Analyzing large biological datasets with association networks
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Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme
The native structure of the Azoarcus group I ribozyme is stabilized by the cooperative formation of tertiary interactions between double helical domains. Thus, even single mutations that break this network of tertiary interactions reduce ribozyme activity in physiological Mg2+ concentrations. Here, we report that molecular crowding comparable to that in the cell compensates for destabilizing mutations in the Azoarcus ribozyme. Small angle X-ray scattering, native polyacrylamide gel electrophoresis and activity assays were used to compare folding free energies in dilute and crowded solutions containing 18% PEG1000. Crowder molecules allowed the wild-type and mutant ribozymes to fold at similarly low Mg2+ concentrations and stabilized the active structure of the mutant ribozymes under physiological conditions. This compensation helps explains why ribozyme mutations are often less deleterious in the cell than in the test tube. Nevertheless, crowding did not rescue the high fraction of folded but less active structures formed by double and triple mutants. We conclude that crowding broadens the fitness landscape by stabilizing compact RNA structures without improving the specificity of self-assembly.
Lee, Hui-Ting↗
Return of the Lemnaceae: duckweed as a model plant system in the genomics and postgenomics era
Abstract The aquatic Lemnaceae family, commonly called duckweed, comprises some of the smallest and fastest growing angiosperms known on Earth. Their tiny size, rapid growth by clonal propagation, and facile uptake of labeled compounds from the media were attractive features that made them a well-known model for plant biology from 1950 to 1990. Interest in duckweed has steadily regained momentum over the past decade, driven in part by the growing need to identify alternative plants from traditional agricultural crops that can help tackle urgent societal challenges, such as climate change and rapid population expansion. Propelled by rapid advances in genomic technologies, recent studies with duckweed again highlight the potential of these small plants to enable discoveries in diverse fields from ecology to chronobiology. Building on established community resources, duckweed is reemerging as a platform to study plant processes at the systems level and to translate knowledge gained for field deployment to address some of society’s pressing needs. This review details the anatomy, development, physiology, and molecular characteristics of the Lemnaceae to introduce them to the broader plant research community. We highlight recent research enabled by Lemnaceae to demonstrate how these plants can be used for quantitative studies of complex processes and for revealing potentially novel strategies in plant defense and genome maintenance.
Biochemistry & Molecular Biology↗
Time for a drought experiment: Do you know your plants’ water status?
Abstract Drought stress is an increasing concern because of climate change and increasing demands on water for agriculture. There are still many unknowns about how plants sense and respond to water limitation, including which genes and cellular mechanisms are impactful for ecology and crop improvement in drought-prone environments. A better understanding of plant drought resistance will require integration of several research disciplines. A common set of parameters to describe plant water status and quantify drought severity can enhance data interpretation and research integration across the research disciplines involved in understanding drought resistance and would be especially useful in integrating the flood of genomic data being generated in drought studies. Water potential (ψw) is a physical measure of the free energy status of water that, along with related physiological measurements, allows unambiguous description of plant water status that can apply across various soil types and environmental conditions. ψw and related physiological parameters can be measured with relatively modest investment in equipment and effort. Thus, we propose that increased use of ψw as a fundamental descriptor of plant water status can enhance the insight gained from many drought-related experiments and facilitate data integration and sharing across laboratories and research disciplines.
Juenger, Thomas E. (ORCID:0000000195509288)↗
Daylength variation affects growth, photosynthesis, leaf metabolism, partitioning, and metabolic fluxes
Abstract Daylength, a seasonal and latitudinal variable, exerts a substantial impact on plant growth. However, the relationship between daylength and growth is nonproportional, suggesting the existence of adaptive mechanisms. Thus, our study aimed to comprehensively investigate the adaptive strategies employed by plants in response to daylength variation. We grew false flax (Camelina sativa) plants, a model oilseed crop, under long-day (LD) and short-day (SD) conditions and used growth measurements, gas exchange measurements, and isotopic labeling techniques, including 13C, 14C, and 2H2O, to determine responses to different daylengths. Our findings revealed that daylength influences various growth parameters, photosynthetic physiology, carbon partitioning, metabolic fluxes, and metabolite levels. SD plants employed diverse mechanisms to compensate for reduced CO2 fixation in the shorter photoperiod. These mechanisms included enhanced photosynthetic rates and reduced respiration in the light (RL), leading to increased shoot investment. Additionally, SD plants exhibited reduced rates of the glucose 6-phosphate (G6P) shunt and greater partitioning of sugars into starch, thereby sustaining carbon availability during the longer night. Isotopic labeling results further demonstrated substantial alterations in the partitioning of amino acids and TCA cycle intermediates between rapidly and slowly turning over pools. Overall, the results point to multiple developmental, physiological, and metabolic ways in which plants adapt to different daylengths to maintain growth.
59 BASIC BIOLOGICAL SCIENCES↗
Stomata in-sight: Integrating live confocal microscopy with leaf gas exchange and environmental control
Stomatal anatomy (aperture area, length, and width) influences leaf-level physiology traits including conductance to water vapor. Stomatal anatomy can be visualized in situ by microscopy, but the difficulty of regulating the atmospheric environment of a microscope stage means that the conditions under which imaging is done are rarely physiologically relevant. Alternatively, leaf gas exchange instruments that measure gas fluxes reflect stomatal anatomical characteristics in aggregate, but the relative strengths of anatomical traits to control water use (e.g. size vs density) cannot be firmly established. To reconcile the microscopic stomatal characteristics with leaf-level gas exchange, we describe a tool that combines laser scanning confocal microscopy, gas exchange instruments, and machine-learning image analysis to simultaneously observe anatomical characteristics of many (>40) stomata alongside leaf-level traits like photosynthesis, transpiration, and stomatal conductance. We demonstrate how the tool has the resolution capable of quantifying aperture sizes and variability in maize (Zea mays) leaves under 5 steady-state light/pCO 2 treatments while tightly controlling other environmental variables like relative humidity and temperature. A model used to calculate stomatal conductance from measured apertures and stomatal density accurately matched stomatal conductance measured by gas exchange. This technical advancement will provide insight on how stomatal anatomy and function trade off to influence stomatal conductance and leaf-level water use efficiency.
59 BASIC BIOLOGICAL SCIENCES↗
Seasonal trends in photosynthesis and leaf traits in scarlet oak
Understanding seasonal variation in photosynthesis is important for understanding and modelling plant productivity. Here, we used shotgun sampling to examine physiological, structural and spectral leaf traits of upper canopy, sun-exposed leaves in Quercus coccinea Münchh (scarlet oak) across the growing season in order to understand seasonal trends, explore the mechanisms underpinning physiological change, and investigate the impact of extrapolating measurements from a single date to the whole season. We tested the hypothesis that photosynthetic rates and capacities would peak at the summer solstice i.e., at the time of peak photoperiod. Contrary to expectations, our results reveal a late-season peak in both photosynthetic capacity and rate before the expected sharp decrease at the start of senescence. This late-season maximum occurred after the higher summer temperatures and VPD, and was correlated with the recovery of leaf water content and increased stomatal conductance. We modelled photosynthesis at the top of the canopy and found that the simulated results closely tracked the maximum carboxylation capacity of Rubisco. For both photosynthetic capacity and modelled top-of-canopy photosynthesis, the maximum value was therefore not observed at the summer solstice. Rather, in each case the measurements at and around the solstice were close to the overall seasonal mean, with values later in the season leading to deviations from the mean by up to 41% and 52% respectively. Overall, we found that the expected Gaussian pattern of photosynthesis was not observed. We conclude that an understanding of species- and environment-specific changes in photosynthesis across the season is essential for correct estimation of seasonal photosynthetic capacity.
54 ENVIRONMENTAL SCIENCES↗
Intra-canopy leaf trait variation facilitates high leaf area index and compensatory growth in a clonal woody encroaching shrub
Leaf trait variation enables plants to utilize large gradients of light availability that exist across canopies of high leaf area index (LAI), allowing for greater net carbon gain while reducing light availability for understory competitors. While these canopy dynamics are well understood in forest ecosystems, studies of canopy structure of woody shrubs in grasslands are lacking. To evaluate the investment strategy used by these shrubs, we investigated the vertical distribution of leaf traits and physiology across canopies of Cornus drummondii, the predominant woody encroaching shrub in the Kansas tallgrass prairie. We also examined the impact of disturbance by browsing and grazing on these factors. Our results reveal that leaf mass per area (LMA) and leaf nitrogen per area (Na) varied approximately threefold across canopies of C. drummondii, resulting in major differences in the physiological functioning of leaves. High LMA leaves had high photosynthetic capacity, while low LMA leaves had a novel strategy for maintaining light compensation points below ambient light levels. The vertical allocation of leaf traits in C. drummondii canopies was also modified in response to browsing, which increased light availability at deeper canopy depths. As a result, LMA and Na increased at lower canopy depths, leading to a greater photosynthetic capacity deeper in browsed canopies compared to control canopies. This response, along with increased light availability, facilitated greater photosynthesis and resource-use efficiency deeper in browsed canopies compared to control canopies. Furthermore, our results illustrate how C. drummondii facilitates high LAI canopies and a compensatory growth response to browsing—both of which are key factors contributing to the success of C. drummondii and other species responsible for grassland woody encroachment.
54 ENVIRONMENTAL SCIENCES↗
At least it is a dry cold: the global distribution of freeze–thaw and drought stress and the traits that may impart poly-tolerance in conifers
Abstract Conifers inhabit some of the most challenging landscapes where multiple abiotic stressors (e.g., aridity, freezing temperatures) often co-occur. Physiological tolerance to multiple stressors (‘poly-tolerance’) is thought to be rare because exposure to one stress generally limits responses to another through functional trade-offs. However, the capacity to exhibit poly-tolerance may be greater when combined abiotic stressors have similar physiological impacts, such as the disruption of hydraulic function imposed by drought or freezing. Here, we reviewed empirical data in light of theoretical expectations for conifer adaptations to drought and freeze–thaw cycles with particular attention to hydraulic traits of the stem and leaf. Additionally, we examined the commonality and spatial distribution of poly-stress along indices of these combined stressors. We found that locations with the highest values of our poly-stress index (PSi) are characterized by moderate drought and moderate freeze–thaw, and most of the global conifer distribution occupies areas of moderate poly-stress. Among traits examined, we found diverse responses to the stressors. Turgor loss point did not correlate with freeze–thaw or drought stress individually, but did with the PSi, albeit inverse to what was hypothesized. Leaf mass per area was more strongly linked with drought stress than the poly-stress and not at all with freeze–thaw stress. In stems, the water potential causing 50% loss of hydraulic conductivity became more negative with increasing drought stress and poly-stress but did not correlate with freeze–thaw stress. For these traits, we identified a striking lack of coverage for substantial portions of species ranges, particularly at the upper boundaries of their respective PSis, demonstrating a critical gap in our understanding of trait prevalence and plasticity along these stress gradients. Future research should investigate traits that confer tolerance to both freeze–thaw and drought stress in a wide range of species across broad geographic scales.
54 ENVIRONMENTAL SCIENCES↗
Partitioning in trees and soil (PiTS) - a experimental approach to improve knowledge of forest carbon dynamics
Summary The dynamics of rapid changes in carbon (C) partitioning within forest ecosystems are not well understood, which limits improvement of mechanistic models of C cycling. Our objective was to inform model processes by describing relationships between C partitioning and accessible environmental or physiological measurements, with a special emphasis on belowground C flux. We exposed eight 7-year-old loblolly pine trees to air enriched with 13CO2 and then implemented adjacent light shade (LS) and heavy shade (HS) treatments in order to manipulate C uptake and flux. A soil pit was dug adjacent to the trees to provide greater access belowground. The impacts of shading on photosynthesis, plant water potential, sap flow, basal area growth, root growth, and soil C exchange rate (CER) were assessed for each tree over a three-week period. The progression of the 13C label was concurrently tracked from the atmosphere through foliage, phloem, roots, and soil CO2 efflux. The HS treatment significantly reduced C uptake, sap flow, stem growth and root standing crop, and resulted in greater residual soil water content to 1 m depth. Sap flow was strongly correlated with CER on the previous day, but not the current day, with no apparent treatment effect on the relationship. The 13C label was immediately detected in foliage on label day (half-life = 0.5 d), progressed through phloem by day 2 (half-life = 4.7 d), roots by day 2-4, and subsequently was evident as respiratory release from soil which peaked between days 3-6. The 13C of soil CO2 efflux was strongly correlated with phloem 13C on the previous day, or two days earlier. These data detail the timing and relative magnitude of C flux through a young pine stand in relation to environmental conditions. Refinement of belowground sampling will be necessary to adequately separate and quantify the flux of recently fixed C into roots, and fate of that new C as respiratory, mycorrhizal or exudative release, storage or partitioning into new root biomass.
09 BIOMASS FUELS↗
A test of the hydraulic vulnerability segmentation hypothesis in angiosperm and conifer tree species
Water transport from soils to the atmosphere is critical for plant growth and survival. However, we have a limited understanding about many portions of the whole-tree hydraulic pathway, because the vast majority of published information is on terminal branches. Our understanding of mature tree trunk hydraulic physiology, in particular, is limited. The hydraulic vulnerability segmentation hypothesis (HVSH) stipulates that distal portions of the plant (leaves, branches and roots) should be more vulnerable to embolism than trunks, which are non-redundant organs that require a massive carbon investment. In the current study, we compared vulnerability to loss of hydraulic function, leaf and xylem water potentials and the resulting hydraulic safety margins (in relation to the water potential causing 50% loss of hydraulic conductivity) in leaves, branches, trunks and roots of four angiosperms and four conifer tree species. Across all species, our results supported strongly the HVSH as leaves and roots were less resistant to embolism than branches or trunks. However, branches were consistently more resistant to embolism than any other portion of the plant, including trunks. Also, calculated whole-tree vulnerability to hydraulic dysfunction was much greater than vulnerability in branches. This was due to hydraulic dysfunction in roots and leaves at less negative water potentials than those causing branch or trunk dysfunction. Leaves and roots had narrow or negative hydraulic safety margins, but trunks and branches maintained positive safety margins. By using branch-based hydraulic information as a proxy for entire plants, much research has potentially overestimated embolism resistance, and possibly drought tolerance, for many species. This study highlights the necessity to reconsider past conclusions made about plant resistance to drought based on branch xylem only. As a result, this study also highlights the necessity for more research of whole-plant hydraulic physiology to better understand strategies of plant drought tolerance and the critical control points within the hydraulic pathway.
59 BASIC BIOLOGICAL SCIENCES↗
Distinct xylem responses to acute vs prolonged drought in pine trees
Increasing dryness challenges trees’ ability to maintain water transport to the leaves. Most plant hydraulics models use a static xylem response to water stress. Yet, in reality, lower soil moisture and warmer temperatures during growing seasons feed back onto xylem development. In turn, adjustments to water stress in the newly built xylem influence future physiological responses to droughts. In this study, we investigate the annual variation of anatomical traits in branch xylem in response to different soil and atmospheric moisture conditions and tree stress levels, as indicated by seasonal predawn leaf water potential (??L,pd). We used a 6-year field experiment in southwestern USA with three soil water treatments applied to Pinus edulis Engelm trees—ambient, drought (45% rain reduction) and irrigation (15–35% annual water addition). All trees were also subject to a natural 1-year acute drought (soil and atmospheric) that occurred during the experiment. The irrigated trees showed only moderate changes in anatomy-derived hydraulic traits compared with the ambient trees, suggesting a generally stable, well-balanced xylem structure under unstressed conditions. The artificial prolonged soil drought increased hydraulic efficiency but lowered xylem construction costs and decreased tracheid implosion safety ((t/b)2), suggesting that annual adjustments of xylem structure follow a safety–efficiency trade-off. The acute drought plunged hydraulic efficiency across all treatments. The combination of acute and prolonged drought resulted in vulnerable and inefficient new xylem, disrupting the stability of the anatomical trade-off observed in the rest of the years. The xylem hydraulic traits showed no consistent direct link to ??L,pd. In the future, changes in seasonality of soil and atmospheric moisture are likely to have a critical impact on the ability of P. edulis to acclimate its xylem to warmer climate. Furthermore, the increasing frequency of acute droughts might reduce hydraulic resilience of P. edulis by repeatedly creating vulnerable and less efficient anatomical structure.
Guerin, Marceau↗
Impacts of Soil Microbiome Variations on Root Colonization by Fungi and Bacteria and on the Metabolome of Populus tremula × alba
Trees depend on beneficial interactions between roots and soil microbes for their nutrition and protection against stresses. The soil microbiome provides the main reservoir of microbes for root colonization and is subject to natural variations that can affect its composition. It is not clear whether the tree’s root system is able to buffer the natural variations occurring in the soil microbiome to capture a stable and effective microbiome or whether these variations affect its microbiome to impact its physiology. To address this question, we planted cuttings of Gray Poplar (Populus tremula × alba clone 717-1B4) in natural soil taken from a poplar stand under the same tree over two consecutive years and grew them in a greenhouse. We analyzed the soil and root microbiomes by high throughput Illumina MiSeq sequencing of fungal rDNA internal transcribed spacer and bacterial 16S rRNA amplicons and we characterized the root metabolome by gas chromatography-mass spectrometry. Soil and root microbial communities significantly shifted over the 2 years. A modification of the balance between endophytes, saprophytes, and mycorrhizal fungi occurred in the roots as well as a replacement of some dominant operational taxonomic units by others. These modifications were correlated with a significant alteration of the levels of about 10% of primary and secondary metabolites, suggesting that natural fluctuations in soil microbial communities can have a profound impact on tree root metabolism and physiology. Tree roots functioning may thus be indirectly strongly affected by the effects of future extreme climatic variations on the soil microbiome.
59 BASIC BIOLOGICAL SCIENCES↗
Interrelationship between sex, age, blood volume and VO 2 max
Background Circulating blood volume (BV) and maximal oxygen uptake (VO 2 max) are physiological characteristics important for optimal human performance in aerospace and military operational environments. Addressing the interrelationships between BV, VO 2 max, sex, and age together is relevant to identifying those individuals with greatest risk of poor outcomes from hemorrhage, as well as assessing the levels of performance competence of individuals deployed in operational environments. In the present investigation, we report and compare for the first time BV and VO 2 max in a cohort of males and females together to test the hypothesis that BV and VO 2 max is lower in older people independent of sex. Methods To accomplish this, a ‘data mining’ effort of an historic database generated from NASA and U.S. Air Force experiments was conducted. BV, red cell volume, plasma volume, hematocrit, and VO 2 max were measured in 94 healthy individuals (28 females, 66 males) across an age range of 23 to 65 years to assess the interrelationship between sex, age, BV, and VO 2 max. Subjects were classified in age groups by < 40 years and ≥ 40 years; these groups identified females as pre‐ vs. post‐menopausal. Results Consistent with our hypothesis, comparisons revealed that males had higher (p < 0.01) BV, red cell volume, hematocrit, and VO 2 max than females when standardized for body size. Against expectations, BV was not different in older compared with younger males and females. VO 2 max was not different in older compared with younger females, while VO 2 max was lower in older males (p < 0.01). Conclusion We conclude that physiological mechanisms other than BV associated with aging appear to be responsible for a decline in VO 2 max of our older male subjects. Furthermore, factors other than menopause may also influence the control of BV in the female population. Our results provide evidence that aging may not compromise males or females in scenarios where BV can affect performance in aerospace and military environments. Support or Funding Information This research was supported in part by appointment of Ms. Koons to the Postgraduate Research Fellowship Program at the US Army Institute of Surgical Research administered by the Oak Ridge Institute for Science and Education through an interagency agreement between the US Department of Energy and USAMRMC. Study funding was provided by a grant from the US Army Combat Casualty Care Research Program (D‐009‐2014‐USAISR). This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Convertino, Victor↗
39th Lauriston S. Taylor Lecture
Since the early days of the Manhattan Engineer District, Oak Ridge National Laboratory (ORNL) has served to advance the dosimetry models used to set protection standards for radionuclides taken into the body. Throughout the years, this effort benefited significantly from ORNL staff's active participation in national and international scientific bodies. The first such interaction was in 1946 with the National Committee on Radiation Protection (NCRP), chaired by L.S. Taylor, which led to the 1949 to 1953 series of tripartite conferences of experts from Canada, the United Kingdom, and the United States. These conferences addressed the need for standardization of dosimetry models and led to the establishment of an anatomic and physiologic model called “Standard Man,” a precursor of the reference worker defined in Publication 23 of the International Commission on Radiological Protection (ICRP). Standard Man was used in setting the maximum permissible concentrations in air and water published in NBS Handbook 52 and subsequent reports by NCRP and ICRP. K.Z. Morgan, then director of the Health Physics Division at ORNL, participated in the tripartite conferences and subsequently established ORNL as a modeling and computational resource for development of radiation protection standards. ORNL’s role expanded with participation in the work of the Medical Internal Radiation Dose (MIRD) Committee of the Society of Nuclear Medicine. Results of interactions with the MIRD Committee are evident in the radiation protection guidance for internal emitters in ICRP Publication 30. The annual limit on intake and derived air concentration values tabulated in Publication 30 were computed by an ORNL-based task group of ICRP Committee 2. A few years after the appearance of Publication 30, the Chernobyl nuclear reactor accident made clear the need to develop standard dosimetry models for pre-adult ages as members of the public. In the late 1980s, ICRP began an effort to extend its reference worker concept to a reference family and develop dosimetric models for application to intake of radionuclides by members of the public. However, the modeling approach underlying the ICRP Publication 30 computational framework was not amenable to age and gender considerations. With support of U.S. federal agencies, ORNL had begun efforts in the early 1980s to develop age- and gender-specific dosimetric models, including physiologically informed biokinetic models and age-specific dosimetric phantoms. ORNL’s models and methods became the starting point for the ICRP’s series of reports on dose coefficients for radionuclide intake by the public. Currently ICRP Committee 2 is overseeing development of a second generation of post-Chernobyl models and methods, with updates of Publications 30 and 68 soon to appear and new models for members of the public in preparation. The goal of this Lauriston S. Taylor Lecture is to chronicle advancements in the dosimetry of internal emitters with some discussion of models and methods but with due deference to decisions within scientific bodies and stimulated by radiological events.
61 RADIATION PROTECTION AND DOSIMETRY↗
Constraints and variation in food web link-species space
Predicting food web structure in future climates is a pressing goal of ecology. These predictions may be impossible without a solid understanding of the factors that structure current food webs. Here, the most fundamental aspect of food web structure—the relationship between the number of links and species—is still poorly understood. Some species interactions may be physically or physiologically ‘forbidden'—like consumption by non-consumer species—with possible consequences for food web structure. We show that accounting for these ‘forbidden interactions' constrains the feasible link-species space, in tight agreement with empirical data. Rather than following one particular scaling relationship, food webs are distributed throughout this space according to shared biotic and abiotic features. Our study provides new insights into the long-standing question of which factors determine this fundamental aspect of food web structure.
59 BASIC BIOLOGICAL SCIENCES↗
Enzyme activities predicted by metabolite concentrations and solvent capacity in the cell
Experimental measurements or computational model predictions of the post-translational regulation of enzymes needed in a metabolic pathway is a difficult problem. Consequently, regulation is mostly known only for well-studied reactions of central metabolism in various model organisms. In this study, we use two approaches to predict enzyme regulation policies and investigate the hypothesis that regulation is driven by the need to maintain the solvent capacity in the cell. The first predictive method uses a statistical thermodynamics and metabolic control theory framework while the second method is performed using a hybrid optimization–reinforcement learning approach. Efficient regulation schemes were learned from experimental data that either agree with theoretical calculations or result in a higher cell fitness using maximum useful work as a metric. As previously hypothesized, regulation is herein shown to control the concentrations of both immediate and downstream product concentrations at physiological levels. Model predictions provide the following two novel general principles: (1) the regulation itself causes the reactions to be much further from equilibrium instead of the common assumption that highly non-equilibrium reactions are the targets for regulation; and (2) the minimal regulation needed to maintain metabolite levels at physiological concentrations maximizes the free energy dissipation rate instead of preserving a specific energy charge. The resulting energy dissipation rate is an emergent property of regulation which may be represented by a high value of the adenylate energy charge. In addition, the predictions demonstrate that the amount of regulation needed can be minimized if it is applied at the beginning or branch point of a pathway, in agreement with common notions. The approach is demonstrated for three pathways in the central metabolism of E. coli (gluconeogenesis, glycolysis-tricarboxylic acid (TCA) and pentose phosphate-TCA) that each require different regulation schemes. It is shown quantitatively that hexokinase, glucose 6-phosphate dehydrogenase and glyceraldehyde phosphate dehydrogenase, all branch points of pathways, play the largest roles in regulating central metabolism.
59 BASIC BIOLOGICAL SCIENCES↗
Description of Rhodanobacter denitrificans sp. nov., isolated from nitrate-rich zones of a contaminated aquifer
Bacterial strains 2APBS1T and 116-2 were isolated from the subsurface of a nuclear legacy waste site where sediments are co-contaminated with large amounts of acidity, nitrate, metal radionuclides and other heavy metals. A combination of physiological and genetic assays indicated that these strains represent the first members of the Rhodanobacter genus shown to be capable of complete denitrification. Cells of strain 2APBS1T and 116-2 were Gram negative, non-spore-forming, rods, 3-5 micro;m long and 0.25-0.5 m in diameter. The isolates were facultative anaerobes, and had temperature and pH optima for growth at 30 C and pH 6.5, respectively, and could tolerate up to 2.0 % NaCl, though growth improved in its absence. Strains 2APBS1T and 116-2 contained fatty acid profiles and 100 % Q-8 ubiquinone, that are characteristic features of the genus Rhodanobacter. Although strains 2APBS1T and 116-2 share high SSU rRNA gene sequence similarity to R. thiooxydans (>99%), DNA-DNA hybridization values were substantially below the 70% threshold used to designate novel species. Thus, based on genotypic, phylogenetic, chemotaxonomic and physiological differences, strains 2APBS1T and 116-2 are considered to represent a novel species of the genus Rhodanobacter, for which the name Rhodanobacter denitrificans sp. nov is proposed. The type strain is 2APBS1T (=DSM 23569T =JCM 17641T). Strain 116-2 (=DSM 24678 = JCM 17642) is a reference strain.
Prakash, Om↗