Effect of growth conditions and staining procedure upon the subsurface transport and attachment behaviors of a groundwater protist

The transport and attachment behaviors of Spumella guttula (Kent), a nanoflagellate (protist) found in contaminated and uncontaminated aquifer sediments in Cape Cod, Mass., were assessed in flowthrough and static columns and in a field injection-and-recovery transport experiment involving an array of multilevel samplers. Transport of S. guttula harvested from low-nutrient (10 mg of dissolved organic carbon per liter), slightly acidic, granular (porous) growth media was compared to earlier observations involving nanoflagellates grown in a traditional high-nutrient liquid broth. In contrast to the highly retarded (retardation factor of approximately 3) subsurface transport previously reported for S. guttula, the peak concentration of porous-medium-grown S. guttula traveled concomitantly with that of a conservative (bromide) tracer. About one-third of the porous-medium-grown nanoflagellates added to the aquifer were transported at least 2.8 m downgradient, compared to only approximately 2% of the broth-grown nanoflagellates. Flowthrough column studies revealed that a vital (hydroethidine [HE]) staining procedure resulted in considerably less attachment (more transport) of S. guttula in aquifer sediments than did a staining-and-fixation procedure involving 4',6'-diamidino-2-phenylindole (DAPI) and glutaraldehyde. The calculated collision efficiency (approximately 10(-2) for porous-medium-grown, DAPI-stained nanoflagellates) was comparable to that observed earlier for the indigenous community of unattached groundwater bacteria that serve as prey. The attachment of HE-labeled S. guttula onto aquifer sediment grains was independent of pH (over the range from pH 3 to 9) suggesting a primary attachment mechanism that may be fundamentally different from that of their prey bacteria, which exhibit sharp decreases in fractional attachment with increasing pH. The high degree of mobility of S. guttula in the aquifer sediments has important ecological implications for the protistan community within the temporally changing plume of organic contaminants in the Cape Cod aquifer.     

Transport Behavior of Groundwater Protozoa and Protozoan-Sized Microspheres in Sandy Aquifer Sediments

Transport behaviors of unidentified flagellated protozoa (flagellates) and flagellate-sized carboxylated microspheres in sandy, organically contaminated aquifer sediments were investigated in a small-scale (1 to 4-m travel distance) natural-gradient tracer test on Cape Cod and in flow-through columns packed with sieved (0.5-to 1.0-mm grain size) aquifer sediments. The minute (average in situ cell size, 2 to 3 (mu)m) flagellates, which are relatively abundant in the Cape Cod aquifer, were isolated from core samples, grown in a grass extract medium, labeled with hydroethidine (a vital eukaryotic stain), and coinjected into aquifer sediments along with bromide, a conservative tracer. The 2-(mu)m flagellates appeared to be near the optimal size for transport, judging from flowthrough column experiments involving a polydispersed (0.7 to 6.2 (mu)m in diameter) suspension of carboxylated microspheres. However, immobilization within the aquifer sediments accounted for a log unit reduction over the first meter of travel compared with a log unit reduction over the first 10 m of travel for indigenous, free-living groundwater bacteria in earlier tests. High rates of flagellate immobilization in the presence of aquifer sediments also was observed in the laboratory. However, immobilization rates for the laboratory-grown flagellates (initially 4 to 5 (mu)m) injected into the aquifer were not constant and decreased noticeably with increasing time and distance of travel. The decrease in propensity for grain surfaces was accompanied by a decrease in cell size, as the flagellates presumably readapted to aquifer conditions. Retardation and apparent dispersion were generally at least twofold greater than those observed earlier for indigenous groundwater bacteria but were much closer to those observed for highly surface active carboxylated latex microspheres. Field and laboratory results suggest that 2-(mu)m carboxylated microspheres may be useful as analogs in investigating several abiotic aspects of flagellate transport behavior in groundwater.     

Phylogenetic Study of Methanol Oxidizers from Chilika-Lake Sediments Using Genomic and Metagenomic Approaches

Group-wise diversity of sediment methylotrophs of Chilika lake (Lat. 19°28′–19°54′N; Long. 85°06′–85°35′E) Odisha, India at various identified sites was studied. Both the culturable and unculturable (metagenome) methylotrophs were investigated in the lake sediments employing both mxaF and 16S rRNA genes as markers. ARDRA profiling, 16S rRNA gene sequencing, PAGE profiling of HaeIII, EcoRI restricted mxaF gene and the mxaF gene sequences using culture-dependent approach revealed the relatedness of α-proteobacteria and Methylobacterium, Hyphomicrobium and Ancyclobacter sp. The total viable counts of the culturable aerobic methylotrophs were relatively higher in sediments near the sea mouth (S3; Panaspada), also demonstrated relatively high salinity (0.1 M NaCl) tolerance. Metagenomic DNA from the sediments, amplified using GC clamp mxaF primers and resolved through DGGE, revealed the diversity within the unculturable methylotrophic bacterium Methylobacterium organophilum, Ancyclobacter aquaticus, Burkholderiales and Hyphomicrobium sp. Culture-independent analyses revealed that up to 90 % of the methylotrophs were unculturable. The study enhances the general understandings of the metagenomic methylotrophs from such a special ecological niche.

Electronic supplementary material

The online version of this article (doi:10.1007/s12088-015-0510-3) contains supplementary material, which is available to authorized users.     

Size-Selective Predation on Groundwater Bacteria by Nanoflagellates in an Organic-Contaminated Aquifer

Time series incubations were conducted to provide estimates for the size selectivities and rates of protistan grazing that may be occurring in a sandy, contaminated aquifer. The experiments involved four size classes of fluorescently labeled groundwater bacteria (FLB) and 2- to 3-μm-long nanoflagellates, primarily Spumella guttula (Ehrenberg) Kent, that were isolated from contaminated aquifer sediments (Cape Cod, Mass.). The greatest uptake and clearance rates (0.77 bacteria · flagellate⁻¹ · h⁻¹ and 1.4 nl · flagellate⁻¹ · h⁻¹, respectively) were observed for 0.8- to 1.5-μm-long FLB (0.21-μm³ average cell volume), which represent the fastest growing bacteria within the pore fluids of the contaminated aquifer sediments. The 19:1 to 67:1 volume ratios of nanoflagellate predators to preferred bacterial prey were in the lower end of the range commonly reported for other aquatic habitats. The grazing data suggest that the aquifer nanoflagellates can consume as much as 12 to 74% of the unattached bacterial community in 1 day and are likely to have a substantive effect upon bacterial degradation of organic groundwater contaminants.While heterotrophic protists have been found in pristine and contaminated aquifers (3, 29, 34, 37, 54–57), very little research has been performed to elucidate their role in the subsurface. In other environments (e.g., surface and marine waters, topsoil, and wastewater treatment plants), it is well documented that they typically consume bacteria (2, 11, 15, 41, 42, 47), although some have been observed to consume high-molecular-weight organics (48, 59) and even viruses (20, 39). Protists typically graze selectively, depending upon the size (1, 9, 17, 25, 52), growth condition (18, 53), species (16, 17, 35), and motility (18) of their prey. In carbon-limited environments, protists decrease bacterial competition, resulting in a greater bacterial uptake rate for organic substrate per unit of bacterial biomass (27). Based upon indirect field observations, it is also hypothesized that this may be the role they play in organically contaminated aquifers (31). In nutrient-limited environments, protists may release nitrogen or phosphorus needed by bacteria (10, 28, 44, 61).Studies at the U.S. Geological Survey’s (USGS) Toxic Substances Hydrology Program research site at the Massachusetts Military Reservation (MMR) on Cape Cod, Mass., have shown that sandy aquifer sediments can harbor large protistan populations even at relatively low levels (≤2 mg/liter) of dissolved organic matter (30). Protistan abundances in the MMR aquifer plume range from 1 × 10⁴ to 7 × 10⁴ g (dry weight)⁻¹ (30) and consist primarily of nanoflagellates (2 to 3 μm in length) (29) that belong to the genera Bodo, Cercomonas, Cryptaulax, Cyanthomonas, Goniomonas, and Spumella, along with some undescribed species (37). A few amoebae (63) and no ciliates (29) have been observed.Results of a principal-component factor analysis of protistan and bacterial abundances and chemical constituents in the MMR plume suggested that the flagellates were preying upon unattached bacteria (30). Additional evidence of predation was obtained from flowthrough columns of aquifer sediment from which fluorescently labeled unattached bacteria eluted at much lower rates than they did from sterile (protist-free) controls (31). However, these results provide only indirect evidence of predation because no enumerations of the bacteria within the flagellates were performed.The purpose of the research reported in this paper was to directly determine whether the MMR nanoflagellates can consume unattached bacteria in the plume and the extent to which they engage in size-selective grazing. Rates of bacterivory (grazing and clearance rates) were estimated in the laboratory by using fluorescently labeled, monodispersed bacteria (FLB) and nanoflagellates that had been isolated from the MMR aquifer plume. Although other methods exist (19, 26, 38, 43, 45, 62, 64–66), we chose to use fluorescent labeling to study flagellate bacterivory because this procedure requires shorter incubation times and relies upon direct visual observation of the prey within the predator. In addition, experiments could be designed with different sizes of FLB to determine if the nanoflagellates can discriminate between prey. This involved using FLB with cell lengths of 0.1 to 0.5, 0.5 to 0.8, 0.8 to 1.5, and >1.5 μm (average cell volumes of 0.06, 0.14, 0.21, and 0.87 μm³, respectively) in the grazing experiments.     

In Situ Exposure to Low Herbicide Concentrations Affects Microbial Population Composition and Catabolic Gene Frequency in an Aerobic Shallow Aquifer

The aim of this study was to evaluate how the in situ exposure of a Danish subsurface aquifer to phenoxy acid herbicides at low concentrations (<40 μg l⁻¹) changes the microbial community composition. Sediment and groundwater samples were collected inside and outside the herbicide-exposed area and were analyzed for the presence of general microbial populations, Pseudomonas bacteria, and specific phenoxy acid degraders. Both culture-dependent and culture-independent methods were applied. The abundance of microbial phenoxy acid degraders (10⁰ to 10⁴ g⁻¹ sediment) was determined by most probable number assays, and their presence was only detected in herbicide-exposed sediments. Similarly, PCR analysis showed that the 2,4-dichlorophenoxyacetic acid degradation pathway genes tfdA and tfdB (10² to 10³ gene copies g⁻¹ sediment) were only detected in sediments from contaminated areas of the aquifer. PCR-restriction fragment length polymorphism measurements demonstrated the presence of different populations of tfd genes, suggesting that the in situ herbicide degradation was caused by the activity of a heterogeneous population of phenoxy acid degraders. The number of Pseudomonas bacteria measured by either PCR or plating on selective agar media was higher in sediments subjected to high levels of phenoxy acid. Furthermore, high numbers of CFU compared to direct counting of 4′,6-diamidino-2-phenylindole-stained cells in the microscope suggested an increased culturability of the indigenous microbial communities from acclimated sediments. The findings of this study demonstrate that continuous exposure to low herbicide concentrations can markedly change the bacterial community composition of a subsurface aquifer.     

THE DISTRIBUTION, ABUNDANCE AND SELECTED PREY OF THE HARBOR SEAL, PHOCA VITULINA CONCOLOR, IN SOUTHERN NEW ENGLAND

The seasonal distribution and abundance of harbor seals occurring south of Maine were documented by counting the number of seals at traditional haulout locations. The average number of seals counted during each survey in Massachusetts and New Hampshire was 3,560 ± 255 (95% CI), 1983–1987. The maximum number of seals counted on any individual survey was 4,736 individuals. Fifty percent of all the surveys since January 1985 have resulted in counts greater than 4,000 seals reflecting a 27% increase in the abundance of seals in our study area since that date. Seventy-five percent of the seals in southern New England are located at haulout sites on Cape Cod and Nantucket Island. The largest aggregation of seals in the eastern United States occurs mid-winter at Monomoy Island and adjacent shoals. A single high count of 1,672 seals occurred at this site during the study period. An additional 271–374 seals were also counted in Rhode Island, Connecticut and eastern Long Island Sound during surveys conducted in March 1986 and 1987. The American sandlance Ammodytes americanus was the single dominant prey item of harbor seals in waters adjacent to Cape Cod based on the modified frequency of occurrence of each prey species in scat samples collected from three haulout sites on Cape Cod between 1984–1987. During January and February sandlance was the near exclusive prey item at Monomoy (99%, n= 80). During March and April, the frequency of Atlantic herring Clupea harengus increased in the scat samples at this site. Regional differences in the diet of seals reflect distinct prey communities throughout the study area. Since 1986, the percent occurrence and importance of sandlance in the diet of seals has decreased, reflecting an overall decrease in abundance of this prey species in waters adjacent to Cape Cod. In spite of fluctuations in abundance, and regional differences in the diet of seals throughout the study area, sandlance still comprised a minimum 55% of the total prey species of harbor seals throughout the study area.     

Whole-Cell versus Total RNA Extraction for Analysis of Microbial Community Structure with 16S rRNA-Targeted Oligonucleotide Probes in Salt Marsh Sediments

rRNA-targeted oligonucleotide probes have become powerful tools for describing microbial communities, but their use in sediments remains difficult. Here we describe a simple technique involving homogenization, detergents, and dispersants that allows the quantitative extraction of cells from formalin-preserved salt marsh sediments. Resulting cell extracts are amenable to membrane blotting and hybridization protocols. Using this procedure, the efficiency of cell extraction was high (95.7% ± 3.7% [mean ± standard deviation]) relative to direct DAPI (4′,6′-diamidino-2-phenylindole) epifluorescence cell counts for a variety of salt marsh sediments. To test the hypothesis that cells were extracted without phylogenetic bias, the relative abundance (depth distribution) of five major divisions of the gram-negative mesophilic sulfate-reducing delta proteobacteria were determined in sediments maintained in a tidal mesocosm system. A suite of six 16S rRNA-targeted oligonucleotide probes were utilized. The apparent structure of sulfate-reducing bacteria communities determined from whole-cell and RNA extracts were consistent with each other (r² = 0.60), indicating that the whole-cell extraction and RNA extraction hybridization approaches for describing sediment microbial communities are equally robust. However, the variability associated with both methods was high and appeared to be a result of the natural heterogeneity of sediment microbial communities and methodological artifacts. The relative distribution of sulfate-reducing bacteria was similar to that observed in natural marsh systems, providing preliminary evidence that the mesocosm systems accurately simulate native marsh systems.     

A simple temperature-based model predicts the upper latitudinal limit of the temperate coral Astrangia poculata

A few hardy ahermatypic scleractinian corals occur in shallow waters well outside of the tropics, but little is known concerning their distribution limits at high latitudes. Using field data on the growth of Astrangia poculata over an annual period near its northern range limit in Rhode Island, USA, we tested the hypothesis that the distribution of this coral is limited by low temperature. A simple model based on satellite sea surface temperature and field growth data at monthly temporal resolution was used to estimate annual net coral growth north and south of the known range limit of A. poculata. Annual net coral growth was the result of new polyp budding above ~10 °C minus polyp loss below ~10 °C, which is caused by a state of torpor that leads to overgrowth by encroaching and settling organisms. The model accurately predicted A. poculata’s range limit around Cape Cod, Massachusetts, predicting no net growth northward as a result of corals’ inability to counteract polyp loss during winter with sufficient polyp budding during summer. The model also indicated that the range limit of A. poculata coincides with a decline in the benefit of associating with symbiotic dinoflagellates (Symbiodinium B2/S. psygmophilum), suggesting that symbiosis may become a liability under colder temperatures. While we cannot exclude the potential role of other coral life history traits or environmental factors in setting A. poculata’s northern range limit, our analysis suggests that low temperature constrains the growth and persistence of adult corals and would preclude coral growth northward of Cape Cod.     

Effect of DNA target sequence on triplex formation by oligo-2'-deoxy- and 2'-O-methylribonucleotides

The interactions of pyrimidine deoxyribo- or 2′-O-methylribo-psoralen-conjugated, triplex-forming oligonucleotides, psTFOs, with a 17-bp env-DNA whose purine tract is 5′-AGAGAGAAAAAAGAG-3′, or an 18-bp gag-DNA whose purine tract is 5′-AGG GGGAAAGAAAAAA-3′, were studied over the pH range 6.0–7.5. The stability of the triplex formed by a deoxy-env-psTFO containing 5-methylcytosines and thymines decreased with increasing pH (T_m = 56°C at pH 6.0; 27°C at pH 7.5). Replacement of 5-methylcytosines with 8-oxo-adenines reduced the pH dependence, but lowered triplex stability. A 2′-O-methyl-env-psTFO containing uracil and cytosine did not form a triplex at pH 7.5. Surprisingly, replacement of the cytosines in this oligomer with 5-methylcytosines dramatically increased triplex stability (T_m = 25°C at pH 7.5), and even greater stability was achieved by selective replacement of uracils with thymines (T_m = 37°C at pH 7.5). Substitution of the contiguous 5-methylcytosines of the deoxy-gag-psTFO with 8-oxo-adenines significantly reduced pH dependence and increased triplex stability. In contrast to the behavior of env-specific TFOs, triplexes formed by 2′-O-methyl-gag-psTFOs did not show enhanced stability. Replacement of the 3′-terminal phosphodiester of the TFO with a methylphosphonate group significantly increased the resistance of both deoxy- and 2′-O-methyl-TFOs to degradation by 3′-exonucleases, while maintaining triplex stability.     

Identification, Cloning, and Characterization of a Novel Ketoreductase from the Cyanobacterium Synechococcus sp. Strain PCC 7942

A new ketoreductase useful for asymmetric synthesis of chiral alcohols was identified in the cyanobacterium Synechococcus sp. strain PCC 7942. Mass spectrometry of trypsin-digested peptides identified the protein as 3-ketoacyl-[acyl-carrier-protein] reductase (KR) (EC 1.1.1.100). The gene, referred to as fabG, was cloned, functionally expressed in Escherichia coli, and subsequently purified to homogeneity. The enzyme displayed a temperature optimum at 44°C and a broad pH optimum between pH 7 and pH 9. The NADPH-dependent KR was able to asymmetrically reduce a variety of prochiral ketones with good to excellent enantioselectivities (>99.8%). The KR showed particular high specific activity for asymmetric reduction of ethyl 4-chloroacetoacetate (38.29 ± 2.15 U mg⁻¹) and 2′,3′,4′,5′,6′-pentafluoroacetophenone (8.57 ± 0.49 U mg⁻¹) to the corresponding (S)-alcohols. In comparison with an established industrial enzyme like the alcohol dehydrogenase from Lactobacillus brevis, the KR showed seven-times-higher activity toward 2′,3′,4′,5′,6′-pentafluoroacetophenone, with a remarkably higher enantiomeric excess (>99.8% [S] versus 43.3% [S]).     

Reductive Reactivity of Iron(III) Oxides in the East China Sea Sediments: Characterization by Selective Extraction and Kinetic Dissolution

Reactive Fe(III) oxides in gravity-core sediments collected from the East China Sea inner shelf were quantified by using three selective extractions (acidic hydroxylamine, acidic oxalate, bicarbonate-citrate buffered sodium dithionite). Also the reactivity of Fe(III) oxides in the sediments was characterized by kinetic dissolution using ascorbic acid as reductant at pH 3.0 and 7.5 in combination with the reactive continuum model. Three parameters derived from the kinetic method: m ₀ (theoretical initial amount of ascorbate-reducible Fe(III) oxides), k′ (rate constant) and γ (heterogeneity of reactivity), enable a quantitative characterization of Fe(III) oxide reactivity in a standardized way. Amorphous Fe(III) oxides quantified by acidic hydroxylamine extraction were quickly consumed in the uppermost layer during early diagenesis but were not depleted over the upper 100 cm depth. The total amounts of amorphous and poorly crystalline Fe(III) oxides are highly available for efficient buffering of dissolved sulfide. As indicated by the m ₀, k′ and γ, the surface sediments always have the maximum content, reactivity and heterogeneity of reactive Fe(III) oxides, while the three parameters simultaneously downcore decrease, much more quickly in the upper layer than at depth. Albeit being within a small range (within one order of magnitude) of the initial rates among sediments at different depths, incongruent dissolution could result in huge discrepancies of the later dissolution rates due to differentiating heterogeneity, which cannot be revealed by selective extraction. A strong linear correlation of the m ₀ at pH 3.0 with the dithionite-extractable Fe(III) suggests that the m ₀ may represent Fe(III) oxide assemblages spanning amorphous and crystalline Fe(III) oxides. Maximum microbially available Fe(III) predicted by the m ₀ at pH 7.5 may include both amorphous and a fraction of other less reactive Fe(III) phases.     

Characterization of in vitro proton pumping by microsomal vesicles isolated from corn coleoptiles

Corn (Zea mays L. cv Golden Cross Bantam) coleoptile microsomal vesicles have been isolated which are capable of ATP-driven H⁺-transport as measured by [¹⁴C]methylamine accumulation and quinacrine fluorescence quenching. Formation of the pH gradient in vitro shows a high specificity for ATP·Mg, is temperature-sensitive, exhibits a pH optimum at 7.5, and is inhibited by carbonyl cyanide-m-chlorophenylhydrazone. Of the divalent cations tested, Mn²⁺ is almost as effective as Mg²⁺, while Ca²⁺ is ineffective. Excess divalent cations, particularly Ca²⁺, reduces the pH gradient. H⁺ transport is strongly promoted by anions, especially chloride, while potassium does not affect pump activity. Studies with ³⁶Cl⁻ indicate that ATP-driven H⁺ transport into the vesicles is associated with chloride uptake. Both carbonyl cyanide-m-chlorophenylhydrazone and the anion transport inhibitor, 4,4′-diisothiocyano-2,2′-disulfonic acid stilbene, inhibit methylamine accumulation and ³⁶Cl⁻ uptake. Proton pumping is also blocked by diethyl stilbestrol and N,N′-dicyclohexylcarbodiimide, but is insensitive to oligomycin and vanadate. These properties of the pump are inconsistent with either a mitochondrial or plasma membrane origin.     

C5'- and C3'-sugar radicals produced via photo-excitation of one-electron oxidized adenine in 2'-deoxyadenosine and its derivatives

We report that photo-excitation of one-electron-oxidized adenine [A(-H)•] in dAdo and its 2′-deoxyribonucleotides leads to formation of deoxyribose sugar radicals in remarkably high yields. Illumination of A(-H)• in dAdo, 3′-dAMP and 5′-dAMP in aqueous glasses at 143 K leads to 80-100% conversion to sugar radicals at C5′ and C3′. The position of the phosphate in 5′- and 3′-dAMP is observed to deactivate radical formation at the site of substitution. In addition, the pH has a crucial influence on the site of sugar radical formation; e.g. at pH ~5, photo-excitation of A(-H)• in dAdo at 143 K produces mainly C5′• whereas only C3′• is observed at high pH ~12. ¹³C substitution at C5′ in dAdo yields ¹³C anisotropic couplings of (28, 28, 84) G whose isotropic component 46.7 G identifies formation of the near planar C5′•. A β-¹³C 16 G isotropic coupling from C3′• is also found. These results are found to be in accord with theoretically calculated ¹³C couplings at C5′ [DFT, B3LYP, 6-31(G) level] for C5′• and C3′•. Calculations using time-dependent density functional theory [TD-DFT B3LYP, 6-31G(d)] confirm that transitions in the near UV and visible induce hole transfer from the base radical to the sugar group leading to sugar radical formation.     

Polyadenylation of genomic RNA and initiation of antigenomic RNA in a positive-strand RNA virus are controlled by the same cis-element

Genomes and antigenomes of many positive-strand RNA viruses contain 3′-poly(A) and 5′-poly(U) tracts, respectively, serving as mutual templates. Mechanism(s) controlling the length of these homopolymeric stretches are not well understood. Here, we show that in coxsackievirus B3 (CVB3) and three other enteroviruses the poly(A) tract is ~80–90 and the poly(U) tract is ~20 nt-long. Mutagenesis analysis indicate that the length of the CVB3 3′-poly(A) is determined by the oriR, a cis-element in the 3′-noncoding region of viral RNA. In contrast, while mutations of the oriR inhibit initiation of (−) RNA synthesis, they do not affect the 5′-poly(U) length. Poly(A)-lacking genomes are able to acquire genetically unstable AU-rich poly(A)-terminated 3′-tails, which may be generated by a mechanism distinct from the cognate viral RNA polyadenylation. The aberrant tails ensure only inefficient replication. The possibility of RNA replication independent of oriR and poly(A) demonstrate that highly debilitated viruses are able to survive by utilizing ‘emergence’, perhaps atavistic, mechanisms.     

Effects of Iron and Nitrogen Limitation on Sulfur Isotope Fractionation during Microbial Sulfate Reduction

Sulfate-reducing microbes utilize sulfate as an electron acceptor and produce sulfide that is depleted in heavy isotopes of sulfur relative to sulfate. Thus, the distribution of sulfur isotopes in sediments can trace microbial sulfate reduction (MSR), and it also has the potential to reflect the physiology of sulfate-reducing microbes. This study investigates the relationship between the availability of iron and reduced nitrogen and the magnitude of S-isotope fractionation during MSR by a marine sulfate-reducing bacterium, DMSS-1, a Desulfovibrio species, isolated from salt marsh in Cape Cod, MA. Submicromolar levels of iron increase sulfur isotope fractionation by about 50% relative to iron-replete cultures of DMSS-1. Iron-limited cultures also exhibit decreased cytochrome c-to-total protein ratios and cell-specific sulfate reduction rates (csSRR), implying changes in the electron transport chain that couples carbon and sulfur metabolisms. When DMSS-1 fixes nitrogen in ammonium-deficient medium, it also produces larger fractionation, but it occurs at faster csSRRs than in the ammonium-replete control cultures. The energy and reducing power required for nitrogen fixation may be responsible for the reverse trend between S-isotope fractionation and csSRR in this case. Iron deficiency and nitrogen fixation by sulfate-reducing microbes may lead to the large observed S-isotope effects in some euxinic basins and various anoxic sediments.     

Identification of the parasitoid community associated with an outbreaking gall wasp,Zapatella davisae,and their relative abundances in New England and Long Island,New York

Gall wasps (Hymenoptera: Cynipidae) are phytophagous insects that often go unnoticed; however, when they are introduced to a new area or released from their natural enemies, they have the capacity to outbreak and cause extensive foliar damage. One such outbreaking pest, Zapatella davisae (Cynipidae: Cynipini), causes significant damage and mortality to black oak, Quercus velutina, in the northeastern United States. In this study, we aimed to identify the parasitoid community associated with Z. davisae, compare differences in percent parasitism of Z. davisae in Cape Cod and Long Island, and determine which parasitoid species contribute most to parasitism in each region. From both locations, we reared parasitoids, identified morphological groups, analyzed percent parasitism rates for each group, and used DNA barcoding to provide species‐level identifications. On Long Island, there was nearly 100% parasitism in 2015 followed by a near total collapse of the population in 2016. In contrast, parasitism rates were lower and remained consistent on Cape Cod between 2015 and 2016, which may explain the greater canopy damage observed in that region. Species of Sycophila were the dominant parasitoids, with one species Sycophila nr. novascotiae representing ~65% of reared parasitoids from Long Island, and two species of Sycophila (S. nr. novascotiae and S. foliatae) with near equal representations on Cape Cod. In order to manage an insect pest, it is important to understand factors that influence its mortality and survival. An understanding of how these infestations progress overtime can help predict the impact that newer infestations in Nantucket, MA, and coastal Rhode Island will have on black oak populations and will aid in the management of this rapidly spreading gall wasp pest.     

Spatially Explicit Estimates of Prey Consumption Reveal a New Krill Predator in the Southern Ocean

Development in foraging behaviour and dietary intake of many vertebrates are age-structured. Differences in feeding ecology may correlate with ontogenetic shifts in dispersal patterns, and therefore affect foraging habitat and resource utilization. Such life-history traits have important implications in interpreting tropho-dynamic linkages. Stable isotope ratios in the whiskers of sub-yearling southern elephant seals (Mirounga leonina; n = 12) were used, in conjunction with satellite telemetry and environmental data, to examine their foraging habitat and diet during their first foraging migration. The trophic position of seals from Macquarie Island (54°30′S, 158°57′E) was estimated using stable carbon (δ^{1 3}C) and nitrogen (δ¹⁵N) ratios along the length of the whisker, which provided a temporal record of prey intake. Satellite-relayed data loggers provided details on seal movement patterns, which were related to isotopic concentrations along the whisker. Animals fed in waters south of the Polar Front (>60°S) or within Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) Statistical Subareas 88.1 and 88.2, as indicated by both their depleted δ^{1 3}C (<−20‰) values, and tracking data. They predominantly exploited varying proportions of mesopelagic fish and squid, and crustaceans, such as euphausiids, which have not been reported as a prey item for this species. Comparison of isotopic data between sub-yearlings, and 1, 2 and 3 yr olds indicated that sub-yearlings, limited by their size, dive capabilities and prey capture skills to feeding higher in the water column, fed at a lower trophic level than older seals. This is consistent with the consumption of euphausiids and most probably, Antarctic krill (Euphausia superba), which constitute an abundant, easily accessible source of prey in water masses used by this age class of seals. Isotopic assessment and concurrent tracking of seals are successfully used here to identify ontogenetic shifts in broad-scale foraging habitat use and diet preferences in a highly migratory predator.     

Cell-free Transport to Distinct Golgi Cisternae Is Compartment Specific and ARF Independent

The small GTPase ADP-ribosylation factor (ARF) is absolutely required for coatomer vesicle formation on Golgi membranes but not for anterograde transport to the medial-Golgi in a mammalian in vitro transport system. This might indicate that the in vivo mechanism of intra-Golgi transport is not faithfully reproduced in vitro, or that intra-Golgi transport occurs by a nonvesicular mechanism. As one approach to distinguishing between these possibilities, we have characterized two additional cell-free systems that reconstitute transport to the trans-Golgi (trans assay) and trans-Golgi network (TGN assay). Like in vitro transport to the medial-Golgi (medial assay), transport to the trans-Golgi and TGN requires cytosol, ATP, and N-ethylmaleimide–sensitive fusion protein (NSF). However, each assay has its own distinct characteristics of transport. The kinetics of transport to late compartments are slower, and less cytosol is needed for guanosine-5′-O-(3-thiotriphosphate) (GTPγS) to inhibit transport, suggesting that each assay reconstitutes a distinct transport event. Depletion of ARF from cytosol abolishes vesicle formation and inhibition by GTPγS, but transport in all assays is otherwise unaffected. Purified recombinant myristoylated ARF1 restores inhibition by GTPγS, indicating that the GTP-sensitive component in all assays is ARF. We also show that asymmetry in donor and acceptor membrane properties in the medial assay is a unique feature of this assay that is unrelated to the production of vesicles. These findings demonstrate that characteristics specific to transport between different Golgi compartments are reconstituted in the cell-free system and that vesicle formation is not required for in vitro transport at any level of the stack.