Potential Application of N-Carbamoyl-β-Alanine Amidohydrolase from Agrobacterium tumefaciens C58 for β-Amino Acid Production

An N-carbamoyl-β-alanine amidohydrolase of industrial interest from Agrobacterium tumefaciens C58 (βcar_At) has been characterized. βcar_At is most active at 30°C and pH 8.0 with N-carbamoyl-β-alanine as a substrate. The purified enzyme is completely inactivated by the metal-chelating agent 8-hydroxyquinoline-5-sulfonic acid (HQSA), and activity is restored by the addition of divalent metal ions, such as Mn²⁺, Ni²⁺, and Co²⁺. The native enzyme is a homodimer with a molecular mass of 90 kDa from pH 5.5 to 9.0. The enzyme has a broad substrate spectrum and hydrolyzes nonsubstituted N-carbamoyl-α-, -β-, -γ-, and -δ-amino acids, with the greatest catalytic efficiency for N-carbamoyl-β-alanine. βcar_At also recognizes substrate analogues substituted with sulfonic and phosphonic acid groups to produce the β-amino acids taurine and ciliatine, respectively. βcar_At is able to produce monosubstituted β²- and β³-amino acids, showing better catalytic efficiency (k_cat/K_m) for the production of the former. For both types of monosubstituted substrates, the enzyme hydrolyzes N-carbamoyl-β-amino acids with a short aliphatic side chain better than those with aromatic rings. These properties make βcar_At an outstanding candidate for application in the biotechnology industry.N-Carbamoyl-β-alanine amidohydrolase (NCβAA) (EC 3.5.1.6), also known as β-alanine synthase or β-ureidopropionase, catalyzes the third and final step of reductive pyrimidine degradation. In this reaction, N-carbamoyl-β-alanine or N-carbamoyl-β-aminoisobutyric acid is irreversibly hydrolyzed to CO₂, NH₃, and β-alanine or β-aminoisobutyric acid, respectively (43). Eukaryotic NCβAAs have been purified from several sources (10, 25, 33, 39, 42, 44). Nevertheless, only two prokaryotic NCβAAs, belonging to the Clostridium and Pseudomonas genera (4, 29), have been purified to date, although this activity has been inferred for several microorganisms due to the appearance of the reductive pathway of pyrimidine degradation (38, 45). Pseudomonas NCβAA is also able to hydrolyze l-N-carbamoyl-α-amino acids, and indeed, this activity is widespread in the bacterial kingdom (3, 23, 26, 46).β-Amino acids have unique pharmacological properties, and their utility as building blocks of β-peptides, pharmaceutical compounds, and natural products is of growing interest (14). β-Alanine, a natural β-amino acid, is a precursor of coenzyme A and pantothenic acid in bacteria and fungi (vitamin B₅) (7). β-Alanine is widely distributed in the central nervous systems of vertebrates and is a structural analogue of γ-amino-n-butyric acid and glycine, major inhibitory neurotransmitters, suggesting that it may be involved in synaptic transmissions (20). Another important natural β-amino acid is taurine (2-aminoethanesulfonic acid), which plays an important role in several essential processes, such as membrane stabilization, osmoregulation, glucose metabolism, antioxidation, and development of the central nervous system and the retina (9, 28, 33). 2-Aminoethylphosphonate, the most common naturally occurring phosphonate, also known as ciliatine, is an important precursor used in the biosynthesis of phosphonolipids, phosphonoproteins, and phosphonoglycans (5). β-Homoalanine (β-aminobutyric acid) has been used successfully for the design of nonnatural ligands for therapeutic application against autoimmune diseases such as rheumatoid arthritis, multiple sclerosis, or autoimmune uveitis (30). Substituted β-amino acids can be denominated β², β³, and β^2,3, depending on the position of the side chain(s) (R) on the amino acid skeleton (18). β²-Amino acids are not yet as readily available as their β³-counterparts, as they must be prepared using multistep procedures (17).We decided to characterize NCβAA (β-carbamoylase) from Agrobacterium tumefaciens C58 (βcar_At) after showing that some dihydropyrimidinases belonging to the Arthrobacter and Sinorhizobium genera are able to hydrolyze different 5- or 6-substituted dihydrouracils to the corresponding N-carbamoyl-β-amino acids (18, 22). If βcar_At could decarbamoylate the reaction products of dihydrouracils, different β-amino acids would be obtained enzymatically in the same way that α-amino acids are produced via the hydantoinase process (6, 21). We therefore describe the physical, biochemical, kinetic, and substrate specificity properties of recombinant βcar_At.     

CO2 Uptake and Fixation by a Thermoacidophilic Microbial Community Attached to Precipitated Sulfur in a Geothermal Spring

Carbon fixation at temperatures above 73°C, the upper limit for photosynthesis, is carried out by chemosynthetic thermophiles. Yellowstone National Park (YNP), Wyoming possesses many thermal features that, while too hot for photosynthesis, presumably support chemosynthetic-based carbon fixation. To our knowledge, in situ rates of chemosynthetic reactions at these high temperatures in YNP or other high-temperature terrestrial geothermal springs have not yet been reported. A microbial community attached to precipitated elemental sulfur (S^o floc) at the source of Dragon Spring (73°C, pH 3.1) in Norris Geyser Basin, YNP, exhibited a maximum rate of CO₂ uptake of 21.3 ± 11.9 μg of C 10⁷ cells⁻¹ h⁻¹. When extrapolated over the estimated total quantity of S^o floc at the spring''s source, the S^o floc-associated microbial community accounted for the uptake of 121 mg of C h⁻¹ at this site. On a per-cell basis, the rate was higher than that calculated for a photosynthetic mat microbial community dominated by Synechococcus spp. in alkaline springs at comparable temperatures. A portion of the carbon taken up as CO₂ by the S^o floc-associated biomass was recovered in the cellular nucleic acid pool, demonstrating that uptake was coupled to fixation. The most abundant sequences in a 16S rRNA clone library of the S^o floc-associated community were related to chemolithoautotrophic Hydrogenobaculum strains previously isolated from springs in the Norris Geyser Basin. These microorganisms likely contributed to the uptake and fixation of CO₂ in this geothermal habitat.The upper temperature limit for primary production via photosynthesis is ∼73°C (7, 8, 11). At this temperature, photosynthesis is restricted to cyanobacteria of the genus Synechococcus, which generally inhabit alkaline environments (11). In acidic environments (pH < 4.0), the upper temperature limit for photosynthetic-based primary production is ∼56°C. Under these conditions, phototrophic activity is restricted to the unicellular eukaryotic red algae Cyanidium, Galdieria, and Cyanidioschyzon, collectively referred to as “cyanidia” (6, 12, 31, 48). Primary production above this temperature in acidic environments occurs through chemoautotrophy, a metabolism restricted to prokaryotes.Yellowstone National Park (YNP), WY, possesses numerous high-temperature (73 to 93°C) geothermal environments that are thought to support communities of microorganisms through chemoautotrophic-based primary production. Evidence for chemosynthesis in these environments is based on the recovery of 16S rRNA gene sequences that are affiliated with cultivated representatives of the phyla Aquificae and Crenarchaeota, many of which are capable of CO₂ fixation via the oxidation of hydrogen (H₂) and/or sulfide (HS⁻) (15, 17, 21, 24, 26, 28, 41, 46). Surprisingly, CO₂ fixation has yet to be demonstrated in situ in YNP hot spring environments (acidic or alkaline) where temperatures exceed the limits of photosynthesis and where primary production is thought to be driven by chemoautotrophic metabolism (14, 15, 28, 29).Dragon Spring, an acid-sulfate-chloride (ASC) spring located in the Norris Geyser Basin of YNP, is a likely habitat for chemoautotrophic primary production. The pH of the water is ∼3.1, and the temperature of the water at the source fluctuates from 65 to 78°C, which is well above the upper temperature limit for photosynthesis under acidic conditions. Potential electron donors for chemolithoautotrophic growth in the source water include hydrogen (H₂) and sulfide (S²⁻) at concentrations of 13 nM and 65 μM, respectively (15). In addition, submerged substrata at the spring''s source are blanketed by precipitates of elemental sulfur (S°), hereafter referred to as S^o floc (23). Inventories of bacterial and archaeal 16S rRNA genes recovered from S^o floc collected from the source of Dragon Spring indicate the presence of Crenarchaeota and Aquificae (4, 15). The latter are related to chemolithoautotrophic Hydrogenobaculum spp., representatives of which have recently been isolated from the spring (15). In the present study, we demonstrate uptake and fixation of CO₂ at a temperature of 73°C by a Hydrogenobaculum-dominated microbial community associated with S^o floc collected from the source of Dragon Spring. This is the first direct evidence of CO₂ uptake in situ by a thermoacidophilic microbial community at a temperature that precludes photosynthesis in terrestrial geothermal springs.     

Detection of a Reproducible,Single-Member Shift in Soil Bacterial Communities Exposed to Low Levels of Hydrogen

Soil is exposed to hydrogen when symbiotic rhizobia in legume root nodules cannot recycle the hydrogen that is generated during nitrogen fixation. The hydrogen emitted is most likely taken up by free-living soil bacteria that use hydrogen as an energy source, though the bacteria that do this in situ remain unclear. In this study, we investigated the effect of hydrogen exposure on the bacteria of two different soils in a microcosm setup designed to simulate hydrogen-emitting root nodules. Although the size and overall composition of the soil bacterial community did not significantly alter after hydrogen exposure, one ribotype increased in relative abundance within each soil. This single-ribotype shift was identified by generating multiple terminal restriction fragment length polymorphism (T-RFLP) profiles of 16S rRNA genes from each soil sample, with gene sequence confirmation to identify terminal restriction fragments. The increased abundance of a single ribotype after hydrogen exposure, within an otherwise similar community, was found in replicate samples taken from each microcosm and was reproducible across replicate experiments. Similarly, only one member of the soil bacterial community increased in abundance in response to hydrogen exposure in soil surrounding the root nodules of field-grown soybean (Glycine max). The ribotypes that increased after hydrogen exposure in each soil system tested were all from known hydrogen-oxidizing lineages within the order Actinomycetales. We suggest that soil actinomycetes are important utilizers of hydrogen at relevant concentrations in soil and could be key contributors to soil''s function as a sink in the global hydrogen cycle.Soil is the major sink in the global hydrogen cycle and accounts for approximately 75 to 80% of uptake from the atmosphere (7, 11). Soil is such a strong sink that the atmospheric mixing ratio of molecular hydrogen, H₂, is hemispherically asymmetric because of the greater landmass in the Northern Hemisphere (11). Many nitrogen-fixing bacteria that form symbiotic relationships with legume plants cannot recycle the H₂ that is generated during N₂ fixation (2, 13). Most of the H₂ emitted from legume root nodules is taken up by the surrounding soil, within a few centimeters of the nodule surface, and is not released to the atmosphere (20). Although the H₂ emitted by the rhizobial symbionts costs the legume approximately 5% of its daily photosynthate and “represents a significant investment by the plant” (9), there is growing evidence to suggest that soil exposed to H₂ is beneficial to plant growth, separate from the benefits derived from N₂ fixation (8, 10, 28). Previously, La Favre and Focht have hypothesized that “the hydrogen which is evolved during N₂ fixation represents an additional energy input into the plant-soil ecosystem… since metabolism of H₂ by chemolithotrophic bacteria results in an input of fixed carbon to the system” (20). A number of studies have found that when H₂ is taken up by soil, net CO₂ fixation occurs at the rate of 7 to 8 nmol CO₂ per g of soil per h (22, 34). For a legume fixing 200 kg of atmospheric N₂ per hectare, over 200,000 liters of H₂ could be released into the legume''s rhizosphere over the duration of the growing season and CO₂ fixation could result in an extra 25 kg of soil carbon fixed per hectare (9, 10, 28).Many bacteria isolated from soil are able to utilize H₂ as an energy source (2, 5-7, 21), and free-living bacteria are most likely responsible for the H₂ uptake observed by soil surrounding legume roots (22). Adding a bacterial energy source, such as H₂, could affect the microbial population size, as has been observed previously (34), but more specific shifts within the bacterial community may occur if just the microorganisms able to utilize the energy source multiply. Their activity could also have downstream consequences specifically on other members of the community. Most H₂-oxidizing cultures have required enrichment with concentrations of H₂ that are not environmentally relevant and therefore cannot be assumed to be carrying out H₂ oxidation at much lower, naturally occurring concentrations (5-7). Recent surveys of microbes present in soil samples, via their nucleic acids, have revealed many novel bacterial inhabitants that have been little studied and thus may also be contributing to the repertoire of bacterial soil processes, such as H₂ uptake (16). A recent study into the effect of H₂ on soil bacteria focused on a few groups of H₂-oxidizing, autotrophic bacteria and thus ignored many other H₂ utilizers potentially present in soil (34).There are now many ways of characterizing the entire microbial community in environmental samples, either via their entire genomic content, though metagenomic analysis of soil is difficult at present, or via analysis of the lineages present according to 16S rRNA gene sequences, or ribotypes (36). A recent study comparing high-throughput pyrosequencing of 16S rRNA genes and an easily accessible profiling method, known as terminal restriction fragment length polymorphism (T-RFLP), found the simpler profiles were appropriate for comparing the dominant ribotypes in multiple samples (24). Although T-RFLP profiles only provide a simplified snapshot of the dominant members in microbial communities, compared to the deeper analyses provided by microarrays or high-throughput sequencing technologies, T-RFLP profiling is a cost-effective, reproducible, and robust method of “fingerprinting” many soil samples rapidly and efficiently (14, 24, 25, 32).In this study, we chose to assess the dominant members of the soil bacterial community via T-RFLP profiles of ribotypes present in H₂-treated and control soils to avoid a narrow focus on well-studied H₂ oxidizers. We investigated the bacterial community structure in two different soils, utilizing a microcosm setup with concentrations of H₂ calculated to occur in the rhizosphere of N₂-fixing legumes, to determine whether common responses to H₂ exposure could be predicted from soils that differ by climate, edaphic characteristics, and starting communities. Soil in microcosms has previously been shown to have similar H₂ uptake properties to soil close to H₂-emitting legume nodules (9), but we also complemented our plant-free microcosm work with an examination of soil collected from the root systems of field-grown soybean (Glycine max (L.) Merr.).     

A Role for DNA Polymerase μ in the Emerging DJH Rearrangements of the Postgastrulation Mouse Embryo

The molecular complexes involved in the nonhomologous end-joining process that resolves recombination-activating gene (RAG)-induced double-strand breaks and results in V(D)J gene rearrangements vary during mammalian ontogeny. In the mouse, the first immunoglobulin gene rearrangements emerge during midgestation periods, but their repertoires have not been analyzed in detail. We decided to study the postgastrulation DJ_H joints and compare them with those present in later life. The embryo DJ_H joints differed from those observed in perinatal life by the presence of short stretches of nontemplated (N) nucleotides. Whereas most adult N nucleotides are introduced by terminal deoxynucleotidyl transferase (TdT), the embryo N nucleotides were due to the activity of the homologous DNA polymerase μ (Polμ), which was widely expressed in the early ontogeny, as shown by analysis of Polμ^−/− embryos. Based on its DNA-dependent polymerization ability, which TdT lacks, Polμ also filled in small sequence gaps at the coding ends and contributed to the ligation of highly processed ends, frequently found in the embryo, by pairing to internal microhomology sites. These findings show that Polμ participates in the repair of early-embryo, RAG-induced double-strand breaks and subsequently may contribute to preserve the genomic stability and cellular homeostasis of lymphohematopoietic precursors during development.The adaptive immune system is characterized by the great diversity of its antigen receptors, which result from the activities of enzymatic complexes that cut and paste the genomic DNA of antigen receptor loci. The nonhomologous end-joining (NHEJ) machinery is then recruited to repair the double-strand DNA breaks (DSBs) inflicted by the products of the recombination-activating genes (RAGs) (45, 65). Within B cells, each immunoglobulin (Ig) receptor represents a singular shuffling of two heavy (H) and two light (L) chains, which are derived from the recombination of V, D, and J gene segments of the IgH locus and of V and J for IgL (71). Besides these combinatorial possibilities, most Ig variability derives from extensive processing of the coding ends, including exonucleolytic trimming of DNA ends, together with the addition of palindromic (P) nucleotides templated by the adjacent germ line sequence and of nontemplated (N) nucleotides secondary to the activity of the terminal deoxynucleotidyl transferase (TdT), a lymphoid-specific member of family X of DNA polymerases (reviewed in reference 56). During B-lineage differentiation, IgH rearrangements occur before those of the IgL locus, and D-to-J_H rearrangements precede V-to-DJ_H rearrangements (62). DJ_H joints are formed in any of the three open reading frames (ORFs). ORF1 is predominantly used in mature Igs, ORF2 is transcribed as a Dμ protein that provides negative signals to the B-cell precursors, and ORF3 frequently leads to stop codons (32, 33, 37). Germ line V, D, and J gene segments display short stretches of mutually homologous nucleotides (SSH), which are frequently used in gene rearrangements during perinatal periods, when N additions are absent (27, 32, 55, 57). The actual Ig V-region repertoires represent both the results of the NHEJ process associated with genomic VDJ recombination and those of antigen-independent and -dependent selection events. Although the core NHEJ components (Ku-Artemis-DNA-PK and XLF-XRCC4-DNA ligase IV) are by themselves able to join RAG-induced, incompatible DNA ends, family X DNA polymerases can be recruited to fill gaps created by imprecise coding ends with 3′ overhangs (DNA polymerase μ [Polμ] and Polλ) and/or to promote diversity through the addition of N nucleotides (TdT) (34, 56).The lymphoid differentiation pathways and clonotypic repertoires are developmentally regulated and differ between the embryo-fetal and adult periods (2, 44, 68). The perinatal B cells result from a wave of B lymphopoiesis occurring during the last third of mouse gestation (13, 14, 21, 70). Perinatal V_H gene usage differs from that predominating in the adult (1, 69), and the former VDJ joints rarely display N additions, leading to V-region repertoires enriched in multi- and self-reactive specificities (36, 40). The program of B-cell differentiation starts at embryonic days 10 to 11 (E10 to E11) in embryo hematopoietic sites, after the emergence of multipotent progenitors (at E8.5 to E9.5) (18, 19, 23, 31, 51, 73). DJ_H rearrangements were detected in these early embryos, whereas full VDJ_H sequences were not observed before E14 (14, 18, 51, 66), when VJκ rearrangements were also found (63). The earliest mouse DJ_H/VDJ_H Ig sequences analyzed to date corresponded to late fetuses (E16) (14, 53). We reasoned that the true baseline of the Ig rearrangement process occurs in midgestation embryos, when the first DJ_Hs are not yet transcribed and, consequently, not subjected to selection and are conditioned only for the evolutionarily established and developmentally regulated usage of distinct NHEJ machineries.We report here the sequence profiles of the earliest embryo E10 to E12 DJ_H joints. Unexpected frequencies of embryonic DJ_H joints bearing N nucleotides, in the absence of detectable TdT expression, were found. Moreover, the embryo DJ_H joints lacking N nucleotides (N⁻) used fewer SSH to recombine than newborn DJ_Hs, and these SSH were widely dispersed along the embryo D sequences, in contrast to the most joint-proximal ones, which predominated in newborn DJ_Hs. Considering that Polμ is the closest relative of TdT (42% amino acid identity) (22), which is able to introduce N nucleotides in vitro (4, 22, 34, 39, 49) and to join DNA ends with minimal or even null complementarity (17, 58), and that it is expressed in early-embryo organs, we decided to investigate its putative contribution to the first embryo DJ_H joints. The DJ_H joints obtained from Polμ^−/− embryos (48) showed a significant reduction of N nucleotides compared to wild-type (WT) embryos. Moreover, highly preserved DJ_H joints (with <3 deleted nucleotides) were selectively depleted in the Polμ^−/− mouse embryos, while the remaining DJ_Hs preferentially relied upon longer stretches of homology for end ligation. These findings support the idea that Polμ is active during early-embryo DJ_H rearrangements and that both its template-dependent and -independent ambivalent functions may be used to fill in small nucleotide gaps generated after asymmetric hairpin nicking and also to extend coding ends via a limited TdT-like activity.     

Composition and Activity of an Autotrophic Fe(II)-Oxidizing,Nitrate-Reducing Enrichment Culture

16S rRNA gene libraries from the lithoautotrophic Fe(II)-oxidizing, nitrate-reducing enrichment culture described by Straub et al. (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl. Environ. Microbiol. 62:1458-1460, 1996) were dominated by a phylotype related (95% 16S rRNA gene homology) to the autotrophic Fe(II) oxidizer Sideroxydans lithotrophicus. The libraries also contained phylotypes related to known heterotrophic nitrate reducers Comamonas badia, Parvibaculum lavamentivorans, and Rhodanobacter thiooxidans. The three heterotrophs were isolated and found to be capable of only partial (12 to 24%) Fe(II) oxidation, suggesting that the Sideroxydans species has primary responsibility for Fe(II) oxidation in the enrichment culture.A variety of microorganisms oxidize Fe(II) with nitrate under anaerobic, circumneutral pH conditions (29) and may contribute to an active microbially driven anoxic Fe redox cycle (1, 27-29, 31, 32). Straub et al. (28) obtained the first Fe(II)-oxidizing, nitrate-reducing (enrichment) culture capable of fully autotrophic growth by a reaction such as 5Fe²⁺ + NO₃⁻ + 12H₂O → 5Fe(OH)₃ + 0.5N₂ + 9H⁺. This process has since been demonstrated in detail with the hyperthermophilic archaeon Ferroglobus placidus (9) and with the mesophilic Proteobacteria Chromobacterium violacens strain 2002 (34) and Paracoccus ferrooxidans strain BDN-1 (16). Nitrate-dependent Fe(II) oxidation in the presence of fixed carbon has been documented for Dechlorosoma suillum strain PS (4), Geobacter metallireducens (7), Desulfitobacterium frappieri (23), and Acidovorax strain BoFeN1 (15). In addition to oxidizing insoluble Fe(II)-bearing minerals (33), the enrichment culture described by Straub et al. (28) is the only autotrophic Fe(II)-oxidizing, nitrate-reducing culture capable of near-complete oxidation of uncomplexed Fe(II) with reduction of nitrate to N₂. During Fe(II) oxidation, F. placidus reduces nitrate to nitrite, which may play a significant role in overall Fe(II) oxidation. Although both C. violacens and Paracoccus ferrooxidans reduce nitrate to N₂, C. violacens oxidizes only 20 to 30% of the initial Fe(II), and P. ferrooxidans uses FeEDTA²⁻ but not free (uncomplexed) Fe(II) in medium analogous to that used for cultivation of the enrichment culture described by Straub et al. (28). The enrichment culture described by Straub et al. (28) is thus the most robust culture capable of autotrophic growth coupled to nitrate-dependent Fe(II) oxidation available at present. The composition and activity of this culture was investigated with molecular and cultivation techniques. The culture examined is one provided by K. L. Straub to E. E. Roden in 1998 for use in studies of nitrate-dependent oxidation of solid-phase Fe(II) compounds (33) and has been maintained in our laboratory since that time.     

Combined Gel Probe and Isotope Labeling Technique for Measuring Dissimilatory Nitrate Reduction to Ammonium in Sediments at Millimeter-Level Resolution

Dissimilatory NO₃⁻ reduction in sediments is often measured in bulk incubations that destroy in situ gradients of controlling factors such as sulfide and oxygen. Additionally, the use of unnaturally high NO₃⁻ concentrations yields potential rather than actual activities of dissimilatory NO₃⁻ reduction. We developed a technique to determine the vertical distribution of the net rates of dissimilatory nitrate reduction to ammonium (DNRA) with minimal physical disturbance in intact sediment cores at millimeter-level resolution. This allows DNRA activity to be directly linked to the microenvironmental conditions in the layer of NO₃⁻ consumption. The water column of the sediment core is amended with ¹⁵NO₃⁻ at the in situ ¹⁴NO₃⁻ concentration. A gel probe is deployed in the sediment and is retrieved after complete diffusive equilibration between the gel and the sediment pore water. The gel is then sliced and the NH₄⁺ dissolved in the gel slices is chemically converted by hypobromite to N₂ in reaction vials. The isotopic composition of N₂ is determined by mass spectrometry. We used the combined gel probe and isotopic labeling technique with freshwater and marine sediment cores and with sterile quartz sand with artificial gradients of ¹⁵NH₄⁺. The results were compared to the NH₄⁺ microsensor profiles measured in freshwater sediment and quartz sand and to the N₂O microsensor profiles measured in acetylene-amended sediments to trace denitrification.Nitrate accounts for the eutrophication of many human-affected aquatic ecosystems (19, 21). Sediment bacteria may mitigate NO₃⁻ pollution by denitrification and anaerobic ammonium oxidation (anammox), which produce N₂ (13, 18). However, inorganic nitrogen is retained in aquatic ecosystems when sediment bacteria reduce NO₃⁻ to NH₄⁺ by dissimilatory nitrate reduction to ammonium (DNRA) (5, 12, 16, 39). Hence, DNRA contributes to rather than counteracts eutrophication (23). DNRA may be the dominant pathway of dissimilatory NO₃⁻ reduction in sediments that are rich in electron donors, such as labile organic carbon and sulfide (4, 8, 17, 38, 55). High rates of DNRA are thus found in sediments affected by coastal aquaculture (8, 36) and settling algal blooms (16).DNRA, denitrification, and the chemical factors that control the partitioning between them (e.g., sulfide) should ideally be investigated in undisturbed sediments. The redox stratification of sediments involves vertical concentration gradients of pore water solutes. These gradients are often very steep, and their measurement requires high-resolution techniques, such as microsensors (26, 42) and gel probes (9, 54). If, for instance, the influence of sulfide on DNRA and denitrification is to be investigated, one wants to know exactly the sulfide concentration in the layers of DNRA and denitrification activity, as well as the flux of sulfide into these layers. This information can easily be obtained using H₂S and pH microsensors (22, 43). It is less trivial to determine the vertical distribution of DNRA and denitrification activity in undisturbed sediments. Denitrification activity can be traced using a combination of the acetylene inhibition technique (51) and N₂O microsensors (1). Acetylene inhibits the last step of denitrification, and therefore, N₂O accumulates in the layer of denitrification activity (44). This method underestimates the denitrification activity in sediments with high rates of coupled nitrification-denitrification because acetylene also inhibits nitrification (50).The vertical distribution of DNRA activity in undisturbed sediment has, to the best of our knowledge, never been determined; thus, the microenvironmental conditions in the layer of DNRA activity remain unknown. Until now, the influence of chemical factors on DNRA and denitrification in sediments has been assessed by slurry incubations (4, 12, 30), by flux measurements with sealed sediment cores (7, 47) or flowthrough sediment cores (16, 27, 37), and in one case, in reconstituted sediment cores sliced at centimeter-level resolution (39). Here, we present a new method, the combined gel probe and isotope labeling technique, to determine the vertical distribution of the net rates of DNRA in sediments. The sediments remain largely undisturbed and the NO₃⁻ amendments are within the range of in situ concentrations. The DNRA measurements can be related to the microprofiles of potential influencing factors measured in close vicinity of the gel probe. This allows DNRA activity to be directly linked with the microenvironmental conditions in the sediment.     

Identification of a Novel Class of Membrane-Bound [NiFe]-Hydrogenases in Thermococcus onnurineus NA1 by In Silico Analysis

In silico analysis of group 4 [NiFe]-hydrogenases from a hyperthermophilic archaeon, Thermococcus onnurineus NA1, revealed a novel tripartite gene cluster consisting of dehydrogenase-hydrogenase-cation/proton antiporter subunits, which may be classified as the new subgroup 4b of [NiFe]-hydrogenases-based on sequence motifs.Hydrogenases are the key enzymes involved in the metabolism of H₂, catalyzing the following chemical reaction: 2H⁺ + 2e⁻ ↔ H₂. Hydrogenases can be classified into [NiFe]-hydrogenases, [FeFe]-hydrogenases, and [Fe]-hydrogenases, based on their distinctive functional core containing the catalytic metal center (11, 17).The genomic analysis of Thermococcus onnurineus NA1, a hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent area, revealed the presence of several distinct gene clusters encoding seven [NiFe]-hydrogenases and one homolog similar to Mbx (membrane-bound oxidoreductase) from Pyrococcus furiosus (1, 6, 8, 12). According to the classification system of hydrogenases by Vignais et al. (17), three hydrogenases (one F₄₂₀-reducing and two NADP-reducing hydrogenases) belong to group 3 [NiFe]-hydrogenases, and four hydrogenases belong to group 4 [NiFe]-hydrogenases. The group 4 hydrogenases are widely distributed among bacteria and archaea (17), with Hyc and Hyf (hydrogenase 3 and 4, respectively) from Escherichia coli (19), Coo (CO-induced hydrogenase) from Rhodospirillum rubrum (4), Ech (energy-converting hydrogenase) from Methanosarcina barkeri (7), and Mbh (membrane-bound hydrogenase) from P. furiosus (6, 10, 12) being relatively well-characterized hydrogenases in this group. One of the four group 4 hydrogenases from T. onnurineus NA1 was found to be similar in sequence to that of P. furiosus Mbh (10).     

Novel Denitrifying Bacterium Ochrobactrum anthropi YD50.2 Tolerates High Levels of Reactive Nitrogen Oxides

Most studies of bacterial denitrification have used nitrate (NO₃⁻) as the first electron acceptor, whereas relatively less is understood about nitrite (NO₂⁻) denitrification. We isolated novel bacteria that proliferated in the presence of high levels of NO₂⁻ (72 mM). Strain YD50.2, among several isolates, was taxonomically positioned within the α subclass of Proteobacteria and identified as Ochrobactrum anthropi YD50.2. This strain denitrified NO₂⁻, as well as NO₃⁻. The gene clusters for denitrification (nar, nir, nor, and nos) were cloned from O. anthropi YD50.2, in which the nir and nor operons were linked. We confirmed that nirK in the nir-nor operon produced a functional NO₂⁻ reductase containing copper that was involved in bacterial NO₂⁻ reduction. The strain denitrified up to 40 mM NO₂⁻ to dinitrogen under anaerobic conditions in which other denitrifiers or NO₃⁻ reducers such as Pseudomonas aeruginosa and Ralstonia eutropha and nitrate-respiring Escherichia coli neither proliferated nor reduced NO₂⁻. Under nondenitrifying aerobic conditions, O. anthropi YD50.2 and its type strain ATCC 49188^T proliferated even in the presence of higher levels of NO₂⁻ (100 mM), and both were considerably more resistant to acidic NO₂⁻ than were the other strains noted above. These results indicated that O. anthropi YD50.2 is a novel denitrifier that has evolved reactive nitrogen oxide tolerance mechanisms.Environmental bacteria maintain the global nitrogen cycle by metabolizing organic and inorganic nitrogen compounds. Denitrification is critical for maintenance of the global nitrogen cycle, through which nitrate (NO₃⁻) or nitrite (NO₂⁻) is reduced to gaseous nitrogen forms such as N₂ and nitrous oxide (N₂O) (19, 47). Decades of investigations into denitrifying bacteria have revealed their ecological impact (9), their molecular mechanisms of denitrification (13, 25, 47), and the industrial importance of removing nitrogenous contaminants from wastewater (31, 36). Bacterial denitrification is considered to comprise four successive reduction steps, each of which is catalyzed by NO₃⁻ reductase (Nar), NO₂⁻ reductase (Nir), nitric oxide (NO) reductase (Nor), and N₂O reductase (Nos). The reaction of each enzyme is linked to the electron transport chain on the cellular membrane and accompanies oxidative phosphorylation, implying that bacterial denitrification is of as much physiological significance as anaerobic respiration (25, 47). Most denitrifying bacteria are facultative anaerobes and respire with oxygen under aerobic conditions. Because denitrification is induced in the absence of oxygen, it is considered an alternative mechanism of energy conservation that has evolved as an adaptation to anaerobic circumstances (13, 47).Nitrite and NO are hazardous to bacteria, since they generate highly reactive nitrogen species (RNS) under physiological conditions and damage cellular DNA, lipid, and proteins (28, 37). Denitrifying bacteria are thought to be threatened by RNS since they reduce NO₃⁻ to generate NO₂⁻ and NO as denitrifying intermediates. Furthermore, denitrifying bacteria often inhabit environments where they are exposed to NO₂⁻ and NO and hence high levels of RNS. Recent reports suggest that pathogenic bacteria invading animal tissues are attacked by NO generated by macrophages (12). Such bacteria involve denitrifiers, and some of them, for example, Neisseria meningitidis (1) and Pseudomonas aeruginosa, acquire resistance to NO by producing Nor (44). The utilization (reduction) of NO by Brucella increases the survival of infected mice (2). These examples suggest that production of a denitrifying mechanism affects bacterial survival of threats from both endogenous and extracellular RNS. However, the mechanism of RNS tolerance induced by denitrifying bacteria is not fully understood.Ubiquitous gram-negative Ochrobactrum strains are widely distributed in soils and aqueous environments, where they biodegrade aromatic compounds (11), organophosphorus pesticides (45), and other hydrocarbons (38) and remove heavy metal ions such as chromium and cadmium (24). Having been isolated from clinical specimens, Ochrobactrum anthropi is currently recognized as an emerging opportunistic pathogen, although relatively little is known about its pathogenesis and factors contributing to its virulence (7, 30). Manipulation systems have been developed to investigate these issues at the molecular genetic level (33). Some O. anthropi strains have been identified as denitrifiers (21), although the denitrifying properties of these strains have not been investigated in detail. This study was undertaken to examine the denitrifying properties of O. anthropi in more detail. O. anthropi YD50.2 was selected for this study and was isolated herein. The strain denitrified high levels of NO₂⁻ (up to 40 mM) to dinitrogen under anaerobic conditions. The strain was highly resistant to acidified NO₂⁻ under nondenitrifying aerobic conditions. These results indicate that O. anthropi YD50.2 has mechanisms that produce tolerance to RNS.     

Very Few Substitutions in a Germ Line Antibody Are Required To Initiate Significant Domain Exchange

2G12 is a broadly neutralizing anti-HIV-1 monoclonal human IgG1 antibody reactive with a high-mannose glycan cluster on the surface of glycoprotein gp120. A key feature of this very highly mutated antibody is domain exchange of the heavy-chain variable region (V_H) with the V_H of the adjacent Fab of the same immunoglobulin, which assembles a multivalent binding interface composed of two primary binding sites in close proximity. A non-germ line-encoded proline in the elbow between V_H and C_H1 and an extensive network of hydrophobic interactions in the V_H/V_H′ interface have been proposed to be crucial for domain exchange. To investigate the origins of domain exchange, a germ line version of 2G12 that behaves as a conventional antibody was engineered. Substitution of 5 to 7 residues for those of the wild type produced a significant fraction of domain-exchanged molecules, with no evidence of equilibrium between domain-exchanged and conventional forms. Two substitutions not previously implicated, A^H14 and E^H75, are the most crucial for domain exchange, together with I^H19 at the V_H/V_H′ interface and P^H113 in the elbow region. Structural modeling gave clues as to why these residues are essential for domain exchange. The demonstration that domain exchange can be initiated by a small number of substitutions in a germ line antibody suggests that the evolution of a domain-exchanged antibody response in vivo may be more readily achieved than considered to date.Protein oligomers are able to exchange or swap an element of their secondary structure or an entire protein domain. The functional unit in domain-exchanged proteins thereby stays preserved, as only the linking hinge loop changes conformation significantly (4, 17, 27). Analogous to other domain-swapped proteins, antibodies can exchange an entire domain, in this case the heavy-chain variable region (V_H), with an equivalent heavy-chain variable region of an adjacent Fab (V_H′) within the same immunoglobulin (Ig) molecule (11). The advantages of domain-exchanged proteins, including antibodies, are higher local concentrations of active sites, a larger binding surface, and a potential secondary active site at the new subunit interface (27, 45). The one and only antibody shown to be domain exchanged to date is 2G12 (7, 11), but this arrangement is potentially possible for any Ig and could have been overlooked at least in some instances.2G12 is one of only a few high-affinity monoclonal antibodies with broad neutralizing activity against different subtypes of HIV-1 (5, 30, 40, 43). The antibody binds a dense cluster of N-linked high-mannose glycans (Man_8-9GlcNAc₂) on the envelope surface glycoprotein gp120 (10, 35, 36, 41). The domain-exchanged arrangement forms a multivalent binding site composed of two primary binding sites in close proximity and a proposed secondary binding site formed by the novel V_H/V_H′ interface (11). 2G12 provides protection against infection in animal models (19, 31) and has been shown to induce neutralization escape following passive immunization in humans (39).Consensus has grown that a successful HIV-1 vaccine will need to include a component that elicits broadly neutralizing antibodies (8, 18, 21, 26, 32, 42). All attempts to elicit 2G12-like antibodies with the desired specificity and neutralization activity have failed to date (22, 29, 44), conceivably due to difficulties in generating adequate mimicry of the glycan cluster and tolerance mechanisms or, very likely, the inability to induce domain exchange (1). Unraveling the mechanism of domain exchange and how this conformation might have evolved is highly desirable to direct future HIV-1 vaccine design to elicit 2G12-like antibodies.By comparison with other domain-exchanged proteins (27), the following three mechanisms have been proposed to contribute to the unique structure of 2G12 compared to the structure of a conventional antibody: destabilization of the “closed” V_H/V_L interface, conformational change in the elbow between V_H and C_H1, and an energetically favorable “open” V_H/V_H′ interface (11). Key residues involved in promoting domain exchange were predicted based on examination of interacting residues at the two interfaces and by the effects of alanine substitutions on the binding of wild-type 2G12 to gp120. However, the importance of these key residues for domain exchange was not directly demonstrated experimentally (11).Here, we explored the minimal requirements for domain exchange of 2G12, starting with a germ line version of the antibody that adopts a conventional antibody structure. Although wild-type 2G12 is heavily somatically mutated, only five to seven substitutions in the germ line version of the antibody were shown to produce a significant fraction of domain-exchanged molecules. The results suggest the evolution of domain-exchanged antibody responses may be more facile than considered to date.     

Environmental Factors Shape Sediment Anammox Bacterial Communities in Hypernutrified Jiaozhou Bay,China

Bacterial anaerobic ammonium oxidation (anammox) is an important process in the marine nitrogen cycle. Because ongoing eutrophication of coastal bays contributes significantly to the formation of low-oxygen zones, monitoring of the anammox bacterial community offers a unique opportunity for assessment of anthropogenic perturbations in these environments. The current study used targeting of 16S rRNA and hzo genes to characterize the composition and structure of the anammox bacterial community in the sediments of the eutrophic Jiaozhou Bay, thereby unraveling their diversity, abundance, and distribution. Abundance and distribution of hzo genes revealed a greater taxonomic diversity in Jiaozhou Bay, including several novel clades of anammox bacteria. In contrast, the targeting of 16S rRNA genes verified the presence of only “Candidatus Scalindua,” albeit with a high microdiversity. The genus “Ca. Scalindua” comprised the apparent majority of active sediment anammox bacteria. Multivariate statistical analyses indicated a heterogeneous distribution of the anammox bacterial assemblages in Jiaozhou Bay. Of all environmental parameters investigated, sediment organic C/organic N (OrgC/OrgN), nitrite concentration, and sediment median grain size were found to impact the composition, structure, and distribution of the sediment anammox bacterial community. Analysis of Pearson correlations between environmental factors and abundance of 16S rRNA and hzo genes as determined by fluorescent real-time PCR suggests that the local nitrite concentration is the key regulator of the abundance of anammox bacteria in Jiaozhou Bay sediments.Anaerobic ammonium oxidation (anammox, NH₄⁺ + NO₂⁻ → N₂ + 2H₂O) was proposed as a missing N transformation pathway decades ago. It was found 20 years later to be mediated by bacteria in artificial environments, such as anaerobic wastewater processing systems (see reference 32 and references therein). Anammox in natural environments was found even more recently, mainly in O₂-limited environments such as marine sediments (28, 51, 54, 67, 69) and hypoxic or anoxic waters (10, 25, 39-42). Because anammox may remove as much as 30 to 70% of fixed N from the oceans (3, 9, 64), this process is potentially as important as denitrification for N loss and bioremediation (41, 42, 73). These findings have significantly changed our understanding of the budget of the marine and global N cycles as well as involved pathways and their evolution (24, 32, 35, 72). Studies indicate variable anammox contributions to local or regional N loss (41, 42, 73), probably due to distinct environmental conditions that may influence the composition, abundance, and distribution of the anammox bacteria. However, the interactions of anammox bacteria with their environment are still poorly understood.The chemolithoautotrophic anammox bacteria (64, 66) comprise the new Brocadiaceae family in the Planctomycetales, for which five Candidatus genera have been described (see references 32 and 37 and references therein): “Candidatus Kuenenia,” “Candidatus Brocadia,” “Candidatus Scalindua,” “Candidatus Anammoxoglobus,” and “Candidatus Jettenia.” Due to the difficulty of cultivation and isolation, anammox bacteria are not yet in pure culture. Molecular detection by using DNA probes or PCR primers targeting the anammox bacterial 16S rRNA genes has thus been the main approach for the detection of anammox bacteria and community analyses (58). However, these studies revealed unexpected target sequence diversity and led to the realization that due to biased coverage and specificity of most of the PCR primers (2, 8), the in situ diversity of anammox bacteria was likely missed. Thus, the use of additional marker genes for phylogenetic analysis was suggested in hopes of better capturing the diversity of this environmentally important group of bacteria. By analogy to molecular ecological studies of aerobic ammonia oxidizers, most recent studies have attempted to include anammox bacterium-specific functional genes. All anammox bacteria employ hydrazine oxidoreductase (HZO) (= [Hzo]₃) to oxidize hydrazine to N₂ as the main source for a useable reductant, which enables them to generate proton-motive force for energy production (32, 36, 65). Phylogenetic analyses of Hzo protein sequences revealed three sequence clusters, of which the cladistic structure of cluster 1 is in agreement with the anammox bacterial 16S rRNA gene phylogeny (57). The hzo genes have emerged as an alternative phylogenetic and functional marker for characterization of anammox bacterial communities (43, 44, 57), allowing the 16S rRNA gene-based investigation methods to be corroborated and improved.The contribution of anammox to the removal of fixed N is highly variable in estuarine and coastal sediments (50). For instance, anammox may be an important pathway for the removal of excess N (23) or nearly negligible (48, 54, 67, 68). This difference may be attributable to a difference in the structure and composition of anammox bacterial communities, in particular how the abundance of individual cohorts depends on particular environmental conditions. Anthropogenic disturbance with variable source and intensity of eutrophication and pollution may further complicate the anammox bacterium-environment relationship.Jiaozhou Bay is a large semienclosed water body of the temperate Yellow Sea in China. Eutrophication has become its most serious environmental problem, along with red tides (harmful algal blooms), species loss, and contamination with toxic chemicals and harmful microbes (14, 15, 21, 61, 71). Due to different sources of pollution and various levels of eutrophication across Jiaozhou Bay (mariculture, municipal and industrial wastewater, crude oil shipyard, etc.), a wide spectrum of environmental conditions may contribute to a widely varying community structure of anammox bacteria. This study used both 16S rRNA and hzo genes as targets to measure their abundance, diversity, and spatial distribution and assess the response of the resident anammox bacterial community to different environmental conditions. Environmental factors with potential for regulating the sediment anammox microbiota are discussed.     

Extracellular Iron Biomineralization by Photoautotrophic Iron-Oxidizing Bacteria

Iron oxidation at neutral pH by the phototrophic anaerobic iron-oxidizing bacterium Rhodobacter sp. strain SW2 leads to the formation of iron-rich minerals. These minerals consist mainly of nano-goethite (α-FeOOH), which precipitates exclusively outside cells, mostly on polymer fibers emerging from the cells. Scanning transmission X-ray microscopy analyses performed at the C K-edge suggest that these fibers are composed of a mixture of lipids and polysaccharides or of lipopolysaccharides. The iron and the organic carbon contents of these fibers are linearly correlated at the 25-nm scale, which in addition to their texture suggests that these fibers act as a template for mineral precipitation, followed by limited crystal growth. Moreover, we evidence a gradient of the iron oxidation state along the mineralized fibers at the submicrometer scale. Fe minerals on these fibers contain a higher proportion of Fe(III) at cell contact, and the proportion of Fe(II) increases at a distance from the cells. All together, these results demonstrate the primordial role of organic polymers in iron biomineralization and provide first evidence for the existence of a redox gradient around these nonencrusting, Fe-oxidizing bacteria.Fe(II) can serve as a source of electrons for phylogenetically diverse microorganisms that precipitate iron minerals as products of their metabolism (see, e.g., references 3, 5, 25, and 30). For example, mixotrophic or autotrophic bacteria can couple the oxidation of Fe(II) to the reduction of nitrate in anoxic and neutral-pH environments. With Fe(III) being highly insoluble at neutral pH, this metabolism leads to the formation of poorly to well-crystallized iron minerals (3, 18, 26, 27) that precipitate partly within the cell periplasm for some strains (22). Similar Fe minerals are also synthesized by autotrophic bacteria that perform anoxygenic photosynthesis, using Fe(II) as an electron donor and light as a source of energy for CO₂ fixation (8, 12, 30), according to the equation HCO₃⁻ + 4 Fe²⁺ + 10 H₂O ⇆ <CH₂O> + 4 Fe(OH)₃ + 7 H⁺.However, the biological mechanisms of iron oxidation in these bacteria and in particular the way they cope with the formation of minerals within their ultrastructures are still not fully understood. Indeed, iron minerals are potentially lethal since their precipitation may alter cellular ultrastructures but also catalyze the production of free radicals (2). Recent genetic studies of the phototrophic, iron-oxidizing bacteria Rhodobacter sp. strain SW2 (6) and Rhodopseudomonas palustris strain TIE-1 (16) have identified genes (fox and pio operons, respectively) encoding proteins specific for iron oxidation. Interestingly, Jiao and Newman (16) suggested that one of these proteins could have a periplasmic localization. However, in contrast to what has been observed in some other phototrophic iron oxidizers (25) and in some nitrate-reducing, iron-oxidizing bacteria (22), no iron-mineral precipitation occurs within the periplasm of the purple nonsulfur iron-oxidizing bacterium Rhodobacter sp. strain SW2 (3). Similarly to some other anaerobic neutrophilic (22, 25) and microaerobic iron-oxidizing bacteria (5, 10), this strain seems indeed to have the ability to localize iron biomineralization at a distance from the cells, leaving large areas of the cells free of precipitates (17, 25). While it has been shown that the Gallionella and Leptothrix genera, for example, produce extracellular polymers that facilitate the nucleation of iron minerals outside cells (see, e.g., references 5 and 9), only a little is known about the existence and function of such polymers in anaerobic, neutrophilic iron-oxidizing bacteria and particularly in the phototrophic strain SW2. In the present study, we investigate iron biomineralization by the photoautotrophic iron-oxidizing bacterium Rhodobacter sp. strain SW2. We use scanning transmission X-ray microscopy (STXM) to map and identify organic polymers produced by the cells as well as the redox state of iron at the 25-nanometer scale regularly during a 2 week-period. These results demonstrate the primordial role of organic polymers in iron biomineralization and provide the first evidence for the existence of a redox gradient around SW2 cells.     

Novel Types of Ca2+ Release Channels Participate in the Secretory Cycle of Paramecium Cells

A database search of the Paramecium genome reveals 34 genes related to Ca²⁺-release channels of the inositol-1,4,5-trisphosphate (IP₃) or ryanodine receptor type (IP₃R, RyR). Phylogenetic analyses show that these Ca²⁺ release channels (CRCs) can be subdivided into six groups (Paramecium tetraurelia CRC-I to CRC-VI), each one with features in part reminiscent of IP₃Rs and RyRs. We characterize here the P. tetraurelia CRC-IV-1 gene family, whose relationship to IP₃Rs and RyRs is restricted to their C-terminal channel domain. CRC-IV-1 channels localize to cortical Ca²⁺ stores (alveolar sacs) and also to the endoplasmic reticulum. This is in contrast to a recently described true IP₃ channel, a group II member (P. tetraurelia IP₃R_N-1), found associated with the contractile vacuole system. Silencing of either one of these CRCs results in reduced exocytosis of dense core vesicles (trichocysts), although for different reasons. Knockdown of P. tetraurelia IP₃R_N affects trichocyst biogenesis, while CRC-IV-1 channels are involved in signal transduction since silenced cells show an impaired release of Ca²⁺ from cortical stores in response to exocytotic stimuli. Our discovery of a range of CRCs in Paramecium indicates that protozoans already have evolved multiple ways for the use of Ca²⁺ as signaling molecule.Ca²⁺ is an important component of cell activity in all organisms, from protozoa to mammals. Thereby Ca²⁺ may originate from the outside medium and/or from internal stores (7, 18). Ca²⁺ release from internal stores is mediated by various Ca²⁺ release channels (CRCs), of which the inositol-1,4,5-trisphosphate receptor (IP₃R) and ryanodine receptor (RyR) families have been studied most extensively (8, 9, 29, 63). IP₃Rs and RyRs have been identified in various metazoan organisms (reviewed in references 9, 28, and 104). According to these reviews, there exist three genetically distinct isoforms of each receptor type in mammals and orthologues have been identified in various nonmammalian vertebrates, e.g., frogs, chickens, and fish. RyRs and IP₃Rs were also cloned and sequenced in the invertebrates Drosophila melanogaster and Caenorhabditis elegans, which possess one copy of each receptor type.Functional evidence for Ca²⁺ release in response to ryanodine or IP₃ receptor agonists has been described in several unicellular systems. Treatment of permeabilized Plasmodium chabaudi parasites with IP₃ results in Ca²⁺ release, which is inhibited by the IP₃ receptor antagonist heparin (69). Another apicomplexan parasite, Toxoplasma gondii, responds to agonists and antagonists of both, ryanodine and IP₃ receptors, by mediating increases in intracellular Ca²⁺ concentration ([Ca²⁺]_i) (56). Stimulation of Trypanosoma cruzi with carbachol results in increased [Ca²⁺]_i and IP₃ (59). IP₃ and cyclic ADP-ribose induces Ca²⁺ release in Euglena gracilis microsome fractions in a dose-dependent manner (61). In the giant algae Chara corallina and Nitrella translucens, IP₃ produces action potentials involving increased [Ca²⁺]_i (93). Treatment of vacuolar membrane vesicles from Candida albicans with IP₃ results in Ca²⁺ release, blocked by heparin and ruthenium red (14). IP₃ generates and maintains a Ca²⁺ gradient in the hyphal tip of Neurospora crassa and the IP₃-sensitive channels have been reconstituted and characterized with the planar bilayer method (87). In summary, these publications suggest that IP₃-dependent signaling pathways are conserved among unicellular organisms, including protozoa.Despite these data, the molecular characterization of IP₃ or ryanodine receptors in low eukaryotes is currently a challenge since the identification of orthologues has not been possible thus far, probably because of evolutionary sequence divergence (66). Traynor et al. (96) identified an IP₃ receptor-like protein, IplA, in Dictyostelium discoideum, which possesses regions related to IP₃R sequences, but thus far no evidence for IP₃ interaction exists. We have recently described an IP₃R in the ciliated protozoa Paramecium tetraurelia (referred to here as P. tetraurelia IP₃R_N) (53), with features characteristic of mammalian IP₃Rs in terms of topology and ability for IP₃ binding. The expression level of P. tetraurelia IP₃R_N is modulated by extracellular Ca²⁺ concentrations ([Ca²⁺]_o) and immunofluorescence studies reveal an unexpected localization to the contractile vacuole complex (CVC), the major organelle involved in osmoregulation (2). The ionic composition of the contractile vacuole fluid by ion-selective microelectrodes (91) suggests that the organelle plays a major role in expelling an excess of cytosolic Ca²⁺. Therefore, these IP₃Rs may here mediate a latent, graded reflux of Ca²⁺ for fine-tuning of [Ca²⁺]_i and thus serve [Ca²⁺] homeostasis (53).Besides [Ca²⁺] homeostasis, the Paramecium cell has to regulate a variety of well-characterized processes (75). This includes exocytosis of dense-core secretory vesicles (trichocysts) (71, 74, 99). Each cell possesses up to 1,000 trichocysts attached to the cell membrane. Their contents can be extruded synchronously in response to natural stimuli, i.e., predators (34, as confirmed by Knoll et al. [49]), to artificial polyamine secretagogues such as aminoethyldextran (AED) (78), to caffeine (48) or to the ryanodine substitute, 4-chloro-meta-cresol (4-CmC) (46). Their expulsion strictly depends on Ca²⁺ (10) and is accompanied by an increase of intracellular [Ca²⁺]_i (24, 47). This Ca²⁺ signal originates from rapid mobilization of cortical stores, the alveolar sacs (33, 64, 74), superimposed by Ca²⁺ influx (46, 72). It thus represents a SOC-type mechanism (SOC, store-operated Ca²⁺ entry) known from mammalian systems (81).Upon exocytosis stimulation ∼60% of their total Ca²⁺ is released from alveolar sacs (33). These are Ca²⁺ stores (90) represented by flat membrane compartments tightly attached at the cell membrane surrounding each trichocyst docking site. They possess a SERCA-type pump located at the membrane facing the cell center (36, 37) and a luminal high-capacity/low-affinity CaBP of the calsequestrin type (73). Thus far, Ca²⁺ release channels of these stores were identified only indirectly as cells respond by exocytosis to the RyR activators caffeine (54, 48) and 4-CmC (46). However, an involvement of conserved RyRs has remained questionable as ryanodine is not able to activate Ca²⁺ release from alveolar sacs, as is the case with IP₃ (54). Therefore, one of the most intriguing questions is the elucidation of the molecular nature of the channels mediating Ca²⁺ release from alveolar sacs upon stimulated exocytosis.In the present work we describe a novel family of CRCs (P. tetraurelia CRC-IV-1), whose members display several properties of the channels postulated above. In detail, the identified CRC-IV-1 channels localize to the alveolar sacs. Functional and fluorochrome analyses after gene silencing reveal that they are essential for mediating Ca²⁺ release and exocytosis in response to AED, caffeine, or 4-CmC. Their classification as “novel” CRC type is based on a restricted relationship to the C-terminal channel domains of IP₃Rs and RyRs. The overall size and the number of putative transmembrane domains resemble IP₃Rs, but N-terminal parts of CRC-IV-1 channels do not show any conservation, such as an IP₃-binding domain. Therefore, CRC-IV-1 channels represent distant relatives of IP₃Rs and RyRs and may belong to an ancestral Ca²⁺ signaling pathway.     

Anaerobic Biodegradation of n-Hexadecane by a Nitrate-Reducing Consortium

Nitrate-reducing enrichments, amended with n-hexadecane, were established with petroleum-contaminated sediment from Onondaga Lake. Cultures were serially diluted to yield a sediment-free consortium. Clone libraries and denaturing gradient gel electrophoresis analysis of 16S rRNA gene community PCR products indicated the presence of uncultured alpha- and betaproteobacteria similar to those detected in contaminated, denitrifying environments. Cultures were incubated with H₃₄-hexadecane, fully deuterated hexadecane (d₃₄-hexadecane), or H₃₄-hexadecane and NaH¹³CO₃. Gas chromatography-mass spectrometry analysis of silylated metabolites resulted in the identification of [H₂₉]pentadecanoic acid, [H₂₅]tridecanoic acid, [1-¹³C]pentadecanoic acid, [3-¹³C]heptadecanoic acid, [3-¹³C]10-methylheptadecanoic acid, and d₂₇-pentadecanoic, d₂₅-, and d₂₄-tridecanoic acids. The identification of these metabolites suggests a carbon addition at the C-3 position of hexadecane, with subsequent β-oxidation and transformation reactions (chain elongation and C-10 methylation) that predominantly produce fatty acids with odd numbers of carbons. Mineralization of [1-¹⁴C]hexadecane was demonstrated based on the recovery of ¹⁴CO₂ in active cultures.Linear alkanes account for a large component of crude and refined petroleum products and, therefore, are of environmental significance with respect to their fate and transport (38). The aerobic activation of alkanes is well documented and involves monooxygenase and dioxygenase enzymes in which not only is oxygen required as an electron acceptor but it also serves as a reactant in hydroxylation (2, 16, 17, 32, 34). Alkanes are also degraded under anoxic conditions via novel degradation strategies (34). To date, there are two known pathways of anaerobic n-alkane degradation: (i) alkane addition to fumarate, commonly referred to as fumarate addition, and (ii) a putative pathway, proposed by So et al. (25), involving carboxylation of the alkane. Fumarate addition proceeds via terminal or subterminal addition (C-2 position) of the alkane to the double bond of fumarate, resulting in the formation of an alkylsuccinate. The alkylsuccinate is further degraded via carbon skeleton rearrangement and β-oxidation (4, 6, 8, 12, 13, 21, 37). Alkane addition to fumarate has been documented for a denitrifying isolate (21, 37), sulfate-reducing consortia (4, 8, 12, 13), and five sulfate-reducing isolates (4, 6-8, 12). In addition to being demonstrated in these studies, fumarate addition in a sulfate-reducing enrichment growing on the alicyclic alkane 2-ethylcyclopentane has also been demonstrated (23). In contrast to fumarate addition, which has been shown for both sulfate-reducers and denitrifiers, the putative carboxylation of n-alkanes has been proposed only for the sulfate-reducing isolate strain Hxd3 (25) and for a sulfate-reducing consortium (4). Experiments using NaH¹³CO₃ demonstrated that bicarbonate serves as the source of inorganic carbon for the putative carboxylation reaction (25). Subterminal carboxylation of the alkane at the C-3 position is followed by elimination of the two terminal carbons, to yield a fatty acid that is one carbon shorter than the parent alkane (4, 25). The fatty acids are subject to β-oxidation, chain elongation, and/or C-10 methylation (25).In this study, we characterized an alkane-degrading, nitrate-reducing consortium and surveyed the metabolites of the consortium incubated with either unlabeled or labeled hexadecane in order to elucidate the pathway of n-alkane degradation. We present evidence of a pathway analogous to the proposed carboxylation pathway under nitrate-reducing conditions.     

Activation of the Inositol (1,4,5)-Triphosphate Calcium Gate Receptor Is Required for HIV-1 Gag Release

The structural precursor polyprotein, Gag, encoded by all retroviruses, including the human immunodeficiency virus type 1 (HIV-1), is necessary and sufficient for the assembly and release of particles that morphologically resemble immature virus particles. Previous studies have shown that the addition of Ca²⁺ to cells expressing Gag enhances virus particle production. However, no specific cellular factor has been implicated as mediator of Ca²⁺ provision. The inositol (1,4,5)-triphosphate receptor (IP3R) gates intracellular Ca²⁺ stores. Following activation by binding of its ligand, IP3, it releases Ca²⁺ from the stores. We demonstrate here that IP3R function is required for efficient release of HIV-1 virus particles. Depletion of IP3R by small interfering RNA, sequestration of its activating ligand by expression of a mutated fragment of IP3R that binds IP3 with very high affinity, or blocking formation of the ligand by inhibiting phospholipase C-mediated hydrolysis of the precursor, phosphatidylinositol-4,5-biphosphate, inhibited Gag particle release. These disruptions, as well as interference with ligand-receptor interaction using antibody targeted to the ligand-binding site on IP3R, blocked plasma membrane accumulation of Gag. These findings identify IP3R as a new determinant in HIV-1 trafficking during Gag assembly and introduce IP3R-regulated Ca²⁺ signaling as a potential novel cofactor in viral particle release.Assembly of the human immunodeficiency virus (HIV) is determined by a single gene that encodes a structural polyprotein precursor, Gag (71), and may occur at the plasma membrane or within late endosomes/multivesicular bodies (LE/MVB) (7, 48, 58; reviewed in reference 9). Irrespective of where assembly occurs, the assembled particle is released from the plasma membrane of the host cell. Release of Gag as virus-like particles (VLPs) requires the C-terminal p6 region of the protein (18, 19), which contains binding sites for Alix (60, 68) and Tsg101 (17, 37, 38, 41, 67, 68). Efficient release of virus particles requires Gag interaction with Alix and Tsg101. Alix and Tsg101 normally function to sort cargo proteins to LE/MVB for lysosomal degradation (5, 15, 29, 52). Previous studies have shown that addition of ionomycin, a calcium ionophore, and CaCl₂ to the culture medium of cells expressing Gag or virus enhances particle production (20, 48). This is an intriguing observation, given the well-documented positive role for Ca²⁺ in exocytotic events (33, 56). It is unclear which cellular factors might regulate calcium availability for the virus release process.Local and global elevations in the cytosolic Ca²⁺ level are achieved by ion release from intracellular stores and by influx from the extracellular milieu (reviewed in reference 3). The major intracellular Ca²⁺ store is the endoplasmic reticulum (ER); stores also exist in MVB and the nucleus. Ca²⁺ release is regulated by transmembrane channels on the Ca²⁺ store membrane that are formed by tetramers of inositol (1,4,5)-triphosphate receptor (IP3R) proteins (reviewed in references 39, 47, and 66). The bulk of IP3R channels mediate release of Ca²⁺ from the ER, the emptying of which signals Ca²⁺ influx (39, 51, 57, 66). The few IP3R channels on the plasma membrane have been shown to be functional as well (13). Through proteomic analysis, we identified IP3R as a cellular protein that was enriched in a previously described membrane fraction (18) which, in subsequent membrane floatation analyses, reproducibly cofractionated with Gag and was enriched in the membrane fraction only when Gag was expressed. That IP3R is a major regulator of cytosolic calcium concentration (Ca²⁺) is well documented (39, 47, 66). An IP3R-mediated rise in cytosolic Ca²⁺ requires activation of the receptor by a ligand, inositol (1,4,5)-triphosphate (IP3), which is produced when phospholipase C (PLC) hydrolyzes phosphatidylinositol-4,5-bisphosphate [PI(4,5)P₂] at the plasma membrane (16, 25, 54). Paradoxically, PI(4,5)P₂ binds to the matrix (MA) domain in Gag (8, 55, 59), and the interaction targets Gag to PI(4,5)P₂-enriched regions on the plasma membrane; these events are required for virus release (45). We hypothesized that PI(4,5)P₂ binding might serve to target Gag to plasma membrane sites of localized Ca²⁺ elevation resulting from PLC-mediated PI(4,5)P₂ hydrolysis and IP3R activation. This idea prompted us to investigate the role of IP3R in Gag function.Here, we show that HIV-1 Gag requires steady-state levels of IP3R for its efficient release. Three isoforms of IP3R, types 1, 2, and 3, are encoded in three independent genes (39, 47). Types 1 and 3 are expressed in a variety of cells and have been studied most extensively (22, 39, 47, 73). Depletion of the major isoforms in HeLa or COS-1 cells by small interfering RNA (siRNA) inhibited viral particle release. Moreover, we show that sequestration of the IP3R activating ligand or blocking ligand formation also inhibited Gag particle release. The above perturbations, as well as interfering with receptor expression or activation, led to reduced Gag accumulation at the cell periphery. The results support the conclusion that IP3R activation is required for efficient HIV-1 viral particle release.     

Isolation of Basal Bodies with C-Ring Components from the Na+-Driven Flagellar Motor of Vibrio alginolyticus

To investigate the Na⁺-driven flagellar motor of Vibrio alginolyticus, we attempted to isolate its C-ring structure. FliG but not FliM copurified with the basal bodies. FliM proteins may be easily dissociated from the basal body. We could detect FliG on the MS ring surface of the basal bodies.The basal body, which is the part of the rotor, is composed of four rings and a rod that penetrates them. Three of these rings, the L, P, and MS rings, are embedded in the outer membrane, peptidoglycan layer and in the inner membrane, respectively (1), while the C-ring of Salmonella species is attached to the cytoplasmic side of the basal body (3). The C-ring is composed of the proteins FliG, FliM, and FliN (25), and genetic evidence indicates that the C-ring is important for flagellar assembly, torque generation, and regulation of rotational direction (33, 34). FliG, 26 molecules of which are incorporated into the motor, appears to be the protein that is most directly involved in torque generation (15). Mutational analysis suggests that electrostatic interactions between conserved charged residues in the C-terminal domain of FliG and the cytoplasmic domain of MotA are important in torque generation (14), although this may not be the case for the Na⁺-type motor of Vibrio alginolyticus (32, 35, 36). FliM interacts with the chemotactic signaling protein CheY in its phosphorylated form (CheY-P) to regulate rotational direction (30). It has been reported that 33 to 35 copies of FliM assemble into a ring structure (28, 29). FliN contributes mostly to forming the C-ring structure (37). The crystal structure of FliN revealed a hydrophobic patch formed by several well-conserved hydrophobic residues (2). Mutational analysis showed that this patch is important for flagellar assembly and rotational switching (23, 24). The association state of FliN in solution was studied by analytical ultracentrifugation, which provided clues to the higher-level organization of the protein. Thermotoga maritima FliN exists primarily as a dimer in solution, and T. maritima FliN and FliM together formed a stable FliM₁-FliN₄ complex (2). The spatial distribution of these proteins in the C-ring of Salmonella species was investigated using three-dimensional reconstitution analysis with electron microscopy (28). However, the correct positioning has still not been clarified.The Na⁺-driven motor requires two additional proteins, MotX and MotY, for torque generation (19-21, 22). These proteins form a unique ring structure, the T ring, located below the LP ring in the polar flagellum of V. alginolyticus (9, 26). It has been suggested that MotX interacts with MotY and PomB (11, 27). Unlike peritrichously flagellated Escherichia coli and Salmonella species, V. alginolyticus has two different flagellar systems adapted for locomotion under different circumstances. A single, sheathed polar flagellum is used for motility in low-viscosity environments such as seawater (18). As described above, it is driven by a Na⁺-type motor. However, in high-viscosity environments, such as the mucus-coated surfaces of fish bodies, cells induce numerous unsheathed lateral flagella that have H⁺-driven motors (7, 8). We have been focusing on the Na⁺-driven polar flagellar motor, since there are certain advantages to studying its mechanism of torque generation over the H⁺-type motor: sodium motive force can be easily manipulated by controlling the Na⁺ concentration in the medium, and motor rotation can be specifically inhibited using phenamil (10). Moreover, its rotation rate is surprisingly high, up to 1,700 rps (compared to ∼200 rps and ∼300 rps for Salmonella species flagella and E. coli flagella, respectively) (12, 16, 17).Although understanding the C-ring structure and function is essential for clarifying the mechanism of motor rotation, there is no information about the C-ring of the polar flagellar motor of Vibrio species or the flagella of any genus other than Salmonella. Since Vibrio species have all of the genes coding for C-ring components, we would expect its location to be on the cytoplasmic side of the MS ring, as in Salmonella species. In this study, we attempted to isolate the polar flagellar basal body with the C-ring attached and investigate whether it is organized similarly to the H⁺-driven flagellar motor of Salmonella enterica serovar Typhimurium.     

Sulfur Isotope Enrichment during Maintenance Metabolism in the Thermophilic Sulfate-Reducing Bacterium Desulfotomaculum putei

Values of Δ³⁴S (, where δ³⁴S_HS and indicate the differences in the isotopic compositions of the HS⁻ and SO₄²⁻ in the eluent, respectively) for many modern marine sediments are in the range of −55 to −75‰, much greater than the −2 to −46‰ ɛ³⁴S (kinetic isotope enrichment) values commonly observed for microbial sulfate reduction in laboratory batch culture and chemostat experiments. It has been proposed that at extremely low sulfate reduction rates under hypersulfidic conditions with a nonlimited supply of sulfate, isotopic enrichment in laboratory culture experiments should increase to the levels recorded in nature. We examined the effect of extremely low sulfate reduction rates and electron donor limitation on S isotope fractionation by culturing a thermophilic, sulfate-reducing bacterium, Desulfotomaculum putei, in a biomass-recycling culture vessel, or “retentostat.” The cell-specific rate of sulfate reduction and the specific growth rate decreased progressively from the exponential phase to the maintenance phase, yielding average maintenance coefficients of 10⁻¹⁶ to 10⁻¹⁸ mol of SO₄ cell⁻¹ h⁻¹ toward the end of the experiments. Overall S mass and isotopic balance were conserved during the experiment. The differences in the δ³⁴S values of the sulfate and sulfide eluting from the retentostat were significantly larger, attaining a maximum Δ³⁴S of −20.9‰, than the −9.7‰ observed during the batch culture experiment, but differences did not attain the values observed in marine sediments.Dissimilatory SO₄²⁻ reduction is a geologically ancient, anaerobic, energy-yielding metabolic process during which SO₄²⁻-reducing bacteria (SRB) reduce SO₄²⁻ to H₂S while oxidizing organic molecules or H₂. SO₄²⁻ reduction is a dominant pathway for organic degradation in marine sediments (23) and in terrestrial subsurface settings where sulfur-bearing minerals dominate over Fe³⁺-bearing minerals. For example, at depths greater than 1.5 km below land surface in the fractured sedimentary and igneous rocks of the Witwatersrand Basin of South Africa, SO₄²⁻ reduction is the dominant electron-accepting process (3, 26, 46, 48, 61).The enrichment of ³²S in biogenic sulfides, with respect to the parent SO₄²⁻, imparted by SRB, is traceable through the geologic record (10, 54). The magnitude of the Δ³⁴S (= δ³⁴S_pyrite − δ³⁴S_{barite/gypsum}, where δ³⁴S_pyrite and δ³⁴S_{barite/gypsum} are the isotopic compositions of pyrite and barite or gypsum) increases from −10‰ in the 3.47-billion-year-old North Pole deposits to −30‰ in late-Archaean deposits (55), to −75‰ in Neoproterozoic to modern sulfide-bearing marine sediments (13).The kinetic isotopic enrichment, ɛ³⁴S, deduced from trends in the δ³⁴S values of SO₄²⁻ and HS⁻ in batch culture microbial SO₄²⁻ reduction experiments using the Rayleigh relationship, ranges from −2‰ to −46‰ (6, 7, 11, 17, 22, 27, 28, 30, 31, 38, 39). The variation in ɛ³⁴S values has been attributed to the SO₄²⁻ concentration, the type of electron donor and its concentration, the SO₄²⁻ reduction rate per cell (csSRR) (22), temperature, and species-specific isotope enrichment effects. In these laboratory experiments, doubling times are on the order of hours and csSRRs range from to 0.1 to 18 fmol cell⁻¹ h⁻¹ (7, 12, 17, 22, 30, 32, 39, 40).Experiments performed during the 1960s found that the magnitude of ɛ³⁴S was inversely proportional to the csSRR for organic electron donors (16, 31, 38, 39) when SO₄²⁻ was not limiting. More-recent batch culture experiments on 3 psychrophilic (optimum growth temperature, <20°C) and mesophilic (optimum growth temperature, between 20°C and 45°C) SRB strains (7) and on 32 psychrophilic to thermophilic SRB strains (22), however, have failed to reproduce such a relationship. In 2001, Canfield (11) reported an inverse correlation between ɛ³⁴S and reduction rate using a flowthrough sediment column and demonstrated that ɛ³⁴S values of approximately −35 to −40‰ were produced when organic substrates added by way of amendment were limited with respect to SO₄²⁻. Because it was not possible to readily evaluate changes in biomass in the sediment column with changes in temperature or substrate provision rate, it was inferred that changes in ɛ³⁴S were related to changes in the csSRRs. More recently, Canfield et al. (12) observed a 6‰ variation in ɛ³⁴S values related to the temperature of the batch culture experiments relative to the optimum growth temperature. The few early experiments that were performed using H₂ as the electron donor yielded ɛ³⁴S values ranging from −3 to −19‰ (22, 38, 39), which appear to correlate with the csSRR (39). Hoek et al. (32) also found that the ɛ³⁴S values for the thermophilic SO₄²⁻ reducer Thermodesulfatator indicus increased from between −1.5‰ and −10‰ in batch cultures with high H₂ concentrations to between −24‰ and −37‰ in batch cultures grown under H₂ limitation with respect to SO₄²⁻. Detmers et al. (22) found that the average ɛ³⁴S of SRB that oxidize their organic carbon electron donor completely to CO₂ averaged −25‰, versus −9.5‰ for SRB that release acetate during their oxidation of their organic carbon electron donor. Detmers et al. (22) speculated that the greater free energy yield per mole of SO₄²⁻ from incomplete carbon oxidation relative to that for complete carbon oxidation promotes complete SO₄²⁻ reduction and hinders isotopic enrichment due to isotopic exchange of the intracellular sulfur species pools.None of these experiments, however, have yielded ɛ³⁴S factors capable of producing the Δ³⁴S values of −55 to −75‰ observed in the geological record from ∼1.0 billion years ago to today. Various schemes have been hypothesized, and observations that involve either the disproportionation of S₂O₃²⁻ (36), the disproportionation of S⁰ produced by oxidation of either H₂S or S₂O₃²⁻ (15), or the disproportionation of SO₃²⁻ (29) have been made. Attribution of the increasing Δ³⁴S values recorded for Achaean to Neoproterozoic sediments to the increasing role of H₂S oxidative pathways makes sense in the context of increasing O₂ concentrations in the atmosphere (14) but is not consistent with the lack of significant fractionation observed during oxidative reactions (29). To explain the Δ³⁴S values of −55 to −77‰ reported to occur in interstitial pore waters from 100- to 300-m-deep, hypersulfidic ocean sediments (51, 64, 67), where the presence of a S-oxidative cycle is unlikely, an alternative, elaborate model of the SO₄²⁻-reducing pathway has been proposed by Brunner and Bernasconi (9). This model attributes the large Δ³⁴S values to a multistep, reversible reduction of SO₃²⁻ to HS⁻ involving S₃O₆²⁻ and S₂O₃²⁻ (20, 25, 41, 42, 52, 66). The conditions under which the maximum ɛ³⁴S values might be expressed are a combination of elevated HS⁻ concentrations, electron donor limitations, nonlimiting SO₄²⁻ concentrations, and a very low csSRR. The csSRR for subsurface environments has been estimated from biogeochemical-flux modeling to be 10⁻⁶ to 10⁻⁷ fmol cell⁻¹ h⁻¹ (23), with a corresponding cell turnover rate greater than 1,000 years (37).Batch and chemostat culture systems, despite low growth rates, cannot completely attain a state of zero growth with constant substrate provision and therefore do not accurately reflect the in situ nutritional states of microbes in many natural settings. Retentostats, or recycling fermentor vessels, recycle 100% of biomass to the culturing vessel, allowing experimenters to culture microbial cells to a large biomass with a constant nutrient supply rate until the substrate supply rate itself becomes the growth-limiting factor and cells enter a resting state in which their specific growth rate approaches zero and they carry on maintenance metabolism (1, 47, 53, 58, 59, 62, 63). Utilizing this approach, Colwell et al. (18) were able to obtain a cell-specific respiration rate of 7 × 10⁻⁴ fmol of CH₄ cell⁻¹ h⁻¹ for a mesophilic marine methanogen, a rate that is comparable to that estimated for methanogenic communities in deep marine sediments off the coast of Peru (49).In this study, the conditions that Brunner and Bernasconi (9) hypothesized would lead to the large Δ³⁴S values seen in nature were recreated in the laboratory by limiting the electron donor supply rate with respect to the SO₄²⁻ supply rate in a retentostat vessel. The S isotopic enrichment by a resting culture of Desulfotomaculum putei at an extremely low csSRR was compared to that of a batch culture experiment to determine whether the ɛ³⁴S values produced under the former conditions approach the Δ³⁴S seen in nature.