Meta-analysis of ecological and phylogenetic biomass maturity metrics.

Although a wide variety of biomass sources have been subjected to 16S rRNA gene sequencing, ecological and phylogenetic signatures of maturity have not been identified quantitatively. In this meta-analysis we reanalyzed data from the only published study with publicly available 16S and temperature data (Zhou et al., 2018), and then applied the Zhou results to 705 samples from 13 additional studies.

Draft genome sequences of five strains isolated from soil.

Here, we present genome sequences of five strains, isolated from agricultural soil. strains are commonly associated with the rhizosphere and are well-known for their ability to degrade xenobiotics. Yet, to date, knowledge about is limited.

Metagenome-assembled genomes from sugarcane mill mud.

The genomes of 11 bacteria and 3 archaea were assembled from metagenomic DNA extracted from sugarcane mill mud. These metagenome-assembled genomes ranged from 1.79 to 6.

Limited impact of weathered residues from the Deepwater Horizon oil spill on the gut-microbiome and foraging behavior of sheepshead minnows ().

The Deepwater Horizon disaster of April 2010 was the largest oil spill in U.S. history and exerted catastrophic effects on several ecologically important fish species in the Gulf of Mexico (GoM).

Soil Properties Correlate with Microbial Community Structure in Qatari Arid Soils.

This is the first detailed characterization of the microbiota and chemistry of different arid habitats from the State of Qatar. Analysis of bacterial 16S rRNA gene sequences showed that in aggregate, the dominant microbial phyla were (32.3%), (24.

Chemical and microbial characterization of sugarcane mill mud for soil applications.

Sugarcane mill mud/filter cake is an activated sludge-like byproduct from the clarifier of a raw sugar production factory, where cane juice is heated to ≈90°C for 1-2 hr, after the removal of bagasse. Mill mud is enriched with organic carbon, nitrogen, and nutrient minerals; no prior report utilized 16S rRNA gene sequencing to characterize the microbial composition. Mill mud could be applied to agricultural fields as biofertilizer to replace or supplement chemical fertilizers, and as bio-stimulant to replenish microorganisms and organic carbon depleted by erosion and post-harvest field burning.

Pumping supplies alter the microbiome of pumped human milk: An in-home, randomized, crossover trial.

Background: The human milk microbiome may contribute to the benefits of breastfeeding by providing bacteria to the infant gastrointestinal tract. Many women pump their milk, but the effect of pumping on the milk microbiome is unknown.

Objectives: Our objective was to determine the effects of pumping supplies on the pumped human milk microbiome.

Genome Sequences of Four Strains of Acinetobacter bereziniae Isolated from Human Milk Pumped with a Personal Breast Pump and Hand-Washed Milk Collection Supplies.

, formerly genomospecies 10, is an opportunistic pathogen possessing resistance to multiple antibiotics, and it has been reported to be responsible for hospital-associated infections in immunocompromised individuals. We report the draft genome sequences of four strains that were isolated from a single human milk sample collected with a personal breast pump and a hand-washed milk collection kit.

Magnetic biochar derived from biosolids via hydrothermal carbonization: Enzyme immobilization, immobilized-enzyme kinetics, environmental toxicity.

Magnetic and nonmagnetic biochar (MBC & BC) were produced from biosolids under hydrothermal conditions and characterized in order to understand surface chemistry impacts on enzyme immobilization and activity. Peak surface pore size of MBC was 180 nm and that of BC was 17 nm. Despite similar surface area (≈ 49 m/g) MBC immobilized more laccase (99 mg/g) than biochar (31 mg/g).

Curli production enhances clay-E. coli aggregation and sedimentation.

Curli are amyloid fibrils that polymerize extracellularly from curlin, a protein that is secreted by many enteric bacteria and is important for biofilm formation. Presented here is a systematic study of the effects of curli on bacteria-clay interactions. The aggregation trends of curli-producing and curli-deficient bacteria with clay minerals were followed using gradient-sedimentation experiments, Lumisizer measurements, bright-field and electron microscopy.

Fomesafen impacts bacterial communities and enzyme activities in the rhizosphere.

Fomesafen, a long-lived protoporphyrinogen-oxidase inhibitor, specially developed for post-emergence control of broad-leaf weeds, is used widely in soybean fields in northern China (Dayan and Duke, 2010). The impact of fomesafen on microbial communities in rhizosphere soils, however, is unknown. In this study we examined fomesafen degradation as well as its effects in the rhizosphere of soybean plants grown in a greenhouse.

Absence of genetic selection in a pathogenic Escherichia coli strain exposed to the manure-amended soil environment.

Escherichia coli that express curli are more common in subsurface soil drainage when manure is surface applied. However, it is unknown whether this arises from mutations in individual strains leading to curli expression or by selection for individuals already expressing higher levels of curli. To test this, we examined curli production in pathogenic E.

Detection of glyphosate residues in companion animal feeds.

The widespread adoption of genetically modified, glyphosate-tolerant corn and soybean varieties in US crop production has led to a dramatic increase in glyphosate usage. Though present at or below regulatory limits currently set for human foodstuffs, the concentration of glyphosate in companion animal feed is currently unknown. In the present study, 18 commercial companion animal feeds from eight manufacturers were analyzed for glyphosate residues using ELISA.

Biochar does not attenuate triclosan's impact on soil bacterial communities.

Triclosan, a broad-spectrum antimicrobial, has been widely used in pharmaceutical and personal care products. It undergoes limited degradation during wastewater treatment and is present in biosolids, most of which are land applied in the United States. This study assessed the impact of triclosan (0-100 mg kg) with and without biochar on soil bacterial communities.

A microbial community snapshot of windrows from a commercial composting facility.

The effect of depth on compost microbial communities is unclear but could be relevant to the management of windrows at commercial facilities. DNA extracted from 64 compost samples from seven windrows at a commercial facility were analyzed via deep 16S rRNA gene sequencing. The relative abundance of eight to nine genera was affected by depth during the transition from cooling to maturation phases between 4 and 6 months, whereas very few genera (0-1) showed a depth dependence in young, actively managed windrows or in mature windrows older than 10 months.

Microbial Characterization of Qatari Barchan Sand Dunes.

This study represents the first characterization of sand microbiota in migrating barchan sand dunes. Bacterial communities were studied through direct counts and cultivation, as well as 16S rRNA gene and metagenomic sequence analysis to gain an understanding of microbial abundance, diversity, and potential metabolic capabilities. Direct on-grain cell counts gave an average of 5.

Draft Whole-Genome Sequence of Urease-Producing Sporosarcina koreensis.

Urease-producing microbes are of significance due to their potential application in biocement production. Sporosarcina koreensis Q1 is a urease-producing bacterium belonging to the phylum Firmicutes. Here, we present the draft whole-genome sequence of S.

Triclosan removal in wetlands constructed with different aquatic plants.

Triclosan (TCS) is widely used in consumer products as an antimicrobial agent. Constructed wetlands have the potential for TCS removal, but knowledge about the relative importance of sediment, plants, and microbes is limited. TCS removal performance was investigated in well-operated constructed wetlands planted with three different types of aquatic plants: emergent Cattail (C-T), submerged Hornwort (H-T), and floating Lemnaminor (L-T).

The lysis cassette of DLP12 defective prophage is regulated by RpoE.

Expression of the lysis cassette (essD, ybcT, rzpD/rzoD) from the defective lambdoid prophage at the 12th minute of Escherichia coli's genome (DLP12) is required in some strains for proper curli expression and biofilm formation. Regulating production of the lytic enzymes encoded by these genes is critical for maintaining cell wall integrity. In lambdoid phages, late-gene regulation is mediated by the vegetative sigma factor RpoD and the lambda antiterminator Qλ.

Identification of a gene cluster associated with triclosan catabolism.

Aerobic degradation of bis-aryl ethers like the antimicrobial triclosan typically proceeds through oxygenase-dependent catabolic pathways. Although several studies have reported on bacteria capable of degrading triclosan aerobically, there are no reports describing the genes responsible for this process. In this study, a gene encoding the large subunit of a putative triclosan oxygenase, designated tcsA was identified in a triclosan-degrading fosmid clone from a DNA library of Sphingomonas sp.

The biotransformation of ibuprofen to trihydroxyibuprofen in activated sludge and by Variovorax Ibu-1.

A bacterium was isolated from activated sewage sludge that has the ability to use ibuprofen as its sole carbon and energy source. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the Variovorax genus within the β-proteobacteria. When grown on ibuprofen it accumulated a transient yellow intermediate that disappeared upon acidification, a trait consistent with meta ring-fission metabolites.