Response of 1,2-dichloroethane-adapted microbial communities to ex-situ biostimulation of polluted groundwater

The microbial community of a groundwater system contaminated by 1,2-dichloroethane (1,2-DCA), a toxic and persistent chlorinated hydrocarbon, has been investigated for its response to biostimulation finalized to 1,2-DCA removal by reductive dehalogenation. The microbial population profile of samples from different wells in the aquifer and from microcosms enriched in the laboratory with different organic electron donors was analyzed by ARISA (Amplified Ribosomal Intergenic Spacer Analysis) and DGGE (Denaturing Gradient Gel Electrophoresis) of 16S rRNA genes. 1,2-DCA was completely removed with release of ethene from most of the microcosms supplemented with lactate, acetate plus formate, while cheese whey supported 1,2-DCA dehalogenation only after a lag period. Microbial species richness deduced from ARISA profiles of the microbial community before and after electron donor amendments indicated that the response of the community to biostimulation was heterogeneous and depended on the well from which groundwater was sampled. Sequencing of 16S rRNA genes separated by DGGE indicated the presence of bacteria previously associated with soils and groundwater polluted by halogenated hydrocarbons or present in consortia active in the removal of these compounds. A PCR assay specific for Desulfitobacterium sp. showed the enrichment of this genus in some of the microcosms. The dehalogenation potential of the microbial community was confirmed by the amplification of dehalogenase-related sequences from the most active microcosms. Cloning and sequencing of PCR products indicated the presence in the metagenome of the bacterial community of a new dehalogenase potentially involved in 1,2-DCA reductive dechlorination.     

Response of marine microbial communities to anthropogenic stress

Marine microbial communities adapt rapidly to changingenvironmental conditions, including anthropogenicstress. Adaptation involves a wide range ofstrategies, including, (a) formation of resistant,dormant stages, (b) initiation of repair mechanisms, (c)immobilization of toxic chemicals, (d) active transportof chemicals out of the cell, (e) use of contaminantchemicals as carbon or energy sources, and (f)transformation of contaminants to less toxic or morevolatile forms.Adaptation responses are generally plasmid- orchromosomally-mediated and controlled throughinduction or derepression of a variety of biochemicalpathways. Characterization of microbial communityresponses at the molecular level provides biomarkersof contaminant exposure which in turn may be used toprovide an overall picture of ecosystem health. Thisreview will discuss the interactions betweenmicroorganisms and environmental contaminants and thepotential use of microbial biomarkers to assess thehealth of the microbial ecosystem.     

Chemical and microbial community analysis during aerobic biostimulation assays of non-sulfonated alkyl-benzene-contaminated groundwater

A chemical and microbial characterization of lab-scale biostimulation assays with groundwater samples taken from an industrial site in which the aquifer had been contaminated by linear non-sulfonate alkyl benzenes (LABs) was carried out for further field-scale bioremediation purposes. Two lab-scale biodegradability assays were performed, one with a previously obtained gas-oil-degrading consortium and another with the native groundwater flora. Results for the characterization of the groundwater microbial population of the site revealed the presence of an important LAB-degrading microbial population with a strong degrading capacity. Among the microorganisms identified at the site, the detection of Parvibaculum lavamentivorans, which have been described in other studies as alkyl benzene sulfonates degraders, is worth mentioning. Incubation of P. lavamentivorans DSMZ13023 with LABs as reported in this study shows for the first time the metabolic capacity of this strain to degrade such compounds. Results from the biodegradation assays in this study showed that the indigenous microbial population had a higher degrading capacity than the gas-oil-degrading consortium, indicating the strong ability of the native community to adapt to the presence of LABs. The addition of inorganic nutrients significantly improved the aerobic biodegradation rate, achieving levels of biodegradation close to 90%. The results of this study show the potential effectiveness of oxygen and nutrients as in situ biostimulation agents as well as the existence of a complex microbial community that encompasses well-known hydrocarbon- and LAS-degrading microbial populations in the aquifer studied.     

Effects of temperature and biostimulation on oil-degrading microbial communities in temperate estuarine waters

Improved strategies for oil-spill remediation will follow a better understanding of the nature, activities and regulating parameters of petroleum hydrocarbon-degrading microbial communities in temperate marine environments. The addition of crude oil to estuarine water resulted in an immediate change in bacterial community structure, increased abundance of hydrocarbon-degrading microorganisms and a rapid rate of oil degradation, suggesting the presence of a pre-adapted oil-degrading microbial community and sufficient supply of nutrients. Relatively rapid degradation was found at 4°C, the lowest temperature tested; and it was temperature rather than nutrient addition that most influenced the community structure. A detailed phylogenetic analysis of oil-degrading microcosms showed that known hydrocarbonoclastic organisms like Thalassolituus and Cycloclasticus , as well as proposed oil degraders like Roseobacter , were present at both 4°C and 20°C, demonstrating the thermo-versatility of such organisms. Clones related to Oleispira antarctica (98% 16S rRNA similarity), a psychrophilic alkane degrader, were dominant in the 4°C oil-degrading community, whereas other clones constituting a different clade and showing 94% similarity 16S rRNA with O. antarctica were found in situ. These findings demonstrate the potential for intrinsic bioremediation throughout the course of the year in temperate estuarine waters, and highlight the importance of both versatile psychrotolerant and specialized psychrophilic hydrocarbon-degrading microbes in effecting this process at low temperatures.     

Flooding forested groundwater recharge areas modifies microbial communities from top soil to groundwater table

Subsurface microorganisms are crucial for contaminant degradation and maintenance of groundwater quality. This study investigates the microbial biomass and community composition [by phospholipid fatty acids (PLFAs)], as well as physical and chemical soil characteristics at woodland flooding sites of an artificial groundwater recharge system used for drinking water production. Vertical soil profiles to c . 4 m at two watered and one nonwatered site were analyzed. The microbial biomass was equal in watered and nonwatered sites, and considerable fractions (25–42%) were located in 40–340 cm depth. The microbial community structure differed significantly between watered and nonwatered sites, predominantly below 100 cm depth. Proportions of the bacterial PLFAs 16:1ω5, 16:1ω7, cy17:0 and 18:1ω9t, and the long-chained PLFAs 22:1ω9 and 24:1ω9 were more prominent at the watered sites, whereas branched, saturated PLFAs (iso/anteiso) dominated at the nonwatered site. PLFA community indices indicated stress response ( trans / cis ratio), higher nutrient availability (unsaturation index) and changes in membrane fluidity (iso/anteiso ratio) due to flooding. In conclusion, water recharge processes led to nutrient input and altered environmental conditions, which resulted in a highly active and adapted microbial community residing in the vadose zone that effectively degraded organic compounds.     

微生物燃料电池阳极微生物群落对乳酸-丙酸-乳酸底物转换的响应特征

摘要:【目的】为探讨底物波动对微生物燃料电池(MFC)产电效能和阳极微生物群落的影响,【方法】依次以乳酸-丙酸-乳酸为底物,应用不依赖于培养的微生物分子生态学技术,解析单室MFC 启动及底物替换过程中阳极微生物群落的动态学响应特征。【结果】底物的更换过程降低了MFC的产电效能,当改变为新底物后,MFC需要较长的产电恢复期。同时,底物的转换改变了阳极微生物群落结构,Anaeromusa spp.、Pseudomonas spp．以及Thiobacillus thioparus对乳酸底物具有很好的响应,随着乳酸底物的投加而富集;丙酸底物对Dechloromonas spp.和Comamonas testosteroni等类群表现出较强的选择作用;而产电微生物Geobacter spp.由于利用乳酸、丙酸的共同代谢产物乙酸为底物而被逐渐富集,是多种底物替换过程的重叠种群。【结论】本研究表明,MFC的阳极微生物群落组成与投加的底物有较强的对应性,为了减缓底物波动对MFC产电过程的影响,应尽量采用混合有机底物,以提供宽泛的营养生态位,提高种群的功能重叠性。     

Response of microbial communities of Lake Baikal to extreme temperatures

The survival rate, metabolic activity, and ability for growth of microbial communities of Lake Baikal after exposure to extremely low temperatures (freeze-thawing) for different lengths of time have been first studied. It has been shown that short-term freezing (1-3 days) inhibits the growth and activity of microbial communities. The quantity of microorganisms increased after 7- and 15-day freezing. In the periods of maximums, the total number of microorganisms in the test samples was twice as high as in the control. It was established that after more prolonged freezing the microorganisms required more time after thawing to adapt to new conditions. In the variants with 7- and 15-day freezing, the activities of defrosted microbial communities were three or more times higher than in the control. The survival rate and activity of Baikal microorganisms after freeze-thawing confirms the fact that the Baikal microbial communities are highly resistant to this type of stress impact.     

Response of microbial communities of Lake Baikal to extreme temperatures

The survival rate, metabolic activity, and ability for growth of microbial communities of Lake Baikal have been first studied after exposure to extremely low temperatures (freeze-thawing) for different lengths of time. It has been shown that short-term freezing (1–3 days) inhibits the growth and activity of microbial communities. The quantity of microorganisms increased after 7-and 15-day freezing. In the periods of maximums, the total number of microorganisms in the test samples was twice as high as in the control. It was established that after more prolonged freezing the microorganisms required more time after thawing to adapt to new conditions. In the variants with 7-and 15-day freezing, the activities of defrosted microbial communities were three or more times higher than in the control. The survival rate and activity of Baikal microorganisms after freeze-thawing confirms the fact that the Baikal microbial communities are highly resistant to this type of stress impact.     

地下水微生物功能群及生物地球化学循环

地下水系统是地球关键带的重要组成部分,为微生物提供了特殊的栖息环境和复杂的生存条件,进而演化出复杂的生物地球化学过程.随着多技术、多学科的交叉融合及发展,近几十年地下水微生物功能群及生物地球化学循环研究取得了引人瞩目的 重要进展.本文从地下水中的微生物群功能分区、微生物介导的地球化学元素循环、污染与修复中的生物地球化学...     

Mixed aerobic and anaerobic microbial communities in benzene-contaminated groundwater

Aims:  To investigate the factors affecting benzene biodegradation and microbial community composition in a contaminated aquifer.
Methods and Results:  We identified the microbial community in groundwater samples from a benzene-contaminated aquifer situated below a petrochemical plant. Eleven out of twelve groundwater samples with in situ dissolved oxygen concentrations between 0 and 2·57 mg l⁻¹ showed benzene degradation in aerobic microcosm experiments, whereas no degradation in anaerobic microcosms was observed. The lack of aerobic degradation in the remaining microcosm could be attributed to a pH of 12·1. Three groundwaters, examined by 16S rRNA gene clone libraries, with low in situ oxygen concentrations and high benzene levels, each had a different dominant aerobic (or denitrifying) population, either Pseudomonas , Polaromonas or Acidovorax species. These groundwaters also had syntrophic organisms, and aceticlastic methanogens were detected in two samples. The alkaline groundwater was dominated by organisms closely related to Hydrogenophaga .
Conclusions:  Results show that pH 12·1 is inimical to benzene biodegradation, and that oxygen concentrations below 0·03 mg l⁻¹ can support aerobic benzene-degrading communities.
Significance and Impact of the Study:  These findings will help to guide the treatment of contaminated groundwaters, and raise questions about the extent to which aerobes and anaerobes may interact to effect benzene degradation.     

Local adaptation of microbial communities to heavy metal stress in polluted sediments of Lake Erie

Microbial communities must balance the assimilation of biologically necessary metals with resistance to toxic metal concentrations. To investigate the impact of heavy metal contaminants on microbial communities, we performed two experiments measuring extracellular enzyme activities (EEA) in polluted and unpolluted sediments of Lake Erie. In the first experiment, inoculations with moderate concentrations of copper and zinc appreciably diminished EEA from uncontaminated sites, whereas EEA from contaminated sediments increased or were only negligibly affected. In the second experiment, we compared the effects of three separate metals (i.e. copper, arsenic, and cadmium) on microbial community metabolism in polluted and unpolluted locations. Although copper and arsenic elicited differential effects by inhibiting EEA only in unpolluted sediments, cadmium inhibited EEA in both polluted and unpolluted sediments. Multivariate analyses of EEA from polluted sediments revealed direct associations among hydrolytic enzymes and inverse or absent associations between hydrolases and oxidases; these associations demonstrated resilience to heavy metal stress. In contrast, addition of heavy metals to unpolluted sediments appeared to have a higher impact on the multivariate pattern of EEA associations as revealed by an increase in the number of associations, more inverse relationships, and potential enzymatic trade-offs. The results of this study suggest community-level adaptations through the development of resistance mechanisms to the types and local levels of heavy metals in the environment.     

Response of microbial communities to elevated thallium contamination in river sediments

Abstract

The study of microbial communities in river sediments contaminated by thallium (Tl) is necessary to achieve the information for in-situ microbially mediated bioremediation. However, little is known about the microbial community in Tl-contaminated river sediments. In the present study, we characterized the microbial community and their responses to Tl pollution in river sediments from the Tl-mineralized Lanmuchang area, Southwest Guizhou, China. Illumina sequencing of 16S rRNA amplicons revealed that over 40 phyla belong to the domain bacteria. In all samples, Proteobacteria, Cyanobacteria, and Actinobacteria were the most dominant phyla. Based on the UPGMA (Unweighted Pair Group Method with Arithmetic Mean) tree and PCoA (Principal Coordinates Analysis) analysis, microbial composition of each segment was distinct, indicating in-situ geochemical parameters (including Tl, sulfate, TOC, Eh, and pH) had influenced on the microbial communities. Moreover, canonical correspondence analysis (CCA) was employed to further elucidate the impact of geochemical parameters on the distribution of microbial communities in local river sediments. The results indicated that a number of microbial communities including Cyanobacteria, Spirochaete, Hydrogenophaga, and Acinetobacter were positively correlated with total Tl, suggesting potential roles of these microbes to Tl tolerance or to biogeochemical cycling of Tl. Our results suggested a reliable location for the microbial community’s diversity in the presence of high concentrations of Tl and might have a potential association for in-situ bioremediation strategies of Tl-contaminated river. Overall, in situ microbial community could provide a useful tool for monitoring and assessing geo-environmental stressors in Tl-polluted river sediments.     

Succession of microbial communities during a biostimulation process as evaluated by DGGE and clone library analyses

AIMS: The objective of this study was to investigate the changes in the indigenous bacterial community structure for assessing the impact of biostimulation on spilled oil. METHODS AND RESULTS: Changes in the bacterial community structure were monitored by denaturing gradient gel electrophoresis (DGGE) and clone library methods based on 16S rRNA gene (rDNA) sequences. The results of DGGE, coupled with the use of the Shannon index and principal component analysis (PCA) and clone library analyses, were consistent. In the treated (fertilized) area, one operational taxonomic unit (OTU) became dominant during the fertilization period, and it was most closely related to Pseudomonas putida. CONCLUSIONS: The bacterial community structure in the treated area was markedly different from that in the control (non-fertilized) area during the fertilization period, but in the two areas it became similar at 14 weeks after the end of fertilization. SIGNIFICANCE AND IMPACT OF THE STUDY: The results suggest that the bacterial community structure was disrupted by the biostimulation treatment, but that it recovered immediately after the end of fertilization.     

Two approaches to biological decontamination of groundwater and soil polluted by aromatics-characterization of microbial populations.

As part of the EU project MULTIBARRIERS, six new endogenous aerobic bacterial isolates able to grow in the presence of BTmX (benzene, toluene, m-xylene) were characterized with respect to their growth specificities. Preliminary analysis included restriction fragment length polymorphism profiles and 16S rDNA sequencing. The diversity of these strains was confirmed by denaturing gradient gel electrophoresis. Additional aerobic bacterial strains were isolated from the rhizospheres of plants grown in polychlorinated biphenyl (PCB)-contaminated soils. Pot experiments were designed to show the beneficial effect of plants on the bacterial degradation of PCBs. The effect of PCB removal from soil was evaluated and bacteria isolated from three different plant species were examined for the presence of the bph operon.     

Response of grazing snails to phosphorus enrichment of modern stromatolitic microbial communities

1. The effects of added phosphorus (P) on the growth, P and RNA : DNA contents, and survivorship of snails grazing on laminated microbial mats (living ‘stromatolites’) were examined in the Rio Mesquites at Cuatro Ciénegas, Mexico (total P, c. 0.60 μmol L^?1) to test the hypothesis that strong P‐limitation of microautotroph growth produces a stoichiometric constraint on herbivores because of mineral P‐limitation. 2. In a 3‐week experiment performed in summer 2001, addition of phosphorus (+15 μmol L^?1) resulted in a strong decline in stromatolite biomass C : P ratio from very high levels (c. 2300 : 1 by atoms) to moderate levels (c. 550 : 1). The endemic hydrobiid snail Mexithauma quadripaludium responded to P‐enrichment with elevated body P content and higher RNA : DNA ratios, especially for small animals likely to be actively growing. This positive response is consistent with the existence of a stoichiometric constraint on snail growth. 3. In a longer experiment (8 weeks) involving a more moderate P enrichment (+5 μmol L^?1) in summer 2002, P enrichment reduced stromatolite C : P ratio from moderate values in control treatments (c. 750) to very low values (<100 : 1). Snails responded to stromatolite P‐enrichment with increased body P content but, in contrast to the first experiment, with lower RNA : DNA ratio, lower growth rates, and higher mortality. 4. These contrasting results suggest that both very high and very low biomass C : P ratios in stromatolites are detrimental to M. quadripaludium performance, leading us to hypothesise that these herbivores live on a ‘stoichiometric knife edge’.     

Response of water column microbial communities to sudden exposure to deltamethrin in aquatic mesocosms

Sudden exposure of an aquatic system to an insecticide can have significant effects on populations other than susceptible organisms. Although this is intuitively obvious, little is actually known about how such exposure might affect bacterial communities and their relative metabolic activity in ecosystems. Here, we assessed small sub-unit (ssu)-RNA levels in open and shaded 9 m(3) aquatic mesocosms (16 units - 2 x 2 factorial design in quadruplicate) to examine the effects of sudden addition of deltamethrin to the units. When deltamethrin was added, a cascade of bacterial then phytoplankton "blooms" occurred over time. The bacterial bloom, which most likely included organisms from the plastid/cyanobacterial phylogenetic guild, was almost immediate (within hours), whereas the phytoplankton (algal) bloom lagged by about 4 days. This sequential response can be explained by an apparent sudden release of nutrients consequent to arthropod death that triggered a series of responses in the microbial loop. Interestingly, bacterial blooms were noted in both open and shaded mesocosms, whereas the algal bloom was only seen in open units, suggesting that both deltamethrin addition (and presumptive nutrient release) and an adequate light supply was required for the phytoplankton response. Overall, this work shows that microbial activities as reflected by ssu-rRNA levels can respond dramatically via apparently indirect effects following insecticide application.     

Response of microbial communities to pesticide residues in soil restored with Azolla imbricata

Applied Microbiology and Biotechnology - Under conditions of Azolla imbricata restoration, the high-throughput sequencing technology was employed to determine change trends of microbial community...     

Reclamation of an activated-sludge microbial consortium by selective biostimulation

Our previous study showed that an activated-sludge process broke down at the phenol-loading rate of 1.5 g l⁻¹ day⁻¹, when non-flocculating bacteria (called R6T and R10) overgrew the sludge, resulting in a sludge washout. In this study, we attempted to circumvent this breakdown problem by reclaiming the consortium structure. Activated sludge was fed phenol, and the phenol-loading rate was increased stepwise from 0.5 g l⁻¹ day⁻¹ to 1.0 g l⁻¹ day⁻¹ and then to 1.5 g l⁻¹ day⁻¹. Either galactose or glucose (at 0.5 g l⁻¹ day⁻¹) was also supplied to the activated sludge from the phenol-loading rate of 1.0 g l⁻¹ day⁻¹. Pure culture experiments have suggested galactose to be a preferential substrate for a floc-forming bacterium (R6F) that predominantly degrades phenol under low phenol-loading conditions. Supplying galactose allowed sustainment of the R6F population and suppression of the overgrowth of R6T and R10 at the phenol-loading rate of 1.5 g l⁻¹ day⁻¹. This measure allowed the activated-sludge process to treat phenol at a phenol-loading rate up to 1.5 g l⁻¹ day⁻¹, although it broke down at 2.0 g l⁻¹ day⁻¹. In contrast, supplying glucose reduced the R6F population and allowed the activated-sludge process to break down at the phenol-loading rate of 1.0 g l⁻¹ day⁻¹. This study demonstrated that reclamation of the activated-sludge consortium by selective biostimulation of the floc-forming population improved the phenol-treating ability of the process. Received: 13 January 2000 / Received revision: 10 March 2000 / Accepted: 7 April 2000     

Molecular characterization of microbial communities in deep coal seam groundwater of northern Japan

We investigated microbial methanogenesis and community structure based on 16S rRNA gene sequences from a coal seam aquifer located 843–907 m below ground level in northern Japan; additionally, we studied the δ¹³C and δ²H (δD) of coal‐bed gases and other physicochemical parameters. Although isotopic analysis suggested a thermocatalytic origin for the gases, the microbial activity and community structure strongly implied the existence of methanogenic microbial communities in situ. Methane was generated in the enrichment cultures of the hydrogenotrophic and methylotrophic microorganisms obtained from coal seam groundwater. Methanogen clones dominated the archaeal 16S rRNA gene libraries and were mostly related to the hydrogenotrophic genus Methanoculleus and the methylotrophic genus Methanolobus. Bacterial 16S rRNA gene libraries were dominated by the clones related to the genera Acetobacterium and Syntrophus which have a symbiotic association with methanogens. LIBSHUFF analysis revealed that N₂ gas injected into the coal seam (for enhanced methane production) does not affect the coverage of archaeal and bacterial populations. However, amova analysis does provide evidence for a change in the genetic diversity of archaeal populations that are dominated by methanogens. Therefore, N₂ injection into the coal seam might affect the cycling of matter by methanogens in situ.     

Adaptive response of microbial communities to soluble microbial products

We carried out two experiments to study the influence of soluble microbial products (SMP) on biomass concentration [defined as mixed liquor suspended solids (MLSS)] and removal of soluble biological and chemical oxygen demands (sBOD₅ and sCOD): (1) SMP were allowed to accumulate, and (2) SMP content was artificially reduced by washing the biomass. The daily initial sCOD in both experiments was kept constant at 859±6 mg/l for 16 days. In experiment 1, the highest sCOD removal (80%) occurred during the first day. Thereafter, it decreased successively to 40% [sludge retention time (SRT), 12 days], after which it increased steadily to 50±4%. Variations in residual sCOD were accompanied by variations in sBOD₅, showing that the biodegradability of the accumulated SMP components was changing. MLSS fluctuated within the range 1,200±25–1,993±58 mg/l. We attributed the irregular accumulation of the biomass to variations in the biodegradability of SMP components. The initial sBOD₅/MLSS ratio varied according to variations in initial sBOD₅ and MLSS, whereas the residual ratio was constant at 0.025±0.008. This indicated a direct relationship between the concentrations of biomass and SMP produced. In experiment 2, MLSS increased from 1,200±25 to a constant value (2,810±16 mg/l; SRT, 12 days). After this time, no decrease or increase in MLSS was observed. Correspondingly, sCOD and sBOD₅ removal increased from 80–97 to 84–99%. A stable microbial community that could consume organic matter efficiently was developed under these conditions.