0.05) in species richness and diversity of γ-proteobacteria, firmicutes and archaea between non-supplemented Nellore steers and steers receiving casein supplementation in the rumen. However, species richness and the Shannon–Wiener index were lower (P<0.05) for the phylum bacteroidetes in steers supplemented with casein in the rumen compared with non-supplemented animals. Venn diagrams indicated that the number of unique bands varied considerably among individual animals and was usually higher in number for non-supplemented steers compared with supplemented animals. These results add new knowledge about the effects of ruminal and postruminal protein supplementation on metabolic activities of rumen microbes and the composition of bacterial and archaeal communities in the rumen of steers.

Springtime dynamics, productivity and activity of prokaryotes in two Arctic fjords

In the Kongsfjorden–Krossfjorden system (Spitsbergen), increasing temperatures enhance glacier melting and concomitant intrusion of freshwater. These altered conditions affect the timing, intensity, and composition of the phytoplankton spring bloom in Kongsfjorden; yet, the effects on prokaryotes (bacteria and archaea) are not well understood. The aim of this study was to examine springtime prokaryote communities in both fjords as a function of hydrographic and phytoplankton variability. Prokaryote community composition was studied in two consecutive years by molecular fingerprinting of the 16S rRNA gene. In addition, we measured bacterial abundance, productivity (3H-Leucine uptake), and single-cell activity using catalyzed reporter deposition fluorescence in situ hybridization combined with microautoradiography. Differences in bacterial and archaeal communities were found between Kongsfjorden and Krossfjorden. Furthermore, an increase in productivity, abundance, and proportion of active bacterial cells was observed during the course of spring. Bacteroidetes were the most abundant bacterial group among the assessed taxa in both Kongsfjorden and Krossfjorden. Multivariate analysis of the microbial community fingerprints revealed a strong temporal shaping of both the bacterial and archaeal communities in addition to a spatial separation between the two fjords. A significant part of the observed bacterial variation could be explained by cyanobacterial biomass, as deduced from pigment analysis, and by phosphate concentration. Archaea were mainly controlled by abiotic factors. We speculate that the bacterial response to hydrographic changes and glacier meltwater is mediated through shifts in phytoplankton abundance and composition, whereas archaea are directly influenced by abiotic environmental variables.

Effects of silver nanoparticles on soil microorganisms and maize biomass are linked in the rhizosphere

Silver nanoparticles hold great promise as effective anti-microbial compounds in a myriad of applications but may also pose a threat to non-target bacteria and fungi in the environment. Because microorganisms are involved in extensive interactions with many other organisms, these partner species are also prone to indirect negative effects from silver nanoparticles.Here, we focus on the effects of nanosilver exposure in the rhizosphere. Specifically, we evaluate the effect of 100 mg kg−1 silver nanoparticles on maize plants, as well as on the bacteria and fungi in the plant's rhizosphere and the surrounding bulk soil. Maize biomass measurements, microbial community fingerprints, an indicator of microbial enzymatic activity, and carbon use diversity profiles are used. Hereby, it is shown that 100 mg kg−1 silver nanoparticles in soil increases maize biomass, and that this effect coincides with significant alterations of the bacterial communities in the rhizosphere. The bacterial community in nanosilver exposed rhizosphere shows less enzymatic activity and significantly altered carbon use and community composition profiles. Fungal communities are less affected by silver nanoparticles, as their composition is only slightly modified by nanosilver exposure. In addition, the microbial changes noted in the rhizosphere were significantly different from those noted in the bulk soil, indicated by different nanosilver-induced alterations of carbon use and community composition profiles in bulk and rhizosphere soil.Overall, microorganisms in the rhizosphere seem to play an important role when evaluating the fate and effects of silver nanoparticle exposure in soil, and not only is the nanosilver response different for bacteria and fungi, but also for bulk and rhizosphere soil. Consequently, assessment of microbial populations should be considered an essential parameter when investigating the impacts of nanoparticle exposure.

Soil microbial communities vary as much over time as with chronic warming and nitrogen additions

We examined the effects of simultaneous warming and N additions on soil microbial biomass and community composition and assessed how the microbial community varied over seasonal and interannual timescales. The research took place at the Soil Warming and Nitrogen Addition (SWaN) Study at the Harvard Forest Long Term Ecological Research site. Nitrogen additions suppressed total biomass while warming increased biomass and shifted microbial community fingerprint. However, these responses were inconsistent over time, and seasonal and interannual differences in the microbial community were equal to or greater than treatment effects. For example, microbial biomass in ambient soils was 400% higher in 2008 than in 2010. This was comparable to the 524% difference in biomass between ambient and N addition plots in October, 2008. Our findings suggest that microbial communities can resist increased temperatures and N inputs for years to decades and that long term experiments are necessary to detect significant shifts in biomass and community composition.

Classification methods for the analysis of LH-PCR data associated with inflammatory bowel disease patients.

The human gut is one of the most densely populated microbial communities in the world. The interaction of microbes with human host cells is responsible for several disease conditions and of criticality to human health. It is imperative to understand the relationships between these microbial communities within the human gut and their roles in disease. In this study we analyse the microbial communities within the human gut and their role in Inflammatory Bowel Disease (IBD). The bacterial communities were interrogated using Length Heterogeneity PCR (LH-PCR) fingerprinting of mucosal and luminal associated microbial communities for a class of healthy and diseases patients.

Cytometric fingerprints: evaluation of new tools for analyzing microbial community dynamics.

Optical characteristics of individual bacterial cells of natural communities can be measured with flow cytometry (FCM) in high throughput. The resulting data are visualized in cytometric histograms. These histograms represent individual cytometric fingerprints of microbial communities, e.g., at certain time points or microenvironmental conditions. Up to now four tools for analyzing the variation in these cytometric fingerprints are available but have not yet been systematically compared regarding application: Dalmatian Plot, Cytometric Histogram Image Comparison (CHIC), Cytometric Barcoding (CyBar), and FlowFP. In this article these tools were evaluated concerning (i) the required experience of the operator in handling cytometric data sets, (ii) the detection level of changes, (iii) time demand for analysis, and (iv) software requirements. As an illustrative example, FCM was used to characterize the microbial community structure of electroactive microbial biofilms. Their cytometric fingerprints were determined, analyzed with all four tools, and correlated to experimental and functional parameters. The source of inoculum (four different types of wastewater samples) showed the strongest influence on the microbial community structure and biofilm performance while the choice of substrate (acetate or lactate) had no significant effect in the present study. All four evaluation tools were found suitable to monitor structural changes of natural microbial communities. The Dalmatian Plot was shown to be most sensitive to operator impact but nevertheless provided an overview on community shifts. CHIC, CyBar, and FlowFP showed less operator dependence and gave highly resolved information on community structure variation on different detection levels. In conclusion, experimental and productivity parameters correlated with the biofilm structures and practical process integration details were available from cytometric fingerprint analysis.

Only Simpson diversity can be estimated accurately from microbial community fingerprints.

Lalande et al. (Microb. Ecol. 66(3):647-658, 2013) introduced a promising approach to quantify microbial diversity from fingerprinting profiles. Their analysis is based on extrapolating the abundance of the phylotypes detectable in a fingerprint towards the rare phylotypes of the community. By considering a set of reconstructed communities, Lalande et al. obtained a range of estimates for phylotype richness, Shannon diversity and Simpson diversity. They reported narrow ranges indicating accurate estimation, especially for Shannon and Simpson diversities. Here, we show that a much larger set of reconstructed communities than the one considered by Lalande et al. is consistent with the fingerprint. We find that the estimates for phylotype richness and Shannon diversity vary over orders of magnitude, but that the estimates for Simpson diversity are restricted to a narrow range (around 10 %). We conclude that only Simpson diversity can be estimated accurately from fingerprints.

External resistance as a potential tool for influencing azo dye reductive decolourisation kinetics in microbial fuel cells

Azo moieties of polar and highly charged azo dyes are thought to undergo reductive degradation into constituent amines in the extracellular milieu of bacterial cells due to their inability to penetrate into cellular interior. In this study, experiments were conducted in microbial fuel cells (MFCs) to investigate the influence of applied external resistance (Rext) on the reductive decolourisation kinetics of three structurally different commercial azo dyes. The results indicate that at very high current densities (low Rext) and very low current densities (high Rext), the reductive decolourisation kinetic constants were lower for all three tested azo dyes in comparison to a moderate optimum Rext (2.2 kΩ), close to the internal resistance of the MFC systems. PCR-DGGE of the 16s rRNA gene microbial community fingerprints were distinctly different between experiments that utilised different Rexts. Molecular phylogenetic microbial profiling indicated that the microbial communities selected at different Rexts were distinctly different. The enhanced decolourisation kinetic constants and good effluent quality in terms of chemical oxygen demand (COD) reduction obtained using a moderate Rext indicates that Rext can be used as a potential tool for influencing azo dye reductive degradation in MFCs.

Interactions between accumulated copper, bacterial community structure and histamine levels in crayfish meat during storage

Pollution in aquaculture areas may negatively impact edible species and threaten seafood quality and safety. The aim of this study was to determine the interaction between copper and bacteria in the aquatic habitat and their impact upon crustaceans. Marbled crayfish was chosen as a model of aquatic crustaceans and the influence of metal contamination on bacterial community structure in water used to culture crayfish and in crayfish themselves was investigated. Histamine, an allergen commonly formed by certain groups of bacteria in crustacean edible tissue during storage, was also determined. Copper exposure increased its concentration in crayfish meat by 17.4%, but the copper concentration remained within acceptable food safety limits. Elevated copper levels affected the bacterial community both in the water used to cultivate crayfish and in the marbled crayfish themselves. Cluster analysis of 16S rRNA-gene based microbial community fingerprints revealed that copper impacted the bacterial community in the water and in the crayfish meat. However, copper exposure reduced the formation of histamine in crayfish meat during storage by 66.3%. Copper from the habitat appears to reduce histamine accumulation in crayfish meat during storage by affecting the bacterial community structure of the cultivation water and most likely also in the intestine of the crayfish. From a food safety point of view, copper treatment during the aqua culturing of crustaceans has a positive impact on the postharvest stage.

Fecal microbiomes of non‐human primates in Western Uganda reveal species‐specific communities largely resistant to habitat perturbation

Primate gastrointestinal microbial communities are becoming increasingly appreciated for their relevance to comparative medicine and conservation, but the factors that structure primate "microbiomes" remain controversial. This study examined a community of primates in Kibale National Park, Uganda, to assess the relative importance of host species and location in structuring gastrointestinal microbiomes. Fecal samples were collected from primates in intact forest and from primates in highly disturbed forest fragments. People and livestock living nearby were also included, as was a geographically distant population of related red colobus in Kenya. A culture-free microbial community fingerprinting technique was used to analyze fecal microbiomes from 124 individual red colobus (Procolobus rufomitratus), 100 individual black-and-white colobus (Colobus guereza), 111 individual red-tailed guenons (Cercopithecus ascanius), 578 human volunteers, and 364 domestic animals, including cattle (Bos indicus and B. indicus × B. taurus crosses), goats (Caprus hircus), sheep (Ovis aries), and pigs (Sus scrofa). Microbiomes sorted strongly by host species, and forest fragmentation did not alter this pattern. Microbiomes of Kenyan red colobus sorted distinctly from microbiomes of Ugandan red colobus, but microbiomes from these two red colobus populations clustered more closely with each other than with any other species. Microbiomes from red colobus and black-and-white colobus were more differentiated than would be predicted by the phylogenetic relatedness of these two species, perhaps reflecting heretofore underappreciated differences in digestive physiology between the species. Within Kibale, social group membership influenced intra-specific variation among microbiomes. However, intra-specific variation was higher among primates in forest fragments than among primates in intact forest, perhaps reflecting the physical separation of fragments. These results suggest that, in this system, species-specific processes such as gastrointestinal physiology strongly structure microbial communities, and that primate microbiomes are relatively resistant to perturbation, even across large geographic distances or in the face of habitat disturbance.

Gut Microbiota Affects Sensitivity to Acute DSS-induced Colitis Independently of Host Genotype

Caspase-deficient mice and wild-type (WT) mice show significant differences in their gut microbiota composition. These differences coincide with the observation that caspase-3-deficient mice carrying a natural caspase-11 mutation (Casp3/11(-/-)) are less sensitive to acute dextran sodium sulfate-induced colitis than WT mice. For these reasons, we investigated the role of the microbiota in the development of colitis by cohousing WT and Casp3/11(-/-) mice. Microbial community fingerprinting by denaturing gradient gel electrophoresis analysis revealed that the similarities in gut microbial composition of WT and Casp3/11(-/-) mice increased after cohousing. In the acute dextran sodium sulfate-induced colitis model, Casp3/11(-/-) mice that were cohoused with WT mice showed increased weight loss and disease activity scores and increased neutrophil infiltration and inflammatory cytokine levels in their colon tissue compared with Casp3/11(-/-) mice that were not cohoused with WT mice. Also, we demonstrate that only the microbiota of the Casp3/11(-/-) mice cohoused with WT mice showed an important increase in Prevotella species. In conclusion, our cohousing experiments revealed that the colitogenic activity of the WT microbiota is transferable to Casp3/11(-/-) mice and that Prevotella species are likely to be involved. By contrast, the relative protection of Casp3/11(-/-) mice against dextran sodium sulfate damage is not transferred to WT mice after cohousing. These results underscore the need for in-depth studies of the bilateral interaction of host genes and microbiota to gain insight into the mechanisms of disease pathogenesis. Our findings also have important implications for the experimental design of disease studies in genetically modified mice and conclusions drawn from them.

Improved sensitivity of sedimentary phospholipid analysis resulting from a novel extract cleanup strategy

The detection of intact phospholipids (PLs) in sedimentary extracts using liquid chromatography–electrospray ionization-mass spectrometry (LC–ESI-MS) is commonly limited by ion suppression caused by complex matrices; the effect typically cannot be satisfactorily reduced using traditional column chromatographic cleanup procedures. We therefore implemented a cleanup strategy recently introduced for serum and plasma samples and adapted it for sedimentary lipid extracts. It involves selective retention of PLs on a zirconia-coated silica phase, available as a HybridSPE®-Phospholipid cartridge. Compared with conventional silica gel liquid chromatography, the HybridSPE-based protocol strongly enhances the detection of PLs using LC–ESI-MS as a result of more effective removal of complex environmental matrices, with negligible PL loss. The strength of the protocol was demonstrated by analysis of marine sediment samples from various depths and of different total organic carbon (TOC) content, for which we observed 1.2–2.7 times more intense signals from sedimentary PLs compared with the untreated reference. This new cleanup protocol significantly improves PL fingerprinting of microbial communities in sediments.

Physiological aspects of mangrove (Laguncularia racemosa) grown in microcosms with oil-degrading bacteria and oil contaminated sediment

To assess the severity of oil spills on mangroves, diagnosis of the vegetation health is crucial. Some aspects of photosynthesis such as photochemical efficiency and leaf pigment composition together with the level of oxidative stress may constitute reliable indicators for vegetation health. To test this approach 14 month old Laguncularia racemosa were contaminated with 5 L m−2 of the marine fuel oil MF-380 and treated with an oil degrading bacterial consortium in microcosms. Contamination resulted in a 20% decrease in shoot dry weight after 128 days. Photochemical efficiency, pigment content, catalase and ascorbate peroxidase remained unchanged. Multivariate ordination of DGGE microbial community fingerprints revealed a pronounced separation between the oil contaminated and the non-contaminated samples. Further studies are necessary before physiological parameters can be recommended as indicators for plant's health in oil polluted mangroves.

Capillary electrophoresis ribosomal RNA single-stranded conformation polymorphism: a new approach for characterization of low-diversity microbial communities

Capillary electrophoresis (CE) has been the principle system for nucleic acid analysis since the early 1990s due to its inherent advantages such as fast analysis time, high resolution and efficiency, minimal sample requirement, high detection sensitivity, and automation. In the past few decades, microbial community fingerprinting methods such as terminal restriction fragment length polymorphism and single-stranded conformation polymorphism (SSCP) have migrated to CE to utilize its advantages over conventional slab gel electrophoresis. Recently, a gel-based direct rRNA fingerprint method was demonstrated. Different from other existing microbial community characterization approaches, this novel approach is polymerase chain reaction free and capable of providing information on the relative abundance of rRNA from individual phylotypes in low-diversity samples. As a gel-based method, it has a long analysis time and relatively large reagent and sample requirements. Here, we addressed these limitations by transferring the RNA fingerprint approach to the CE platform. Analysis time significantly improved from 24 h to 60 min, and the use of a fluorescently labeled hybridization probe as the detection strategy decreased the sample requirement by ten-fold. The combination of fast analysis time, low sample requirement, and sensitive fluorescence detection makes CE-RNA-SSCP an appealing new approach for characterizing low-diversity microbial communities.