Effects of mercury contamination on the culturable heterotrophic, functional and genetic diversity of the bacterial community in soil

Tailored bacteria tackling with environmental mercury: Inspired by natural mercuric detoxification operons

Mercury (Hg) and its inorganic and organic compounds significantly threaten the ecosystem and human health. However, the natural and anthropogenic Hg environmental inputs exceed 5000 metric tons annually. Hg is usually discharged in elemental or ionic forms, accumulating in surface water and sediments where Hg-methylating microbes-mediated biotransformation occurs. Microbial genetic factors such as the mer operon play a significant role in the complex Hg biogeochemical cycle. Previous reviews summarize the fate of environmental Hg, its biogeochemistry, and the mechanism of bacterial Hg resistance. This review mainly focuses on the mer operon and its components in detecting, absorbing, bioaccumulating, and detoxifying environmental Hg. Four components of the mer operon, including the MerR regulator, divergent mer promoter, and detoxification factors MerA and MerB, are rare bio-parts for assembling synthetic bacteria, which tackle pollutant Hg. Bacteria are designed to integrate synthetic biology, protein engineering, and metabolic engineering. In summary, this review highlights that designed bacteria based on the mer operon can potentially sense and bioremediate pollutant Hg in a green and low-cost manner.

Application of QSAR Approach to Assess the Effects of Organic Pollutants on Bacterial Virulence Factors

The release of a wide variety of persistent chemical contaminants into wastewater has become a growing concern due to their potential health and environmental risks. While the toxic effects of these pollutants on aquatic organisms have been extensively studied, their impact on microbial pathogens and their virulence mechanisms remains largely unexplored. This research paper focuses on the identification and prioritization of chemical pollutants that increase bacterial pathogenicity, which is a public health concern. In order to predict how chemical compounds, such as pesticides and pharmaceuticals, would affect the virulence mechanisms of three bacterial strains (Escherichia coli K12, Pseudomonas aeruginosa H103, and Salmonella enterica serovar. Typhimurium), this study has developed quantitative structure-activity relationship (QSAR) models. The use of analysis of variance (ANOVA) functions assists in developing QSAR models based on the chemical structure of the compounds, to predict their effect on the growth and swarming behavior of the bacterial strains. The results showed an uncertainty in the created model, and that increases in virulence factors, including growth and motility of bacteria, after exposure to the studied compounds are possible to be predicted. These results could be more accurate if the interactions between groups of functions are included. For that, to make an accurate and universal model, it is essential to incorporate a larger number of compounds of similar and different structures.

Effects of heavy metal pollution and soil physicochemical properties on the Sphagnum farmland soil microbial community structure in Southern Guizhou, China

Farmland soil pollution is a serious problem worldwide threatening environment and human health. Microbial communities plays a key role in soil function. The purpose of this study was to analyze the relationship between microbial structure and soil physicochemical properties under different heavy metal pollution levels, find out heavy metal tolerant species under different environmental conditions, then provide useful reference for the bioremediation of contaminated farmland. In this study, 16s rRNA high-throughput sequencing technology was used, multiple comparisons and correlation analyses of the data were performed using R software. The results showed that study area A was contaminated by heavy metal Cd, and study area A, B and C were contaminated by heavy metal Hg. From the analysis of the community structure of the samples, it can be seen that the dominant bacterial phyla were Proteobacteria, Acidobacteriota, Chloroflexi, Actinobacteria, and 10 others. Correlation and RDA analysis of samples showed that the heavy metals Hg and As in peat were related to dominant bacteria phyla, and the physicochemical properties of soil potential of hydrogen (pH), total nitrogen (TN), available nitrogen (AN), available phosphorus (AP), available potassium (AK), and soil organic matter (SOM) were significantly positively correlated with the bacteria (Acidobacterta and Chloroflexi). Moreover, Chloroflexi was more tolerant to the heavy metals Hg and As. There was a significant correlation between bacterial community abundance and diversity in the four study areas. Soil heavy metal concentration and soil physicochemical properties affected the main phyla, bacterial community abundance and bacterial diversity of peat soil. These results indicate that some microorganisms have strong tolerance to heavy metal pollution and certain heavy metal digestion ability, which can create a good environment for farmland soil remediation.

Biogeographic Patterns and Community Assembly Processes of Bacterioplankton and Potential Pathogens in Subtropical Estuaries in China

Microbial communities in coastal waters are diverse and dynamic and play important roles in ecosystem functions and services. Despite the ecological impact of bacterioplankton or pathogens, little is known about whether bacterioplankton and pathogen communities exhibit similar patterns. Here, using 16S RNA gene amplicon sequencing, the geographic patterns and assembly processes of bacterioplankton and pathogen communities in 30 subtropical estuaries were studied. Results showed that the estuarine bacterioplankton communities mainly consisted of Proteobacteria (49.06%), Actinobacteria (17.62%), and Bacteroidetes (16.33%), among which 31 pathogen genera (186 amplicon sequence variants [ASVs]) were identified. Under the influence of salinity, bacterioplankton and pathogens showed similar biogeographic patterns. Redundancy and correlation analyses indicated that the bacterioplankton communities were strongly correlated with estuarine environmental factors, but potential pathogens were less influenced. Co-occurrence network analysis revealed a close relationship between bacterioplankton and potential pathogens, with two pathogens identified as connectors (i.e., ASV340 [Clostridium perfringens] and ASV1624 [Brevundimonas diminuta]), implying potential impacts of pathogens on structure, function, and stability of estuarine bacterioplankton communities. Null-model analysis revealed that deterministic processes (heterogeneous selection) dominated bacterioplankton community assembly, while stochastic processes (undominated effect) shaped the potential pathogen community. Our findings illustrate the biogeographic patterns and community assembly mechanisms of bacterioplankton and pathogens in estuaries, which should provide guidance and a reference for the control of potential pathogenic bacteria. IMPORTANCE Bacterioplankton play an important role in estuarine ecosystem functions and services; however, potentially pathogenic bacteria may exhibit infectivity and pose a serious threat to environmental and human health. In this study, geographic patterns and assembly processes of bacterioplankton communities in 30 subtropical estuaries were explored, and potential pathogenic bacteria in the estuaries were detected and profiled. Our results demonstrate here that bacterioplankton and pathogens show similar biogeographic patterns under the influence of salinity. Interestingly, heterogeneous selection dominated bacterioplankton assembly, while stochasticity dominated pathogen assembly. This study provides important information for future risk assessment of potential pathogenic bacteria as well as management in estuarine ecosystems.

Seasonal trends of mercury bioaccumulation and assessment of toxic effects in Asian clams and microbial community from field study of estuarine sediment

This study investigated seasonal trends in bioaccumulation potential and toxic effects of mercury (Hg) in Asian clams (Corbicula fluminea) and microbial community. For this, a clam-exposure experiment was performed during summer, fall, and winter seasons in four different sites (HS1: control/clean site; HS2, HS3, and HS4: contaminated sites) of Hyeongsan River estuary, South Korea. Total mercury (THg) and methylmercury (MeHg) in whole sediments were highest at HS4 site during fall, sustained similar levels during winter, but decreased during summer. Unlike whole sediment, pore water reported higher levels in summer, and gradually declined during fall and winter. Asian clams from HS4 site collected during summer presented highest bioaccumulations of THg (521.52 μg/kg, dry weight) and MeHg (161.04 μg/kg, dry weight), which also correlated with the higher levels of Hg present in pore water in the same season. Moreover, biota-sediment-pore water accumulation factor (BSpAF) were comparatively greater in clams collected from HS2∼HS4 compared to HS1 sites, suggesting that porewater was a better indicator of accumulation of Hg. Upregulation of biomarker genes responsible for detoxifying process (gsts1), scavenging oxidative stress (cat), and protein reparation (hsp70 and hsp90) were observed in clams collected from HS2∼HS4. The overexpression of these biomarkers implied that Asian clams can be considered as promising warning tools for Hg-contamination. Both bacterial and metabolic diversities were negatively affected by higher levels of THg and MeHg. Phylum Proteobacteria was enriched in HS2∼HS4 compared to HS1. In contrast, phylum Bacteroidetes showed a reverse trend. The metabolic profile was highest in HS1 and lowest in HS4, revealing higher stress of Hg in HS4 site. Overall, the outcomes of this field study broaden the information on seasonal trends of bioaccumulation of Hg and its toxic effects. These findings may be helpful in Hg monitoring and management programs in other river systems.

Insights into Bacterial Community Structure and Metabolic Diversity of Mercury-Contaminated Sediments from Hyeongsan River, Pohang, South Korea

This study investigated the bacterial community structure and metabolic diversity and their relationship with Hg and other environmental variables in sediments collected from different locations (HSR-1-HSR-6) in the Hyeongsan River estuary in South Korea. The results showed that the highest total mercury (THg) and methylmercury (MeHg) concentrations were in HSR-2, with values of 4585.3 µg/kg and 13.4 µg/kg, respectively. The lowest THg (31.9 µg/kg) and MeHg (0.1 µg/kg) concentrations were found in HSR-1. Sulfate and organic matter (OM) were more influential environmental variables, revealing a positive association with THg and MeHg and negatively affecting bacterial and metabolic diversities. Bacterial and metabolic diversities were also negatively impacted by the THg and MeHg concentrations. Proteobacteria and Bacteroidetes were abundantly distributed in all the sediments. The dominance of Proteobacteria was upscaled in all the heavily Hg-contaminated sites (HSR-2-HSR-6), and it was the only phylum that showed a significant positive correlation with THg, MeHg, and OM. The genera Sulfurovum and Sulfurimonas were abundantly observed in sites with high Hg contamination, whereas Congregibacter, Gaetbulibacter, Ilumatobacter, Methylotenera, Nevskia, and Sediminibacter were only detected in low Hg-contaminated sites (HSR-1). The community-level physiological profile data showed the highest (1.0) average well color development (AWCD) value in HSR-1 and the lowest (0.45) AWCD value in HSR-2. Overall, these results demonstrated the inhibitory effects of THg, MeHg, and other environmental variables on microbial communities and metabolic diversity. These findings broaden the current knowledge on the dynamics of bacterial and metabolic diversities in Hg-contaminated sediments and might be useful in the management of Hg pollution.

Identification and Characterization of Peruvian Native Bacterial Strains as Bioremediation of Hg-Polluted Water and Soils Due to Artisanal and Small-Scale Gold Mining in the Secocha Annex, Arequipa

The water and soils pollution due to mercury emissions from mining industries represents a serious environmental problem and continuous risk to human health. Although many strategies have been designed for the recovery or elimination of this metal from environmental sources, microbial bioremediation has proven to be the most effective and environmentally friendly strategy and thus control heavy metal contamination. The main objective of this work, using native bacterial strains obtained from contaminated soils of the Peruvian region of Secocha, was to identify which of these strains would have growth capacity on mercury substrates to evaluate their adsorption behavior and mercury removal capacity. Through a DNA analysis (99.78% similarity) and atomic absorption spectrometry, the Gram-positive bacterium Zhihengliuella alba sp. T2.2 was identified as the strain with the highest mercury removal capacity from culture solutions with an initial mercury concentration of 162 mg·L−1. The removal capacity reached values close to 39.5% in a period of incubation time of 45 days, with maximum elimination efficiency in the first 48 h. These results are encouraging and show that this native strain may be the key to the bioremediation of water and soils contaminated with mercury.

Interactions between Hg and soil microbes: microbial diversity and mechanisms, with an emphasis on fungal processes

Mercury (Hg) is a highly toxic metal with no known biological function, and it can be highly bioavailable in terrestrial ecosystems. Although fungi are important contributors to a number of soil processes including plant nutrient uptake and decomposition, little is known about the effect of Hg on fungi. Fungi accumulate the largest amount of Hg and are the organisms capable of the highest bioaccumulation of Hg. While referring to detailed mechanisms in bacteria, this mini-review emphasizes the progress made recently on this topic and represents the first step towards a better understanding of the mechanisms underlying Hg tolerance and accumulation in fungal species and hence on the role of fungi within the Hg cycle at Hg-contaminated sites. KEY POINTS: • The fungal communities are more resilient than bacterial communities to Hg exposure. • The exposure to Hg is a threat to microbial soil functions involved in both C and nutrient cycles. • Fungal (hyper)accumulation of Hg may be important for the Hg cycle in terrestrial environments. • Understanding Hg tolerance and accumulation by fungi may lead to new remediation biotechnologies.

The Impact of Mercury Selection and Conjugative Genetic Elements on Community Structure and Resistance Gene Transfer

Carriage of resistance genes can underpin bacterial survival, and by spreading these genes between species, mobile genetic elements (MGEs) can potentially protect diversity within microbial communities. The spread of MGEs could be affected by environmental factors such as selection for resistance, and biological factors such as plasmid host range, with consequences for individual species and for community structure. Here we cultured a focal bacterial strain, Pseudomonas fluorescens SBW25, embedded within a soil microbial community, with and without mercury selection, and with and without mercury resistance plasmids (pQBR57 or pQBR103), to investigate the effects of selection and resistance gene introduction on (1) the focal species; (2) the community as a whole; (3) the spread of the introduced mer resistance operon. We found that P. fluorescens SBW25 only escaped competitive exclusion by other members of community under mercury selection, even when it did not begin with a mercury resistance plasmid, due to its propensity to acquire resistance from the community by horizontal gene transfer. Mercury pollution had a significant effect on community structure, decreasing alpha diversity within communities while increasing beta diversity between communities, a pattern that was not affected by the introduction of mercury resistance plasmids by P. fluorescens SBW25. Nevertheless, the introduced merA gene spread to a phylogenetically diverse set of recipients over the 5 weeks of the experiment, as assessed by epicPCR. Our data demonstrates how the effects of MGEs can be experimentally assessed for individual lineages, the wider community, and for the spread of adaptive traits.

Water-soluble mercury induced by organic amendments affected microbial community assemblage in mercury-polluted paddy soil

Mercury (Hg) pollution or organic amendments (OA) may individually induce changes in the microbial community of paddy soils. However, little is known regarding the interaction of Hg and OA and the effect of different OA applications on the microbial community assemblage in Hg-polluted paddy soil. A soil incubation experiment was performed by applying three organic amendments (OA), namely a food-waste compost (FC), and its HA and FA, into an Hg-polluted paddy soil to examine the changes in the microbial community and merA/merB gene abundance. The results showed that the OA treatments promoted total (SOC) and dissolved organic carbon (DOC) in soils, which may harbor copiotrophic bacteria. The HA and FA treatments decreased microbial diversity and richness along with an increase of water-soluble Hg (WHg) through the complexation of DOC to Hg, which may be mainly attributed to the enhanced Hg biotoxicity to soil microbiome induced by the increased WHg under these two treatments. Additionally, the WHg enhancement also contributed to the increase of Hg-resistant bacteria and merA/merB gene abundance, and consequently, induced changes in the microbial community. These results indicated the interaction of Hg and different OA induced the variation of WHg fraction in paddy soil, which played a fundamental role in the distinct responses of the microbial community assemblage. Collectively, the application of FA and HA to Hg-polluted soil should be limited considering Hg risk to microbiome, and FC can be an alternative.

Critical mercury concentration in tropical soils: Impact on plants and soil biological attributes

Mercury is a toxic element that becomes a problem when present at high concentrations in soils. Mercury toxicity in soils varies depending on chemical species, concentration, exposure routes, and organism vulnerability. There is little information regarding the toxicity of Hg in tropical soils, especially for establishing safe levels of this pollutant. The purpose of this study was to investigate Hg concentrations in two tropical soils and their effect on oats and common beans, as well as on soil biological attributes. The experiment was carried out in a greenhouse, following ISO 11.269-2 and OECD-208 guidelines. Oat and common bean were cultivated in a Typic Hapludox (TyHpx) and Rhodic Acrudox (RhAcx) contaminated with HgCl₂ at the following concentrations: 0, 2.5, 5.0, 10.0, 20.0, 40.0, and 80.0 mg of Hg kg^-1 of dry soil. The biological variables analyzed were seedling emergence, vegetative growth, chlorophyll content (SPAD index), gas exchange (photosynthetic rate, internal CO₂ concentration, transpiration rate, and stomatal conductance), and Hg concentration and accumulation in shoot dry matter. Microbial biomass carbon, soil basal respiration, and metabolic quotient (qCO₂) were also analyzed. Due to the sorptive characteristics of TyHpx, it had higher Hg concentrations than RhAcx. Mercury showed toxic effects on both oat and common bean species. However, common bean was affected only at concentrations higher than 20 mg kg^-1. The microbial community showed high sensitivity to soil Hg concentrations, but external factors, such as the plant species cultivated, influenced the sensitivity of the community. The microbiota was most sensitive in pots with common bean, and this effect was more pronounced at low clay and low organic matter contents (TyHpx). In this study, the concentration of 0.36 mg kg^-1 was critical for Hg in these soils, based on its deleterious effects on oat and common bean and on biological soil attributes.

16S rRNA-Based metagenomic analysis of microbial communities associated with wild Labroides dimidiatus from Karah Island, Terengganu, Malaysia

This study was designed to evaluate the bacterial composition of the Labroides dimidiatus and its surrounding water. Fish and carriage water samples were obtained from corals of the Karah Island in Terengganu Malaysia. DNA was extracted and the bacteria communities on the skin mucus and stomach as well as water sample were classified (to family level) using the 16S rRNA-based metagenomics analysis. 1,426,740 amplicon sequence reads corresponding to 508 total operational taxonomic units were obtained from the three metagenomics libraries in this study. The Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Fusobacteria were the most dominant bacterial phyla in all samples. A total of 36 different classes and 132 families were identified, many of which had shared presence in all samples while others were exclusive to different sample. Thirty-three of these were identified as pathogenic zoonotic bacterial. The results obtained indicate a strong influence of host environment on the composition of its microbiota. Knowing the composition of the microbiota is the first step toward exploring proper management of this ornamental fish in captivity.

Responses of riverbed sediment bacteria to heavy metals: Integrated evaluation based on bacterial density, activity and community structure under well-controlled sequencing batch incubation conditions

Better understanding the responses of riverbed sediment bacteria to heavy metals is a key for considering using riverbed sediment bacterial community as an indicator of river water contamination by heavy metals. For this, integrated evaluation based on bacterial density, activity and community structure through incubation experiments under well-controlled conditions is necessary to obtain more closely relevant findings that are difficult to achieve through field studies. The findings may also include those that can serve as new evidence to clarify contrary findings reported in previous studies. In this study, sequencing batch incubation experiments were performed using sediment suspensions from three rivers with catchment of different land covers and uses. The effects of four metals (Pb, Cr, Cd and Cu) were investigated by spiking them separately under three different concentration levels. Glucose was added once every day as the carbon source throughout the whole incubation lasted for 30 days. The changing trends of the density of general and heterotrophic bacteria showed clearly that the responses of sediment bacteria to Cu were obviously stronger, followed by that to Cd; whereas, the responses to Pb and Cr were not apparent. For incubation with Cu, a short-term inhibition effect appeared in the initial 3 days and was then followed by a long-term promotion effect reflected by obvious increases of bacterial density against control. In regard of bacterial activity evaluated based on the first-order consumption rate for glucose, a trend of decreases was revealed. The results of PCR-DGGE and sequence analysis of extracted 16S rDNA further suggested there were bacterial species that had strong tolerance against the metal and could grow readily to become new dominating ones. The existence of such bacterial species was inferred as the reason leading to the observed increases of bacterial density during incubation with the metal.

Organic and inorganic amendment application on mercury-polluted soils: effects on soil chemical and biochemical properties

On the basis of a previous study performed in our laboratory, the use of organic and inorganic amendments can significantly modify the Hg mobility in soil. We have compared the effectiveness of organic and inorganic amendments such as digestate and fly ash, respectively, reducing the Hg mobility in Chernozem and Luvisol soils differing in their physicochemical properties. Hence, the aim of this work was to compare the impact of digestate and fly ash application on the chemical and biochemical parameters in these two mercury-contaminated soils in a model batch experiment. Chernozem and Luvisol soils were artificially contaminated with Hg and then incubated under controlled conditions for 21 days. Digestate and fly ash were applied to both soils in a dose of 10 and 1.5 %, respectively, and soil samples were collected after 1, 7, 14, and 21 days of incubation. The presence of Hg in both soils negatively affected to processes such as nitrification, provoked a decline in the soil microbial biomass C (soil microbial biomass C (MBC)), and the microbial activities (arylsulfatase, and β-glucosaminidase) in both soils. Meanwhile, the digestate addition to Chernozem and Luvisol soils contaminated with Hg improved the soil chemical properties (pH, dissolved organic carbon (DOC), N (Ntot), inorganic-N forms (N-NH4 (+) and N-NO3 (-))), as consequence of high content in C and N contained in digestate. Likewise, the soil MBC and soil microbial activities (dehydrogenase, arylsulfatase, and β-glucosaminidase) were greatly enhanced by the digestate application in both soils. In contrast, fly ash application did not have a remarkable positive effect when compared to digestate in Chernozem and Luvisol soil contaminated with mercury. These results may indicate that the use of organic amendments such as digestate considerably improved the soil health in Chernozem and Luvisol compared with fly ash, alleviating the detrimental impact of Hg. Probably, the chemical properties present in digestate may determine its use as a suitable amendment for the assisted-natural attenuation of mercury-polluted soils.

Chemical multi-contamination drives benthic prokaryotic diversity in the anthropized Toulon Bay

Investigating the impact of human activities on marine coastal ecosystems remains difficult because of the co-occurrence of numerous natural and human-induced gradients. Our aims were (i) to evaluate the links between the chemical environment as a whole and microbial diversity in the benthic compartment, and (ii) to compare the contributions of anthropogenic and natural chemical gradients to microbial diversity shifts. We studied surface sediments from 54 sampling sites in the semi-enclosed Toulon Bay (NW Mediterranean) exposed to high anthropogenic pressure. Previously published chemical data were completed by new measurements, resulting in an in depth geochemical characterization by 29 representative environmental variables. Bacterial and archaeal diversity was assessed by terminal restriction fragment length polymorphism profiling on a selection of samples distributed along chemical gradients. Multivariate statistical analyses explained from 45% to 80% of the spatial variation in microbial diversity, considering only the chemical variables. A selection of trace metals of anthropogenic origin appeared to be strong structural factors for both bacterial and archaeal communities. Bacterial terminal restriction fragment (T-RF) richness correlated strongly with both anthropogenic and natural chemical gradients, whereas archaeal T-RF richness demonstrated fewer links with chemical variables. No significant decrease in diversity was evidenced in relation to chemical contamination, suggesting a high adaptive potential of benthic microbial communities in Toulon Bay.

Diversity of active microbial communities subjected to long-term exposure to chemical contaminants along a 40-year-old sediment core

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.

Responses of soil ammonia oxidizers to a short-term severe mercury stress

The responses of soil ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) to mercury (Hg) stress were investigated through a short-term incubation experiment. Treated with four different concentrations of Hg (CK, Hg25, Hg50, and Hg100, denoting 0, 25, 50, and 100mgHg/kg dry soil, respectively), samples were harvested after 3, 7, and 28day incubation. Results showed that the soil potential nitrification rate (PNR) was significantly inhibited by Hg stress during the incubation. However, lower abundances of AOA (the highest in CK: 9.20×10(7)copies/g dry soil; the lowest in Hg50: 2.68×10(7)copies/g dry soil) and AOB (the highest in CK: 2.68×10(7)copies/g dry soil; the lowest in Hg50: 7.49×10(6)copies/g dry soil) were observed only at day 28 of incubation (P<0.05). Moreover, only the community structure of soil AOB obviously shifted under Hg stress as seen through DGGE profiles, which revealed that 2-3 distinct AOB bands emerged in the Hg treatments at day 28. In summary, soil PNR might be a very useful parameter to assess acute Hg stress on soil ecosystems, and the community structure of soil AOB might be a realistic biological indicator for the assessment of heavy metal stress on soil ecosystems in the future.

Patterns of bacterial diversity along a long-term mercury-contaminated gradient in the paddy soils

Mercury (Hg) pollution is usually regarded as an environmental stress in reducing microbial diversity and altering bacterial community structure. However, these results were based on relatively short-term studies, which might obscure the real response of microbial species to Hg contamination. Here, we analysed the bacterial abundance and community composition in paddy soils that have been potentially contaminated by Hg for more than 600 years. Expectedly, the soil Hg pollution significantly influenced the bacterial community structure. However, the bacterial abundance was significantly correlated with the soil organic matter content rather than the total Hg (THg) concentration. The bacterial alpha diversity increased at relatively low levels of THg and methylmercury (MeHg) and subsequently approached a plateau above 4.86 mg kg(-1) THg or 18.62 ng g(-1) MeHg, respectively. Contrasting with the general prediction of decreasing diversity along Hg stress, our results seem to be consistent with the intermediate disturbance hypotheses with the peak biological diversity under intermediate disturbance or stress. This result was partly supported by the inconsistent response of bacterial species to Hg stress. For instance, the relative abundance of Nitrospirae decreased, while that of Gemmatimonadetes increased significantly along the increasing soil THg and MeHg concentrations. In addition, the content of SO(4)(2-), THg, MeHg and soil depth were the four main factors influencing bacterial community structures based on the canonical correspondence analysis (CCA). Overall, our findings provide novel insight into the distribution patterns of bacterial community along the long-term Hg-contaminated gradient in paddy soils.

Stability of soil microbial structure and activity depends on microbial diversity

Despite the central role of microbes in soil processes, empirical evidence concerning the effect of their diversity on soil stability remains controversial. Here, we addressed the ecological insurance hypothesis by examining the stability of microbial communities along a gradient of soil microbial diversity in response to mercury pollution and heat stress. Diversity was manipulated by dilution extinction approach. Structural and functional stabilities of microbial communities were assessed from patterns of genetic structure and soil respiration after the stress. Dilution led to the establishment of a consistent diversity gradient, as revealed by 454 sequencing of ribosomal genes. Diversity stability was enhanced in species-rich communities whatever the stress whereas functional stability was improved with increasing diversity after heat stress, but not after mercury pollution. This discrepancy implies that the relevance of ecological insurance for soil microbial communities might depend on the type of stress. Our results also suggest that the significance of microbial diversity for soil functional stability might increase with available soil resources. This could have strong repercussions in the current 'global changes' context because it suggests that the combined increased frequencies of extreme climatic events, nutrient loading and biotic exploitation may amplify the functional consequences of diversity decrease.

Interactions between snow chemistry, mercury inputs and microbial population dynamics in an Arctic snowpack

We investigated the interactions between snowpack chemistry, mercury (Hg) contamination and microbial community structure and function in Arctic snow. Snowpack chemistry (inorganic and organic ions) including mercury (Hg) speciation was studied in samples collected during a two-month field study in a high Arctic site, Svalbard, Norway (79 °N). Shifts in microbial community structure were determined by using a 16S rRNA gene phylogenetic microarray. We linked snowpack and meltwater chemistry to changes in microbial community structure by using co-inertia analyses (CIA) and explored changes in community function due to Hg contamination by q-PCR quantification of Hg-resistance genes in metagenomic samples. Based on the CIA, chemical and microbial data were linked (p = 0.006) with bioavailable Hg (BioHg) and methylmercury (MeHg) contributing significantly to the ordination of samples. Mercury was shown to influence community function with increases in merA gene copy numbers at low BioHg levels. Our results show that snowpacks can be considered as dynamic habitats with microbial and chemical components responding rapidly to environmental changes.

Mercury induced community tolerance in microbial biofilms is related to pollution gradients in a long-term polluted river

The net toxicity of different forms of mercury, in the long-term during their transformation processes, leads to the selection of resistant bacterial cells and this result in community tolerance which is pollution induced. Accordingly, based on profiles of a bacterial community structure, analysis of Hg resistant culturable bacteria and quantification of merA genes, we assessed development of pollution induced community tolerance in a mercury-polluted gradient in the Idrijca River. TTGE analysis did not show effects of mercury pollution to bacterial community diversity, while quantification of merA genes showed that merA genes can be correlated precisely (R(2)=0.83) with the total concentration of mercury in the biofilm microbial communities in the pollution gradient.

Effect of leaf type and pesticide exposure on abundance of bacterial taxa in mosquito larval habitats

Lentic freshwater systems including those inhabited by aquatic stages of mosquitoes derive most of their carbon inputs from terrestrial organic matter mainly leaf litter. The leaf litter is colonized by microbial communities that provide the resource base for mosquito larvae. While the microbial biomass associated with different leaf species in container aquatic habitats is well documented, the taxonomic composition of these microbes and their response to common environmental stressors is poorly understood. We used indoor aquatic microcosms to determine the abundances of major taxonomic groups of bacteria in leaf litters from seven plant species and their responses to low concentrations of four pesticides with different modes of action on the target organisms; permethrin, malathion, atrazine and glyphosate. We tested the hypotheses that leaf species support different quantities of major taxonomic groups of bacteria and that exposure to pesticides at environmentally relevant concentrations alters bacterial abundance and community structure in mosquito larval habitats. We found support for both hypotheses suggesting that leaf litter identity and chemical contamination may alter the quality and quantity of mosquito food base (microbial communities) in larval habitats. The effect of pesticides on microbial communities varied significantly among leaf types, suggesting that the impact of pesticides on natural microbial communities may be highly complex and difficult to predict. Collectively, these findings demonstrate the potential for detritus composition within mosquito larval habitats and exposure to pesticides to influence the quality of mosquito larval habitats.

Analysis of the bacterial community in the two typical intertidal sediments of Bohai Bay, China by pyrosequencing

For full understanding of the bacterial community in the intertidal zones of Bohai Bay, China, we used pyrosequencing-based approach to analyze the 16S rRNA gene of bacteria in the sediments from the two typically intertidal zones - Qikou (Qi) and Gaoshaling (Ga). Results showed that, at a 0.03 distance, the sequences from the Qi sediment were assigned to 3252 operational taxonomic units (OTUs) which belong to 34 phyla, 69 classes and 119 genera, while the 3740 OTUs from the Ga sediment were affiliated with 33 phyla, 66 classes and 146 genera. Comparing the bacterial communities inhabiting in the two intertidal sediments, we observed significant difference in the dominant composition and distribution at phylum, class and genus levels. Canonical correspondence analysis (CCA) showed that the median grain size and DO were the most important factors regulating the bacterial abundance and diversity, while the other environmental factors have effects with different degree.

Methylation of mercury in earthworms and the effect of mercury on the associated bacterial communities

Methylmercury compounds are very toxic for most organisms. Here, we investigated the potential of earthworms to methylate inorganic-Hg. We hypothesized that the anaerobic and nutrient-rich conditions in the digestive tracts of earthworm's promote the methylation of Hg through the action of their gut bacteria. Earthworms were either grown in sterile soils treated with an inorganic (HgCl₂) or organic (CH₃HgCl) Hg source, or were left untreated. After 30 days of incubation, the total-Hg and methyl-Hg concentrations in the soils, earthworms, and their casts were analyzed. The impact of Hg on the bacterial community compositions in earthworms was also studied. Tissue concentrations of methyl-Hg in earthworms grown in soils treated with inorganic-Hg were about six times higher than in earthworms grown in soils without Hg. Concentrations of methyl-Hg in the soils and earthworm casts remained at significantly lower levels suggesting that Hg was mainly methylated in the earthworms. Bacterial communities in earthworms were mostly affected by methyl-Hg treatment. Terminal-restriction fragments (T-RFs) affiliated to Firmicutes were sensitive to inorganic and methyl-Hg, whereas T-RFs related to Betaproteobacteria were tolerant to the Hg treatments. Sulphate-reducing bacteria were detected in earthworms but not in soils.

Microbial diversity and PAH catabolic genes tracking spatial heterogeneity of PAH concentrations

We analyzed the within-site spatial heterogeneity of microbial community diversity, polyaromatic hydrocarbon (PAH) catabolic genotypes, and physiochemical soil properties at a creosote contaminated site. Genetic diversity and community structure were evaluated from an analysis of denaturant gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified sequences of 16S rRNA gene. The potential PAH degradation capability was determined from PCR amplification of a suit of aromatic dioxygenase genes. Microbial diversity, evenness, and PAH genotypes were patchily distributed, and hot and cold spots of their distribution coincided with hot and cold spots of the PAH distribution. The analyses revealed a positive covariation between microbial diversity, biomass, evenness, and PAH concentration, implying that the creosote contamination at this site promotes diversity and abundance. Three patchily distributed PAH-degrading genotypes, NAH, phnA, and pdo1, were identified, and their abundances were positively correlated with the PAH concentration and the fraction of soil organic carbon. The covariation of the PAH concentration with the number and spatial distribution of catabolic genotypes suggests that a field site capacity to degrade PAHs may vary with the extent of contamination.

GFP-tagged multimetal-tolerant bacteria and their detection in the rhizosphere of white mustard

The introduction of rhizobacteria that tolerate heavy metals is a promising approach to support plants involved in phytoextraction and phytostabilisation. In this study, soil of a metal-mine wasteland was analyzed for the presence of metal-tolerant bacterial isolates, and the tolerance patterns of the isolated strains for a number of heavy metals and antibiotics were compared. Several of the multimetal-tolerant strains were tagged with a broad host range reporter plasmid (i.e. pPROBE-NT) bearing a green fluorescent protein marker gene (gfp). Overall, the metal-tolerant isolates were predominately Gram-negative bacteria. Most of the strains showed a tolerance to five metals (Zn, Cu, Ni, Pb and Cd), but with differing tolerance patterns. From among the successfully tagged isolates, we used the transconjugant Pseudomonas putida G25 (pPROBE-NT) to inoculate white mustard seedlings. Despite a significant decrease in transconjugant abundance in the rhizosphere, the gfp-tagged cells survived on the root surfaces at a level previously reported for root colonisers.

Interactions between Zn and bacteria in marine tropical coastal sediments

PURPOSE

The main goals of this study were (1) to examine the effects of zinc on the microbial community structure of anthropogenically impacted sediments in a tropical coastal ecosystem and (2) to determine whether these microbial benthic communities may enhance the adsorption of zinc.

METHODS

The interactions between zinc and bacteria in tropical sediments were studied in sediment microcosms amended with 2.5 mg L⁻¹ of Zn in the water phase and incubated for 8 days under different environmental conditions, oxic/anoxic and glucose addition. At the end of incubation, microbial structure was assessed by molecular fingerprints (T-RFLP) analysis and Zn speciation in the sediment was determined by sequential extraction.

RESULTS

In the three studied sediments, Zn spiking resulted in only slight changes in bacterial community structure. In contrast, the addition of low concentrations of glucose (5 mM) strongly modified the bacterial community structure: <20% of similarity with the initial structure concomitant with a strong diminution of the specific richness. Overall, these results suggest that highly labile organic matter has a larger impact on microbial structure than heavy metal. These weak impacts of Zn on bacteria diversity might be partly explained by (1) the strong adsorption of Zn in the presence of bacteria and/or (2) the incorporation of Zn into a nonbioavailable fraction. Nevertheless, Zn spiking resulted in significant changes in nutrient cycles, suggesting that bacterial metabolisms were impacted by the heavy metal. This led to an increase in nutrient supplies to the water column, potentially enhancing eutrophication in a nutrient-limited, oligotrophic ecosystem.

Links between bacterial communities in marine sediments and trace metal geochemistry as measured by in situ DET/DGT approaches

Our current view about the relationship between metals and bacteria in marine sediments might be biased because most studies only use ex situ approaches to quantify metals. The aim of the present research was to compare ex situ and in situ methods of metal measurement (DET and DGT--diffusive equilibration or diffusive gradients in thin-films) and relate the results with two commonly used microbiological variables (bacterial biomass and bacterial diversity as revealed by DGGE). No previous studies have used such in situ approaches in microbial ecology. For biomass and most of the investigated trace metals (Ag, Cd, Sn, Cr, Ni, Cu, Pb, and Al) no significant correlations were found. The exceptions were Fe, Mn, Co, and As which behave like micronutrients. For bacterial diversity, no relevant relationships were found. We conclude that in situ methods are more adapted tools for microbial ecologists but that ex situ approaches are still necessary.

Genetic difference but functional similarity among fish gut bacterial communities through molecular and biochemical fingerprints

Considering the major involvement of gut microflora in the digestive function of various macro-organisms, bacterial communities inhabiting fish guts may be the main actors of organic matter degradation by fish. Nevertheless, the extent and the sources of variability in the degradation potential of gut bacterial communities are largely overlooked. Using Biolog Ecoplate™ and denaturing gradient gel electrophoresis (DGGE), we explored functional (i.e. the ability to degrade organic matter) and genetic (i.e. identification of DGGE banding patterns) diversity of fish gut bacterial communities, respectively. Gut bacterial communities were extracted from fish species characterized by different diets sampled along a salinity gradient in the Patos-Mirim lagoons complex (Brazil). We found that functional diversity was surprisingly unrelated to genetic diversity of gut bacterial communities. Functional diversity was not affected by the sampling site but by fish species and diet, whereas genetic diversity was significantly influenced by all three factors. Overall, the functional diversity was consistently high across fish individuals and species, suggesting a wide functional niche breadth and a high potential of organic matter degradation. We conclude that fish gut bacterial communities may strongly contribute to nutrient cycling regardless of their genetic diversity and environment.

Bacterial mer operon-mediated detoxification of mercurial compounds: a short review

Mercury pollution has emerged as a major problem in industrialized zones and presents a serious threat to environment and health of local communities. Effectiveness and wide distribution of mer operon by horizontal and vertical gene transfer in its various forms among large community of microbe reflect importance and compatibility of this mechanism in nature. This review specifically describes mer operon and its generic molecular mechanism with reference to the central role played by merA gene and its related gene products. The combinatorial action of merA and merB together maintains broad spectrum mercury detoxification system for substantial detoxification of mercurial compounds. Feasibility of mer operon to coexist with antibiotic resistance gene (ampr, kanr, tetr) clusters enables extensive adaptation of bacterial species to adverse environment. Flexibility of the mer genes to exist as intricate part of chromosome, plasmids, transposons, and integrons enables high distribution of these genes in wider microbial gene pool. Unique ability of this system to manipulate oligodynamic property of mercurial compounds for volatilization of mercuric ions (Hg2+) makes it possible for a wide range of microbes to tolerate mercury-mediated toxicity.

Microbial characterization of mercury-reducing mixed cultures enriched with different carbon sources

The use of mixed microbial cultures enriched for biological mercury removal is explored in this paper, focusing on the ecological shifts occurring throughout acclimatization to mercury and on the long-term stability of four microbial enrichments. The 16S rRNA genetic profiles obtained by denaturing gradient gel electrophoresis (DGGE) revealed that the glucose and ethanol cultures had similar profiles, whereas the acetate cultures diverged into a totally dissimilar cluster. Quantification of the merA gene copies in each enrichment showed higher values for the glucose culture, followed by the ethanol and then the acetate cultures, which was consistent with the mercury removal performance throughout the study. Isolates were obtained from the four cultures and analyzed with respect to their genetic (16S rRNA) and functional (merA) phylogenies in order to identify mercury-resistant species enriched with different carbon sources. All mercury-resistant isolates obtained from the glucose and ethanol cultures belonged to the Gammaproteobacteria, whereas acetate cultures also contained members of other phyla, with differences in merA sequences. Higher phylogenetic than functional diversity of the isolates, together with increasing merA copies even after culture stabilisation, highlight the role of horizontal gene transfer in the acclimatization process.

Diversity and characterization of mercury-resistant bacteria in snow, freshwater and sea-ice brine from the High Arctic

It is well-established that atmospheric deposition transports mercury from lower latitudes to the Arctic. The role of bacteria in the dynamics of the deposited mercury, however, is unknown. We characterized mercury-resistant bacteria from High Arctic snow, freshwater and sea-ice brine. Bacterial densities were 9.4 × 10(5), 5 × 10(5) and 0.9-3.1 × 10(3) cells mL(-1) in freshwater, brine and snow, respectively. Highest cultivability was observed in snow (11.9%), followed by freshwater (0.3%) and brine (0.03%). In snow, the mercury-resistant bacteria accounted for up to 31% of the culturable bacteria, but <2% in freshwater and brine. The resistant bacteria belonged to the Alpha-, Beta- and Gammaproteobacteria, Firmicutes, Actinobacteria, and Bacteriodetes. Resistance levels of most isolates were not temperature dependent. Of the resistant isolates, 25% reduced Hg(II) to Hg(0). No relation between resistance level, ability to reduce Hg(II) and phylogenetic group was observed. An estimation of the potential bacterial reduction of Hg(II) in snow suggested that it was important in the deeper snow layers where light attenuation inhibited photoreduction. Thus, by reducing Hg(II) to Hg(0), mercury-resistant bacteria may limit the supply of substrate for methylation processes and, hence, contribute to lowering the risk that methylmercury is being incorporated into the Arctic food chains.

Determining the effects of a spatially heterogeneous selection pressure on bacterial population structure at the sub-millimetre scale

A key interest of microbial ecology is to understand the role of environmental heterogeneity in shaping bacterial diversity and fitness. However, quantifying relevant selection pressures and their effects is challenging due to the number of parameters that must be considered and the multiple scales over which they act. In the current study, a model system was employed to investigate the effects of a spatially heterogeneous mercuric ion (Hg(2+)) selection pressure on a population comprising Hg-sensitive and Hg-resistant pseudomonads. The Hg-sensitive bacteria were Pseudomonas fluorescens SBW25::rfp and Hg-resistant bacteria were P. fluorescens SBW25 carrying a gfp-labelled, Hg resistance plasmid. In the absence of Hg, the plasmid confers a considerable fitness cost on the host, with µ(max) for plasmid-carrying cells relative to plasmid-free cells of only 0.66. Two image analysis techniques were developed to investigate the structure that developed in biofilms about foci of Hg (cellulose fibres imbued with HgCl(2)). Both techniques indicated selection for the resistant phenotype occurred only in small areas of approximately 178-353 μm (manually defined contour region analysis) or 275-350 μm (daime analysis) from foci. Hg also elicited toxic effects that reduced the growth of both Hg-sensitive and Hg-resistant bacteria up to 250 μm from foci. Selection for the Hg resistance phenotype was therefore highly localised when Hg was spatially heterogeneous. As such, for this model system, we define here the spatial scale over which selection operates. The ability to quantify changes in the strength of selection for particular phenotypes over sub-millimetre scales is useful for understanding the scale over which environmental variables affect bacterial populations.

Long-term Hg pollution-induced structural shifts of bacterial community in the terrestrial isopod (Porcellio scaber) gut

In previous studies we detected lower species richness and lower Hg sensitivity of the bacteria present in egested guts of Porcellio scaber (Crustacea, Isopoda) from chronically Hg polluted than from unpolluted environment. Basis for such results were further investigated by sequencing of 16S rRNA genes of mercury-resistant (Hgr) isolates and clone libraries. We observed up to 385 times higher numbers of Hgr bacteria in guts of animals from polluted than from unpolluted environment. The majority of Hgr strains contained merA genes. Sequencing of 16S rRNA clones from egested guts of animals from Hg-polluted environments showed elevated number of bacteria from Pseudomonas, Listeria and Bacteroidetes relatives groups. In animals from pristine environment number of bacteria from Achromobacter relatives, Alcaligenes, Paracoccus, Ochrobactrum relatives, Rhizobium/Agrobacterium, Bacillus and Microbacterium groups were elevated. Such bacterial community shifts in guts of animals from Hg-polluted environment could significantly contribute to P. scaber Hg tolerance.

Growth responses to and accumulation of mercury by ectomycorrhizal fungi

Heavy metals have been shown to negatively affect the growth of ectomycorrhizal fungi (ECMF). In addition, ECMF have been shown to accumulate heavy metals and to protect host trees from metal toxicity. However, specific literature on the interactions between ECMF and mercury (Hg) is scant. This paper describes the responses of ECMF to Hg in axenic culture conditions. Six ECMF from an area with no known history of direct Hg contamination were tested to determine their sensitivity to Hg. ECMF were incubated on solid medium amended with Hg (0-50μM) as HgCl₂ and the effect of Hg on radial growth was determined. The effect of preexposure cultivation on Hg sensitivity, the effect of Hg on biomass production, and the ability to accumulate Hg were determined for four of the ECMF. At micromolar concentrations, Hg significantly inhibited the radial growth rate of ECMF. This inhibitory effect was lessened in some ECMF when an established colony was exposed to Hg. Mercury lowered biomass production by some ECMF, and ECMF accumulate Hg from a solid growth substrate in direct relation to the amount of Hg added to the media. Possible implications for ECMF communities in Hg-impacted areas are discussed.

Organic matter control of mercury and lead toxicity in mor layers

This study evaluated the effect of organic matter composition on Hg and Pb toxicity for heterotrophic respiration in mor layers in long-term in vitro dose-response experiments. Pb proved to be a more potent toxin than Hg at comparable metal additions. The degree of litter decomposition and fragmentation and background Hg concentration levels were key factors determining metal toxicity. Higher sensitivity to metal additions in the fermentation layer than in litter and humification layers was corroborated. The role of organic matter composition was further examined in litter after structural disintegration by milling, which significantly increased the sensitivity of heterotrophic respiration to metal additions. A threshold value causing 5% reduction in heterotrophic respiration was estimated at 800 microg Hg kg(-1). In boreal forests in the northern hemisphere, the mean regional Hg concentrations in mor layers amount to approximately half this threshold value.

Effects of mercury on the activity and community composition of soil ammonia oxidizers

PURPOSE

Experiments were conducted to examine the effects of mercury (Hg) on soil nitrification activities and the microbial communities of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA).

METHODS

The soil samples spiked with different Hg concentrations were incubated for a period of 1, 2, 4, and 8 weeks in triplicate and the potential nitrification rate (PNR) of the samples was determined. The abundance of AOB and AOA was measured after an 8-week incubation by real-time polymerase chain reaction (PCR) assay of the amoA genes, while the community compositions by cloning and sequencing approaches.

RESULTS

The soil PNR differed with different incubation periods. It tended to decrease with increasing soil Hg concentrations at week 1, basing on which the half-maximal effective concentration (EC50) was 1.59 mg kg(-1). There was no significant difference in the abundance of AOB or AOA among the treatments. The AOB community was dominated by Nitrosospira-like sequences and more than 70% of the obtained clones were affiliated with the cluster 3a.2. The percentage of cluster 3a.1 in AOB community appeared to a consistent trend of decreasing with ascending soil Hg concentrations. While all the AOA sequences in the clone libraries were grouped into cluster S (soil and sediment origin).

CONCLUSIONS

This study revealed that Hg could inhibit soil potential nitrification and the extent varied with incubation periods. Soil Hg pollution changed the composition of soil AOB to some extent. These findings will be helpful to recognize the effects of Hg on the activity and community composition of soil ammonia oxidizers.

Temporal bacterial diversity associated with metal-contaminated river sediments

The temporal activity, abundance and diversity of microbial communities were evaluated across a metal-contamination gradient around a Superfund site in Montana. In order to analyze short-term variability, samples were collected from six sites on four occasions over 12 months. Measurements of community activity, diversity and richness, quantified by dehydrogenase activity and through denaturant gradient gel electrophoresis (DGGE), respectively, were higher at contaminated sites adjacent to the smelter, relative to reference sites. 16S rRNA gene copy numbers, measured by quantitative PCR, showed seasonal variability, yet were generally higher within polluted sediments. Jaccard similarity coefficients of DGGE profiles, found sites to cluster based primarily on geographical proximity rather than geochemical similarities. Intra-site clustering of the most polluted sites also suggests a stable metal-tolerant community. Sequences from DGGE-extracted bands were predominantly Beta and Gammaproteobacteria, although the communities at all sites generally maintained a diverse phylogeny changing in composition throughout the sampling period. Spearman's rank correlations analysis found statistically significant relationships between community composition and organic carbon (r-value = 0.786) and metals (r-values As = 0.65; Cu = 0.63; Zn = 0.62). A diverse and abundant community at the most polluted site indicates that historical contamination selects for a metal-resistant microbial community, a finding that must be accounted for when using the microbial community within ecosystem monitoring studies. This study highlights the importance of using multiple time-points to draw conclusions on the affect of metal contamination.

Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants

The diversity of bacterial groups of activated sludge samples that received wastewater from four different types of industry was investigated by a nested PCR-DGGE (denaturing gradient gel electrophoresis) approach. Specific 16S rRNA primers were chosen for large bacterial groups (Bacteria and alpha-Proteobacteria in particular), which dominate activated sludge communities, as well as for actinomycetes, ammonium oxidisers and methanotrophs (types I and II). In addition primers for the new Acidobacterium kingdom were used to observe their community structure in activated sludge. After this first PCR amplification, a second PCR with bacterial primers yielded 16S rRNA gene fragments that were subsequently separated by DGGE, thus generating 'group-specific DGGE patterns'. The community structure and diversity of the bacterial groups from the different samples was further analysed using different techniques, such as statistical analysis and Shannon diversity index evaluation of the band patterns. By combining the seven DGGE gels, cluster analysis, multidimensional scaling and principal component analysis clearly clustered two of the four activated sludge types separately. It was shown that the combination of molecular and statistical methods can be very useful to differentiate microbial communities.

Impact of 4-chlorophenol contamination and/or inoculation with the 4-chlorophenol-degrading strain, Arthrobacter chlorophenolicus A6L, on soil bacterial community structure

The 4-chlorophenol-degrading strain, Arthrobacter chlorophenolicus A6L (chromosomally tagged with the firefly luciferase gene, luc) was inoculated into 4-chlorophenol-contaminated soil to assess the impact of bioaugmentation with a biodegrading strain on the indigenous microbiota. Simultaneously, the impact of 4-chlorophenol alone, or inoculation with A. chlorophenolicus into non-contaminated soil, was addressed. Using terminal restriction fragment length polymorphism (T-RFLP) several significant changes were detected in community fingerprint patterns obtained from soil microcosms treated under the different conditions. The relative abundances of some populations, as judged by the relative intensity of terminal restriction fragments, were significantly impacted by either 4-chlorophenol, A. chlorophenolicus inoculation, or by a combination of both inoculation and 4-chlorophenol contamination. Some populations were significantly stimulated and others were significantly repressed when compared to control soil with no additions. For several peaks, the positive or negative impact imposed by the treatments increased over the 13-day incubation period. Some members of the bacterial community were specifically sensitive to A. chlorophenolicus inoculation or to 4-chlorophenol contamination, whereas other populations remained relatively unaffected by any of the treatments. The A. chlorophenolicus inoculum was also monitored by T-RFLP and was found to have a significantly higher relative abundance in soil contaminated with 4-chlorophenol. These results were substantiated by a high correlation to luciferase activity measurements and the number of colony forming units of the inoculum. Therefore, the A. chlorophenolicus A6L population was positively stimulated by the presence of the 4-chlorophenol substrate (180 microg g(-1) soil) that it catabolized during the first 8 days of the incubation period as a carbon and energy source. Together, these results demonstrate that specific populations in the soil bacterial community rapidly fluctuated in response to specific disturbances and the resulting shifts in the community may therefore represent an adjustment in community structure favoring those populations best capable of responding to novel stress scenarios.

Characterization of microbial community during Asian dust events in Korea

An Asian dust event, also sometimes known as a Yellow Sand event, is a seasonal meteorological phenomenon affecting East Asia, typically in the early spring. Because of the significant ecological and health effects of these events on East Asia, and the large amount of dust that is transported from the desert in China to Korea and Japan, these events have been receiving increased attention. It is likely that these storms often provide long-range transport to various microorganisms. However, despite a certain level of attention to the chemical analysis of these storms, microbiological studies of Yellow Sand dust have been scarce. We collected a total of 30 microbiological air samples using a PM(2.5) cyclone sampler in Seoul, Korea from April 2007 to March 2008. Six of these samples were collected during Yellow Sand events, while 24 were from non-Yellow Sand events. Chemical analysis was performed on the samples using a thermal-optical transmittance (TOT) method. Total nucleic acids were also extracted, and the 16S rDNA was amplified by PCR and analyzed by denaturing gradient gel electrophoresis (DGGE). Dendrogram analysis, based on DGGE, indicated that the microbial profiles from the Yellow Sand were distinctive from those of the non-Yellow Sand samples. Microorganisms identified in Yellow Sand samples included Aquabacterium sp., Flavobacteriales bacterium sp., Prevotellaceae bacterium sp., and others, whereas microorganisms in non-Yellow Sand samples included Propionibacterium sp., Bacillus sp., Acinetobacter sp., and others. These results suggest that, as a result of Yellow Sand events, humans in the affected regions are exposed to communities of microorganisms that might cause various adverse health effects.

Bacterial diversity and community structure of a sub-surface aquifer exposed to realistic low herbicide concentrations

An increasing number of herbicides are found in our groundwater environments. This underlines the need for examining the effects of herbicide exposure on the indigenous groundwater microbial communities, as microbial degradation is the major process responsible for the complete removal of most contaminants. We examined the effect of in situ exposure to realistic low concentrations of herbicides on the microbial diversity and community structure of sub-surface sediments from a shallow aquifer near Vejen (Denmark). Three different community analyses were performed: colony morphology typing, sole-carbon source utilisation in Biolog EcoPlates, and denaturing gradient gel electrophoresis. Cluster analysis demonstrated that the microbial communities of those aquifer sediments that acclimated to the herbicide exposure also had similar community structure. This observation was concurrent for all three community analyses. In contrast, no significant effect was found on the bacterial diversity, except for the culturable fraction where a significantly increased richness and Shannon index was found in the herbicide acclimated sediments. The results of this study show that in situ exposure of sub-surface aquifers to realistic low concentrations of herbicides may alter the overall structure of a natural bacterial community, although significant effects on the genetic diversity and carbon substrate usage cannot be detected. The observed impact was probably due to indirect effects. In future investigations, the inclusion of methods that specifically detect relevant microbial sub-populations and functional genes is therefore recommended.

Confocal laser scanning microscopy image analysis for cyanobacterial biomass determined at microscale level in different microbial mats

We recently published a new method based on determining cyanobacterial biomass by confocal laser scanning microscopy image analysis (CLSM-IA) (Solé et al., Ultramicrosc 107:669-673, 2007). CLSM-IA allows biomass calculation for microorganisms of a small size, since the limit of the technique's resolution is that generated by a voxel, the smallest unit of a three-dimensional digital image, equivalent to 1.183 x 10(-3) mgC/cm(3) of sediment. This method is especially suitable for the quantitative analysis of a large number of CLSM images generated from benthic sediments in which complex populations of cyanobacteria are abundant, such as microbial mats. In order to validate the new CLSM approach, mats with varying structural characteristics were studied. We have grouped them into three types: Microcoleus mats (laminated), sandy mats (nonlaminated and composed of well-sorted quartz sands), and oil-polluted mats. In this work, we applied CLSM-IA in natural [the Ebro delta and Sant Jordi colony (Spain), Salins-de-Giraud and Etang de Berre (France), and Orkney Islands (Scotland)] and artificial [mesocosms (Israel)] microbial mats. A total of 4,103 confocal images were obtained in order to determine total and individual cyanobacteria biomass profiles, at microscale level. The data presented in this paper show the efficacy of the method, as it can be applied to highly diverse mat samples.