Measurement and modeling of multiple substrate oxidation by methanotrophs at 20 degrees C

Earlier experiments have shown that when Methylosinus trichosporium OB3b was grown at 30 degrees C, greater growth and degradation of chlorinated ethenes was observed under particulate methane monooxygenase (pMMO)-expressing conditions than sMMO-expressing conditions. The effect of temperature on the growth and ability of methanotrophs to degrade chlorinated ethenes, however, has not been examined, particularly temperatures more representative of groundwater systems. Thus, experiments were performed at 20 degrees C to examine the effect of mixtures of trichloroethylene, trans-dichloroethylene and vinyl chloride in the presence of methane on the growth and ability of Methylosinus trichosporium OB3b cells to degrade these pollutants. Although the maximal rates of chlorinated ethane degradation were greater by M. trichosporium OB3b expressing sMMO as compared with the same cell expressing pMMO, the growth and ability of sMMO-expressing cells to degrade these cosubstrates was substantially inhibited in their presence as compared with the same cell expressing pMMO. The Delta model developed earlier was found to be useful for predicting the effect of chlorinated ethenes on the growth and ability of M. trichosporium OB3b to degrade these compounds at a growth temperature of 20 degrees C. Finally, it was also discovered that at 20 degrees C, cells expressing pMMO exhibited faster turnover of methane than sMMO-expressing cells, unlike that found earlier at 30 degrees C, suggesting that temperature may exert selective pressure on methanotrophic communities to express sMMO or pMMO.     

The natural chlorine cycle – fitting the scattered pieces

Chlorine is one of the most abundant elements on the surface of the earth. Until recently, it was widely believed that all chlorinated organic compounds were xenobiotic, that chlorine does not participate in biological processes and that it is present in the environment only as chloride. However, over the years, research has revealed that chlorine takes part in a complex biogeochemical cycle, that it is one of the major elements of soil organic matter and that the amount of naturally formed organic chlorine present in the environment can be counted in tons per km(2). Interestingly enough, some of the pieces of the chlorine puzzle have actually been known for decades, but the information has been scattered among a number of different disciplines with little or no exchange of information. The lack of communication appears to be due to the fact that the points of departure in the various fields have not corresponded; a number of paradoxes are actually revealed when the known pieces of the chlorine puzzle are fit together. It appears as if a number of generally agreed statements or tacit understandings have guided perceptions, and that these have obstructed the understanding of the chlorine-cycle as a whole. The present review enlightens four paradoxes that spring up when some persistent tacit understandings are viewed in the light of recent work as well as earlier findings in other areas. The paradoxes illuminated in this paper are that it is generally agreed that: (1) chlorinated organic compounds are xenobiotic even though more than 1,000 naturally produced chlorinated compounds have been identified; (2) only a few, rather specialised, organisms are able to convert chloride to organic chlorine even though it appears as if the ability among organisms to transform chloride to organic chlorine is more the rule than the exception; (3) all chlorinated organic compounds are persistent and toxic even though the vast majority of naturally produced organic chlorine is neither persistent nor toxic; (4) chlorine is mainly found in its ionic form in the environment even though organic chlorine is as abundant or even more abundant than chloride in soil. Furthermore, the contours of the terrestrial chlorine cycle are outlined and put in a concrete form by constructing a rough chlorine budget over a small forested catchment. Finally, possible ecological roles of the turnover of chlorine are discussed.     

Biodegradation of chlorinated ethenes by a methane-utilizing mixed culture.

Chlorinated ethenes are toxic substances which are widely distributed groundwater contaminants and are persistent in the subsurface environment. Reports on the biodegradation of these compounds under anaerobic conditions which might occur naturally in groundwater show that these substances degrade very slowly, if at all. Previous attempts to degrade chlorinated ethenes aerobically have produced conflicting results. A mixed culture containing methane-utilizing bacteria was obtained by methane enrichment of a sediment sample. Biodegradation experiments carried out in sealed culture bottles with radioactively labeled trichloroethylene (TCE) showed that approximately half of the radioactive carbon had been converted to 14CO2 and bacterial biomass. In addition to TCE, vinyl chloride and vinylidene chloride could be degraded to products which are not volatile chlorinated substances and are therefore likely to be further degraded to CO2. Two other chlorinated ethenes, cis and trans-1,2-dichloroethylene, were shown to degrade to chlorinated products, which appeared to degrade further. A sixth chlorinated ethene, tetrachloroethylene, was not degraded by the methane-utilizing culture under these conditions. The biodegradation of TCE was inhibited by acetylene, a specific inhibitor of methane oxidation by methanotrophs. This observation supported the hypothesis that a methanotroph is responsible for the observed biodegradations.     

Biodegradation of chlorinated ethenes by a methane-utilizing mixed culture

Chlorinated ethenes are toxic substances which are widely distributed groundwater contaminants and are persistent in the subsurface environment. Reports on the biodegradation of these compounds under anaerobic conditions which might occur naturally in groundwater show that these substances degrade very slowly, if at all. Previous attempts to degrade chlorinated ethenes aerobically have produced conflicting results. A mixed culture containing methane-utilizing bacteria was obtained by methane enrichment of a sediment sample. Biodegradation experiments carried out in sealed culture bottles with radioactively labeled trichloroethylene (TCE) showed that approximately half of the radioactive carbon had been converted to 14CO2 and bacterial biomass. In addition to TCE, vinyl chloride and vinylidene chloride could be degraded to products which are not volatile chlorinated substances and are therefore likely to be further degraded to CO2. Two other chlorinated ethenes, cis and trans-1,2-dichloroethylene, were shown to degrade to chlorinated products, which appeared to degrade further. A sixth chlorinated ethene, tetrachloroethylene, was not degraded by the methane-utilizing culture under these conditions. The biodegradation of TCE was inhibited by acetylene, a specific inhibitor of methane oxidation by methanotrophs. This observation supported the hypothesis that a methanotroph is responsible for the observed biodegradations.     

Plant acquisition of organic nitrogen in boreal forests

Research on plant nitrogen (N) uptake and metabolism has more or less exclusively concerned inorganic N, particularly nitrate. Nevertheless, recent as well as older studies indicate that plants may have access to organic N sources. Laboratory studies have shown that ectomycorrhizal and ericoid mycorrhizal plants can degrade polymeric N and absorb the resulting products. Recent studies have also shown that some non‐mycorrhizal plants are able to absorb amino acids. Moreover, amino acid transporters have been shown to be present in both plant roots and in mycorrhizal hyphae. Although both mycorrhizal and non‐mycorrhizal plants appear to have a capacity for absorbing a range of organic N compounds, is this capacity realized in the field? Several lines of evidence show that plants are outcompeted by microorganisms for organic N sources. Such studies, however, have not addressed the issue of spatial and temporal separation between plants and microorganisms. Moreover, competition studies have not been able to separate uptake by symbiotic and non‐symbiotic microorganisms. Qualitative assessment of organic N uptake by plants has been performed with dual‐labelled glycine in several studies. These studies arrive at different conclusions: some indicate that plants do not absorb this organic N source when competing with other organisms in soil, while others conclude that significant fractions of amino acid N are absorbed as intact amino acid. These variable results may reflect species differences in the ability to absorb glycine as well as differences in experimental conditions and analytical techniques. Although theoretical calculations indicate that organic N might add significant amounts of N to plant N uptake, direct quantitative assessment of the fraction of plant N derived from uptake by organic N sources is a challenge for future research.     

Total biodegradation of 4-chlorobiphenyl (4 CB) by a two-membered bacterial culture

Summary Several bacterial strains that can oxidize mono- and dichlorinated biphenyls with one unsubstituted ring have already been described. The major route for this biodegradation leads ultimately to the corresponding chlorobenzoic acid, but several other minor chlorinated metabolites that might possibly be of concern for the environment have also been described previously. Since none of the bacterial strains that are able to oxidize these chlorinated biphenyls in pure culture are known to degrade chlorobenzoic acid, the oxidation of these substrates by axenic cultures always generates chlorobenzoates plus several other metabolites. In the present study, we have estimated the biodegradation of 4-chlorobiphenyl (4CB) by a two-membered bacterial culture containing one strain able to grow on 4CB and to transform it into 4-chlorobenzoate (4CBA) and one strain able to degrade 4CBA. The results were encouraging, since it was shown that the degradation of 4CB was more rapid and complete with the double bacterial culture.     

Molecular characteristics of xenobiotic-degrading sphingomonads

The genus Sphingomonas (sensu latu) belongs to the α-Proteobacteria and comprises strictly aerobic chemoheterotrophic bacteria that are widespread in various aquatic and terrestrial environments. The members of this genus are often isolated and studied because of their ability to degrade recalcitrant natural and anthropogenic compounds, such as (substituted) biphenyl(s) and naphthalene(s), fluorene, (substituted) phenanthrene(s), pyrene, (chlorinated) diphenylether(s), (chlorinated) furan(s), (chlorinated) dibenzo-p-dioxin(s), carbazole, estradiol, polyethylene glycols, chlorinated phenols, nonylphenols, and different herbicides and pesticides. The metabolic versatility of these organisms suggests that they have evolved mechanisms to adapt quicker and/or more efficiently to the degradation of novel compounds in the environment than members of other bacterial genera. Comparative analyses demonstrate that sphingomonads generally use similar degradative pathways as other groups of microorganisms but deviate from competing microorganisms by the existence of multiple hydroxylating oxygenases and the conservation of specific gene clusters. Furthermore, there is increasing evidence for the existence of plasmids that only can be disseminated among sphingomonads and which undergo after conjugative transfer pronounced rearrangements.     

Iron--dioxygen-dependent changes to the biological activities of bleomycin

Antitumor antibiotic bleomycin can bind to and degrade DNA, both in vivo and in vitro. This DNA damaging property in vitro can be related to its ability to chelate ferrous ions under aerobic conditions leading to the formation of "active oxygens," which are thought to be directly responsible for the damage. At present, evidence points to the hydroxyl radical formed by an iron-catalyzed Haber-Weiss reaction as the free radical most likely to be involved in this damage. When these same reactions occur in the absence of DNA, the free radicals then damage the bleomycin molecule, resulting in changes to its DNA-degrading activity, antibacterial properties, and chemical composition. Attempts to protect both bleomycin and DNA with a variety of specific and nonspecific scavengers have been unsuccessful, with several even showing pro-oxidant activity towards the iron-dependent damage. Only the metal chelators were effective inhibitors of bleomycin-iron-dependent damage to DNA. The damaged bleomycin lost some 50% of its ability to degrade DNA in vitro. This activity was closely paralleled by a loss in antibacterial activity against two different strains of bacteria.     

Isolation and Characterization of a Mixed Culture That Degrades Polychlorinated Biphenyls

A mixed culture composed of two Pseudomonas strains, designated as KKL101 and KKS102, was isolated from soil. This mixed culture had an enhanced ability to degrade various polychlorinated biphenyls (PCBs) which include highly chlorinated components. They did not grow individually on the mineral salts medium supplemented with a highly chlorinated PCB (PCB48, a mixture of mainly tetrachlorobiphenyl) and biphenyl. When the spent medium of KKL101 was added to the washed cell preparation of KKS102, however, the latter grew on these carbon sources, producing yellow compounds which were identified as metabolic intermediates of the carbon sources, biphenyl and PCBs. These results suggest that KKL101 produces a growth factor(s) essential for KKS102 to grow on PCBs and that the growth of KKL101 is supported by the metabolic intermediates produced by KKS102. It appears that these two bacterial strains have a symbiotic relationship. From the analysis of the degradation products of various PCB congeners, it was found that strain KKS102 degrades a wide range of PCBs which have been considered to be refractory to biological degradation.     

Induction of temperate cyanophage AS-1 by heavy metal - copper

Background  

It has been reported that some marine cyanophage are temperate and can be induced from a lysogenic phase to a lytic phase by different agents such as heavy metals. However, to date no significant reports have focused on the temperate nature of freshwater cyanophage/cyanobacteria. Previous experiments with cyanophage AS-1 and cyanobacteria Anacystis nidulans have provided some evidence that AS-1 may have a lysogenic life cycle in addition to the characterized lytic cycle.     

Genotoxic activity of organic chemicals in drinking water

The information summarized in this review provides substantial evidence for the widespread presence of genotoxins in drinking water. In many, if not most cases, the genotoxic activity can be directly attributed to the chlorination stage of drinking water treatment. The genotoxic activity appears to originate primarily from reactions of chlorine with humic substances in the source waters. Genotoxic activity in drinking water concentrates has been most frequently demonstrated using bacterial mutagenicity tests but results with mammalian cell assay systems are generally consistent with the findings from the bacterial assays. There is currently no evidence for genotoxic damage following in vivo exposures to animals. In some locations genotoxic contaminants of probable industrial and/or agricultural origin occur in the source waters and contribute substantially to the genotoxic activity of finished drinking waters. The method used for sample concentration can have an important bearing on study results. In particular, organic acids account for most of the mutagenicity of chlorinated drinking water, and their recovery from water requires a sample acidification step prior to extraction or XAD resin adsorption. Considerable work has been done to determine the identity of the compounds responsible for the mutagenicity of organic concentrates of drinking water. Recently, one class of acidic compounds, the chlorinated hydroxyfuranones, has been shown to be responsible for a major part of the mutagenic activity. Strategies for drinking water treatment that have been evaluated with respect to reduction of genotoxins in drinking water include granular activated carbon (GAC) filtration, chemical destruction, and the use of alternative means of treatment (i.e., ozone, chlorine dioxide, and monochloramine). GAC treatment has been found to be effective for removal of mutagens from drinking water even after the GAC is beyond its normal use for organic carbon removal. All disinfectant chemicals appear to have the capacity of forming mutagenic chemicals during water treatment. However, the levels of mutagenicity formed with the alternative disinfectants have been generally less than those seen with chlorine and, especially in the case of ozone, highly dependent on the source water.(ABSTRACT TRUNCATED AT 400 WORDS)     

Degradation of the disease-associated prion protein by a serine protease from lichens

The disease-associated prion protein (PrP(TSE)), the probable etiological agent of the transmissible spongiform encephalopathies (TSEs), is resistant to degradation and can persist in the environment. Lichens, mutualistic symbioses containing fungi, algae, bacteria and occasionally cyanobacteria, are ubiquitous in the environment and have evolved unique biological activities allowing their survival in challenging ecological niches. We investigated PrP(TSE) inactivation by lichens and found acetone extracts of three lichen species (Parmelia sulcata, Cladonia rangiferina and Lobaria pulmonaria) have the ability to degrade prion protein (PrP) from TSE-infected hamsters, mice and deer. Immunoblots measuring PrP levels and protein misfolding cyclic amplification indicated at least two logs of reductions in PrP(TSE). Degradative activity was not found in closely related lichen species or in algae or a cyanobacterium that inhabit lichens. Degradation was blocked by Pefabloc SC, a serine protease inhibitor, but not inhibitors of other proteases or enzymes. Additionally, we found that PrP levels in PrP(TSE)-enriched preps or infected brain homogenates are also reduced following exposure to freshly-collected P. sulcata or an aqueous extract of the lichen. Our findings indicate that these lichen extracts efficiently degrade PrP(TSE) and suggest that some lichens could have potential to inactivate TSE infectivity on the landscape or be a source for agents to degrade prions. Further work to clone and characterize the protease, assess its effect on TSE infectivity and determine which organism or organisms present in lichens produce or influence the protease activity is warranted.     

Transformation capacities of chlorinated organics by mixed cultures enriched on methane, propane, toluene, or phenol

The degradation of trichloroethylene (TCE), chloroform (CF), and 1,2-dichloroethane (1,2-DCA) by four aerobic mixed cultures (methane, propane, toluene, and phenol oxidizers) grown under similar chemostat conditions was measured. Methane and propane oxidizers were capable of degrading both saturated and unsaturated chlorinated organics (TCE, CF, and 1,2-DCA). Toluene and phenol oxidizers degraded TCE but were not able to degrade CF, 1,2-DCA, or other saturated organics. None of the cultures tested were able to degrade perchloroethylene (PCE) or carbon tetrachloride (CC(4)). For the four cultures tested, degradation of each of the chlorinated organics resulted in cell inactivation due to product toxicity. In all cases, the toxic products were rapidly depleted, leaving no toxic residues in solution. Among the four tested cultures, the resting cells of methane oxidizers exhibited the highest transformation capacities (T(c)) for TCE, CF, and 1,2-DCA. The T(c) for each chlorinated organic was observed to be inversely proportional to the chlorine carbon ratio (Cl/C). The addition of low concentrations of growth substrate or some catabolic intermediates enhanced TCE transformation capacities and degradation rates, presumably due to the regeneration of reducing energy (NADH); however, addition of higher concentrations of most amendments reduced TCE transformation capacities and degradation rates. Reducing energy limitations and amendment toxicity may significantly affect T(c) measurements, causing a masking of the toxicity associated with chlorinated organic degradation. (c) 1995 John Wiley & Sons, Inc.     

Biodeterioration of Mayan buildings at uxmal and tulum,Mexico

Uxmal and Tulum are two important Mayan sites in the Yucatan peninsula. The buildings are mainly composed of limestone and grey/black discoloration is seen on exposed walls and copious greenish biofilms on inner walls. The principal microorganisms detected on interior walls at both Uxmal and Tulum were cyanobacteria; heterotrophic bacteria and filamentous fungi were also present. A dark‐pigmented mitosporic fungus and Bacillus cereus, both isolated from Uxmal, were shown to be acidogenic in laboratory cultures. Cyanobacteria belonging to rock‐degrading genera Synechocystis and Gloeocapsa were identified at both sites. Surface analysis previously showed that calcium ions were present in the biofilms on buildings at Uxmal and Tulum, suggesting the deposition of biosolubilized stone. Apart from their potential to degrade the substrate, the coccoid cyanobacteria supply organic nutrients for bacteria and fungi, which can produce organic acids, further increasing stone degradation.     

Methanogenic transformation of aromatic hydrocarbons and phenols in groundwater aquifers

Fermentative and methanogenic bacteria have been found repeatedly as important members of microbial flora in anoxic zones of the subsurface—in pristine as well as in contaminated groundwater aquifers. These bacteria, which together with obligate proton reducers form complex methanogenic communities, are significant as decomposers of organic matter under conditions of exogenous electron acceptor depletion. Their metabolic activity has been demonstrated in laboratory microcosms derived from aquifer material, and also in the subsurface in situ. Methanogenic communities have been shown to transform numerous organic pollutants, or even to completely degrade these compounds with the production of carbon dioxide and methane. Depending on the chemical structure of the pollutant, such a compound can be used as an electron donor and a carbon/energy source for fermentative microorganisms (which is typically the case with highly reduced compounds); alternatively, a highly oxidized pollutant can be used as a potential electron acceptor or electron sink. This review addresses fermentative/methanogenic degradation of chlorinated and nonchlorinated aromatic hydrocarbons and phenols by subsurface microorganisms; for comparison, it briefly relates also other types of anaerobic transformations (under sulfate‐reducing, iron‐reducing, and denitrifying conditions). Furthermore, it outlines transformation pathways, those that are proposed as well as those that are already partially proved, for aromatic hydrocarbons and phenols under fermentative/methanogenic conditions; finally, it discusses the relevance of these processes to bioremediation of contaminated groundwater aquifers.     

Mineralization of biphenyl and PCBs by the white rot fungus Phanerochaete chrysosporium

The white rot fungus Phanerochaete chrysosporium is unique in its ability to totally degrade a wide variety of recalcitrant pollutants. We have investigated the degradation of biphenyl and two model chlorinated biphenyls, 2,2',4,4'-tetrachlorobiphenyl and 2-chlorobiphenyl by suspended cultures of P. chrysosporium grown under conditions that maximize the synthesis of lignin-oxidizing enzymes. Radiolabeled biphenyl and 2'-chlorobiphenyl added to cultures at concentrations in the range 260 nM to 8.8 muM were degraded extensively to CO(2) within 30 days. In addition, from 40% to 60% of the recovered radioactivity was found in water-soluble compounds. A correlation between the rate of degradation and the synthesis of ligninases or Mn-dependent peroxidases could not be observed, indicating that yet unknown enzymatic system may be resonsible for the initial oxidation of PCBs. The more heavily chlorinated PCB congener, 2,2',4,4'-tetrachlorobiphenyl was converted to CO(2) less readily; approximately 9% and 0.9% mineralization was observed in cultures incubated with 40 nM and 5.3 muM, respectively. Overall, our results indicate that P. chrysosporium is a promising organism for the treatment of wastes contaminatd with lightly and moderately chlorinated PCBs. (c) 1992 John Wiley & Sons, Inc.     

Biodegradation and Rhodococcus--masters of catabolic versatility

The genus Rhodococcus is a very diverse group of bacteria that possesses the ability to degrade a large number of organic compounds, including some of the most difficult compounds with regard to recalcitrance and toxicity. They achieve this through their capacity to acquire a remarkable range of diverse catabolic genes and their robust cellular physiology. Rhodococcus appear to have adopted a strategy of hyper-recombination associated with a large genome. Notably, they harbour large linear plasmids that contribute to their catabolic diversity by acting as 'mass storage' for a large number of catabolic genes. In addition, there is increasing evidence that multiple pathways and gene homologues are present that further increase the catabolic versatility and efficiency of Rhodococcus.     

Molecular analysis and development of 16S rRNA oligonucleotide probes to characterize a diclofop-methyl-degrading biofilm consortium

Genomic DNA from nine individual bacteria, isolated from a diclofop-methyl-degrading biofilm consortium, was extracted for genetic characterization. The degradation of diclofop-methyl produces metabolites that are known intermediates or substrates for bacteria that degrade a variety of chlorinated aromatic compounds. Accordingly, oligonucleotide primers were designed from specific catabolic genes for chlorinated organic degradation pathways, and tested by PCR to determine if these genes are involved in diclofop-methyl degradation. DNA homology between the PCR products and the known catabolic genes investigated by Southern hybridization analysis and by sequencing, suggested that novel catabolic genes are functioning in the isolates. Specific fluorescent oligonucleotides were designed for two of the isolates, following 16S rDNA sequencing and identification of each of the isolates. These probes were successfully used for fluorescent in situ hybridization (FISH) studies of the two isolates in the biofilm consortium.     

Molecular phylogeny and evogenomics of heterocystous cyanobacteria using rbcl gene sequence data

Taxonomic affiliations and molecular diversity of 41 heterocystous cyanobacteria representing 12 genera have been assessed on an evolutionary landscape using rbcl gene sequence data-based phylogenomics and evogenomics approaches. Phylogenetic affiliations have clearly demonstrated the polyphyly of the true branching cyanobacteria, along with a frequent intermixing amongst the heterocystous cyanobacteria. The monophyletic origin of the heterocystous cyanobacteria was also quite evident from maximum parsimony and neighbor joining analyses. Incongruency with the traditional scheme of cyanobacterial taxonomy was frequently observed, thus advocating towards some re-amendments in the cyanobacterial classificatory schemes. Evogenomics analyses of gene sequence data gave a clear indication about the greater evolutionary pace of the unbranched cyanobacteria as compared to the branched forms. It was evident that the order Nostocales would be controlling the future pace of evolution of heterocystous cyanobacteria. The cyanobacteria Nostoc was found to have the greatest genetic heterogeneity amongst the studied genera, along with some evidence towards events of lateral gene transfer amongst the heterocystous cyanobacteria in case of the rbcl gene. Thus, heterocystous cyanobacteria were found to be a fast evolving group, with estimates of gene conversion tracts pointing towards the unbranched heterocystous cyanobacteria being at the base of evolutionary diversifications of the complete heterocystous lineage.     

Bioconcentration of chlorinated anilines and benzene in fish: preliminary results.

1. Seven chlorinated anilines and one chlorinated benzene were tested for their ability to bioconcentrate in guppies (Poecilia reticulata) under different experimental conditions. 2. Interactions between compounds in a mixture influence the bioconcentration of some chlorinated anilines. These interactions result in either an increase or a decrease of bioconcentration, depending on the compound studied. 3. Exposure concentration can have an effect on the extent of bioconcentration of some chlorinated anilines.