MicrobiologyOpen

The study reported here is the first specific study about the distribution and characteristics of carbapenem-resistant bacteria (CRB) in urban and agricultural environmental soils in the United States. We have found that the soils from Los Angeles–Southern California area are an underappreciated reservoir of bacteria resistant to carbapenems and other antibiotics, including carbapenemase-producing CRB. Our findings also show a much higher relative frequency of CRB on soils from locations adjacent to farms compared to soils from urban locations.

This study outlines an overview of the discovery and development of commonly used antibiotics; the timeline of resistance development; drivers and hotspots of environmental antimicrobial resistance; transmission routes of antimicrobial resistance in the agro-ecosystem; detection methods of environmental antimicrobial resistance determinants; factors involved in the evolution and transmission of antibiotic resistance in the environment and the agro-ecosystem; and possible ways to curtail the menace of antimicrobial resistance.

Porcine deltacoronavirus (PDCoV) is a novel enteropathogenic coronavirus that causes watery diarrhea in piglets. Gut microbiota profiles in the colon and feces of piglets inoculated with PDCoV were investigated using 16S rRNA sequencing. The results showed that PDCoV infection altered the composition of the microbiota in the colon and feces of piglets. The current study provides new insight into the pathology and physiology of PDCoV.

We investigated the gut bacterial communities of lesser white-fronted geese wintering at Shengjin Lake and Caizi Lake, China, the results showed that the differentiation significantly between the samples from both lakes. These findings suggest that diet may be an important driver of gut microbial community structure in the birds from each lake, and the obvious differentiation in their gut microbial structures may indicate that the bacteria are highly sensitive to food sources at both lakes.

PBANKA_1115200, which we named Gamete Egress Protein (GEP), is a gametocyte protein found only in malaria parasites. GEP partly localizes to osmophilic bodies. A mutant lacking this protein showed aberrant rupture of the parasitophorous vacuole and the red blood cell membranes. Axonemes of the male flagellar gametes gep(-) were not motile.

Known oil-degrading bacteria isolated from contaminated marine sediment impacted by the Deepwater Horizon oil spill were unable to degrade members of the six-ring dibenzopyrene PAH family. Dibenzo[a,h]pyrene appeared more toxic of the five different PAH isomers, as fewer unique microbial species were able to survive in its presence. Resistance to biodegradation may lead to environmental accumulation of these highly toxic hydrocarbons.

Functional screening of a water sample metagenomic library led to the discovery of a new type of class A beta lactamase. Analysis of the genomic context revealed the presence of genes coding for type II toxin-antitoxin systems, which were experimentally validated.

This article demonstrates the involvement of CodY as a direct regulator of cid and lrg operons, key players in the integration of complex environmental signals into regulatory networks that modulate virulence and cell homeostasis in Streptococcus mutans. It also improves our understanding of the functional links between stress response and cell death/lysis process.

After the expression of ompR was inhibited, the virulence of Aeromonas hydrophila B11 decreased, which suggested that ompR is involved in the bacterial virulence regulation. Comparative transcriptome analysis revealed that the expression of ompR can directly regulate the expression of some important virulence-related genes, especially the bacterial type II secretion system, as well as regulate the expression of multiple genes related to bacterial chemotaxis, motility, adhesion, and biofilm formation.

Algicidal process of fungus Bjerkandera adusta T1 was investigated by a time-course transcriptomic analysis. The results showed that most differentially expressed genes exhibited high endopeptidase activity, cellulose catabolic process, and transmembrane transporter activity. Comparison of gene expression between B. adusta T1 and Trametes versicolor F21a during the algicidal process suggested that endopeptidases together with enzymes of the polysaccharide lyases family 8 might be responsible for the strong algicidal activity of B. adusta T1 as well as T. versicolor F21a.

Certain parameters for the preparation of TG1 competent cells include optimum culture time of monoclonal bacteria, amplification growth concentration, and culture volume. The optimized transformation efficiency of TG1 (≥8 × 10¹⁰ cfu/μg DNA) was observed under suitable electric voltage (2.5 kV), electric intensity (15 kV/cm), and electric time (3.5 ms) of electricity for plasmid transformation. Optimized DNA amount (0.01–100 ng) dissolved in water led to the high efficiency of plasmid transformation but had low efficiency when dissolved in the T4 ligation buffer.

Microbial biomass shows different decomposition patterns among tropical caves, which could be interpreted by two theories: stoichiometric decomposition and microbial nitrogen mining. Our results indicate that nutrient flow and ecological dynamics, such as microbial parameters related to decomposition processes, cannot be generalized to all subterranean environments.

Tilling the soil down to a depth of 40 cm in combination with Dazomet soil fumigation and the application of biofertilizer promoted chrysanthemum growth, provided substantial control over Fusarium wilt disease, and altered the composition of the rhizosphere soil microbiome, through enhancing the availability of plant nutrients and promoting the presence of plant growth-promoting rhizomicrobes. The redundancy analysis implied that the composition of the microbiome was correlated to soil enzymatic activities and soil potassium availability in the rhizosphere soil.

eNAT® medium is a guanidine thiocyanate-based medium that stabilizes microbial DNA and allows safe specimen handling and shipping by inactivating live microorganisms. In comparing eNAT samples frozen immediately to eNAT samples stored at ambient temperature, we identified no detectable differences in Shannon diversity (p = .65), Chao1 richness (p = .87), overall microbiome composition (p > .99), or the relative abundances of highly abundant genera. eNAT may be a useful medium for fecal microbiome studies, particularly when cold chain storage is unavailable.

The significance of archaellin multiplicity remains unclear. We compared two Halorubrum lacusprofundi strains, one of them has two extraordinarily diverged archaellin genes, while another one has only one gene. In addition we engineered Haloferax volcanii strains synthesizing recombinant archaella of Hrr. lacusprofundi archaellins. The results suggest that functional supercoiled archaella can be composed from only one archaellin. However, interaction of two different archaellins provides additional stabilization to the archaellum structure and thus adaptation to a wider range of environments.

In this study, we characterized the shared microbiome of the phyllosphere and rhizosphere among three plants on Yongxing Island, South China Sea. We found that about 10%~27% of bacteria, including diazotrophs, and fungi overlapped between the phyllosphere and rhizosphere of these host plants. No significant difference in microbial community structure was found among the rhizosphere samples, and soil properties had a higher influence on soil community structure than on the host plant species.

Activation of the chlorite dismutase (cld) gene, located in the chlorate composite transposon of the chlorate reducer Ideonella dechloratans, was studied in a transcriptional reporter system in an fnr-deficient Escherichia coli strain. The results demonstrate that an fnr-type regulator of I. dechloratans, not present in the chlorate composite transposon, induces this gene under anaerobic conditions. Implications for horizontal gene transfer of the capability of dissimilatory chlorate reduction are discussed.

A potential influence of subspecies, diet, and age on the gut microbiota in tigers was investigated in this study to provide a better understanding of the response of the tiger gut microbiota to external changes. The results revealed that the impact of these factors on gut bacterial and fungal communities are versatile.

Several metabolic engineering strategies were successfully applied in this study towards direct fatty acid ethyl esters (FAEE) overproduction in the nonconventional oleaginous yeast Yarrowia lipolytica. Additionally, we examined the performance of a microbial consortium for its potential application in FAEE production. The results obtained in this work lay the foundation for future development of more efficient yeast cell factories for the sustainable production of FAEE biodiesel.

Nudix proteins catalyze the hydrolysis of pyrophosphate bonds in a variety of substrates and are ubiquitous in all domains of life. The genome of an important opportunistic human pathogen, Pseudomonas aeruginosa, encodes multiple Nudix proteins. Most of them are important for different cellular activities.