Microbial degradation of tannins – A current perspective

Tannins are water-soluble polyphenolic compounds having wide prevalence in plants. Hydrolysable and condensed tannins are the two major classes of tannins. These compounds have a range of effects on various organisms – from toxic effects on animals to growth inhibition of microorganisms. Some microbes are, however, resistant to tannins, and have developed various mechanisms and pathways for tannin degradation in their natural milieu. The microbial degradation of condensed tannins is, however, less than hydrolysable tannins in both aerobic and anaerobic environments. A number of microbes have also been isolated from the gastrointestinal tract of animals, which have the ability to break tannin-protein complexes and degrade tannins, especially hydrolysable tannins. Tannase, a key enzyme in the degradation of hydrolysable tannins, is present in a diverse group of microorganisms, including rumen bacteria. This enzyme is being increasingly used in a number of processes. Presently, there is a need for increased understanding of the biodegradation of condensed tannins, particularly in ruminants.     

Trophic state indicators are a better predictor of Florida bass condition compared to temperature in Florida’s freshwater bodies

Forecasted increases in global temperatures will likely have profound effects on freshwater fishes. Overlaid on increasing global temperatures, human populations are expected to grow, which will increase anthropogenic nutrient enrichment in freshwater ecosystems. Florida (US) represents the equatorial range limit for many freshwater fishes, thus these species are potentially at risk to climate warming. Likewise, Florida’s population is expected to aggressively expand, increasing risk for nutrient enrichment. In this study, we examined whether maximum water temperatures or trophic state indicators (a proxy for nutrient enrichment) better explains variation in Florida Bass (Micropterus salmoides floridanus) condition across 23 different Florida freshwater bodies distributed throughout the state. Florida Bass lengths and weights, temperature, and chlorophyll-α, total phosphorous (TP), and total nitrogen (TN) measures were collected in the late summer and fall from 2010 to 2012. We described relationships between bass relative condition and environmental measurements (temperature, and trophic state indicators) across these lake-year combinations using linear and non-linear regressions. We found no significant relationship between temperature and bass condition (r² = 0.01). However, we found that trophic state indicators did predict bass condition (r² = 0.39–0.50). Though research is needed to more rigorously assess the effects of rising temperature on bass condition, our results may suggest that lake productivity is currently an influential driver on Florida Bass. As such, management efforts should continue to closely monitor and manage water quality and potential nutrient enrichment in Florida’s freshwater waters, as bass condition appears to be closely tied to lake productivity.     

Microbial degradation and deterioration of polyethylene – A review

The ability of microorganisms to use polyethylene as a carbon source has only been recently established. This result has significance both from an environmental point of view, due to the accumulation of millions of tons of waste plastics every year, but also regarding the conservation of integrity for infrastructures incorporating this plastic. A number of microorganisms with the ability to grow on polyethylene have been isolated. The effects of these microorganisms on the physiochemical properties of this polymer have been described; these include changes in crystallinity, molecular weight, topography of samples and the functional groups found on the surface. Although the bio-degradation and bio-deterioration of polyethylene has been demonstrated by several researchers, the enzymes involved and mechanisms associated with these phenomena are still unclear. Nevertheless, it is recognized that both enzymatic and abiotic factors (such UV light) can mediate the initial oxidation of polyethylene chains, and given the chemical similarity between polyethylene and olefins it has been suggested that the metabolic pathways for degradation of hydrocarbons can be used once the size of polyethylene molecules decrease to an acceptable range for enzyme action (typically from 10 to 50 carbons). The long-range structure and morphology of polyethylene have shown important roles, with amorphous regions being more prone to microbial attack than crystalline ones. This review focuses on the recent hypotheses and experimental findings regarding the biodegradation of polyethylene.     

Yield trials of steroid-producingDioscorea on Florida’s Everglades peat soils

Four steroid-bearing clones of Dioscorea tested in a replicated varietal trial on Everglades peat soil near Belle Glade, Florida, included three introductions of D. spiculiflora Hemsl. and one selection of D. composita Hemsl. On an acre basis, D. composita, P. I. 201783, produced over 21 tons of dry tubers and 1,049 lbs of crude sapogenins. Tuber and sapogenin yields front the highest producing D. spiculiflora, P. I. 252887, were approximately 1/3 and 1/2 respectively, of these amounts. Yield differences were not significant between plots harvested 2 1/2 and 3 1/2 years after planting. The failure of tubers to increase in size in the last growing season was attributed to the restriction on growth imposed by the high water table at the test site.     

Regulation of metabolic pathways PVY-RNA biosynthesis in tobacco: Host’s RNA degradation

Tobacco plants infected with the potato virus Y (PVY) were studied during the acute-infection period. The control enzymes of metabolic pathway of hosts RNA degradation tending to biosynthesis of PVY-RNA, its coarse/fine regulation and content of hosts RNA were monitored. Activities of ribonucleases, phosphomonoesterases and phosphodiesterases in both the crude homogenates and the partially purified enzyme preparations from the diseased leaves were markedly increased when compared to the tissues from healthy plants. The curves of enzyme activities positively correlated with the multiplication curve of the PVY and negatively correlated with the decreased contents of hosts RNA. The enzyme activity in homogenate samples did not significantly differ from the corresponding purified enzyme preparations.     

Mango introduction in Florida and the ’haden’ cultivar’s significance to the modern industry

Mango (Mangifera indica L.) introductions to Florida began in 1861 with the importation of ’No. 11’, a polyembryonic, seed-propagated (nucellar) cultivarfrom Cuba. In the 1880s a collection of Cuban mangos was established near Bradenton. One resulting popular cultivar was ’Turpentine’, now widely used as a rootstock. The U. S. Department of Agriculture introduced ’Mulgoba’, an improved cultivarfrom India, in 1889. Other mangos were later brought from India, Vietnam, the Philippines, Thailand, Israel, Australia and Kenya. Related Mangifera species were collected in East Malaysian Borneo in 1990. Inasmuch as the breeding system of Mangifera favors outcrossing, the proximity of numerous genotypes of disparate geographic origin in Florida has made that state a secondary center of diversity for the mango and enabled it to make a unique contribution to the fruit industry.     

Do no-take reserves benefit Florida’s corals? 14 years of change and stasis in the Florida Keys National Marine Sanctuary

With coral populations in decline globally, it is critical that we tease apart the relative impacts of ecological and physical perturbations on reef ecosystems to determine the most appropriate management actions. This study compared the trajectories of benthic assemblages from 1998 to 2011 in three no-take reserves and three sites open to fishing, at 7–9 and 15–18 m depth in the Florida Keys. We evaluated temporal changes in the benthic assemblage to infer whether fisheries bans in no-take reserves could have cascading effects on the benthos in this region. Coral cover declined significantly over time at our sites and that trend was driven almost exclusively by decline of the Orbicella (formerly Montastraea) annularis species complex. Other coral taxa showed remarkable stasis and resistance to a variety of environmental perturbations. Protection status did not influence coral or macroalgal cover. The dynamics of corals and macroalgae in the 15 years since the reserves were established in 1997 suggest that although the reserves protected fish, they were of no perceptible benefit to Florida’s corals.     

Microbial degradation of nonylphenol and other alkylphenols—our evolving view

Because the endocrine disrupting effects of nonylphenol (NP) and octylphenol became evident, the degradation of long-chain alkylphenols (AP) by microorganisms was intensively studied. Most NP-degrading bacteria belong to the sphingomonads and closely related genera, while NP metabolism is not restricted to defined fungal taxa. Growth on NP and its mineralization was demonstrated for bacterial isolates, whereas ultimate degradation by fungi still remains unclear. While both bacterial and fungal degradation of short-chain AP, such as cresols, and the bacterial degradation of long-chain branched AP involves aromatic ring hydroxylation, alkyl chain oxidation and the formation of phenolic polymers seem to be preferential elimination pathways of long-chain branched AP in fungi, whereby both intracellular and extracellular oxidative enzymes may be involved. The degradation of NP by sphingomonads does not proceed via the common degradation mechanisms reported for short-chain AP, rather, via an unusual ipso-substitution mechanism. This fact underlies the peculiarity of long-chain AP such as NP isomers, which possess highly branched alkyl groups mostly containing a quaternary α-carbon. In addition to physicochemical parameters influencing degradation rates, this structural characteristic confers to branched isomers of NP a biodegradability different to that of the widely used linear isomer of NP. Potential biotechnological applications for the removal of AP from contaminated media and the difficulties of analysis and application inherent to the hydrophobic NP, in particular, are also discussed. The combination of bacteria and fungi, attacking NP at both the phenolic and alkylic moiety, represents a promising perspective.     

Florida’s efforts to assume section 404 permitting

Wetlands Ecology and Management - Section 404 of the federal Clean Water Act prohibits disposing of dredged and fill materials into the waters of the United States (WOTUS) absent a permit...     

The Root-Associated Microbial Community of the World’s Highest Growing Vascular Plants

Upward migration of plants to barren subnival areas is occurring worldwide due to raising ambient temperatures and glacial recession. In summer 2012, the presence of six vascular plants, growing in a single patch, was recorded at an unprecedented elevation of 6150 m.a.s.l. close to the summit of Mount Shukule II in the Western Himalayas (Ladakh, India). Whilst showing multiple signs of stress, all plants have managed to establish stable growth and persist for several years. To learn about the role of microbes in the process of plant upward migration, we analysed the root-associated microbial community of the plants (three individuals from each) using microscopy and tagged amplicon sequencing. No mycorrhizae were found on the roots, implying they are of little importance to the establishment and early growth of the plants. However, all roots were associated with a complex bacterial community, with richness and diversity estimates similar or even higher than the surrounding bare soil. Both soil and root-associated communities were dominated by members of the orders Sphingomonadales and Sphingobacteriales, which are typical for hot desert soils, but were different from communities of temperate subnival soils and typical rhizosphere communities. Despite taxonomic similarity on the order level, the plants harboured a unique set of highly dominant operational taxonomic units which were not found in the bare soil. These bacteria have been likely transported with the dispersing seeds and became part of the root-associated community following germination. The results indicate that developing soils act not only as a source of inoculation to plant roots but also possibly as a sink for plant-associated bacteria.     

Dead land walking: the value of continued conservation efforts in South Florida’s imperiled pine rocklands

Pine rocklands are deeply imperiled habitats restricted to South Florida and the Caribbean. In South Florida, more than 98% of pine rockland habitat has been destroyed in the past century (outside of Everglades National Park). Due to their proximity to human populations, management options in the remaining fragments are sometimes limited, and fires that are necessary to maintain healthy habitat structure are often excluded. Despite these pressures, conservation initiatives in pine rocklands have been surprisingly successful, and plant extinction has been avoided. In the coming decades, however, sea-level rise threatens to all but eliminate the pine rocklands, and efforts to preserve their many endemic species will likely fail. We synthesize the results of numerous ecological studies and review the successes and failures of conservation in South Florida’s pine rocklands. Further, we illustrate the value of continued conservation efforts, and provide direction in the light of the habitats long-term fate. We advocate the increased use of prescribed fire and, as the effects of climate change become more apparent, the translocation of some endemic species. Finally, we acclaim pine rocklands as a model system for studying how plant communities respond to environmental change. South Florida’s fragmented landscape, with shifting gradients of elevation, salinity, inundation and nutrient availability, should continue to inspire ecologists to address important questions, and better prepare the region, and the world, for the challenges of the coming decades.     

Diversity of ‘benzenetriol dioxygenase’ involved in p-nitrophenol degradation in soil bacteria

Ring hydroxylating dioxygenases (RHDOs) are one of the most important classes of enzymes featuring in the microbial metabolism of several xenobiotic aromatic compounds. One such RHDO is benzenetriol dioxygenase (BtD) which constitutes the metabolic machinery of microbial degradation of several mono- phenolic and biphenolic compounds including nitrophenols. Assessment of the natural diversity of benzenetriol dioxygenase (btd) gene sequence is of great significance from basic as well as applied study point of view. In the present study we have evaluated the gene sequence variations amongst the partial btd genes that were retrieved from microorganisms enriched for PNP degradation from pesticide contaminated agriculture soils. The gene sequence analysis was also supplemented with an in silico restriction digestion analysis. Furthermore, a phylogenetic analysis based on the deduced amino acid sequence(s) was performed wherein the evolutionary relatedness of BtD enzyme with similar aromatic dioxygenases was determined. The results obtained in this study indicated that this enzyme has probably undergone evolutionary divergence which largely corroborated with the taxonomic ranks of the host microorganisms.     

Kinetics of degradation of ‘short-’ and ‘long-lived’ proteins in cultured mammalian cells

Two distinct classes of protein referred to as short- and long-lived (Poole and Wibo, 1973) were found in pulse-chased HeLa S-3 and BHK 21/C13 cells. From experiments with pulse times ranging from 1 min to 20 h, a clear inverse correlation emerged between the pulse length and the percentage of protein which was hydrolysed intracellularly in the first h of chase. Using a 5 min pulse labelling with ³H-leucine, cells were either harvested immediately or after a 2 h chase. Approximately 35% of the label incorporated by cells was lost in a 2h chase; however, electrophoretic separation of cytosol and residual cytoplasmic fractions revealed no significant alteration in their protein profiles. The technique of selectively labelling ‘short’ and ‘long-lived’ proteins, which implies qualitative differences between them, is more readily interpreted as an artificial polarisation of a declining statistical probability curve of proteolysis with time which is similar for all nascent proteins.     

Parkin promotes proteasomal degradation of p62: implication of selective vulnerability of neuronal cells in the pathogenesis of Parkinson’s disease

Mutations or inactivation of parkin, an E3 ubiquitin ligase, are associated with familial form or sporadic Parkinson’s disease (PD), respectively, which manifested with the selective vulnerability of neuronal cells in substantia nigra (SN) and striatum (STR) regions. However, the underlying molecular mechanism linking parkin with the etiology of PD remains elusive. Here we report that p62, a critical regulator for protein quality control, inclusion body formation, selective autophagy and diverse signaling pathways, is a new substrate of parkin. P62 levels were increased in the SN and STR regions, but not in other brain regions in parkin knockout mice. Parkin directly interacts with and ubiquitinates p62 at the K13 to promote proteasomal degradation of p62 even in the absence of ATG5. Pathogenic mutations, knockdown of parkin or mutation of p62 at K13 prevented the degradation of p62. We further showed that parkin deficiency mice have pronounced loss of tyrosine hydroxylase positive neurons and have worse performance in motor test when treated with 6-hydroxydopamine hydrochloride in aged mice. These results suggest that, in addition to their critical role in regulating autophagy, p62 are subjected to parkin mediated proteasomal degradation and implicate that the dysregulation of parkin/p62 axis may involve in the selective vulnerability of neuronal cells during the onset of PD pathogenesis.     

Prevention of progression in Parkinson’s disease

Environmental influences affecting genetically susceptible individuals seem to contribute significantly to the development of Parkinson’s disease (PD). Xenobiotic exposure including transitional metal deposition into vulnerable CNS regions appears to interact with PD genes. Such exposure together with mitochondrial dysfunction evokes a destructive cascade of biochemical events, including oxidative stress and degeneration of the sensitive dopamine (DA) production system in the basal ganglia. Recent research indicates that the substantia nigra degeneration can be decelerated by treatment with iron binding compounds such as deferiprone. Interestingly compounds known to decrease PD risk including caffeine, niacin, nicotine and salbutamol also possess iron binding properties. Adequate function of antioxidative mechanisms in the vulnerable brain cells can be restored by acetylcysteine supplementation to normalize intracellular glutathione activity. Other preventive measures to reduce deterioration of dopaminergic neurons may involve life-style changes such as intake of natural antioxidants and physical exercise. Further research is recommended to identify therapeutic targets of the proposed interventions, in particular protection of the DA biosynthesis by oxygen radical scavengers and iron binding agents.     

Transport of ethanol in baker’s yeast

Ethanol is transported into various strains of baker's yeast by simple diffusion (no effect of inhibitors and a linear concentration dependence of the initial rate of uptake and final distribution in cells). It distributes itself in 96.6 +/- 16.2% of intracellular water.     

Role of RAGE in Alzheimer’s Disease

Receptor for advanced glycation end products (RAGE) is a receptor of the immunoglobulin super family that plays various important roles under physiological and pathological conditions. Compelling evidence suggests that RAGE acts as both an inflammatory intermediary and a critical inducer of oxidative stress, underlying RAGE-induced Alzheimer-like pathophysiological changes that drive the process of Alzheimer’s disease (AD). A critical role of RAGE in AD includes beta-amyloid (Aβ) production and accumulation, the formation of neurofibrillary tangles, failure of synaptic transmission, and neuronal degeneration. The steady-state level of Aβ depends on the balance between production and clearance. RAGE plays an important role in the Aβ clearance. RAGE acts as an important transporter via regulating influx of circulating Aβ into brain, whereas the efflux of brain-derived Aβ into the circulation via BBB is implemented by LRP1. RAGE could be an important contributor to Aβ generation via enhancing the activity of β- and/or γ-secretases and activating inflammatory response and oxidative stress. However, sRAGE–Aβ interactions could inhibit Aβ neurotoxicity and promote Aβ clearance from brain. Meanwhile, RAGE could be a promoting factor for the synaptic dysfunction and neuronal circuit dysfunction which are both the material structure of cognition, and the physiological and pathological basis of cognition. In addition, RAGE could be a trigger for the pathogenesis of Aβ and tau hyper-phosphorylation which both participate in the process of cognitive impairment. Preclinical and clinical studies have supported that RAGE inhibitors could be useful in the treatment of AD. Thus, an effective measure to inhibit RAGE may be a novel drug target in AD.