Enrichment of Members of the Family Geobacteraceae Associated with Stimulation of Dissimilatory Metal Reduction in Uranium-Contaminated Aquifer Sediments

Stimulating microbial reduction of soluble U(VI) to insoluble U(IV) shows promise as a strategy for immobilizing uranium in uranium-contaminated subsurface environments. In order to learn more about which microorganisms might be involved in U(VI) reduction in situ, the changes in the microbial community when U(VI) reduction was stimulated with the addition of acetate were monitored in sediments from three different uranium-contaminated sites in the floodplain of the San Juan River in Shiprock, N.Mex. In all three sediments U(VI) reduction was accompanied by concurrent Fe(III) reduction and a dramatic enrichment of microorganisms in the family Geobacteraceae, which are known U(VI)- and Fe(III)-reducing microorganisms. At the point when U(VI) reduction and Fe(III) reduction were nearing completion, Geobacteraceae accounted for ca. 40% of the 16S ribosomal DNA (rDNA) sequences recovered from the sediments with bacterial PCR primers, whereas Geobacteraceae accounted for fewer than 5% of the 16S rDNA sequences in control sediments that were not amended with acetate and in which U(VI) and Fe(III) reduction were not stimulated. Between 55 and 65% of these Geobacteraceae sequences were most similar to sequences from Desulfuromonas species, with the remainder being most closely related to Geobacter species. Quantitative analysis of Geobacteraceae sequences with most-probable-number PCR and TaqMan analyses indicated that the number of Geobacteraceae sequences increased from 2 to 4 orders of magnitude over the course of U(VI) and Fe(III) reduction in the acetate-amended sediments from the three sites. No increase in Geobacteraceae sequences was observed in control sediments. In contrast to the predominance of Geobacteraceae sequences, no sequences related to other known Fe(III)-reducing microorganisms were detected in sediments. These results compare favorably with an increasing number of studies which have demonstrated that Geobacteraceae are important components of the microbial community in a diversity of subsurface environments in which Fe(III) reduction is an important process. The combination of these results with the finding that U(VI) reduction takes place during Fe(III) reduction and prior to sulfate reduction suggests that Geobacteraceae will be responsible for much of the Fe(III) and U(VI) reduction during uranium bioremediation in these sediments.     

Bacterial diversity in deep-sea sediments from different depths

Seven sediment samples have been examined, taken from different depths of the deep-sea in the range of 1159m to 6482m. A total of 75 different 16S rDNA sequences (149 clones) analyzed clustered into the Proteobacteria, Gram-positive bacteria, Cytophaga, Planctomyces, and Actinomycetes and many sequences were from microorganisms that showed no phylogenetic affiliation with known bacteria. Clones identical to 16S rDNA sequences of members of the genus Pseudomonas were observed in all of the sediments examined. The second group of common sequences cloned from six sediment samples was related to the 16S rDNA sequence of a chemoautotrophic bacterium, the Solemya velum symbiont. Five 16S rDNA sequences from three sediments were related to those of the Alvinella pompejana epibiont which is a member of the -Proteobacteria. Only one sequence was obtained that was closely related to the 16S rDNA of the barophilic bacterium, Shewanella benthica, which might be a minor population in the deeper sediments. -Proteobacteria-related sequences were cloned from sediments obtained from sites near man-made garbage deposits and a Calyptogena community. These environments obviously would be richer in nutrients than other sites, and might be expected to show more types of bacteria than other deep-sea sediments. A large number of cloned sequences in this study showed very low identity to known sequences. These sequences may represent communities of as-yet-uncultivated microorganisms in the sediments.     

Optimal and central-place foraging theory applied to a desert harvester ant,Pogonomyrmex californicus

Summary Certain predictions of optimal- and central place-foraging theory were tested on the desert harvester ant, Pogonomyrmex californicus. Colonies were offered three different sizes of oat seed and found to maximize net energy intake (ei) over time (t _i ) by harvesting the seed sizes with the highest e _i /t _i rank. Two aspects of t _i were measured that were assumed constant in previous studies. The handling components of t _i (time required to manipulate the seed and travel time back to the colony with the food) were measured and found to be positively correlated with seed size. The manipulation success rate (the percentage of handled seeds successfully picked up) decreased with increased seed size. These results point out how important it is to measure all parameters of e _i /t _i rather than to assume constancy with both prey type and foraging distance. The relative abundance of less preferred food types was important in determining the proportion of preferred types in the diet. The food supply of eight colonies was manipulated experimentally over a 25-day period. Four deprived colonies were constrained within aluminum enclosures to prevented foraging. The remaining four satiated colonies were given food ad libitum. The niche breadths of the treated colonies were then compared to controls, but found not to differ significantly. Seed baits were offered at three distances from the colony to test whether selectivity increased with disance. Contrary to theoretical predictions, all colonies harcested about the same proportion of each seed size at each distance.     

Comparative Metagenomics of Anode-Associated Microbiomes Developed in Rice Paddy-Field Microbial Fuel Cells

In sediment-type microbial fuel cells (sMFCs) operating in rice paddy fields, rice-root exudates are converted to electricity by anode-associated rhizosphere microbes. Previous studies have shown that members of the family Geobacteraceae are enriched on the anodes of rhizosphere sMFCs. To deepen our understanding of rhizosphere microbes involved in electricity generation in sMFCs, here, we conducted comparative analyses of anode-associated microbiomes in three MFC systems: a rice paddy-field sMFC, and acetate- and glucose-fed MFCs in which pieces of graphite felt that had functioned as anodes in rice paddy-field sMFC were used as rhizosphere microbe-bearing anodes. After electric outputs became stable, microbiomes associated with the anodes of these MFC systems were analyzed by pyrotag sequencing of 16S rRNA gene amplicons and Illumina shotgun metagenomics. Pyrotag sequencing showed that Geobacteraceae bacteria were associated with the anodes of all three systems, but the dominant Geobacter species in each MFC were different. Specifically, species closely related to G. metallireducens comprised 90% of the anode Geobacteraceae in the acetate-fed MFC, but were only relatively minor components of the rhizosphere sMFC and glucose-fed MFC, whereas species closely related to G. psychrophilus were abundantly detected. This trend was confirmed by the phylogenetic assignments of predicted genes in shotgun metagenome sequences of the anode microbiomes. Our findings suggest that G. psychrophilus and its related species preferentially grow on the anodes of rhizosphere sMFCs and generate electricity through syntrophic interactions with organisms that excrete electron donors.     

Vertical distribution and diversity of bacteria and archaea in sulfide and methane-rich cold seep sediments located at the base of the Florida Escarpment

The bacterial and archaeal communities of the sediments at the base of the Florida Escarpment (Gulf of Mexico, USA) were investigated using molecular phylogenetic analysis. The total microbial community DNA of each of three vertical zones (top, middle and bottom) of a sediment core was extracted and the 16S rRNA genes were amplified by PCR, cloned and sequenced. Shannon–Weaver Diversity measures of bacteria were high in all three zones. For the archaea, diversity was generally low, but increased with depth. The archaeal clonal libraries were dominated by representatives of four groups of organisms involved in the anaerobic oxidation of methane (ANME groups). Phylogenetic analysis of bacteria suggests the dominance of -proteobacteria in the top zone, the -, - and -proteobacteria in the middle zone and the -proteobacteria in the bottom zone of the core. Members of the Cytophaga–Flexibacter–Bacteroidetes group, the Chloroflexi/green non-sulfur bacteria, the Gram+ (Firmicutes), the Planctomyces, candidate division WS3 and Fusobacterium were also detected. Our data suggest that the community structure and diversity of microorganisms can shift greatly within small vertical distances, possibly in response to changes in the physical and chemical conditions.     

Bacterial and Fungal Diversity of Quaternary Cave Sediment Deposits

The bacterial and fungal assemblages of clastic sediments collected from two caves located in north-western Romania were investigated by assessing ITS and 16S rRNA gene diversity. Bacterial members belonging to Chloroflexi, Nitrospirae, Proteobacteria, Firmicutes, Acidobacteria, Gemmatimonadetes, and fungal members of Ascomycota were identified. Except for Bacillus sp., all bacteria were related to uncultured or unknown species and the majority (86%) of the bacterial sequences from one of the caves had no close GenBank relatives. The bacterial sequences obtained clustered with species found in extreme environments. Half of the bacterial operational taxonomic units were clustered with clones isolated from deep subsurface sediments of a radioactively contaminated site in the USA. The present study represents the first attempt to identify microorganisms in Quaternary cave sediments.

Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the supplemental file.     

Sources of organic carbon in mangrove sediments: variability and possible ecological implications

Mangrove sediments from three different mangrove ecosystems (Coringa Wildlife Sanctuary in the Godavari Delta, Andhra Pradesh, India, and Galle and Pambala, south-west Sri Lanka) were analysed for their organic carbon content, elemental ratios (C:N) and carbon stable isotope composition. Organic carbon content (0.6 – 31.7% dry weight), C/N ratios (7.0 – 27.3) and ¹³C (between –29.4 and –20.6) showed a wide range of values. Lower stocks of organic carbon coincided with low C/N (atom) ratios and less negative ¹³C values, indicating import of marine or estuarine particulate suspended matter. High organic carbon stocks coincided with high C/N ratios and ¹³C values close, but not equal, to those of the mangrove vegetation. The variations observed in this study and published literature data could be adequately described by a simple two-end mixing model, whereby marine/estuarine suspended matter and mangrove litter were taken as end members. Thus, while in some mangrove ecosystems or vegetation zones, organic carbon stocks can be very high and are almost entirely of mangrove origin, there also appear to be cases in which deposited estuarine or marine suspended matter is the dominant source of organic carbon and nitrogen in mangrove sediments. This situation is remarkably similar to that observed in temperate salt marsh ecosystems where the importance of local vascular plant production to the sediment organic carbon pool is equally variable. The observed high variability in organic matter origin is thought to have a major impact on the overall carbon dynamics in intertidal mangrove ecosystems.     

δ13C signature of organic carbon in estuarine bottom sediment as an indicator of carbon export from adjacent marshes

The ¹³C signature of organic carbon in estuarine bottom sediment in Louisiana Barataria Basin was used for estimating carbon flux from adjacent marsh. The stable carbon isotope composition of plants, soils and sediments from the basin were determined. The ¹³C content of marsh vegetation ranged from -26.3 to -27.8% for C₃ freshwater vegetation in the upper basin to -13.0 to -13.3% for C₄ vegetation in the lower basin. The ¹³C content of the highly organic marsh soils were similar to ¹³C content of vegetation present. The ¹³C content of organic carbon from bottom sediment of open water bodies ranged from 27.3 in the upper basin (freshwater) to 16.4 in bottom sediment of salt marsh ponds. The¹³C signature of organic carbon in bottom sediment from saline regions corresponded to the size of the body of water. The smaller salt marsh ponds contain sediment with ¹³C values close to that of the C₄ plantSpartina alterniflora. Results suggest that phytoplankton rather thanSpartina alterniffora is the likely organic source in bottom sediment of the larger bay near the coast (e.g. Caminada Bay).     

Bacterial diversity of the Inner Mongolian Baer Soda Lake as revealed by 16S rRNA gene sequence analyses

Bacterial diversity associated with Baer Soda Lake in Inner Mongolia of China was investigated using a culture-independent method. Bacterial 16S rRNA gene libraries were generated using bacterial oligonucleotide primers, and 16S rRNA gene sequences of 58 clones were analyzed phylogenetically. The library was dominated by 16S rDNAs of Gram-negative bacteria (24% -Proteobacteria, 31% -Proteobacteria, 33% -Proteobacteria, and 2% -Proteobacteria), with a lower percentage of clones corresponding to Gram-positive bacteria. Forty cloned sequences were similar to that of known bacterial isolates (>97% sequence similarity), represented by the species of the genera Brevundimonas, Comamonas, Alcaligenes, Stenotrophomonas, and Klebsiella. Eighteen cloned sequences showed less affiliation with known taxa (<97% sequence similarity) and may represent novel taxa.Communicated by K. Horikoshi     

Effects of estuarine infauna on sediment stability and particle sedimentation

Secretions produced by the two estuarine benthic invertebrates Corophium volutator and Nereis diversicolor stabilise sediments by increasing their shear strength, and reduce sedimentation of previously resuspended particles. The secretions consist of 1 to 2 m threads which bind the particles together. They are used by both species in the production of complex burrow systems in the top 15 cm of sediment. The burrow systems have been demonstrated by a new resin impregnation technique. These results have widespread implications for the stability and erosion of estuarine sediments.     

Parametric and jackknife confidence interval estimators for two-factor mating design genetic variance ratios

Summary Confidence interval estimators have not been defined for dominance to additive genetic variance () and average degree of dominance () for the nested, factorial, and backcross mating designs. The objective of this paper was to describe interval estimators for these parameters. Approximate F random variables were defined for expected mean square (EMS) ratios for linear models with one environmental effect. Approximate 1– parametric interval estimators were defined for and using these random variables. Random variables defined for linear models with no environmental effects are not approximately distributed as F random variables because common EMS are involved in the numerators and denominators of the EMS ratios. Delete-one jackknife (jackknife) interval estimators were defined for and for linear models with zero or one environmental effect(s); In transformed analysis of variance point estimates were used in pseudovalue estimators.Oregon Agricultural Experiment Station Technical Paper No. 8067     

Microbial fuel cell energy from an ocean cold seep

Benthic microbial fuel cells are devices that generate modest levels of electrical power in seafloor environments by a mechanism analogous to the coupled biogeochemical reactions that transfer electrons from organic carbon through redox intermediates to oxygen. Two benthic microbial fuel cells were deployed at a deep-ocean cold seep within Monterey Canyon, California, and were monitored for 125 days. Their anodes consisted of single graphite rods that were placed within microbial mat patches of the seep, while the cathodes consisted of carbon-fibre/titanium wire brushes attached to graphite plates suspended ∼0.5 m above the sediment. Power records demonstrated a maximal sustained power density of 34 mW·m⁻² of anode surface area, equating to 1100 mW m⁻² of seafloor. Molecular phylogenetic analyses of microbial biofilms that formed on the electrode surfaces revealed changes in microbial community composition along the anode as a function of sediment depth and surrounding geochemistry. Near the sediment surface (20–29 cm depth), the anodic biofilm was dominated by micro-organisms closely related to Desulfuromonas acetoxidans. At horizons 46–55 and 70–76 cm below the sediment–water interface, clone libraries showed more diverse populations, with increasing representation of δ-proteobacteria such as Desulfocapsa and Syntrophus, as well as ɛ-proteobacteria. Genes from phylotypes related to Pseudomonas dominated the cathode clone library. These results confound ascribing a single electron transport role performed by only a few members of the microbial community to explain energy harvesting from marine sediments. In addition, the microbial fuel cells exhibited slowly decreasing current attributable to a combination of anode passivation and sulfide mass transport limitation. Electron micrographs of fuel cell anodes and laboratory experiments confirmed that sulfide oxidation products can build up on anode surfaces and impede electron transfer. Thus, while cold seeps have the potential to provide more power than neighbouring ocean sediments, the limits of mass transport as well as the proclivity for passivation must be considered when developing new benthic microbial fuel cell designs to meet specific power requirements.     

The Hawaiian Archipelago: A Microbial Diversity Hotspot

The Hawaiian Archipelago is a biodiversity hotspot where significant endemism among eukaryotes has evolved through geographic isolation and local topography. To address the absence of corresponding region-wide data on Hawaiis microbiota, we compiled the first 16S SSU rDNA clone libraries and cultivated bacteria from five Hawaiian lakes, an anchialine pool, and the Lihi submarine volcano. These sites offer diverse niches over ~5000 m elevation and ~1150 nautical miles. Each site hosted a distinct prokaryotic community dominated by Bacteria. Cloned sequences fell into 158 groups from 18 Bacteria phyla, while seven were unassigned and two belonged in the Euryarchaeota. Only seven operational taxonomic units (each OTU comprised sequences that shared 97% sequence identity) occurred in more than one site. Pure bacterial cultures from all sites fell into 155 groups (each group comprised pure cultures that shared 97% 16S SSU rDNA sequence identity) from 10 Bacteria phyla; 15 Proteobacteria and Firmicutes were cultivated from more than one site. One hundred OTUs (60%) and 52 (33.3%) cultures shared <97% 16S SSU rDNA sequence identity with published sequences. Community structure reflected habitat chemistry; most -Proteobacteria occurred in anoxic and sulfidic waters of one lake, while -Proteobacteria were cultivated exclusively from fresh or brackish waters. Novel sequences that affiliate with an Antarctic-specific clade of Deinococci, and Candidate Divisions TM7 and BRC1, extend the geographic ranges of these phyla. Globally and locally remote, as well as physically and chemically diverse, Hawaiian aquatic habitats provide unique niches for the evolution of novel communities and microorganisms.     

Plating/Stripping Behavior of Actual Lithium Metal Anode

Lithium (Li) metal anodes exhibits the potential to enable rechargeable Li batteries with a high energy density. However, the irreversible plating and stripping behaviors of Li metal anodes with high reactivity and dendrite growth when matching different cathodes in working cells are not fully understood yet. Herein the working manner of very thin Li metal anodes (50 µm, 10 mAh cm^?2) is probed with different sequences of Li plating and stripping at 3.0 mA cm^?2 and 3.0 mAh cm^?2. Dendrite growth and dead Li forms on the surface of the initially plated Li electrode (P‐Li), while Li dendrites form in the pit of the initially stripped Li electrode (S‐Li). This induces the differences in reactive sites, distribution of dead Li, and voltage polarization of Li metal anodes. There is a gap of 15–20 and 13–16 mV for the end voltages between S‐Li and P‐Li during stripping and plating, respectively. When matching LiFePO₄ and FePO₄ cathodes, P‐Li | LiFePO₄ cells exhibit a 30‐cycle longer lifespan with smaller end polarization due to differences in the sequences of Li plating and stripping. This contribution affords emerging working principles for actual Li metal anodes when matching lithium‐containing and lithium‐free cathodes.     

Microbial Communities Associated with Anaerobic Benzene Degradation in a Petroleum-Contaminated Aquifer

Microbial community composition associated with benzene oxidation under in situ Fe(III)-reducing conditions in a petroleum-contaminated aquifer located in Bemidji, Minn., was investigated. Community structure associated with benzene degradation was compared to sediment communities that did not anaerobically oxidize benzene which were obtained from two adjacent Fe(III)-reducing sites and from methanogenic and uncontaminated zones. Denaturing gradient gel electrophoresis of 16S rDNA sequences amplified with bacterial or Geobacteraceae-specific primers indicated significant differences in the composition of the microbial communities at the different sites. Most notable was a selective enrichment of microorganisms in the Geobacter cluster seen in the benzene-degrading sediments. This finding was in accordance with phospholipid fatty acid analysis and most-probable-number–PCR enumeration, which indicated that members of the family Geobacteraceae were more numerous in these sediments. A benzene-oxidizing Fe(III)-reducing enrichment culture was established from benzene-degrading sediments and contained an organism closely related to the uncultivated Geobacter spp. This genus contains the only known organisms that can oxidize aromatic compounds with the reduction of Fe(III). Sequences closely related to the Fe(III) reducer Geothrix fermentans and the aerobe Variovorax paradoxus were also amplified from the benzene-degrading enrichment and were present in the benzene-degrading sediments. However, neither G. fermentans nor V. paradoxus is known to oxidize aromatic compounds with the reduction of Fe(III), and there was no apparent enrichment of these organisms in the benzene-degrading sediments. These results suggest that Geobacter spp. play an important role in the anaerobic oxidation of benzene in the Bemidji aquifer and that molecular community analysis may be a powerful tool for predicting a site’s capacity for anaerobic benzene degradation.     

Enumeration and Characterization of Iron(III)-Reducing Microbial Communities from Acidic Subsurface Sediments Contaminated with Uranium(VI)

Iron(III)-reducing bacteria have been demonstrated to rapidly catalyze the reduction and immobilization of uranium(VI) from contaminated subsurface sediments. Thus, these organisms may aid in the development of bioremediation strategies for uranium contamination, which is prevalent in acidic subsurface sediments at U.S. government facilities. Iron(III)-reducing enrichment cultures were initiated from pristine and contaminated (high in uranium, nitrate; low pH) subsurface sediments at pH 7 and pH 4 to 5. Enumeration of Fe(III)-reducing bacteria yielded cell counts of up to 240 cells ml⁻¹ for the contaminated and background sediments at both pHs with a range of different carbon sources (glycerol, acetate, lactate, and glucose). In enrichments where nitrate contamination was removed from the sediment by washing, MPN counts of Fe(III)-reducing bacteria increased substantially. Sediments of lower pH typically yielded lower counts of Fe(III)-reducing bacteria in lactate- and acetate-amended enrichments, but higher counts were observed when glucose was used as an electron donor in acidic enrichments. Phylogenetic analysis of 16S rRNA gene sequences extracted from the highest positive MPN dilutions revealed that the predominant members of Fe(III)-reducing consortia from background sediments were closely related to members of the Geobacteraceae family, whereas a recently characterized Fe(III) reducer (Anaeromyxobacter sp.) and organisms not previously shown to reduce Fe(III) (Paenibacillus and Brevibacillus spp.) predominated in the Fe(III)-reducing consortia of contaminated sediments. Analysis of enrichment cultures by terminal restriction fragment length polymorphism (T-RFLP) strongly supported the cloning and sequencing results. Dominant members of the Fe(III)-reducing consortia were observed to be stable over several enrichment culture transfers by T-RFLP in conjunction with measurements of Fe(III) reduction activity and carbon substrate utilization. Enrichment cultures from contaminated sites were also shown to rapidly reduce millimolar amounts of U(VI) in comparison to killed controls. With DNA extracted directly from subsurface sediments, quantitative analysis of 16S rRNA gene sequences with MPN-PCR indicated that Geobacteraceae sequences were more abundant in pristine compared to contaminated environments,whereas Anaeromyxobacter sequences were more abundant in contaminated sediments. Thus, results from a combination of cultivation-based and cultivation-independent approaches indicate that the abundance/community composition of Fe(III)-reducing consortia in subsurface sediments is dependent upon geochemical parameters (pH, nitrate concentration) and that microorganisms capable of producing spores (gram positive) or spore-like bodies (Anaeromyxobacter) were representative of acidic subsurface environments.     

Characterization of riparian species and stream detritus using multiple stable isotopes

Multiple stable isotopes were used to determine the effectiveness of distinguishing among several dominant riparian species and aquatic macrophytes both spatially (three sites) and temporally (three seasons) along an 8-km reach of a blackwater stream. The differences in isotopic composition were used to assess contributions of various organic matter sources to the detrital pool of the stream. Samples of riparian and aquatic macrophyte vegetation and detritus were collected at three times to represent early leaf-out (April), mid-summer (August), and just prior to abscission (October). Each sample was analyzed for stable isotopes of carbon ¹³C, nitrogen ¹⁵N, and sulfur ³⁴S Within a site and sampling date, ¹³C-values were significantly different among certain riparian species and detritus samples. Species differences persisted between seasons. ³⁴S values were the most variable of the three elements examined although they remained fairly constant through time within each species and site. The results suggest that temporal changes in isotopic compositions of riparian species and aquatic macrophytes are site-specific. Discriminant analysis dissimilarity plots (based on all three isotopes) demonstrated that the contribution of species to the detrital pool depended on the site and season. At the upper site, detritus was isotopically most similar to Quercus laurifolia and Sparganium americanum in April, and the aquatic macrophytes (S. americanum and Potamogeton spp.) in August and October. At the middle site, detritus was most similar to Carpinus caroliniana and Q. nigra in April but no single source was similar to detritus in August or October. At the lower site, detritus was most similar to Taxodium distichum for all three seasons.     

Molecular diversity and distribution of aromatic hydrocarbon-degrading anaerobes across a landfill leachate plume

Natural attenuation of the mono‐aromates benzene, toluene, ethylbenzene and xylene occurs under iron‐reducing conditions in a leachate‐contaminated aquifer near the Banisveld landfill, the Netherlands. The diversity of mono‐aromate‐degrading microorganisms was studied by targeting functional genes encoding benzylsuccinate synthase α‐subunit (bssA) and 6‐oxocyclohex‐1‐ene‐1‐carbonyl‐CoA hydrolase (bamA). Sixty‐four bssA and 188 bamA variants were sequenced from groundwater sampled along the pollution plume in 1999 and 2004. Species containing bssA sequences closest affiliated (> 91%) with the betaprotebacterium Georgfuchsia toluolica were the dominant alkylbenzene degraders (89% of bssA sequences). bssA genes were found at more than 10‐fold lower copy numbers than bamA genes, of which only a small fraction (< 2%) was closely related to the genes of Georgfuchsia. bamA gene diversity was high and bamA‐based community composition was primarily affected by dissolved organic carbon (DOC) and ferrous iron concentrations. bamA sequences closest related to Geobacteraceae were dominantly (43.2%) observed and the presence of Geobacteraceae‐related bamA sequences was associated with DOC. Our results indicate a key role for specialized Georgfuchsia spp. in the degradation of alkylbenzenes, whereas Geobacteraceae are involved in degradation of aromatics other than toluene and xylene.     

Biosynthesis,cDNA and amino acid sequences of a precursor of conglutin δ, a sulphur-rich protein from Lupinus angustifolius

The biosynthesis of conglutin has been studied in developing cotyledons of Lupinus angustifolius L. Precursors of conglutin formed the major sink for [³⁵S]-cysteine incorporated by developing lupin cotyledons, and these precursors were rapidly sequestered into the endoplasmic reticulum. The sequence of a cDNA clone coding for one such precursor of conglutin was determined. The structure of the precursor polypeptide for conglutin predicted from the cDNA sequence contained an N-terminal leader peptide of 22 amino acids directly preceding a subunit polypeptide of M _r 4520, together with a linking region of 13 amino acids and a subunit polypeptide of M _r 9558 at the C-terminus. The amino acid sequence predicted from the cDNA sequence showed minor variations from that established by sequencing of the protein purified from mature dried seeds (Lilley and Inglis, 1986). These were consistent with the existence of a multi-gene family coding for conglutin . Comparison of the sequences of conglutin with those of other 2S storage proteins showed that the cysteines involved in internal disulphide bridges between the mature subunits of conglutin , were maintained throughout this family of proteins but that little else was conserved either at the protein or DNA level.     

Phylogenetic analysis of photosynthetic genes of Rhodocyclus gelatinosus: Possibility of horizontal gene transfer in purple bacteria

Nucleotide sequences of the genes coding for the M and cytochrome subunits of the photosynthetic reaction center of Rhodocyclus gelatinosus, a purple bacterium in the subdivision, were determined. The deduced amino acid sequences of these proteins were compared with those of other photosynthetic bacteria. Based on the homology of these two photosynthetic proteins, Rc. gelatinosus was placed in the subdivision of purple bacteria, which disagrees with the phylogenetic trees based on 16S rRNA and soluble cytochrome c ₂. Horizontal transfer of the genes which code for the photosynthetic apparatus in purple bacteria can be postulated if the phylogenetic trees based on 16S rRNA and soluble cytochrome c ₂ reflect the real history of purple bacteria.Abbreviations LH I light harvesting complex I - RC reaction center