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Appl Environ Microbiol 2022 May 25:e0051922. Epub 2022 May 25.

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.

Bacteria coping with oxygen deficiency use alternative terminal electron acceptors for NADH regeneration, particularly fumarate. Fumarate is reduced by the domain of cytoplasmic fumarate reductase in many bacteria. The variability of the primary structure of this domain in homologous proteins suggests the existence of reducing activities with different specificities. Read More

Appl Environ Microbiol 2022 May 25:e0046622. Epub 2022 May 25.

Department of Pathology, College of Veterinary Medicine, University of Georgiagrid.213876.9, Athens, Georgia, USA.

Avian paramyxoviruses (APMVs) (subfamily ) have been isolated from over 200 species of wild and domestic birds around the world. The International Committee on Taxonomy of Viruses (ICTV) currently defines 22 different APMV species, with (whose viruses are designated APMV-1) being the most frequently studied due to its economic burden to the poultry industry. Less is known about other APMV species, including limited knowledge on the genetic diversity in wild birds, and there is a paucity of public whole-genome sequences for APMV-2 to -22. Read More

Appl Environ Microbiol 2022 May 25:e0027022. Epub 2022 May 25.

Department of Chemistry, University of Utah, Salt Lake City, Utah, USA.

Bacterial symbionts often provide critical functions for their hosts. For example, wood-boring bivalves called shipworms rely on cellulolytic endosymbionts for wood digestion. However, how the relationship between shipworms and their bacterial symbionts is formed and maintained remains unknown. Read More

Appl Environ Microbiol 2022 May 24;88(10):e0078622. Epub 2022 May 24.

Appl Environ Microbiol 2022 May 24:e0046822. Epub 2022 May 24.

Department of Earth System Science, Stanford University, Stanford, California, USA.

Marine cold seeps are natural sites of methane emission and harbor distinct microbial communities capable of oxidizing methane. The majority of known cold seeps are on tectonically active continental margins, but recent discoveries have revealed abundant seeps on passive margins as well, including on the U.S. Read More

Appl Environ Microbiol 2022 May 23:e0038822. Epub 2022 May 23.

Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía, Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain.

Ibuprofen is one of the most common drugs found as a contaminant in soils, sediments, and waters. Although several microorganisms able to metabolize ibuprofen have been described, the metabolic pathways and factors limiting biodegradation in nature remain poorly characterized. Among the bacteria able to grow on ibuprofen, three different strains belonging to and isolated from different geographical locations carry the same set of genes required for the upper part of the ibuprofen metabolic pathway. Read More

Appl Environ Microbiol 2022 May 23:e0064522. Epub 2022 May 23.

Johannes Gutenberg University Mainz, Institute of Molecular Physiology (imP), Biocenter II, Microbiology and Biotechnology, Mainz, Germany.

Phytopathogens represent a large agricultural challenge. The use of chemical pesticides is harmful to the environment, animals, and humans. Therefore, new sustainable and biological alternatives are urgently needed. Read More

Appl Environ Microbiol 2022 May 23:e0008522. Epub 2022 May 23.

Institute of Microbiology, Faculty of Biosciences, Friedrich Schiller University Jenagrid.9613.d, Jena, Germany.

The extreme metal tolerance of up to 130 mM NiSO in Streptomyces mirabilis P16B-1 was investigated. Genome sequencing revealed the presence of a large linear plasmid, pI. To identify plasmid-encoded determinants of metal resistance, a newly established transformation system was used to characterize the predicted plasmid-encoded loci , and . Read More

Appl Environ Microbiol 2022 May 23:e0017222. Epub 2022 May 23.

Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural Universitygrid.27871.3b, Nanjing, China.

Picolinic acid (PA) is a natural toxic pyridine derivative as well as an important intermediate used in the chemical industry. In a previous study, we identified a gene cluster, , that responsible for the catabolism of PA in Alcaligenes faecalis JQ135. However, the transcriptional regulation of the cluster remains known. Read More

Appl Environ Microbiol 2022 May 23:e0251821. Epub 2022 May 23.

Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA.

Blooms of many dinoflagellates, including several harmful algal bloom (HAB) species, are seeded and revived through the germination of benthic resting cysts. Temperature is a key determinant of cysts' germination rate, and temperature-germination rate relationships are therefore fundamental to understanding species' germling cell production, cyst bed persistence, and resilience to climate warming. This study measured germination by cysts of the HAB dinoflagellate Alexandrium catenella using a growing degree-day () approach that accounts for the time and intensity of warming above a critical temperature. Read More

Appl Environ Microbiol 2022 May 23:e0210921. Epub 2022 May 23.

Division of Geological and Planetary Sciences, California Institute of Technologygrid.20861.3d, Pasadena, California, USA.

Syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) consume large amounts of methane and serve as the foundational microorganisms in marine methane seeps. Despite their importance in the carbon cycle, research on the physiology of ANME-SRB consortia has been hampered by the slow growth and complex physicochemical environment the consortia inhabit. Here, we report successful sediment-free enrichment of ANME-SRB consortia from deep-sea methane seep sediments in the Santa Monica Basin, California. Read More

Appl Environ Microbiol 2022 May 19:e0045222. Epub 2022 May 19.

State Key Laboratory of Veterinary Biotechnology, National High-Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institutegrid.38587.31, Chinese Academy of Agricultural Sciences, Harbin, China.

African swine fever (ASF) is a highly contagious disease of domestic pigs and wild boar with high morbidity and mortality caused by African swine fever virus (ASFV). Due to the lack of commercial vaccines and treatments for ASF, cleaning and disinfection remain one of the most effective biosecurity measures to control ASF. Our previous studies have shown that ASFV can be inactivated by 0. Read More

Appl Environ Microbiol 2022 May 19:e0016422. Epub 2022 May 19.

Institute of Molecular Microbiology and Biotechnology, University of Münstergrid.5949.1, Münster, Germany.

Despite being unicellular organisms, bacteria undergo complex regulation mechanisms which coordinate different physiological traits. Among others, DegU, DegS, and Spo0A are the pleiotropic proteins which govern various cellular responses and behaviors. However, the functions and regulatory networks between these three proteins are rarely described in the highly interesting bacterium Paenibacillus polymyxa. Read More

Appl Environ Microbiol 2022 May 19:e0048622. Epub 2022 May 19.

Department of Food Science, Cornell Universitygrid.5386.8, Ithaca, New York, USA.

Selection for Listeria monocytogenes strains that are tolerant to quaternary ammonium compounds (such as benzalkonium chloride [BC]) is a concern across the food industry, including in fresh produce processing environments. This study evaluated the ability of 67 strains of produce-associated L. monocytogenes and other spp. Read More

Appl Environ Microbiol 2022 May 19:e0043922. Epub 2022 May 19.

Division of Biology and Biological Engineering, Caltech, Pasadena, California, USA.

Gaining insight into the behavior of bacteria at the single-cell level is important given that heterogeneous microenvironments strongly influence microbial physiology. The hybridization chain reaction (HCR) is a technique that provides molecular signal amplification, enabling simultaneous mapping of multiple target RNAs at small spatial scales. To refine this method for biofilm applications, we designed and validated new probes to visualize the expression of key catabolic genes in Pseudomonas aeruginosa aggregates. Read More

Appl Environ Microbiol 2022 May 18:e0033022. Epub 2022 May 18.

Bacterial Stress Response Group, Microbiology, Ryan Institute, School of Biological and Chemical Sciences, National University of Ireland, Galwaygrid.6142.1, Ireland.

The alternative sigma factor B (σ) contributes to the stress tolerance of the foodborne pathogen Listeria monocytogenes by upregulating the general stress response. We previously showed that σ loss-of-function mutations arise frequently in strains of L. monocytogenes and suggested that mild stresses might favor the selection of such mutations. Read More

Appl Environ Microbiol 2022 May 17:e0054322. Epub 2022 May 17.

Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural Universitygrid.27871.3b, Nanjing, Jiangsu, People's Republic of China.

Phenazines are an important class of secondary metabolites and are primarily named for their heterocyclic phenazine cores, including phenazine-1-carboxylic acid (PCA) and its derivatives, such as phenazine-1-carboxamide (PCN) and pyocyanin (PYO). Although several genes involved in the degradation of PCA and PYO have been reported so far, the genetic foundations of PCN degradation remain unknown. In this study, a PCN-degrading bacterial strain, Sphingomonas histidinilytica DS-9, was isolated. Read More

Appl Environ Microbiol 2022 May 16:e0022022. Epub 2022 May 16.

Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, APHP, Créteil, France.

Genus bacteria include important agricultural pathogens. Pectobacterium versatile isolates contain a chromosome-borne beta-lactamase, PEC-1. This enzyme is the closest relative of TEM-1, a plasmid-borne beta-lactamase widespread in the . Read More

Appl Environ Microbiol 2022 May 16:e0003822. Epub 2022 May 16.

Single Cell Research Center, School of Agriculture and Life Sciences, Shanghai Jiao Tong Universitygrid.16821.3c, Shanghai, China.

Reactive oxygen species (ROS) can cause destructive damage to biological macromolecules and protein dysfunction in bacteria. Methionine sulfoxide reductase (Msr) with redox-active Cys and/or seleno-cysteine (Sec) residues can restore physiological functions of the proteome, which is essential for oxidative stress tolerance of the extremophile Deinococcus radiodurans. However, the underlying mechanism regulating MsrA enzyme activity in D. Read More

Appl Environ Microbiol 2022 May 16:e0240921. Epub 2022 May 16.

Shanghai Veterinary Research Institutegrid.464410.3, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, China.

Riemerella anatipestifer is a major pathogenic agent of duck septicemic and exudative diseases. Recent studies have shown that the R. anatipestifer type IX secretion system (T9SS) is a crucial factor in bacterial virulence. Read More

Appl Environ Microbiol 2022 May 12:e0050622. Epub 2022 May 12.

State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciencesgrid.410727.7, Beijing, China.

The good thermostability of enzymes is an important basis for their wide application in industry. In this study, the phytase APPA from Yersinia intermedia was designed by evolution-guided design. Through the collection of homologous sequences in the NCBI database, we obtained a sequence set composed of 5,569 sequences, counted the number and locations of motif N-X-T/S, and selected the sites with high frequency in evolution as candidate sites for experiments. Read More

Appl Environ Microbiol 2022 May 10:e0038322. Epub 2022 May 10.

Experimental Zooprophylactic Institute in Lombardy and Emilia Romagna, Brescia, Italy.

We report here on an outbreak of mastitis caused by Streptococcus agalactiae, or group B Streptococcus, in a northern Italy (Lombardy Region) free stall dairy farm. This outbreak was unusual because it occurred in a closed dairy herd and proved to be extremely difficult to resolve even after the application of the classical control procedures, which are specifically focused on the contagious nature of S. agalactiae. Read More

Appl Environ Microbiol 2022 May 10:e0022622. Epub 2022 May 10.

Department of Horticulture and Landscape Architecture, Colorado State Universitygrid.47894.36, Fort Collins, Colorado, USA.

Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix, yet the mechanisms by which exudation alters microbial metabolism in soils have been challenging to unravel. Here, utilizing distinct sorghum genotypes, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolism. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments: a high-organic-acid treatment (HOT) and a high-sugar treatment (HST). Read More

Appl Environ Microbiol 2022 May 10;88(9):e0072922. Epub 2022 May 10.

Appl Environ Microbiol 2022 May 9;88(10):e0039322. Epub 2022 May 9.

Bacterial Epidemiology and Antimicrobial Resistance Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia, USA.

As the cases of Salmonella enterica infections associated with contaminated water are increasing, this study was conducted to address the role of surface water as a reservoir of S. enterica serotypes. We sampled rivers and streams ( = 688) over a 3-year period (2015 to 2017) in a mixed-use watershed in Georgia, USA, and 70. Read More

Appl Environ Microbiol 2022 May 9;88(10):e0008422. Epub 2022 May 9.

Laboratory of Entomology, Plant Sciences Group, Wageningen University & Research, Wageningen, the Netherlands.

Saprophagous fly larvae interact with a rich community of bacteria in decomposing organic matter. Larvae of some species, such as the black soldier fly, can process a wide range of organic residual streams into edible insect biomass and thus produce protein as a sustainable component of livestock feed. The microbiological safety of the insects and substrates remains a point of concern. Read More

Appl Environ Microbiol 2022 May 4;88(10):e0011622. Epub 2022 May 4.

Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan Universitygrid.13291.38, Chengdu, China.

Candida albicans can coaggregate with Streptococcus gordonii and cocolonize in the oral cavity. Saliva provides a vital microenvironment for close interactions of oral microorganisms. However, the level of fermentable carbohydrates in saliva is not sufficient to support the growth of multiple species. Read More

Appl Environ Microbiol 2022 May 2;88(10):e0247821. Epub 2022 May 2.

Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium.

The infection of a bacterium by a tailed phage starts from the adsorption process, which consists of a specific and strong interaction between viral proteins called receptor binding proteins (RBPs) and receptors located on the bacterial surface. In addition to RBPs, other tail proteins, such as evolved distal tail (evoDit) proteins and tail lysins, harboring carbohydrate binding modules (CBMs) have been shown to facilitate the phage adsorption by interacting with host polysaccharides. In this work, the proteins involved in the adsorption of Deep-Purple, a siphovirus targeting bacteria of the Bacillus cereus group, were studied. Read More

Appl Environ Microbiol 2022 May 2;88(10):e0037122. Epub 2022 May 2.

College of Food Science and Technology, Nanjing Agricultural Universitygrid.27871.3b, Nanjing, Jiangsu, People's Republic of China.

The outer membrane of Gram-negative bacteria is one of the major factors contributing to the development of antibiotic resistance, resulting in a lack of effectiveness of several hydrophobic antibiotics. Plantaricin A (PlnA) intensifies the potency of antibiotics by increasing the permeability of the bacterial outer membrane. Moreover, it has been proven to bind to the lipopolysaccharide of Escherichia coli via electrostatic and hydrophobic interactions and to interfere with the integrity of the bacterial outer membrane. Read More

Appl Environ Microbiol 2022 May 2;88(10):e0013222. Epub 2022 May 2.

State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciencesgrid.162107.3, Wuhan, China.

Nitrate-reducing Fe(II)-oxidizing (NRFeOx) microorganisms contribute to nitrogen, carbon, and iron cycling in freshwater and marine ecosystems. However, NRFeOx microorganisms have not been investigated in hypersaline lakes, and their identity, as well as their activity in response to salinity, is unknown. In this study, we combined cultivation-based most probable number (MPN) counts with Illumina MiSeq sequencing to analyze the abundance and community compositions of NRFeOx microorganisms enriched from five lake sediments with different salinities (ranging from 0. Read More