Spatiotemporal Characteristics Determining the Multifaceted Nature of Reactive Oxygen, Nitrogen, and Sulfur Species in Relation to Proton Homeostasis.

Reactive oxygen species (ROS), reactive nitrogen species (RNS), and reactive sulfur species (RSS) act as signaling molecules, regulating gene expression, enzyme activity, and physiological responses. However, excessive amounts of these molecular species can lead to deleterious effects, causing cellular damage and death. This dual nature of ROS, RNS, and RSS presents an intriguing conundrum that calls for a new paradigm.

Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes.

Exploring the natural diversity of functional genes/proteins from environmental DNA in high throughput remains challenging. In this study, we developed a sequence-based functional metagenomics procedure for mining the diversity of copper (Cu) resistance gene copA in global microbiomes, by combining the metagenomic assembly technology, local BLAST, evolutionary trace analysis (ETA), chemical synthesis, and conventional functional genomics. In total, 87 metagenomes were collected from a public database and subjected to copA detection, resulting in 93,899 hits.

Genomic and metabolomic profiling of endolithic Rhodococcus fascians strain S11 isolated from an arid serpentine environment.

Genomic and metabolomic studies of endolithic bacteria are essential for understanding their adaptations to extreme conditions of the rock environment and their contributions to mineralization and weathering processes. The endoliths of arid serpentine rocks are exposed to different environmental stresses, including desiccation and re-hydration, temperature fluctuations, oligotrophy, and high concentrations of heavy metals. Bacteria of the genus Rhodococcus commonly inhabit endolithic environments.

Genomic and phenotypic analysis of siderophore-producing Rhodococcus qingshengii strain S10 isolated from an arid weathered serpentine rock environment.

The success of members of the genus Rhodococcus in colonizing arid rocky environments is owed in part to desiccation tolerance and an ability to extract iron through the secretion and uptake of siderophores. Here, we report a comprehensive genomic and taxonomic analysis of Rhodococcus qingshengii strain S10 isolated from eathered serpentine rock at the arid Khalilovsky massif, Russia. Sequence comparisons of whole genomes and of selected marker genes clearly showed strain S10 to belong to the R.

Deconstruction of plant biomass by a Cellulomonas strain isolated from an ultra-basic (lignin-stripping) spring.

Plant material falling into the ultra-basic (pH 11.5-11.9) springs within The Cedars, an actively serpentinizing site in Sonoma County, California, is subject to conditions that mimic the industrial pretreatment of lignocellulosic biomass for biofuel production.

Microbial diversity and mineral composition of weathered serpentine rock of the Khalilovsky massif.

Endolithic microbial communities survive nutrient and energy deficient conditions while contributing to the weathering of their mineral substrate. This study examined the mineral composition and microbial communities of fully serpentinized weathered rock from 0.1 to 6.

d-Cysteine-Induced Rapid Root Abscission in the Water Fern : Implications for the Linkage between d-Amino Acid and Reactive Sulfur Species (RSS) in Plant Environmental Responses.

Reactive Oxygen Species (ROS) and Reactive Nitrogen Species (RNS) have been proposed as universal signaling molecules in plant stress responses. There are a growing number of studies suggesting that hydrogen sulfide (HS) or Reactive Sulfur Species (RSS) are also involved in plant abiotic as well as biotic stress responses. However, it is still a matter of debate as to how plants utilize those RSS in their signaling cascades.

Comparative Metagenomic Analysis of Electrogenic Microbial Communities in Differentially Inoculated Swine Wastewater-Fed Microbial Fuel Cells.

Bioelectrochemical systems such as microbial fuel cells (MFCs) are promising new technologies for efficient removal of organic compounds from industrial wastewaters, including that generated from swine farming. We inoculated two pairs of laboratory-scale MFCs with sludge granules from a beer wastewater-treating anaerobic digester (IGBS) or from sludge taken from the bottom of a tank receiving swine wastewater (SS). The SS-inoculated MFC outperformed the IGBS-inoculated MFC with regard to COD and VFA removal and electricity production.

An Overview of Methods in Plant Nitric Oxide (NO) Research: Why Do We Always Need to Use Multiple Methods?

The free radical nitric oxide (NO) is a universal signaling molecule among living organisms. To investigate versatile functions of NO in plants it is essential to analyze biologically produced NO with an appropriate method. Owing to the uniqueness of NO, plant researchers may encounter difficulties in applying methods that have been developed for mammalian study.

Biological consilience of hydrogen sulfide and nitric oxide in plants: Gases of primordial earth linking plant, microbial and animal physiologies.

Hydrogen sulfide (H2S) is produced in the mammalian body through the enzymatic activities of cystathionine β-synthase (CBS), cystathionine γ-lyase (CSE) and 3-mercaptopyruvate sulfurtransferase (3MST). A growing number of studies have revealed that biogenic H2S produced in tissues is involved in a variety of physiological responses in mammals including vasorelaxation and neurotransmission. It is now evident that mammals utilize H2S to regulate multiple signaling systems, echoing the research history of the gaseous signaling molecules nitric oxide (NO) and carbon monoxide (CO) that had previously only been recognized for their cytotoxicity.

Host Phenology and Leaf Effects on Susceptibility of California Bay Laurel to Phytophthora ramorum.

Spread of the plant pathogen Phytophthora ramorum, causal agent of the forest disease sudden oak death, is driven by a few competent hosts that support spore production from foliar lesions. The relationship between traits of a principal foliar host, California bay laurel (Umbellularia californica), and susceptibility to P. ramorum infection were investigated with multiple P.

Bimodal effect of hydrogen peroxide and oxidative events in nitrite-induced rapid root abscission by the water fern Azolla pinnata.

In the genus Azolla rapid abscission of roots from floating fronds occurs within minutes in response to a variety of stresses, including exposure to nitrite. We found that hydrogen peroxide, though itself not an inducer of root abscission, modulates nitrite-induced root abscission by Azolla pinnata in a dose-dependent manner, with 2 mM H2O2 significantly diminishing the responsiveness to 2 mM NaNO2, and 10 mM H2O2 slightly enhancing it. Hypoxia, which has been found in other plants to result in autogenic production of H2O2, dramatically stimulated root abscission of A.

Genome Sequence of the Alkaline-Tolerant Cellulomonas sp. Strain FA1.

We present the genome of the cellulose-degrading Cellulomonas sp. strain FA1 isolated from an actively serpentinizing highly alkaline spring. Knowledge of this genome will enable studies into the molecular basis of plant material degradation in alkaline environments and inform the development of lignocellulose bioprocessing procedures for biofuel production.

Genome Sequence of the Electrogenic Petroleum-Degrading Thalassospira sp. Strain HJ.

We present the draft genome of the petroleum-degrading Thalassospira sp. strain HJ, isolated from tidal marine sediment. Knowledge of this genomic information will inform studies on electrogenesis and means to degrade environmental organic contaminants, including compounds found in petroleum.

Controlled free radical attack in the apoplast: a hypothesis for roles of O, N and S species in regulatory and polysaccharide cleavage events during rapid abscission by Azolla.

Shedding of organs by abscission is a key terminal step in plant development and stress responses. Cell wall (CW) loosening at the abscission zone can occur through a combination chain breakage of apoplastic polysaccharides and tension release of cellulose microfibrils. Two distinctly regulated abscission cleavage events are amenable to study in small water ferns of the genus Azolla; one is a rapid abscission induced by environmental stimuli such as heat or chemicals, and the other is an ethylene-induced process occurring more slowly through the action of hydrolytic enzymes.

Wastewater polishing by a channelized macrophyte-dominated wetland and anaerobic digestion of the harvested phytomass.

Constructed wetlands (CW) offer a mechanism to meet increasingly stringent regulatory standards for wastewater treatment while minimizing energy inputs. Additionally, harvested wetland phytomass subjected to anaerobic digestion can serve as a source of biogas methane. To investigate CW wastewater polishing activities and potential energy yield we constructed a pair of secondary wastewater-fed channelized CW modules designed to retain easily harvestable floating aquatic vegetation and maximize exposure of water to roots and sediment.

Polyamine-Induced Rapid Root Abscission in Azolla pinnata.

Floating ferns of the genus Azolla detach their roots under stress conditions, a unique adaptive response termed rapid root abscission. We found that Azolla pinnata plants exhibited dose-dependent rapid root abscission in response to the polyamines spermidine and spermine after a substantial time lag (>20 min). The duration of the time lag decreased in response to high pH and high temperature whereas high light intensity increased the time lag and markedly lowered the rate of abscission.

Image-Based Remodeling.

Imagining what a proposed home remodel might look like without actually performing it is challenging. We present an image-based remodeling methodology that allows real-time photorealistic visualization during both the modeling and remodeling process of a home interior. Large-scale edits, like removing a wall or enlarging a window, are performed easily and in real time, with realistic results.

Video Snapshots: Creating High-Quality Images from Video Clips.

We describe a unified framework for generating a single high-quality still image ("snapshot") from a short video clip. Our system allows the user to specify the desired operations for creating the output image, such as super resolution, noise and blur reduction, and selection of best focus. It also provides a visual summary of activity in the video by incorporating saliency-based objectives in the snapshot formation process.

Protozoan-induced regulation of cyclic lipopeptide biosynthesis is an effective predation defense mechanism for Pseudomonas fluorescens.

Environmental bacteria are exposed to a myriad of biotic interactions that influence their function and survival. The grazing activity of protozoan predators significantly impacts the dynamics, diversification, and evolution of bacterial communities in soil ecosystems. To evade protozoan predation, bacteria employ various defense strategies.

Mechanism of action and efficacy of seed meal-induced pathogen suppression differ in a brassicaceae species and time-dependent manner.

ABSTRACT The effect of seed meals derived from Brassica juncea, B. napus, or Sinapis alba on suppression of soilborne pathogens inciting replant disease of apple was evaluated in greenhouse trials. Regardless of plant source, seed meal amendment significantly improved apple growth in all orchard soils; however, relative differences in pathogen suppression were observed.

NO signal at the crossroads: polyamine-induced nitric oxide synthesis in plants?

Polyamines, such as spermine, spermidine and putrescine, are ubiquitous polycationic compounds that are produced by almost all living organisms, including plants, animals, fungi and bacteria. Polyamines are multifunctional and interact with polyanionic biomolecules such as DNA or protein. However, despite their potential significance, the polyamine-dependent signal transduction system has not been revealed yet.

Molecular and physiological comparison of Azospirillum spp. isolated from Rhizoctonia solani mycelia, wheat rhizosphere, and human skin wounds.

Four phenotypically similar bacterial strains isolated from fungal, plant, and human sources were identified as Azospirillum species. Strains RC1 and LOD4 were isolated from the mycelium of the apple root pathogen Rhizoctonia solani AG 5 and from the rhizosphere of wheat grown in apple orchard soil, respectively. Strains C610 and F4626 isolated from human wounds were previously misclassified as Roseomonas genomospecies 3 and 6.