Publications by authors named "Amisha Poret-Peterson"

Successive plantings of Prunus species produce suboptimal growth and yield in many California soils due to a poorly understood soilborne disease complex, Prunus replant disease (PRD). We explored the hypothesis that PRD is mediated by microbial taxa in roots of Nemaguard peach, a rootstock for almond and other stone fruits. In a greenhouse bioassay, portions of 10 replant soils were treated with fumigation or pasteurization or left untreated as a control before being planted with peach seedlings.

View Article and Find Full Text PDF

Inefficient nitrogen (N) fertilization and irrigation have led to unhealthy nitrate levels in groundwater bodies of agricultural areas in California. Simultaneously, high commodity prices and drought have encouraged perennial crop growers to turnover less-productive orchards, providing opportunities to recycle tree biomass in situ and to use high-carbon (C) residues to conserve soil and water resources. Although climate change adaptation and mitigation benefits of high-C soil amendments have been shown, uncertainties remain regarding the benefits and trade-offs of this practice for N cycling and retention.

View Article and Find Full Text PDF

Successive orchard plantings of almond and other Prunus species exhibit reduced growth and yield in many California soils. This phenomenon, known as Prunus replant disease (PRD), can be prevented by preplant soil fumigation or anaerobic soil disinfestation, but its etiology is poorly understood and its incidence and severity are hard to predict. We report here on relationships among physicochemical variables, microbial community structure, and PRD induction in 25 diverse replant soils from California.

View Article and Find Full Text PDF

Background: The geographic and temporal distributions of bacterial and fungal populations are poorly understood within the same wine grape cultivar. In this work, we describe the microbial composition from 'Pinot noir' must with respect to vintage, growing region, climate, and must chemistry across the states of California and Oregon, USA.

Materials And Methods: We sampled 'Pinot noir' clone 667 clusters from 15 vineyards existing in a latitudinal gradient spanning nearly 1,200 km in California and Oregon for two vintages (2016 and 2017).

View Article and Find Full Text PDF

Plant-microbe interactions in the rhizosphere influence rates of organic matter mineralization and nutrient cycling that are critical to sustainable agricultural productivity. Agricultural intensification, particularly the introduction of synthetic fertilizer in the USA, altered the abundance and dominant forms of nitrogen (N), a critical plant nutrient, potentially imposing selection pressure on plant traits and plant-microbe interactions regulating N cycling and acquisition. We hypothesized that maize adaptation to synthetic N fertilization altered root functional traits and rhizosphere microbial nutrient cycling, reducing maize ability to acquire N from organic sources.

View Article and Find Full Text PDF

Several universal genomic traits affect trade-offs in the capacity, cost, and efficiency of the biochemical information processing that underpins metabolism and reproduction. We analyzed the role of these traits in mediating the responses of a planktonic microbial community to nutrient enrichment in an oligotrophic, phosphorus-deficient pond in Cuatro Ciénegas, Mexico. This is one of the first whole-ecosystem experiments to involve replicated metagenomic assessment.

View Article and Find Full Text PDF

Anaerobic soil disinfestation (ASD) is an organic amendment-based management tool for controlling soil-borne plant diseases and is increasingly used in a variety of crops. ASD results in a marked decrease in soil redox potential and other physicochemical changes, and a turnover in the composition of the soil microbiome. Mechanisms of ASD-mediated pathogen control are not fully understood, but appear to depend on the carbon source used to initiate the process and involve a combination of biological (i.

View Article and Find Full Text PDF

and , respectively, cause deep and shallow bark canker disease in walnut. exhibits quorum sensing-controlled virulence and rubrifacine pigment production. The complete genome sequences of these species will be useful for studying the role of genes regulated by quorum sensing, including pathways mediating pathogenesis.

View Article and Find Full Text PDF

biovar 1 strain 186 was isolated from a walnut tree expressing crown gall symptoms. The draft genome sequence of this strain harbored genes for crown gall formation and will be useful for understanding its virulence on Paradox, the predominant hybrid rootstock used for the cultivation of English walnut in California.

View Article and Find Full Text PDF

In January 2014, approximately 37 800 L of crude 4-methylcyclohexanemethanol (crude MCHM) spilled into the Elk River, West Virginia. To understand the long-term fate of 4-MCHM, we conducted experiments under environmentally relevant conditions to assess the potential for the 2 primary compounds in crude MCHM (1) to undergo biodegradation and (2) for sediments to serve as a long-term source of 4-MCHM. We developed a solid phase microextraction (SPME) method to quantify the cis- and trans-isomers of 4-MCHM.

View Article and Find Full Text PDF

Acetylene (CH) is a trace constituent of the present Earth's oxidizing atmosphere, reflecting a mixture of terrestrial and marine emissions from anthropogenic, biomass-burning, and unidentified biogenic sources. Fermentation of acetylene was serendipitously discovered during CH block assays of NO reductase, and was shown to grow on CH via acetylene hydratase (AH). AH is a W-containing, catabolic, low-redox-potential enzyme that, unlike nitrogenase (Nase), is specific for acetylene.

View Article and Find Full Text PDF

Nutrient availability and ratios can play an important role in shaping microbial communities of freshwater ecosystems. The Cuatro Ciénegas Basin (CCB) in Mexico is a desert oasis where, perhaps paradoxically, high microbial diversity coincides with extreme oligotrophy. To better understand the effects of nutrients on microbial communities in CCB, a mesocosm experiment was implemented in a stoichiometrically imbalanced pond, Lagunita, which has an average TN:TP ratio of 122 (atomic).

View Article and Find Full Text PDF

Acetylene fermentation is a rare metabolism that was previously reported as being unique to Here, we report the genome sequence of sp. strain SFB93, an acetylene-fermenting bacterium isolated from sediments collected in San Francisco Bay, CA.

View Article and Find Full Text PDF

Acetylene fermentation is a rare metabolism that was serendipitously discovered during CH-block assays of NO reductase. Here, we report the genome sequences of two type strains of acetylene-fermenting , the freshwater bacterium DSM 3246 and the estuarine bacterium DSM 3247.

View Article and Find Full Text PDF

Cuatro Ciénegas Basin (CCB) is a desert ecosystem that hosts a large diversity of water bodies. Many surface waters in this basin have imbalanced nitrogen (N) to phosphorus (P) stoichiometry (total N:P > 100 by atoms), where P is likely to be a limiting nutrient. To investigate the effects of nutrient stoichiometry on planktonic and sediment ecosystem components and processes, we conducted a replicated in situ mesocosm experiment in Lagunita, a shallow pond located in the southwest region of the basin.

View Article and Find Full Text PDF

Massilia sp. BSC265 was isolated from a biological soil crust near Moab, Utah. The strain appears to be capable of chemotaxis and exopolysaccharide synthesis for biofilm adhesion.

View Article and Find Full Text PDF

Bacillus sp. BSC154 was isolated from a biological soil crust near Moab, Utah. The strain appears to be capable of chemotaxis and biofilm production.

View Article and Find Full Text PDF

Microvirga sp. BSC39 was isolated from a biological soil crust near Moab, Utah. The strain appears to be capable of chemotaxis and exopolysaccharide synthesis for biofilm adhesion.

View Article and Find Full Text PDF

Genes encoding nitrogenase (nifH) were amplified from sediment and photosynthetic mat samples collected in the outflow channel of Mound Spring, an alkaline thermal feature in Yellowstone National Park. Results indicate the genetic capacity for nitrogen fixation over the entire range of temperatures sampled (57.2°C to 80.

View Article and Find Full Text PDF

Many methane-oxidizing bacteria (MOB) have been shown to aerobically oxidize ammonia and hydroxylamine (NH(2)OH) to produce nitrite and nitrous oxide (N(2)O). Genome sequences of alphaproteobacterial, gammaproteobacterial, and verrucomicrobial methanotrophs revealed the presence of haoAB, cytL, cytS, nirS or nirK, and norCB genes that may be responsible for N(2)O production, and additional haoAB genes were sequenced from two strains of Methylomicrobium album. The haoAB genes of M.

View Article and Find Full Text PDF

Natural clays have been used in ancient and modern medicine, but the mechanism(s) that make certain clays lethal against bacterial pathogens has not been identified. We have compared the depositional environments, mineralogies, and chemistries of clays that exhibit antibacterial effects on a broad spectrum of human pathogens including antibiotic resistant strains. Natural antibacterial clays contain nanoscale (<200 nm), illite-smectite and reduced iron phases.

View Article and Find Full Text PDF

Methylococcus capsulatus strain Bath, a methane-oxidizing bacterium, and ammonia-oxidizing bacteria (AOB) carry out the first step of nitrification, the oxidation of ammonia to nitrite, through the intermediate hydroxylamine. AOB use hydroxylamine oxidoreductase (HAO) to produce nitrite. M.

View Article and Find Full Text PDF

The alphaproteobacterium Nitrobacter hamburgensis X14 is a gram-negative facultative chemolithoautotroph that conserves energy from the oxidation of nitrite to nitrate. Sequencing and analysis of the Nitrobacter hamburgensis X14 genome revealed four replicons comprised of one chromosome (4.4 Mbp) and three plasmids (294, 188, and 121 kbp).

View Article and Find Full Text PDF

Molecular analysis of the amo gene cluster in Nitrosococcus oceani revealed that it consists of five genes, instead of the three known genes, amoCAB. The two additional genes, orf1 and orf5, were introduced as amoR and amoD, respectively. Putative functions of the AmoR and AmoD proteins are discussed.

View Article and Find Full Text PDF

The gammaproteobacterium Nitrosococcus oceani (ATCC 19707) is a gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; G+C content of 50.4%) and a plasmid (40,420 bp) that contain 3,052 and 41 candidate protein-encoding genes, respectively.

View Article and Find Full Text PDF