2024-03-28T12:00:29Zhttp://repository.helmholtz-hzi.de/oai/requestoai:repository.helmholtz-hzi.de:10033/85452019-08-30T11:24:30Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Holtel, A
author
Goldenberg, D
author
Giladi, H
author
Oppenheim, A B
author
Timmis, K N
author
1995-06
Journal of Bacteriology 1995 177(11):3312-3315
0021-9193
1098-5530
7768832
http://hdl.handle.net/10033/8545
177025
Involvement of IHF protein in expression of the Ps promoter of the Pseudomonas putida TOL plasmid.
oai:repository.helmholtz-hzi.de:10033/85922019-08-30T11:37:44Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Karlson, U
author
Dwyer, D F
author
Hooper, S W
author
Moore, E R
author
Timmis, K N
author
Eltis, L D
author
1993-03
Images
Journal of Bacteriology 1993 175(5):1467-1474
0021-9193
1098-5530
8444808
http://hdl.handle.net/10033/8592
193234
Two independently regulated cytochromes P-450 in a Rhodococcus rhodochrous strain that degrades 2-ethoxyphenol and 4-methoxybenzoate.
oai:repository.helmholtz-hzi.de:10033/86332019-08-30T11:26:13Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Horn, Joanne M.
author
Brunke, Maren
author
Deckwer, W.-D.
author
Timmis, Kenneth N.
author
1994-01
Images
Applied and Environmental Microbiology 1994 60(1):357-362
0099-2240
1098-5336
http://hdl.handle.net/10033/8633
201314
Pseudomonas putida Strains Which Constitutively Overexpress Mercury Resistance for Biodetoxification of Organomercurial Pollutants
oai:repository.helmholtz-hzi.de:10033/86342019-08-30T11:25:43Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Holtel, A
author
Marqués, S
author
Möhler, I
author
Jakubzik, U
author
Timmis, K N
author
1994-03
Images
Journal of Bacteriology 1994 176(6):1773-1776
0021-9193
1098-5530
8132475
http://hdl.handle.net/10033/8634
205268
Carbon source-dependent inhibition of xyl operon expression of the Pseudomonas putida TOL plasmid.
oai:repository.helmholtz-hzi.de:10033/86362019-08-30T11:32:36Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Kessler, B
author
Herrero, M
author
Timmis, K N
author
de Lorenzo, V
author
1994-06
Journal of Bacteriology 1994 176(11):3171-3176
0021-9193
1098-5530
8195070
http://hdl.handle.net/10033/8636
205485
Genetic evidence that the XylS regulator of the Pseudomonas TOL meta operon controls the Pm promoter through weak DNA-protein interactions.
oai:repository.helmholtz-hzi.de:10033/86402019-08-30T11:26:13Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Happe, B
author
Eltis, L D
author
Poth, H
author
Hedderich, R
author
Timmis, K N
author
1993-11
Images
Journal of Bacteriology 1993 175(22):7313-7320
0021-9193
1098-5530
8226678
http://hdl.handle.net/10033/8640
206875
Characterization of 2,2',3-trihydroxybiphenyl dioxygenase, an extradiol dioxygenase from the dibenzofuran- and dibenzo-p-dioxin-degrading bacterium Sphingomonas sp. strain RW1.
oai:repository.helmholtz-hzi.de:10033/86522019-08-30T11:25:39Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Schmeisser, C.
author
Stöckigt, C.
author
Raasch, C.
author
Wingender, J.
author
Timmis, K. N.
author
Wenderoth, D. F.
author
Flemming, H.-C.
author
Liesegang, H.
author
Schmitz, R. A.
author
Jaeger, K.-E.
author
Streit, W. R.
author
2003-12
Applied and Environmental Microbiology 2003 69(12):7298-7309
0099-2240
1098-5336
14660379
10.1128/AEM.69.12.7298-7309.2003
http://hdl.handle.net/10033/8652
309957
Metagenome Survey of Biofilms in Drinking-Water Networks
oai:repository.helmholtz-hzi.de:10033/86712019-08-30T11:24:26Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Ferrer, Manuel
author
Chernikova, Tatyana N.
author
Timmis, Kenneth N.
author
Golyshin, Peter N.
author
2004-08
Applied and Environmental Microbiology 2004 70(8):4499-4504
0099-2240
1098-5336
15294778
10.1128/AEM.70.8.4499-4504.2004
http://hdl.handle.net/10033/8671
492381
Expression of a Temperature-Sensitive Esterase in a Novel Chaperone-Based Escherichia coli Strain
oai:repository.helmholtz-hzi.de:10033/86942019-08-30T11:26:13Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
de Lorenzo, V
author
Herrero, M
author
Metzke, M
author
Timmis, K N
author
1991-05
Images
The EMBO Journal 1991 10(5):1159-1167
0261-4189
1460-2075
2022186
http://hdl.handle.net/10033/8694
452769
An upstream XylR- and IHF-induced nucleoprotein complex regulates the sigma 54-dependent Pu promoter of TOL plasmid.
oai:repository.helmholtz-hzi.de:10033/87792019-08-30T11:30:30Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Sabirova, Julia S
author
Ferrer, Manuel
author
Regenhardt, Daniela
author
Timmis, Kenneth N.
author
Golyshin, Peter N.
author
2006-06
Journal of Bacteriology 2006 188(11):3763-3773
0021-9193
1098-5530
16707669
10.1128/JB.00072-06
http://hdl.handle.net/10033/8779
1482905
Proteomic Insights into Metabolic Adaptations in Alcanivorax borkumensis Induced by Alkane Utilization
oai:repository.helmholtz-hzi.de:10033/151122019-08-30T11:35:39Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Sabirova, Julia S
author
Ferrer, Manuel
author
Lünsdorf, Heinrich
author
Wray, Victor
author
Kalscheuer, Rainer
author
Steinbüchel, Alexander
author
Timmis, Kenneth N
author
Golyshin, Peter N
author
2006-12
A novel mutant of the marine oil-degrading bacterium Alcanivorax borkumensis SK2, containing a mini-Tn5 transposon disrupting a "tesB-like" acyl-coenzyme A (CoA) thioesterase gene, was found to hyperproduce polyhydroxyalkanoates (PHA), resulting in the extracellular deposition of this biotechnologically important polymer when grown on alkanes. The tesB-like gene encodes a distinct novel enzyme activity, which acts exclusively on hydroxylated acyl-CoAs and thus represents a hydroxyacyl-CoA-specific thioesterase. Inactivation of this enzyme results in the rechanneling of CoA-activated hydroxylated fatty acids, the cellular intermediates of alkane degradation, towards PHA production. These findings may open up new avenues for the development of simplified biotechnological processes for the production of PHA as a raw material for the production of bioplastics.
Mutation in a "tesB-like" hydroxyacyl-coenzyme A-specific thioesterase gene causes hyperproduction of extracellular polyhydroxyalkanoates by Alcanivorax borkumensis SK2. 2006, 188 (24):8452-9 J. Bacteriol.
0021-9193
16997960
10.1128/JB.01321-06
http://hdl.handle.net/10033/15112
Journal of bacteriology
Mutation in a "tesB-like" hydroxyacyl-coenzyme A-specific thioesterase gene causes hyperproduction of extracellular polyhydroxyalkanoates by Alcanivorax borkumensis SK2.
oai:repository.helmholtz-hzi.de:10033/187322019-08-30T11:36:33Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Kotsyurbenko, O R
author
Friedrich, M W
author
Simankova, M V
author
Nozhevnikova, A N
author
Golyshin, P N
author
Timmis, K N
author
Conrad, R
author
2007-04
Methane production and archaeal community composition were studied in samples from an acidic peat bog incubated at different temperatures and pH values. H(2)-dependent methanogenesis increased strongly at the lowest pH, 3.8, and Methanobacteriaceae became important except for Methanomicrobiaceae and Methanosarcinaceae. An acidophilic and psychrotolerant Methanobacterium sp. was isolated using H(2)-plus-CO(2)-supplemented medium at pH 4.5.
shift from acetoclastic to H2-dependent methanogenesis in a west Siberian peat bog at low pH values and isolation of an acidophilic Methanobacterium strain. 2007, 73 (7):2344-8 Appl. Environ. Microbiol.
0099-2240
17277200
10.1128/AEM.02413-06
http://hdl.handle.net/10033/18732
Applied and environmental microbiology
shift from acetoclastic to H2-dependent methanogenesis in a west Siberian peat bog at low pH values and isolation of an acidophilic Methanobacterium strain.
oai:repository.helmholtz-hzi.de:10033/195922019-08-30T11:37:23Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Kalscheuer, Rainer
author
Stöveken, Tim
author
Malkus, Ursula
author
Reichelt, Rudolf
author
Golyshin, Peter N
author
Sabirova, Julia S
author
Ferrer, Manuel
author
Timmis, Kenneth N
author
Steinbüchel, Alexander
author
2007-02
Marine hydrocarbonoclastic bacteria, like Alcanivorax borkumensis, play a globally important role in bioremediation of petroleum oil contamination in marine ecosystems. Accumulation of storage lipids, serving as endogenous carbon and energy sources during starvation periods, might be a potential adaptation mechanism for coping with nutrient limitation, which is a frequent stress factor challenging those bacteria in their natural marine habitats. Here we report on the analysis of storage lipid biosynthesis in A. borkumensis strain SK2. Triacylglycerols (TAGs) and wax esters (WEs), but not poly(hydroxyalkanoic acids), are the principal storage lipids present in this and other hydrocarbonoclastic bacterial species. Although so far assumed to be a characteristic restricted to gram-positive actinomycetes, substantial accumulation of TAGs corresponding to a fatty acid content of more than 23% of the cellular dry weight is the first characteristic of large-scale de novo TAG biosynthesis in a gram-negative bacterium. The acyltransferase AtfA1 (ABO_2742) exhibiting wax ester synthase/acyl-coenzyme A:diacylglycerol acyltransferase (WS/DGAT) activity plays a key role in both TAG and WE biosynthesis, whereas AtfA2 (ABO_1804) was dispensable for storage lipid formation. However, reduced but still substantial residual TAG levels in atfA1 and atfA2 knockout mutants compellingly indicate the existence of a yet unknown WS/DGAT-independent alternative TAG biosynthesis route. Storage lipids of A. borkumensis were enriched in saturated fatty acids and accumulated as insoluble intracytoplasmic inclusions exhibiting great structural variety. Storage lipid accumulation provided only a slight growth advantage during short-term starvation periods but was not required for maintaining viability and long-term persistence during extended starvation phases.
Analysis of storage lipid accumulation in Alcanivorax borkumensis: Evidence for alternative triacylglycerol biosynthesis routes in bacteria. 2007, 189 (3):918-28 J. Bacteriol.
0021-9193
17122340
10.1128/JB.01292-06
http://hdl.handle.net/10033/19592
Journal of bacteriology
Analysis of storage lipid accumulation in Alcanivorax borkumensis: Evidence for alternative triacylglycerol biosynthesis routes in bacteria.
oai:repository.helmholtz-hzi.de:10033/196932019-08-30T11:37:24Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Kim, Hyun-Soo
author
Golyshin, Peter N
author
Timmis, Kenneth N
author
2007-11
A metalloprotease induced by chitin in a new chitinolytic bacterium Serratia sp. Strain KCK was purified and characterized. Compared with other Serratia enzymes, it exhibited a rather broad pH activity range (pH 5.0-8.0), and thermostability. The cognate ORF, mpr, was cloned and expressed. Its deduced amino acid sequence showed high similarity to those of bacterial zinc-binding metalloproteases and a well-conserved serralysin family motif. Pretreatment of chitin with the Mpr protein promoted chitin degradation by chitinase A, which suggests that Mpr participates in, and facilitates, chitin degradation by this microorganism.
Characterization and role of a metalloprotease induced by chitin in Serratia sp. KCK. 2007, 34 (11):715-21 J. Ind. Microbiol. Biotechnol.
1367-5435
17668255
10.1007/s10295-007-0245-1
http://hdl.handle.net/10033/19693
Journal of industrial microbiology & biotechnology
Characterization and role of a metalloprotease induced by chitin in Serratia sp. KCK.
oai:repository.helmholtz-hzi.de:10033/197782019-08-30T11:37:23Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Khachane, Amit N
author
Timmis, Kenneth N
author
Martins dos Santos, Vítor A P
author
2007-02
Reductive evolution in mitochondria and obligate intracellular microbes has led to a significant reduction in their genome size and guanine plus cytosine content (GC). We show that genome shrinkage during reductive evolution in prokaryotes follows an exponential decay pattern and provide a method to predict the extent of this decay on an evolutionary timescale. We validated predictions by comparison with estimated extents of genome reduction known to have occurred in mitochondria and Buchnera aphidicola, through comparative genomics and by drawing on available fossil evidences. The model shows how the mitochondrial ancestor would have quickly shed most of its genome, shortly after its incorporation into the protoeukaryotic cell and prior to codivergence subsequent to the split of eukaryotic lineages. It also predicts that the primary rickettsial parasitic event would have occurred between 180 and 425 million years ago (MYA), an event of relatively recent evolutionary origin considering the fact that Rickettsia and mitochondria evolved from a common alphaproteobacterial ancestor. This suggests that the symbiotic events of Rickettsia and mitochondria originated at different time points. Moreover, our model results predict that the ancestor of Wigglesworthia glossinidia brevipalpis, dated around the time of origin of its symbiotic association with the tsetse fly (50-100 MYA), was likely to have been an endosymbiont itself, thus supporting an earlier proposition that Wigglesworthia, which is currently a maternally inherited primary endosymbiont, evolved from a secondary endosymbiont.
Dynamics of reductive genome evolution in mitochondria and obligate intracellular microbes. 2007, 24 (2):449-56 Mol. Biol. Evol.
0737-4038
17108184
10.1093/molbev/msl174
http://hdl.handle.net/10033/19778
Molecular biology and evolution
Dynamics of reductive genome evolution in mitochondria and obligate intracellular microbes.
oai:repository.helmholtz-hzi.de:10033/197932019-08-30T11:30:32Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Yakimov, Michail M
author
Timmis, Kenneth N
author
Golyshin, Peter N
author
2007-06
Over the past few years, a new and ecophysiologically unusual group of marine hydrocarbon-degrading bacteria - the obligate hydrocarbonoclastic bacteria (OHCB) - has been recognized and shown to play a significant role in the biological removal of petroleum hydrocarbons from polluted marine waters. The introduction of oil or oil constituents into seawater leads to successive blooms of a relatively limited number of indigenous marine bacterial genera--Alcanivorax, Marinobacter, Thallassolituus, Cycloclasticus, Oleispira and a few others (the OHCB)--which are present at low or undetectable levels before the polluting event. The types of OHCB that bloom depend on the latitude/temperature, salinity, redox and other prevailing physical-chemical factors. These blooms result in the rapid degradation of many oil constituents, a process that can be accelerated further by supplementation with limiting nutrients. Genome sequencing and functional genomic analysis of Alcanivorax borkumensis, the paradigm of OHCB, has provided significant insights into the genomic basis of the efficiency and versatility of its hydrocarbon utilization, the metabolic routes underlying its special hydrocarbon diet, and its ecological success. These and other studies have revealed the potential of OHCB for multiple biotechnological applications that include not only oil pollution mitigation, but also biopolymer production and biocatalysis.
Obligate oil-degrading marine bacteria. 2007, 18 (3):257-66 Curr. Opin. Biotechnol.
0958-1669
17493798
10.1016/j.copbio.2007.04.006
http://hdl.handle.net/10033/19793
Current opinion in biotechnology
Obligate oil-degrading marine bacteria.
oai:repository.helmholtz-hzi.de:10033/198322019-08-30T11:37:23Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Khomiakov, N V
author
Kharin, S A
author
Nechitaĭlo, T Iu
author
Golyshin, P N
author
Kurakov, A V
author
Byzov, B A
author
Zviagintsev, D G
author
2008-03-05T13:32:08Z
The reaction of soil bacteria and fungi to the digestive fluid of the earthworm Aporrectodea caliginosa was studied. The fluid was obtained by centrifugation of the native enzymes of the digestive tract. The inhibition of growth of certain bacteria, spores, and fungal hyphae under the effect of extracts from the anterior and middle sections of the digestive tract of A. caliginosa was discovered for the first time. In bacteria, microcolony formation was inhibited as early as 20-30 s after the application of the gut extracts, which may indicate the nonenzymatic nature of the effect. The digestive fluid exhibited the same microbicidal activity whether the earthworms were feeding on soil or sterile sand. This indicates that the microbicidal agents are formed within the earthworm's body, rather than by soil microorganisms. The effect of the digestive fluid from the anterior and middle divisions is selective in relation to different microorganisms. Of 42 strains of soil bacteria, seven were susceptible to the microbicidal action of the fluid (Alcaligenes.faecalis 345-1, Microbacterium sp. 423-1, Arthrobacter sp. 430-1, Bacillus megaterium 401-1, B. megaterium 413-1, Kluyvera ascorbata 301-1, Pseudomonas reactans 387-2). The remaining bacteria did not die in the digestive fluid. Of 13 micromycetes, the digestive fluid inhibited spore germination in Aspergillus terreus and Paecilomyces lilacinus and the growth of hyphae in Trichoderma harzianum and Penicillium decumbens. The digestive fluid stimulated spore germination in Alternaria alternata and the growth of hyphae in Penicillium chrysogenum. The reaction of the remaining micromycetes was neutral. The gut fluid from the posterior division of the abdominal tract did not possess microbicidal activity. No relation was found between the reaction of microorganisms to the effects of the digestive fluid and the taxonomic position of the microorganisms. The effects revealed are similar to those shown earlier for millipedes and wood lice in the following parameters: quick action of the digestive fluid on microorganisms, and the selectivity of the action on microorganisms revealed at the strain level. The selective effect of the digestive gut fluid of the earthworms on soil microorganisms is important for animal feeding, maintaining the homeostasis of the gut microbial community, and the formation of microbial communities in soils.
[Reaction of microorganisms to the digestive fluid of the earthworms], 76 (1):55-65 Mikrobiologiia
0026-3656
17410875
http://hdl.handle.net/10033/19832
Mikrobiologiia
[Reaction of microorganisms to the digestive fluid of the earthworms]
oai:repository.helmholtz-hzi.de:10033/199122019-08-30T11:37:44Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Gattinger, Andreas
author
Höfle, Manfred G
author
Schloter, Michael
author
Embacher, Arndt
author
Böhme, Frank
author
Munch, Jean Charles
author
Labrenz, Matthias
author
2007-03
Based on lipid analyses, 16S rRNA/rRNA gene single-strand conformation polymorphism fingerprints and methane flux measurements, influences of the fertilization regime on abundance and diversity of archaeal communities were investigated in soil samples from the long-term (103 years) field trial in Bad Lauchstädt, Germany. The investigated plots followed a gradient of increasing fertilization beginning at no fertilization and ending at the 'cattle manure' itself. The archaeal phospholipid etherlipid (PLEL) concentration was used as an indicator for archaeal biomass and increased with the gradient of increasing fertilization, whereby the concentrations determined for organically fertilized soils were well above previously reported values. Methane emission, although at a low level, were occasionally only observed in organically fertilized soils, whereas the other treatments showed significant methane uptake. Euryarchaeotal organisms were abundant in all investigated samples but 16S rRNA analysis also demonstrated the presence of Crenarchaeota in fertilized soils. Lowest molecular archaeal diversity was found in highest fertilized treatments. Archaea phylogenetically most closely related to cultured methanogens were abundant in these fertilized soils, whereas Archaea with low relatedness to cultured microorganisms dominated in non-fertilized soils. Relatives of Methanoculleus spp. were found almost exclusively in organically fertilized soils or cattle manure. Methanosarcina-related microorganisms were detected in all soils as well as in the cattle manure, but soils with highest organic application rate were specifically dominated by a close phylogenetic relative of Methanosarcina thermophila. Our findings suggest that regular application of cattle manure increased archaeal biomass, but reduced archaeal diversity and selected for methanogenic Methanoculleus and Methanosarcina strains, leading to the circumstance that high organic fertilized soils did not function as a methane sink at the investigated site anymore.
Traditional cattle manure application determines abundance, diversity and activity of methanogenic Archaea in arable European soil. 2007, 9 (3):612-24 Environ. Microbiol.
1462-2912
17298362
10.1111/j.1462-2920.2006.01181.x
http://hdl.handle.net/10033/19912
Environmental microbiology
Traditional cattle manure application determines abundance, diversity and activity of methanogenic Archaea in arable European soil.
oai:repository.helmholtz-hzi.de:10033/244322019-08-30T11:27:16Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Böckelmann, Uta
author
Lünsdorf, Heinrich
author
Szewzyk, Ulrich
author
2007-09
Strain F8, a bacterial isolate from 'river snow', was found to produce extracellular fibres in the form of a filamentous network. These extracellular filaments, which were previously shown to be composed of DNA, have been studied for the first time by ultrastructural and electron energy-loss spectroscopy in the present work. 'Whole mount' preparations of strain F8 indicate these polymers are ultrastructurally homogeneous and form a network of elemental filaments, which have a width of 1.8-2.0 nm. When incubated at pH 3.5 with colloidal cationic ThO(2) tracers they become intensely stained (electron dense), affording direct evidence that the fibres are negatively charged and thus acidic chemically. Elemental analysis of the extracellular filaments by Energy-filtered Transmission Electron Microscopy revealed phosphorus to be the main element present and, because pretreatment of F8 cells with DNase prevented thorium labelling, the fibres must be composed of extracellular DNA (eDNA). Neither ultrathin sections nor 'whole mount negative stain' caused DNA release by general cell lysis. Additionally, cells infected with phages were never observed in ultrathin sections and phage particles were never detected in whole mount samples, which rules out the possibility of phages being directly involved in eDNA release.
Ultrastructural and electron energy-loss spectroscopic analysis of an extracellular filamentous matrix of an environmental bacterial isolate. 2007, 9 (9):2137-44 Environ. Microbiol.
1462-2912
17686013
10.1111/j.1462-2920.2007.01325.x
http://hdl.handle.net/10033/24432
Environmental microbiology
Ultrastructural and electron energy-loss spectroscopic analysis of an extracellular filamentous matrix of an environmental bacterial isolate.
oai:repository.helmholtz-hzi.de:10033/303242019-08-30T11:29:47Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Blasco, Rafael
author
Ramos, Juan-Luis
author
Wittich, Rolf-Michael
author
2008-06
Pseudomonas aeruginosa RW41 is the first bacterial strain, which could be isolated by virtue of its capability to mineralize 4-chlorobenzenesulfonic acid (4CBSA), the major polar by-product of the chemical synthesis of 1,1,1-trichloro-2,2-bis-(4-chlorophenyl)ethane (DDT). This capability makes the isolate a promising candidate for the development of bioremediation technologies. The bacterial mineralization of 4CBSA proceeds under oxygenolytic desulfonation and transient accumulation of sulfite which then is oxidized to sulfate. High enzyme activities for the turnover of 4-chlorocatechol were measured. The further catabolism proceeded through 3-chloromuconate and, probably, the instable 4-chloromuconolactone, which is directly hydrolyzed to maleylacetate. Detectable levels of maleylacetate reductase were only present when cells were grown with 4CBSA. When the ordinary catechol pathway was induced during growth on benzenesulfonate, catechol was ortho-cleaved to cis,cis-muconate and a partially purified muconate cycloisomerase transformed it to muconolactone in vitro. The same enzyme transformed 3-chloro-cis,cis-muconate into cis-dienelactone (76%) and the antibiotically active protoanemonin (24%). These observations are indicative for a not yet highly evolved catabolism for halogenated substrates by bacterial isolates from environmental samples which, on the other hand, are able to productively recycle sulfur and chloride ions from synthetic haloorganosulfonates.
Pseudomonas aeruginosa strain RW41 mineralizes 4-chlorobenzenesulfonate, the major polar by-product from DDT manufacturing. 2008, 10 (6):1591-600 Environ. Microbiol.
1462-2920
18331335
10.1111/j.1462-2920.2008.01575.x
http://hdl.handle.net/10033/30324
Environmental microbiology
Pseudomonas aeruginosa strain RW41 mineralizes 4-chlorobenzenesulfonate, the major polar by-product from DDT manufacturing.
oai:repository.helmholtz-hzi.de:10033/360322019-08-30T11:32:17Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Fahy, A
author
Ball, A S
author
Lethbridge, G
author
Timmis, K N
author
McGenity, T J
author
2008-07
AIMS: To isolate benzene-degrading strains from neutral and alkaline groundwaters contaminated by benzene, toluene, ethylbenzene, xylenes (BTEX) from the SIReN aquifer, UK, and to test their effective pH range and ability to degrade TEX. METHODS AND RESULTS: The 14 isolates studied had an optimum pH for growth of 8, and could degrade benzene to below detection level (1 microg l(-1)). Five Rhodococcus erythropolis strains were able to metabolize benzene up to pH 9, two distinct R. erythropolis strains to pH 10, and one Arthrobacter strain to pH 8.5. These Actinobacteria also degraded benzene at least down to pH 5.5. Six other isolates, a Hydrogenophaga and five Pseudomonas strains, had a narrower pH tolerance for benzene degradation (pH 6 to 8.5), and could metabolize toluene; in addition, the Hydrogenophaga and two Pseudomonas strains utilized o-, m- or p-xylenes. None of these strains degraded ethylbenzene. CONCLUSIONS: Phylogenetically distinct isolates, able to degrade BTX compounds, were obtained, and some degraded benzene at high pH. SIGNIFICANCE AND IMPACT OF THE STUDY: High pH has previously been found to inhibit in situ degradation of benzene, a widespread, carcinogenic groundwater contaminant. These benzene-degrading organisms therefore have potential applications in the remediation or natural attenuation of alkaline waters.
Isolation of alkali-tolerant benzene-degrading bacteria from a contaminated aquifer. 2008, 47 (1):60-6 Lett. Appl. Microbiol.
1472-765X
18544140
10.1111/j.1472-765X.2008.02386.x
http://hdl.handle.net/10033/36032
Letters in applied microbiology
Isolation of alkali-tolerant benzene-degrading bacteria from a contaminated aquifer.
oai:repository.helmholtz-hzi.de:10033/485412019-08-30T11:32:17Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Sabirova, Julia S
author
Ferrer, Manuel
author
Regenhardt, Daniela
author
Timmis, Kenneth N
author
Golyshin, Peter N
author
2006-06
Alcanivorax borkumensis is a ubiquitous marine petroleum oil-degrading bacterium with an unusual physiology specialized for alkane metabolism. This "hydrocarbonoclastic" bacterium degrades an exceptionally broad range of alkane hydrocarbons but few other substrates. The proteomic analysis presented here reveals metabolic features of the hydrocarbonoclastic lifestyle. Specifically, hexadecane-grown and pyruvate-grown cells differed in the expression of 97 cytoplasmic and membrane-associated proteins whose genes appeared to be components of 46 putative operon structures. Membrane proteins up-regulated in alkane-grown cells included three enzyme systems able to convert alkanes via terminal oxidation to fatty acids, namely, enzymes encoded by the well-known alkB1 gene cluster and two new alkane hydroxylating systems, a P450 cytochrome monooxygenase and a putative flavin-binding monooxygenase, and enzymes mediating beta-oxidation of fatty acids. Cytoplasmic proteins up-regulated in hexadecane-grown cells reflect a central metabolism based on a fatty acid diet, namely, enzymes of the glyoxylate bypass and of the gluconeogenesis pathway, able to provide key metabolic intermediates, like phosphoenolpyruvate, from fatty acids. They also include enzymes for synthesis of riboflavin and of unsaturated fatty acids and cardiolipin, which presumably reflect membrane restructuring required for membranes to adapt to perturbations induced by the massive influx of alkane oxidation enzymes. Ancillary functions up-regulated included the lipoprotein releasing system (Lol), presumably associated with biosurfactant release, and polyhydroxyalkanoate synthesis enzymes associated with carbon storage under conditions of carbon surfeit. The existence of three different alkane-oxidizing systems is consistent with the broad range of oil hydrocarbons degraded by A. borkumensis and its ecological success in oil-contaminated marine habitats.
Proteomic insights into metabolic adaptations in Alcanivorax borkumensis induced by alkane utilization. 2006, 188 (11):3763-73 J. Bacteriol.
0021-9193
16707669
10.1128/JB.00072-06
http://hdl.handle.net/10033/48541
Journal of bacteriology
Proteomic insights into metabolic adaptations in Alcanivorax borkumensis induced by alkane utilization.
oai:repository.helmholtz-hzi.de:10033/500532019-08-30T11:25:43Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Golyshina, Olga V
author
Golyshin, Peter N
author
Timmis, Kenneth N
author
Ferrer, Manuel
author
2006-03
A wide range of microorganisms, the so-called acidophiles, inhabit acidic environments and grow optimally at pH values between 0 and 3. The intracellular pH of these organisms is, however, close to neutrality or slightly acidic. It is to be expected that enzymatic activities dedicated to extracellular functions would be adapted to the prevailing low pH of the environment (0-3), whereas intracellular enzymes would be optimally active at the near-neutral pH of the cytoplasm (4.6-7.0). The genes of several intracellular or cell-bound enzymes, a carboxylesterase and three alpha-glucosidases, from Ferroplasma acidiphilum, a cell wall-lacking acidophilic archaeon with a growth optimum at pH 1.7, were cloned and expressed in Escherichia coli, and their products purified and characterized. The Ferroplasmaalpha-glucosidases exhibited no sequence similarity to known glycosyl hydrolases. All enzymes functioned and were stable in vitro in the pH range 1.7-4.0, and had pH optima much lower than the mean intracellular pH of 5.6. This 'pH optimum anomaly' suggests the existence of yet-undetected cellular compartmentalization providing cytoplasmic pH patchiness and low pH environments for the enzymes we have analysed.
The 'pH optimum anomaly' of intracellular enzymes of Ferroplasma acidiphilum. 2006, 8 (3):416-25 Environ. Microbiol.
1462-2912
16478448
10.1111/j.1462-2920.2005.00907.x
http://hdl.handle.net/10033/50053
Environmental microbiology
The 'pH optimum anomaly' of intracellular enzymes of Ferroplasma acidiphilum.
oai:repository.helmholtz-hzi.de:10033/902582019-08-30T11:35:14Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Golyshina, Olga V
author
Yakimov, Michail M
author
Lünsdorf, Heinrich
author
Ferrer, Manuel
author
Nimtz, Manfred
author
Timmis, Kenneth N
author
Wray, Victor
author
Tindall, Brian J
author
Golyshin, Peter N
author
2009-11
A novel acidophilic, cell-wall-less archaeon, strain V(T), was isolated from a hydrothermal pool on Vulcano Island, Italy. The morphology of cells was observed to vary from pleomorphic to coccoid. The temperature range for growth of strain V(T) was 15-65 degrees C with an optimum at 45 degrees C. The pH for growth ranged from pH 0 to 4 with an optimal at pH 1.4-1.6. Strain V(T) was able to grow aerobically and anaerobically, oxidizing ferrous iron and reducing ferric iron, respectively. The isolate grew chemo-organotrophically with yeast extract and yeast extract with glucose as the sources of energy and carbon. The molar G+C content in the DNA was 36 mol%. 16S rRNA gene sequence analysis demonstrated that strain V(T) was a member of the family Ferroplasmaceae, order Thermoplasmatales, phylum Euryarchaeota, showing sequence identities of 100 % with Ferroplasma cupricumulans BH2(T), 95.4 % with Ferroplasma acidiphilum Y(T), 94 % with Picrophilus torridus DSM 9790(T) and 92 % with Picrophilus oshimae DSM 9789(T). 16S rRNA gene sequence-based phylogenetic analysis showed that strain V(T) formed a monophyletic cluster together with F. cupricumulans BH2(T) and all other thermophilic isolates with available 16S rRNA gene sequences, whereas F. acidiphilum Y(T) formed another cluster with mesophilic isolates within the family Ferroplasmaceae. DNA-DNA hybridization values between strain V(T) and F. cupricumulans BH2(T) were well below 70 %, indicating that the two strains belong to separate species. Principal membrane lipids of strain V(T) were dibiphytanyl-based tetraether lipids containing pentacyclic rings. The polar lipids were dominated by a single phosphoglycolipid derivative based on a galactosyl dibiphytanyl phosphoglycerol tetraether, together with smaller amounts of monoglycosyl and diglycosyl dibiphytanyl ether lipids and the corresponding phosphoglycerol derivatives. The major respiratory quinones present were naphthoquinone derivatives. Given the notable physiological and chemical differences as well as the distinct phylogenetic placement of the new isolate relative to the type species of the genus Ferroplasma, we propose strain V(T) as a member of a new genus and species, Acidiplasma aeolicum gen. nov., sp. nov. The type strain of Acidiplasma aeolicum is strain V(T) (=DSM 18409(T) =JCM 14615(T)). In addition, we propose to transfer Ferroplasma cupricumulans Hawkes et al. 2008 to the genus Acidiplasma as Acidiplasma cupricumulans comb. nov. (type strain BH2(T) =DSM 16551(T) =JCM 13668(T)).
Acidiplasma aeolicum gen. nov., sp. nov., a euryarchaeon of the family Ferroplasmaceae isolated from a hydrothermal pool, and transfer of Ferroplasma cupricumulans to Acidiplasma cupricumulans comb. nov. 2009, 59 (Pt 11):2815-23 Int. J. Syst. Evol. Microbiol.
1466-5026
19628615
10.1099/ijs.0.009639-0
http://hdl.handle.net/10033/90258
International journal of systematic and evolutionary microbiology
Acidiplasma aeolicum gen. nov., sp. nov., a euryarchaeon of the family Ferroplasmaceae isolated from a hydrothermal pool, and transfer of Ferroplasma cupricumulans to Acidiplasma cupricumulans comb. nov.
oai:repository.helmholtz-hzi.de:10033/963152019-08-30T11:33:30Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Alvarez, Laura Acuña
author
Exton, Daniel A
author
Timmis, Kenneth N
author
Suggett, David J
author
McGenity, Terry J
author
2009-12
Isoprene is a volatile and climate-altering hydrocarbon with an atmospheric concentration similar to that of methane. It is well established that marine algae produce isoprene; however, until now there was no specific information about marine isoprene sinks. Here we demonstrate isoprene consumption in samples from temperate and tropical marine and coastal environments, and furthermore show that the most rapid degradation of isoprene coincides with the highest rates of isoprene production in estuarine sediments. Isoprene-degrading enrichment cultures, analysed by denaturing gradient gel electrophoresis and 454 pyrosequencing of the 16S rRNA gene and by culturing, were generally dominated by Actinobacteria, but included other groups such as Alphaproteobacteria and Bacteroidetes, previously not known to degrade isoprene. In contrast to specialist methane-oxidizing bacteria, cultivated isoprene degraders were nutritionally versatile, and nearly all of them were able to use n-alkanes as a source of carbon and energy. We therefore tested and showed that the ubiquitous marine hydrocarbon-degrader, Alcanivorax borkumensis, could also degrade isoprene. A mixture of the isolates consumed isoprene emitted from algal cultures, confirming that isoprene can be metabolized at low, environmentally relevant concentrations, and suggesting that, in the absence of spilled petroleum hydrocarbons, algal production of isoprene could maintain viable populations of hydrocarbon-degrading microbes. This discovery of a missing marine sink for isoprene is the first step in obtaining more robust predictions of its flux, and suggests that algal-derived isoprene provides an additional source of carbon for diverse microbes in the oceans.
Characterization of marine isoprene-degrading communities. 2009, 11 (12):3280-91 Environ. Microbiol.
1462-2920
19807779
10.1111/j.1462-2920.2009.02069.x
http://hdl.handle.net/10033/96315
Environmental microbiology
Characterization of marine isoprene-degrading communities.
oai:repository.helmholtz-hzi.de:10033/1219162019-08-30T11:31:49Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Martin-Arjol, I
author
Bassas-Galia, M
author
Bermudo, E
author
Garcia, F
author
Manresa, A
author
2010-05
In microorganisms hydroxy fatty acids are produced from the biotransformation of unsaturated fatty acids. Such compounds belong to a class of oxylipins which are reported to perform a variety of biological functions such as anti-inflammatory or cytotoxic activity. These compounds have been found in rice and timothy plants after being infected by specific fungus. When grown in submerged culture with linoleic acid, Pseudomonas 42A2 accumulated in the supernatant several hydroxy fatty acids. In this work LC-MS/MS has been used to elucidate the structure of the components form the organic extract: 9-hydroxy-10,12-octadecadienoic acid; 13-hydroxy-9,11-octadecadienoic acid; 7,10-dihydroxy-8E-octadecenoic acid; 9,10,13-trihydroxy-11-octadecenoic acid and 9,12,13-trihydroxy-10-octadecenoic acid. Antimicrobial activity against several pathogenic fungal strains is presented: MIC (microg/mL) Verticillium dhaliae, 32; Macrophonia phaesolina, 32; Arthroderma uncinatum, 32; Trycophyton mentagrophytes, 64.
Identification of oxylipins with antifungal activity by LC-MS/MS from the supernatant of Pseudomonas 42A2. 2010, 163 (4-5):341-6 Chem. Phys. Lipids
1873-2941
20188718
10.1016/j.chemphyslip.2010.02.003
http://hdl.handle.net/10033/121916
Chemistry and physics of lipids
Identification of oxylipins with antifungal activity by LC-MS/MS from the supernatant of Pseudomonas 42A2.
oai:repository.helmholtz-hzi.de:10033/1456112019-08-30T11:30:32Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Sabirova, Julia S
author
Becker, Anke
author
Lünsdorf, Heinrich
author
Nicaud, Jean-Marc
author
Timmis, Kenneth N
author
Golyshin, Peter N
author
2011-06
The marine oil-degrading bacterium Alcanivorax borkumensis SK2 has attracted significant interest due to its hydrocarbonoclastic lifestyle, its alkane-centered metabolism, and for playing an important ecological role in cleaning up marine oil spills. In this study, we used microarray technology to characterize the transcriptional responses of A. borkumensis to n-hexadecane exposure as opposed to pyruvate, which led to the identification of a total of 220 differentially expressed genes, with 109 genes being upregulated and 111 genes being downregulated. Among the genes upregulated on alkanes are systems predicted to be involved in the terminal oxidation of alkanes, biofilm formation, signal transduction, and regulation.
Transcriptional profiling of the marine oil-degrading bacterium Alcanivorax borkumensis during growth on n-alkanes. 2011, 319 (2):160-8 FEMS Microbiol. Lett.
1574-6968
21470299
10.1111/j.1574-6968.2011.02279.x
http://hdl.handle.net/10033/145611
FEMS microbiology letters
Transcriptional profiling of the marine oil-degrading bacterium Alcanivorax borkumensis during growth on n-alkanes.
oai:repository.helmholtz-hzi.de:10033/2464432019-08-30T11:27:46Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Ferrer, Manuel
author
Ghazi, Azam
author
Beloqui, Ana
author
Vieites, José María
author
López-Cortés, Nieves
author
Marín-Navarro, Julia
author
Nechitaylo, Taras Y
author
Guazzaroni, María-Eugenia
author
Polaina, Julio
author
Waliczek, Agnes
author
Chernikova, Tatyana N
author
Reva, Oleg N
author
Golyshina, Olga V
author
Golyshin, Peter N
author
2012
Microbial communities from cow rumen are known for their ability to degrade diverse plant polymers at high rates. In this work, we identified 15 hydrolases through an activity-centred metagenome analysis of a fibre-adherent microbial community from dairy cow rumen. Among them, 7 glycosyl hydrolases (GHs) and 1 feruloyl esterase were successfully cloned, expressed, purified and characterised. The most striking result was a protein of GH family 43 (GHF43), hereinafter designated as R_09-02, which had characteristics very distinct from the other proteins in this family with mono-functional β-xylosidase, α-xylanase, α-L-arabinase and α-L-arabinofuranosidase activities. R_09-02 is the first multifunctional enzyme to exhibit β-1,4 xylosidase, α-1,5 arabinofur(pyr)anosidase, β-1,4 lactase, α-1,6 raffinase, α-1,6 stachyase, β-galactosidase and α-1,4 glucosidase activities. The R_09-02 protein appears to originate from the chromosome of a member of Clostridia, a class of phylum Firmicutes, members of which are highly abundant in ruminal environment. The evolution of R_09-02 is suggested to be driven from the xylose- and arabinose-specific activities, typical for GHF43 members, toward a broader specificity to the glucose- and galactose-containing components of lignocellulose. The apparent capability of enzymes from the GHF43 family to utilise xylose-, arabinose-, glucose- and galactose-containing oligosaccharides has thus far been neglected by, or could not be predicted from, genome and metagenome sequencing data analyses. Taking into account the abundance of GHF43-encoding gene sequences in the rumen (up to 7% of all GH-genes) and the multifunctional phenotype herein described, our findings suggest that the ecological role of this GH family in the digestion of ligno-cellulosic matter should be significantly reconsidered.
Functional metagenomics unveils a multifunctional glycosyl hydrolase from the family 43 catalysing the breakdown of plant polymers in the calf rumen. 2012, 7 (6):e38134 PLoS ONE
1932-6203
22761666
10.1371/journal.pone.0038134
http://hdl.handle.net/10033/246443
PloS one
Functional metagenomics unveils a multifunctional glycosyl hydrolase from the family 43 catalysing the breakdown of plant polymers in the calf rumen.
oai:repository.helmholtz-hzi.de:10033/2640532019-08-30T11:28:51Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Del Pozo, Mercedes V
author
Fernández-Arrojo, Lucía
author
Gil-Martínez, Jorge
author
Montesinos, Alejandro
author
Chernikova, Tatyana N
author
Nechitaylo, Taras Y
author
Waliszek, Agnes
author
Tortajada, Marta
author
Rojas, Antonia
author
Huws, Sharon A
author
Golyshina, Olga V
author
Newbold, Charles J
author
Polaina, Julio
author
Ferrer, Manuel
author
Golyshin, Peter N
author
2012
A complete saccharification of plant polymers is the critical step in the efficient production of bio-alcohols. Beta-glucosidases acting in the degradation of intermediate gluco-oligosaccharides produced by cellulases limit the yield of the final product.
Microbial β-glucosidases from cow rumen metagenome enhance the saccharification of lignocellulose in combination with commercial cellulase cocktail. 2012, 5 (1):73 Biotechnol Biofuels
1754-6834
22998985
10.1186/1754-6834-5-73
http://hdl.handle.net/10033/264053
Biotechnology for biofuels
Microbial β-glucosidases from cow rumen metagenome enhance the saccharification of lignocellulose in combination with commercial cellulase cocktail.
oai:repository.helmholtz-hzi.de:10033/2837782019-08-30T11:30:58Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Sass, Andrea M
author
McKew, Boyd A
author
Sass, Henrik
author
Fichtel, Jörg
author
Timmis, Kenneth N
author
McGenity, Terry J
author
2008
The deep-sea, hypersaline anoxic brine lakes in the Mediterranean are among the most extreme environments on earth, and in one of them, the MgCl2-rich Discovery basin, the presence of active microbes is equivocal. However, thriving microbial communities have been detected especially in the chemocline between deep seawater and three NaCl-rich brine lakes, l'Atalante, Bannock and Urania. By contrast, the microbiota of these brine-lake sediments remains largely unexplored.
Diversity of Bacillus-like organisms isolated from deep-sea hypersaline anoxic sediments. 2008, 4:8 Saline Syst.
1746-1448
18541011
10.1186/1746-1448-4-8
http://hdl.handle.net/10033/283778
Saline systems
Diversity of Bacillus-like organisms isolated from deep-sea hypersaline anoxic sediments.
oai:repository.helmholtz-hzi.de:10033/2943262019-08-30T11:28:51Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Cavaletti, Linda
author
Monciardini, Paolo
author
Bamonte, Ruggiero
author
Schumann, Peter
author
Rohde, Manfred
author
Sosio, Margherita
author
Donadio, Stefano
author
2006-06
A novel bacterial strain that was isolated from an Italian soil and was designated SOSP1-21T forms branched mycelia in solid and liquid media and has a filamentous morphology similar to that of some genera belonging to the Actinobacteria. Electron microscopy showed that this organism has a grape-like appearance, resulting from interlacing of spores originating from sporophoric hyphae. Ten strains that are morphologically related to SOSP1-21T were recovered from soil. Phylogenetic analyses of 16S rRNA gene segments confirmed the relatedness of these strains to SOSP1-21T and indicated that the newly isolated strains form separate clades in a deeply branching lineage. The closest matches for the 16S rRNA sequences of all the strains (around 79% identity) were matches with representatives of the Chloroflexi, although the affiliation with this division was not supported by high bootstrap values. The strains are mesophilic aerobic heterotrophs and are also capable of growing under microaerophilic conditions. They all stain gram positive. Strain SOSP1-21T contains ornithine, alanine, glutamic acid, serine, and glycine as the peptidoglycan amino acids. In addition, an unusual level of C16:1 2OH (30%) was found in the cellular fatty acids. The G+C content of SOSP1-21T genomic DNA is 53.9%, and MK-9(H2) was the only menaquinone detected. All these data suggest that SOSP1-21T and the related strains may constitute a new division of filamentous, spore-forming, gram-positive bacteria. We propose the name Ktedobacter racemifer gen. nov., sp. nov. for strain SOSP1-21T.
New lineage of filamentous, spore-forming, gram-positive bacteria from soil. 2006, 72 (6):4360-9 Appl. Environ. Microbiol.
0099-2240
16751552
10.1128/AEM.00132-06
http://hdl.handle.net/10033/294326
Applied and environmental microbiology
New lineage of filamentous, spore-forming, gram-positive bacteria from soil.
oai:repository.helmholtz-hzi.de:10033/2943252019-08-30T11:34:48Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Eichler, Stefan
author
Christen, Richard
author
Höltje, Claudia
author
Westphal, Petra
author
Bötel, Julia
author
Brettar, Ingrid
author
Mehling, Arndt
author
Höfle, Manfred G
author
2006-03
Bacterial community dynamics of a whole drinking water supply system (DWSS) were studied from source to tap. Raw water for this DWSS is provided by two reservoirs with different water characteristics in the Harz mountains of Northern Germany. Samples were taken after different steps of treatment of raw water (i.e., flocculation, sand filtration, and chlorination) and at different points along the supply system to the tap. RNA and DNA were extracted from the sampled water. The 16S rRNA or its genes were partially amplified by reverse transcription-PCR or PCR and analyzed by single-strand conformation polymorphism community fingerprints. The bacterial community structures of the raw water samples from the two reservoirs were very different, but no major changes of these structures occurred after flocculation and sand filtration. Chlorination of the processed raw water strongly affected bacterial community structure, as reflected by the RNA-based fingerprints. This effect was less pronounced for the DNA-based fingerprints. After chlorination, the bacterial community remained rather constant from the storage containers to the tap. Furthermore, the community structure of the tap water did not change substantially for several months. Community composition was assessed by sequencing of abundant bands and phylogenetic analysis of the sequences obtained. The taxonomic compositions of the bacterial communities from both reservoirs were very different at the species level due to their different limnologies. On the other hand, major taxonomic groups, well known to occur in freshwater, such as Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes, were found in both reservoirs. Significant differences in the detection of the major groups were observed between DNA-based and RNA-based fingerprints irrespective of the reservoir. Chlorination of the drinking water seemed to promote growth of nitrifying bacteria. Detailed analysis of the community dynamics of the whole DWSS revealed a significant influence of both source waters on the overall composition of the drinking water microflora and demonstrated the relevance of the raw water microflora for the drinking water microflora provided to the end user.
Composition and dynamics of bacterial communities of a drinking water supply system as assessed by RNA- and DNA-based 16S rRNA gene fingerprinting. 2006, 72 (3):1858-72 Appl. Environ. Microbiol.
0099-2240
16517632
10.1128/AEM.72.3.1858-1872.2006
http://hdl.handle.net/10033/294325
Applied and environmental microbiology
Composition and dynamics of bacterial communities of a drinking water supply system as assessed by RNA- and DNA-based 16S rRNA gene fingerprinting.
oai:repository.helmholtz-hzi.de:10033/2943292019-08-30T11:33:57Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Labrenz, Matthias
author
Brettar, Ingrid
author
Christen, Richard
author
Flavier, Sebastien
author
Bötel, Julia
author
Höfle, Manfred G
author
2004-08
We have developed a highly sensitive approach to assess the abundance of uncultured bacteria in water samples from the central Baltic Sea by using a noncultured member of the "Epsilonproteobacteria" related to Thiomicrospira denitrificans as an example. Environmental seawater samples and samples enriched for the target taxon provided a unique opportunity to test the approach over a broad range of abundances. The approach is based on a combination of taxon- and domain-specific real-time PCR measurements determining the relative T. denitrificans-like 16S rRNA gene and 16S rRNA abundances, as well as the determination of total cell counts and environmental RNA content. It allowed quantification of T. denitrificans-like 16S rRNA molecules or 16S rRNA genes as well as calculation of the number of ribosomes per T. denitrificans-like cell. Every real-time measurement and its specific primer system were calibrated using environmental nucleic acids obtained from the original habitat for external standardization. These standards, as well as the respective samples to be measured, were prepared from the same DNA or RNA extract. Enrichment samples could be analyzed directly, whereas environmental templates had to be preamplified with general bacterial primers before quantification. Preamplification increased the sensitivity of the assay by more than 4 orders of magnitude. Quantification of enrichments with or without a preamplification step yielded comparable results. T. denitrificans-like 16S rRNA molecules ranged from 7.1 x 10(3) to 4.4 x 10(9) copies ml(-1) or 0.002 to 49.7% relative abundance. T. denitrificans-like 16S rRNA genes ranged from 9.0 x 10(1) to 2.2 x10(6) copies ml(-1) or 0.01 to 49.7% relative abundance. Detection limits of this real-time-PCR approach were 20 16S rRNA molecules or 0.2 16S rRNA gene ml(-1). The number of ribosomes per T. denitrificans-like cell was estimated to range from 20 to 200 in seawater and reached up to 2,000 in the enrichments. The results indicate that our real-time PCR approach can be used to determine cellular and relative abundances of uncultured marine bacterial taxa and to provide information about their levels of activity in their natural environment.
Development and application of a real-time PCR approach for quantification of uncultured bacteria in the central Baltic Sea. 2004, 70 (8):4971-9 Appl. Environ. Microbiol.
0099-2240
15294837
10.1128/AEM.70.8.4971-4979.2004
http://hdl.handle.net/10033/294329
Applied and environmental microbiology
Development and application of a real-time PCR approach for quantification of uncultured bacteria in the central Baltic Sea.
oai:repository.helmholtz-hzi.de:10033/2995232019-08-30T11:35:13Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Kube, Michael
author
Chernikova, Tatyana N
author
Al-Ramahi, Yamal
author
Beloqui, Ana
author
Lopez-Cortez, Nieves
author
Guazzaroni, María-Eugenia
author
Heipieper, Hermann J
author
Klages, Sven
author
Kotsyurbenko, Oleg R
author
Langer, Ines
author
Nechitaylo, Taras Y
author
Lünsdorf, Heinrich
author
Fernández, Marisol
author
Juárez, Silvia
author
Ciordia, Sergio
author
Singer, Alexander
author
Kagan, Olga
author
Egorova, Olga
author
Alain Petit, Pierre
author
Stogios, Peter
author
Kim, Youngchang
author
Tchigvintsev, Anatoli
author
Flick, Robert
author
Denaro, Renata
author
Genovese, Maria
author
Albar, Juan P
author
Reva, Oleg N
author
Martínez-Gomariz, Montserrat
author
Tran, Hai
author
Ferrer, Manuel
author
Savchenko, Alexei
author
Yakunin, Alexander F
author
Yakimov, Michail M
author
Golyshina, Olga V
author
Reinhardt, Richard
author
Golyshin, Peter N
author
2013-07-23
Ubiquitous bacteria from the genus Oleispira drive oil degradation in the largest environment on Earth, the cold and deep sea. Here we report the genome sequence of Oleispira antarctica and show that compared with Alcanivorax borkumensis-the paradigm of mesophilic hydrocarbonoclastic bacteria-O. antarctica has a larger genome that has witnessed massive gene-transfer events. We identify an array of alkane monooxygenases, osmoprotectants, siderophores and micronutrient-scavenging pathways. We also show that at low temperatures, the main protein-folding machine Cpn60 functions as a single heptameric barrel that uses larger proteins as substrates compared with the classical double-barrel structure observed at higher temperatures. With 11 protein crystal structures, we further report the largest set of structures from one psychrotolerant organism. The most common structural feature is an increased content of surface-exposed negatively charged residues compared to their mesophilic counterparts. Our findings are relevant in the context of microbial cold-adaptation mechanisms and the development of strategies for oil-spill mitigation in cold environments.
Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica. 2013, 4:2156 Nat Commun
2041-1723
23877221
10.1038/ncomms3156
http://hdl.handle.net/10033/299523
Nature communications
Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica.
oai:repository.helmholtz-hzi.de:10033/3037682019-08-30T11:37:00Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Dammeyer, Thorben
author
Timmis, Kenneth N
author
Tinnefeld, Philip
author
2013
In current protein research, a limitation still is the production of active recombinant proteins or native protein associations to assess their function. Especially the localization and analysis of protein-complexes or the identification of modifications and small molecule interaction partners by co-purification experiments requires a controllable expression of affinity- and/or fluorescence tagged variants of a protein of interest in its native cellular background. Advantages of periplasmic and/or homologous expressions can frequently not be realized due to a lack of suitable tools. Instead, experiments are often limited to the heterologous production in one of the few well established expression strains.
Broad host range vectors for expression of proteins with (Twin-) Strep-tag, His-tag and engineered, export optimized yellow fluorescent protein. 2013, 12:49 Microb. Cell Fact.
1475-2859
23687945
10.1186/1475-2859-12-49
http://hdl.handle.net/10033/303768
Microbial cell factories
Broad host range vectors for expression of proteins with (Twin-) Strep-tag, His-tag and engineered, export optimized yellow fluorescent protein.
oai:repository.helmholtz-hzi.de:10033/3137182019-08-30T11:30:53Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Arias, Sagrario
author
Bassas-Galia, Monica
author
Molinari, Gabriella
author
Timmis, Kenneth N.
author
2014-03-06
Tight coupling of polymerization and depolymerization of polyhydroxyalkanoates ensures efficient management of carbon resources in Pseudomonas putida 2013, 6 (5):551 Microbial Biotechnology
17517915
10.1111/1751-7915.12040
http://hdl.handle.net/10033/313718
Microbial Biotechnology
Tight coupling of polymerization and depolymerization of polyhydroxyalkanoates ensures efficient management of carbon resources in Pseudomonas putida
oai:repository.helmholtz-hzi.de:10033/6207612019-08-30T11:34:48Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Dammeyer, Thorben
author
Timmis, Kenneth N
author
Tinnefeld, Philip
author
2013-05-20
Abstract Background In current protein research, a limitation still is the production of active recombinant proteins or native protein associations to assess their function. Especially the localization and analysis of protein-complexes or the identification of modifications and small molecule interaction partners by co-purification experiments requires a controllable expression of affinity- and/or fluorescence tagged variants of a protein of interest in its native cellular background. Advantages of periplasmic and/or homologous expressions can frequently not be realized due to a lack of suitable tools. Instead, experiments are often limited to the heterologous production in one of the few well established expression strains. Results Here, we introduce a series of new RK2 based broad host range expression plasmids for inducible production of affinity- and fluorescence tagged proteins in the cytoplasm and periplasm of a wide range of Gram negative hosts which are designed to match the recently suggested modular Standard European Vector Architecture and database. The vectors are equipped with a yellow fluorescent protein variant which is engineered to fold and brightly fluoresce in the bacterial periplasm following Sec-mediated export, as shown from fractionation and imaging studies. Expression of Strep-tag®II and Twin-Strep-tag® fusion proteins in Pseudomonas putida KT2440 is demonstrated for various ORFs. Conclusion The broad host range constructs we have produced enable good and controlled expression of affinity tagged protein variants for single-step purification and qualify for complex co-purification experiments. Periplasmic export variants enable production of affinity tagged proteins and generation of fusion proteins with a novel engineered Aequorea-based yellow fluorescent reporter protein variant with activity in the periplasm of the tested Gram-negative model bacteria Pseudomonas putida KT2440 and Escherichia coli K12 for production, localization or co-localization studies. In addition, the new tools facilitate metabolic engineering and yield assessment for cytoplasmic or periplasmic protein production in a number of different expression hosts when yields in one initially selected are insufficient.
Microbial Cell Factories. 2013 May 20;12(1):49
http://dx.doi.org/10.1186/1475-2859-12-49
http://hdl.handle.net/10033/620761
Broad host range vectors for expression of proteins with (Twin-) Strep-tag, His-tag and engineered, export optimized yellow fluorescent protein
oai:repository.helmholtz-hzi.de:10033/6207032019-08-30T11:26:13Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Del Pozo, Mercedes V
author
Fernández-Arrojo, Lucía
author
Gil-Martínez, Jorge
author
Montesinos, Alejandro
author
Chernikova, Tatyana N
author
Nechitaylo, Taras Y
author
Waliszek, Agnes
author
Tortajada, Marta
author
Rojas, Antonia
author
Huws, Sharon A
author
Golyshina, Olga V
author
Newbold, Charles J
author
Polaina, Julio
author
Ferrer, Manuel
author
Golyshin, Peter N
author
2012-09-21
Abstract Background A complete saccharification of plant polymers is the critical step in the efficient production of bio-alcohols. Beta-glucosidases acting in the degradation of intermediate gluco-oligosaccharides produced by cellulases limit the yield of the final product. Results In the present work, we have identified and then successfully cloned, expressed, purified and characterised 4 highly active beta-glucosidases from fibre-adherent microbial community from the cow rumen. The enzymes were most active at temperatures 45–55°C and pH 4.0-7.0 and exhibited high affinity and activity towards synthetic substrates such as p-nitrophenyl-beta-D-glucopyranoside (pNPbetaG) and pNP-beta-cellobiose, as well as to natural cello-oligosaccharides ranging from cellobiose to cellopentaose. The apparent capability of the most active beta-glucosidase, herein named LAB25g2, was tested for its ability to improve, at low dosage (31.25 units g-1 dry biomass, using pNPbetaG as substrate), the hydrolysis of pre-treated corn stover (dry matter content of 20%; 350 g glucan kg-1 dry biomass) in combination with a beta-glucosidase-deficient commercial Trichoderma reseei cellulase cocktail (5 units g-1 dry biomass in the basis of pNPbetaG). LAB25g2 increased the final hydrolysis yield by a factor of 20% (44.5 ± 1.7% vs. 34.5 ± 1.5% in control conditions) after 96–120 h as compared to control reactions in its absence or in the presence of other commercial beta-glucosidase preparations. The high stability (half-life higher than 5 days at 50°C and pH 5.2) and 2–38000 fold higher (as compared with reported beta-glucosidases) activity towards cello-oligosaccharides may account for its performance in supplementation assays. Conclusions The results suggest that beta-glucosidases from yet uncultured bacteria from animal digestomes may be of a potential interest for biotechnological processes related to the effective bio-ethanol production in combination with low dosage of commercial cellulases.
Biotechnology for Biofuels. 2012 Sep 21;5(1):73
http://dx.doi.org/10.1186/1754-6834-5-73
http://hdl.handle.net/10033/620703
Microbial β-glucosidases from cow rumen metagenome enhance the saccharification of lignocellulose in combination with commercial cellulase cocktail
oai:repository.helmholtz-hzi.de:10033/5944092019-08-30T11:36:33Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Dammeyer, Thorben
author
Steinwand, Miriam
author
Krüger, Sarah-C
author
Dübel, Stefan
author
Hust, Michael
author
Timmis, Kenneth N
author
2011
Recombinant antibody fragments have a wide range of applications in research, diagnostics and therapy. For many of these, small fragments like single chain fragment variables (scFv) function well and can be produced inexpensively in bacterial expression systems. Although Escherichia coli K-12 production systems are convenient, yields of different fragments, even those produced from codon-optimized expression systems, vary significantly. Where yields are inadequate, alternative production systems are needed. Pseudomonas putida strain KT2440 is a versatile biosafety strain known for good expression of heterologous genes, so we have explored its utility as a cell factory for production of scFvs.
Efficient production of soluble recombinant single chain Fv fragments by a Pseudomonas putida strain KT2440 cell factory. 2011, 10:11 Microb. Cell Fact.
1475-2859
21338491
10.1186/1475-2859-10-11
http://hdl.handle.net/10033/594409
Microbial cell factories
Efficient production of soluble recombinant single chain Fv fragments by a Pseudomonas putida strain KT2440 cell factory.
oai:repository.helmholtz-hzi.de:10033/5992772019-08-30T11:37:23Zcom_10033_6853com_10033_6839col_10033_6854
00925njm 22002777a 4500
dc
Sabirova, Julia S
author
Haddouche, R
author
Van Bogaert, I N
author
Mulaa, F
author
Verstraete, W
author
Timmis, K N
author
Schmidt-Dannert, C
author
Nicaud, J M
author
Soetaert, W
author
2011-01
The oleochemical industry is currently still dominated by conventional chemistry, with biotechnology only starting to play a more prominent role, primarily with respect to the biosurfactants or lipases, e.g. as detergents, or for biofuel production. A major bottleneck for all further biotechnological applications is the problem of the initial mobilization of cheap and vastly available lipid and oil substrates, which are then to be transformed into high-value biotechnological, nutritional or pharmacological products. Under the EU-sponsored LipoYeasts project we are developing the oleaginous yeast Yarrowia lipolytica into a versatile and high-throughput microbial factory that, by use of specific enzymatic pathways from hydrocarbonoclastic bacteria, efficiently mobilizes lipids by directing its versatile lipid metabolism towards the production of industrially valuable lipid-derived compounds like wax esters (WE), isoprenoid-derived compounds (carotenoids, polyenic carotenoid ester), polyhydroxyalkanoates (PHAs) and free hydroxylated fatty acids (HFAs). Different lipid stocks (petroleum, alkane, vegetable oil, fatty acid) and combinations thereof are being assessed as substrates in combination with different mutant and recombinant strains of Y. lipolytica, in order to modulate the composition and yields of the produced added-value products.
The 'LipoYeasts' project: using the oleaginous yeast Yarrowia lipolytica in combination with specific bacterial genes for the bioconversion of lipids, fats and oils into high-value products. 2011, 4 (1):47-54 Microb Biotechnol
1751-7915
21255371
10.1111/j.1751-7915.2010.00187.x
http://hdl.handle.net/10033/599277
Microbial biotechnology
The 'LipoYeasts' project: using the oleaginous yeast Yarrowia lipolytica in combination with specific bacterial genes for the bioconversion of lipids, fats and oils into high-value products.