An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments.

Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa. Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences.

In situ bioremediation of uranium with emulsified vegetable oil as the electron donor.

A field test with a one-time emulsified vegetable oil (EVO) injection was conducted to assess the capacity of EVO to sustain uranium bioreduction in a high-permeability gravel layer with groundwater concentrations of (mM) U, 0.0055; Ca, 2.98; NO3(-), 0.11; HCO3(-), 5.07; and SO4(2-), 1.23. Comparison of bromide and EVO migration and distribution indicated that a majority of the injected EVO was retained in the subsurface from the injection wells to 50 m downgradient. Nitrate, uranium, and sulfate were sequentially removed from the groundwater within 1-2 weeks, accompanied by an increase in acetate, Mn, Fe, and methane concentrations. Due to the slow release and degradation of EVO with time, reducing conditions were sustained for approximately one year, and daily U discharge to a creek, located approximately 50 m from the injection wells, decreased by 80% within 100 days. Total U discharge was reduced by 50% over the one-year period. Reduction of U(VI) to U(IV) was confirmed by synchrotron analysis of recovered aquifer solids. Oxidants (e.g., dissolved oxygen, nitrate) flowing in from upgradient appeared to reoxidize and remobilize uranium after the EVO was exhausted as evidenced by a transient increase of U concentration above ambient values. Occasional (e.g., annual) EVO injection into a permeable Ca and bicarbonate-containing aquifer can sustain uranium bioreduction/immobilization and decrease U migration/discharge.

Bringing function to structure: Root-soil interactions shaping phosphatase activity throughout a soil profile in Puerto Rico.

Large areas of highly productive tropical forests occur on weathered soils with low concentrations of available phosphorus (P). In such forests, root and microbial production of acid phosphatase enzymes capable of mineralizing organic phosphorus is considered vital to increasing available P for plant uptake.We measured both root and soil phosphatase throughout depth and alongside a variety of root and soil factors to better understand the potential of roots and soil biota to increase P availability and to constrain estimates of the biochemical mineralization within ecosystem models.We measured soil phosphatase down to 1 m, root phosphatase to 30 cm, and collected data on fine-root mass density, specific root length, soil P, bulk density, and soil texture using soil cores in four tropical forests within the Luquillo Experimental Forest in Puerto Rico.We found that soil phosphatase decreased with soil depth, but not root phosphatase. Furthermore, when both soil and root phosphatase were expressed per soil volume, soil phosphatase was 100-fold higher that root phosphatase.Both root and soil factors influenced soil and root phosphatase. Soil phosphatase increased with fine-root mass density and organic P, which together explained over 50% of the variation in soil phosphatase. Over 80% of the variation in root phosphatase per unit root mass was attributed to specific root length (positive correlation) and available (resin) P (negative correlation). Synthesis: Fine-root traits and soil P data are necessary to understand and represent soil and root phosphatase activity throughout the soil column and across sites with different soil conditions and tree species. These findings can be used to parameterize or benchmark estimates of biochemical mineralization in ecosystem models that contain fine-root biomass and soil P distributions throughout depth.

Nitrogen and phosphorus cycling in an ombrotrophic peatland: a benchmark for assessing change.

Aims: Slow decomposition and isolation from groundwater mean that ombrotrophic peatlands store a large amount of soil carbon (C) but have low availability of nitrogen (N) and phosphorus (P). To better understand the role these limiting nutrients play in determining the C balance of peatland ecosystems, we compile comprehensive N and P budgets for a forested bog in northern Minnesota, USA. Methods: N and P within plants, soils, and water are quantified based on field measurements. The resulting empirical dataset are then compared to modern-day, site-level simulations from the peatland land surface version of the Energy Exascale Earth System Model (ELM-SPRUCE). Results: Our results reveal N is accumulating in the ecosystem at 0.2 ± 0.1 g N m-2 year-1 but annual P inputs to this ecosystem are balanced by losses. Biomass stoichiometry indicates that plant functional types differ in N versus P limitation, with trees exhibiting a stronger N limitation than ericaceous shrubs or Sphagnum moss. High biomass and productivity of Sphagnum results in the moss layer storing and cycling a large proportion of plant N and P. Comparing our empirically-derived nutrient budgets to ELM-SPRUCE shows the model captures N cycling within dominant plant functional types well. Conclusions: The nutrient budgets and stoichiometry presented serve as a baseline for quantifying the nutrient cycling response of peatland ecosystems to both observed and simulated climate change. Our analysis improves our understanding of N and P dynamics within nutrient-limited peatlands and represents a crucial step toward improving C-cycle projections into the twenty-first century.

Natural bacterial communities serve as quantitative geochemical biosensors.

UNLABELLED: Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination, even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. IMPORTANCE: Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts.

Selective sorption of dissolved organic carbon compounds by temperate soils.

BACKGROUND: Physico-chemical sorption onto soil minerals is one of the major processes of dissolved organic carbon (OC) stabilization in deeper soils. The interaction of DOC on soil solids is related to the reactivity of soil minerals, the chemistry of sorbate functional groups, and the stability of sorbate to microbial degradation. This study was conducted to examine the sorption of diverse OC compounds (D-glucose, L-alanine, oxalic acid, salicylic acid, and sinapyl alcohol) on temperate climate soil orders (Mollisols, Ultisols and Alfisols). METHODOLOGY: Equilibrium batch experiments were conducted using 0-100 mg C L(-1) at a solid-solution ratio of 1∶60 for 48 hrs on natural soils and on soils sterilized by γ-irradiation. The maximum sorption capacity, Q(max) and binding coefficient, k were calculated by fitting to the Langmuir model. RESULTS: Ultisols appeared to sorb more glucose, alanine, and salicylic acid than did Alfisols or Mollisols and the isotherms followed a non-linear pattern (higher k). Sterile experiments revealed that glucose and alanine were both readily degraded and/or incorporated into microbial biomass because the observed Q(max) under sterile conditions decreased by 22-46% for glucose and 17-77% for alanine as compared to non-sterile conditions. Mollisols, in contrast, more readily reacted with oxalic acid (Q(max) of 886 mg kg(-1)) and sinapyl alcohol (Q(max) of 2031 mg kg(-1)), and no degradation was observed. The reactivity of Alfisols to DOC was intermediate to that of Ultisols and Mollisols, and degradation followed similar patterns as for Ultisols. CONCLUSION: This study demonstrated that three common temperate soil orders experienced differential sorption and degradation of simple OC compounds, indicating that sorbate chemistry plays a significant role in the sorptive stabilization of DOC.

Activation of VTA GABA neurons disrupts reward consumption.

The activity of ventral tegmental area (VTA) dopamine (DA) neurons promotes behavioral responses to rewards and environmental stimuli that predict them. VTA GABA inputs synapse directly onto DA neurons and may regulate DA neuronal activity to alter reward-related behaviors; however, the functional consequences of selective activation of VTA GABA neurons remains unknown. Here, we show that in vivo optogenetic activation of VTA GABA neurons disrupts reward consummatory behavior but not conditioned anticipatory behavior in response to reward-predictive cues. In addition, direct activation of VTA GABA projections to the nucleus accumbens (NAc) resulted in detectable GABA release but did not alter reward consumption. Furthermore, optogenetic stimulation of VTA GABA neurons directly suppressed the activity and excitability of neighboring DA neurons as well as the release of DA in the NAc, suggesting that the dynamic interplay between VTA DA and GABA neurons can control the initiation and termination of reward-related behaviors.

What causes a prolactinoma to be aggressive or to become a pituitary carcinoma?

INTRODUCTION: Malignant prolactinoma is an exceedingly rare endocrine tumor and cannot be diagnosed on histological grounds alone. Similarly to other neuroendocrine tumors such as pheochromocytoma, the mitoses index, Ki-67, p53, and others are utilized in helping understand whether a tumor is benign or malignant or to better predict tumor behavior. We here present the unusual case of an unfortunate young man with an aggressive prolactinoma, the complications of which led to his premature death. CASE REPORT: A 25-year-old white man developed severe headaches, low energy, and decreased libido. A brain magnetic resonance imaging (MRI) showed a 4 x 3 x 2 cm pituitary tumor invading the left cavernous sinus. Laboratory findings revealed elevated prolactin (470 ng/mL) and adrenocorticotropic hormone (ACTH, 82 pg/ml) and decreased total testosterone (176 ng/dl). Visual fields showed superior quadrantanopia in the left eye. Transsphenoidal pituitary resection was undertaken. Pathology revealed a prolactinoma with atypical cells, diffuse p53 nuclear labeling, and a Ki-67 index of 23% (high). Postoperatively, prolactin remained elevated (725-891 ng/ml) and cabergoline was increased to 1 mg three times weekly, with serum prolactin further increasing to 3507 ng/ml five months postoperatively. Repeat MRI revealed extension of the tumor with optic chiasm compression and left orbit invasion. Because of acute left vision loss with ophthalmoplegia, an urgent left frontotemporal craniotomy and tumor resection were conducted. The Ki-67 index of the tumor was 24.8%, the mitotic figure immunostain phosphohistone-H3 positive. Sixty percent (60%) of tumor cells were positive for p53. Cabergoline was increased to 1 mg daily but prolactin remained elevated (770 ng/ml). The patient then underwent proton beam radiation to the area of concern involving the sella. Prolactin thereafter improved to 44 ng/ml. He then developed acute vision loss of the right eye with an MRI showing tumor in the right cavernous sinus. A 15 mm dural-based right temporal mass believed to be a metastasis was also noted. Following this scan, he was considered too high risk for debulking surgery and instead underwent gamma knife irradiation to the sella area. This shrank the right cavernous sinus tumor mass, while the right temporal mass increased in size. The patient developed blindness and left-sided weakness and required enteral feeding and tracheostomy after prolonged intubation. A trial of chemotherapy with temozolomide (350 mg daily for 5 days) near the end of his life was unsuccessful. He died on home hospice 31 months after his first surgery. CONCLUSION: Headaches, vision changes, and symptoms of androgen deficiency syndrome can be manifestations of an aggressive prolactinoma that might require surgery and additional medical therapy including cabergoline and temozolomide with an unpredictable time of survival.

Systemic gene transfer to skeletal muscle using reengineered AAV vectors.

Gene therapy of musculoskeletal disorders warrants efficient gene transfer to a wide range of muscle groups. Reengineered adeno-associated viral (AAV) vectors that selectively transduce muscle tissue following systemic administration are attractive candidates for such applications. Here we provide examples of several lab-derived AAV vectors that display systemic tissue tropism in mice. Methods to evaluate the efficiency of gene transfer to skeletal muscle following intravenous or isolated limb infusion of AAV -vectors in mice are discussed in detail.

Construction of implantable optical fibers for long-term optogenetic manipulation of neural circuits.

In vivo optogenetic strategies have redefined our ability to assay how neural circuits govern behavior. Although acutely implanted optical fibers have previously been used in such studies, long-term control over neuronal activity has been largely unachievable. Here we describe a method to construct implantable optical fibers to readily manipulate neural circuit elements with minimal tissue damage or change in light output over time (weeks to months). Implanted optical fibers readily interface with in vivo electrophysiological arrays or electrochemical detection electrodes. The procedure described here, from implant construction to the start of behavioral experimentation, can be completed in approximately 2-6 weeks. Successful use of implantable optical fibers will allow for long-term control of mammalian neural circuits in vivo, which is integral to the study of the neurobiology of behavior.

Reengineering a receptor footprint of adeno-associated virus enables selective and systemic gene transfer to muscle.

Reengineering the receptor footprints of adeno-associated virus (AAV) isolates may yield variants with improved properties for clinical applications. We generated a panel of synthetic AAV2 vectors by replacing a hexapeptide sequence in a previously identified heparan sulfate receptor footprint with corresponding residues from other AAV strains. This approach yielded several chimeric capsids displaying systemic tropism after intravenous administration in mice. Of particular interest, an AAV2/AAV8 chimera designated AAV2i8 displayed an altered antigenic profile, readily traversed the blood vasculature, and selectively transduced cardiac and whole-body skeletal muscle tissues with high efficiency. Unlike other AAV serotypes, which are preferentially sequestered in the liver, AAV2i8 showed markedly reduced hepatic tropism. These features of AAV2i8 suggest that it is well suited to translational studies in gene therapy of musculoskeletal disorders.