Environmental Microbiology

The Research Publications track research that is published across national and international peer-reviewed journals. The most recent articles are available ahead of print and searchable by Journal Title, Subject, USDA Grant Funding Agencies or FDA Grant Funding Agencies. The research publications are tracked across five subject areas: Bacterial Pathogens, Chemical Contaminants, Natural Toxins, Parasites, and Viruses.

Mon, 08/10/2020 - 22:09
Research on the initial phage‐host interaction has been conducted on a limited repertoire of phages and their cognate receptors, such as phage λ and the Escherichia coli LamB (EcLamB) protein. Apart from phage λ, little is known about other phages which target EcLamB. Here, we developed a simple method for isolating novel environmental phages in a predictable way, i.e. isolating phages which...
Wed, 07/15/2020 - 22:10
Polycyclic aromatic hydrocarbons (PAHs) are among the most persistent xenobiotic compounds, with high toxicity effects. Mycoremediation with halophilic Aspergillus sydowii was used for their removal from a hypersaline medium (1 M NaCl). A. sydowii used PAHs as sole carbon sources, resulting in the removal of up to 90% for both PAHs (benzo [a] pyrene (BaP) and phenanthrene (Phe)) after 10 days....
Wed, 07/01/2020 - 22:09
The development of sustainable agriculture and the increasing antibiotic resistance of human pathogens call for novel antimicrobial compounds. Here, we describe the extraction and characterization of a class of cationic circular lipopeptides, for which we propose the name relacidines, from the soil bacterium Brevibacillus laterosporus MG64. Relacidines are composed of a fatty acid side chain (4‐...
Sat, 06/27/2020 - 22:08
The type VI nanomachine is critical for Vibrio cholerae to establish infections and to thrive in niches co‐occupied by competing bacteria. The genes for the type VI structural proteins are encoded in one large and two small auxiliary gene clusters. VCA0117 (VasH) – a σ54‐transcriptional activator – is strictly required for functionality of the type VI secretion system since it controls production...
Mon, 06/22/2020 - 22:09
Vibrio vulnificus is a zoonotic pathogen able to cause diseases in humans and fish that occasionally result in sepsis and death. Most reviews about this pathogen (including those related to its ecology) are clearly biased towards its role as a human pathogen, emphasizing its relationship with oysters as its main reservoir, the role of the known virulence factors as well as the clinic and the...
Fri, 06/19/2020 - 22:08
Wetlands are common sites of active Hg methylation by anaerobic microbes; however, the amount of methylmercury produced varies greatly, as Hg methylation is dependent upon both the availability of Hg and the composition and activity of the microbial community involved. In this study, we identified the major microbial guilds responsible for Hg methylation along a trophic gradient composed of two...
Tue, 06/09/2020 - 22:09
With the rapid increase of aquaculture contributing to sustainable food security, comes the need to better understand seafood associated diseases. One of the major aquatic bacterial genera responsible for human infections from seafood is Vibrio, especially from oysters. Currently, in vivo study of bacterial interactions within oysters is limited by the inability to promote high‐level uptake of...
Tue, 06/09/2020 - 22:09
In warm regions, agricultural fields are occupied by complex Aspergillus flavus communities composed of isolates in many vegetative compatibility groups (VCGs) with varying abilities to produce highly toxic, carcinogenic aflatoxins. Aflatoxin contamination is reduced with biocontrol products that enable atoxigenic isolates from atoxigenic VCGs to dominate the population. Shifts in VCG frequencies...
Wed, 06/03/2020 - 03:27
Listeria monocytogenes is a foodborne pathogen causing systemic infection with high mortality. To allow efficient tracing of outbreaks a clear definition of the genomic signature of a cluster of related isolates is required, but lineage specific characteristics call for a more detailed understanding of evolution. In our work we used core genome MLST (cgMLST) to identify new outbreaks combined to...
Fri, 05/29/2020 - 03:26
Lake and adjoining river ecosystems are ecologically and economically valuable and are heavily threatened by anthropogenic activities. Determining the inherent capacity of ecosystems for polycyclic aromatic hydrocarbon (PAH) biodegradation can help quantify environmental impacts on the functioning of ecosystems, especially on that of the microbial community. Here, PAH biodegradation potential was...
Sun, 05/24/2020 - 03:24
Antibiotic‐resistant Vibrio alginolyticus poses a big challenge to human health and food safety. It's urgently needed to understand the mechanisms underlying antibiotic resistance to develop effective approaches for the control. Here we explored the metabolic difference between gentamicin‐resistant V. alginolyticus (VA‐RGEN) and gentamicin‐sensitive V. alginolyticus (VA‐S), and found that the...
Thu, 05/21/2020 - 03:27
To identify the free‐living amoeba (FLA) and amoeba resistant bacteria (ARB) accumulated in zebra mussels and in the water in which they are found, mussels were collected at two locations in the Ebro river basin (North East Spain). Free‐living amoebas and bacteria were isolated from mussel extracts and from natural water. PCR techniques were used to identify the FLAs and endosymbiont bacteria (...
Tue, 05/19/2020 - 03:25
Soil microbial communities are often not resistant to the impact caused by microbial invasions, both in terms of structure and functionality, but it remains unclear whether these changes persist over time. Here we used 3 strains of Escherichia coli O157:H7 (E. coli O157:H7), a species used for modelling bacterial invasions, to evaluate the resilience of the bacterial communities from four Chinese...
Tue, 05/19/2020 - 03:25
Enterotoxigenic Escherichia coli (ETEC) cause acute secretory diarrhea in pigs, posing a great economic loss to swine industry. This study analyzed the prevalence and genetic characteristics of prophages from 132 ETEC isolates from symptomatic pigs to determine their potential for spreading antibiotic resistance. A total of 1105 potential prophages were identified, and the distribution of the...
Tue, 05/05/2020 - 03:25
In livestock production, antibiotics are used to promote animal growth, control infections and thereby increase profitability. This practice has led to the emergence of multi‐resistant bacteria such as Salmonella, of which some serovars are disseminated in the environment. The objective of this study is to evaluate microcin J25 as an inhibitor of Salmonella enterica serovars of various origins...
Tue, 05/05/2020 - 03:25
Environmental monitoring of bacteria using phage‐based biosensors has been widely developed for many different species. However, there are only a few available methods to detect specific bacteriophages in raw environmental samples. In this work, we developed a simple and efficient assay to rapidly monitor the phage content of a given sample. The assay is based on the bistable expression of the...
Tue, 04/28/2020 - 03:24
Trebouxia sp. TR9 and Coccomyxa simplex are desiccation‐tolerant microalgae with flexible cell walls, which undergo species‐specific remodelling during dehydration‐rehydration (D/R) due to their distinct ultrastructure and biochemical composition. Here, we tested the hypothesis that extracellular polysaccharides excreted by each microalga could be quantitatively and/or qualitatively modified by D...
Tue, 04/28/2020 - 03:24
The bacterium Vibrio cholerae is a natural inhabitant of aquatic ecosystems across the planet. V. cholerae serogroups O1 and O139 are responsible for cholera outbreaks in developing countries accounting for 3–5 million infections worldwide and 28.800–130.000 deaths per year according to World Health Organization. In contrast, V. cholerae serogroups other than O1 and O139, also designated as V....
Thu, 04/23/2020 - 03:22
Vibrio cholerae can enter a viable but non‐culturable (VBNC) state when it encounters unfavorable environments; VBNC cells serve as important reservoirs and still pose threats to public health. The genetic regulation of V. cholerae entering its VBNC state is not well understood. Here, we show a confrontation strategy adapted by V. cholerae O1 in which it utilizes a quorum sensing (QS) system to...
Thu, 04/16/2020 - 03:18
In Saccharomyces cerevisiae, vacuolar H+‐ATPase (V‐ATPase) involved in the regulation of intracellular pH homeostasis has been shown to be important for tolerances to cadmium, cobalt, and nickel. However, molecular mechanism underlying the protective role of V‐ATPase against these metals remains unclear. In this study, we show that cadmium, cobalt, and nickel disturbed intracellular pH balance by...
Wed, 04/15/2020 - 03:17
Emergence and expansion of frequent multidrug‐resistant (MDR) major Salmonella clones/serotypes has been a significant threat in the last years. Metal compounds, such as copper, commonly used in animal‐production settings, have been pointed out as possible contributors for the selection of such strains/clones. However, the scarcity of studies limits our understanding of the impact of other metal...
Tue, 04/14/2020 - 03:18
Genetic variation in a pathogen, including the causative agent of salmonellosis, Salmonella enterica, can occur as a result of eco‐evolutionary forces triggered by dissimilarities of ecological niches. Here, we applied comparative genomics to study 90 antimicrobial resistant (AMR) S. enterica isolates from bovine and human hosts in New York state and Washington state to understand host‐ and...
Tue, 04/07/2020 - 03:30
Reactive oxygen species (ROS) induce the synthesis of a myriad of secondary metabolites, including aflatoxins. It raises significant concern as it is a potent environmental contaminant. In Aspergillus flavus (A. flavus), antioxidant enzymes link ROS stress response with coordinated gene regulation of aflatoxin biosynthesis. In this study, we characterized the function of a core component of the...
Tue, 04/07/2020 - 03:30
The second messenger cyclic di‐AMP (c‐di‐AMP) is essential for growth of many bacteria because it controls osmolyte homeostasis. c‐di‐AMP can regulate the synthesis of potassium uptake systems in some bacteria and also directly inhibits and activates potassium import and export systems, respectively. Therefore, c‐di‐AMP production and degradation have to be tightly regulated depending on the...
Thu, 04/02/2020 - 03:16
The genome of Vibrio cholerae, the etiological agent of cholera, is an exception to the single chromosome rule found in the vast majority of bacteria and has its genome partitioned between two unequally sized chromosomes. This unusual two‐chromosome arrangement in V. cholerae has sparked considerable research interest since its discovery. It was demonstrated that the two chromosomes could be...
Tue, 03/31/2020 - 03:18
Bacteria constantly experience changes to their external milieu and need to adapt accordingly to ensure their survival. Certain bacteria adapt by means of cellular differentiation, resulting in the development of a specific cell type that is specialized for life in a distinct environment. Furthermore, to understand how bacteria adapt, it is essential to appreciate the significant changes that...
Mon, 03/23/2020 - 03:19
Many Listeria species including L. monocytogenes contain the pathway for the biosynthesis of protocatechuate from shikimate and quinate. The qui1 and qui2 operons within these Listeria spp. encode enzymes for this pathway. The diversion of shikimate pathway intermediates in some Listeria species to produce protocatechuate suggests an important biological role for this compound to these organisms...
Sat, 03/14/2020 - 03:17
Bacteria in nature often encounter non‐antibiotic antibacterials (NAAs), such as disinfectants and heavy metals, and they can evolve resistance via mechanisms that are also involved in antibiotic resistance. Understanding whether susceptibility to different types of antibacterials is non‐randomly associated across natural and clinical bacteria is therefore important for predicting the spread of...
Thu, 03/05/2020 - 03:19
The Type VI Secretion System (T6SS) is a proteinaceous weapon used by many Gram‐negative bacteria to deliver toxins into adjacent target cells. Vibrio cholerae, the bacterium responsible for the fatal water‐borne cholera disease, uses the T6SS to evade phagocytic eukaryotes, cause intestinal inflammation, and compete against other bacteria with toxins that disrupt lipid membranes, cell walls and...
Wed, 03/04/2020 - 03:29
Fresh fruits and vegetables have numerous benefits to human health. Unfortunately, their consumption is increasingly associated with food‐borne diseases, Salmonella enterica being their most frequent cause in Europe. Agricultural soils were postulated as reservoir of human pathogens, contributing to the contamination of crops during the growing period. Since the competition with the indigenous...
Tue, 03/03/2020 - 03:16
The antibiotic‐resistant bacteria (ARB) and antibiotic‐resistant genes (ARGs) in human gut microbiota have significant impact on human health. Whilst high throughput metagenomic sequencing reveals genotypes of bacteria communities, the functionality, phenotype and heterogeneity of human gut microbiota are still elusive. In this study, we applied Raman microscopy with deuterium isotope probing (...
Tue, 03/03/2020 - 03:16
Sea level rise and the anthropogenic warming of the world's oceans is not only an environmental tragedy, but these changes also result in a significant threat to public health. Along with coastal flooding and the encroachment of saltwater farther inland comes an increased risk of human interaction with pathogenic Vibrio species, such as Vibrio cholerae, V. vulnificus and V. parahaemolyticus. This...
Tue, 02/25/2020 - 03:19
Mercury (Hg) is a highly toxic and widely distributed heavy metal which some Bacteria and Archaea detoxify by the reduction of ionic Hg (Hg[II]) to the elemental volatile form, Hg(0). This activity is specified by the mer operon. The mer operon of the deeply‐branching thermophile Thermus thermophilus HB27 encodes for, an O‐acetyl‐L‐homoacetylserine sulfhydrylase (Oah2), a transcriptional...
Fri, 01/24/2020 - 03:16
Populations of the bacterium Vibrio cholerae consist of dozens of distinct lineages, with primarily (but not exclusively) members of the pandemic generating (PG) lineage capable of causing the diarrheal disease cholera. Assessing composition and temporal dynamics of such populations requires extensive isolation efforts and thus only rarely covers large geographic areas or timeframes exhaustively...
Tue, 12/24/2019 - 03:16
Vibrio cholerae is a waterborne bacterium responsible for worldwide outbreaks of acute and fatal cholera. Recently, small regulatory RNAs (sRNAs) have become increasingly recognized as important regulators of virulence gene expression in response to environmental signals. In this study, we determined that two component system EnvZ/OmpR was required for intestinal colonization in V. cholerae O1 EI...
Tue, 12/24/2019 - 03:16
Bacteria in nature are widely exposed to differential fluid shears which are often a trigger for phenotypic switches. The latter mediates transcriptional and translation remodeling of cellular metabolism impacting among others virulence, antimicrobial resistance and stress resistance. In this study, we evaluated the role of fluid shear on phenotypic switch in an acute hepatopancreatic necrosis...
Tue, 11/26/2019 - 03:17
Fusarium verticillioides is a fungal pathogen that is responsible for maize ear rot and stalk rot diseases worldwide. The fungus also produces carcinogenic mycotoxins, fumonisins, on infested maize. Unfortunately, we still lack clear understanding of how the pathogen responds to host and environmental stimuli to trigger fumonisin biosynthesis. The heterotrimeric G protein complex, consisting of...
Thu, 11/14/2019 - 03:16
SUMMARY Non‐typhoidal Salmonella enterica (NTS) are diverse and important bacterial pathogens consisting of more than 2600 different serovars, with varying host‐specificity. Here, we characterized the poultry‐associated serovars in Israel, analyzed their resistome and illuminated the molecular mechanisms underlying common multidrug resistance (MDR) patterns. We show that at least four serovars...
Tue, 10/15/2019 - 03:23
Aspergillus flavus (A. flavus) is a pathogenic fungus that produces carcinogenic aflatoxins, posing a great threat to crops, animals and humans. Lysine acetylation is one of the most important reversible post‐translational modifications, and plays a vital regulatory role in various cellular processes. However, current information on the extent and function of lysine acetylation and aflatoxin...
Fri, 10/04/2019 - 03:20
Stone surfaces are extreme environments that support microbial life. This microbial growth occurs despite unfavourable conditions associated with stone including limited sources of nutrients and water, high pH and exposure to extreme variations in temperature, humidity and irradiation. These stone‐dwelling microbes are often resistant to extreme environments including exposure to desiccation,...
Fri, 10/04/2019 - 03:20
Successful application of microorganisms to heavy metal remediation depends on their resistance to toxic metals. This study contrasted the differences of tolerant mechanisms between Pb2+ and Cd2+ in Enterobacter sp. Microbial respiration and production of formic acid showed that Enterobacter sp. had a higher tolerant concentration of Pb (>1000 mg l−1) than Cd (about 200 mg l−1). Additionally,...
Fri, 10/04/2019 - 03:20
Iron is essential for most living organisms. In addition, its biogeochemical cycling influences important processes in the geosphere (e.g., the mobilization or immobilization of trace elements and contaminants). The reduction of Fe(III) to Fe(II) can be catalysed microbially, particularly by metal‐respiring bacteria utilizing Fe(III) as a terminal electron acceptor. Furthermore, Gram‐positive...
Tue, 09/24/2019 - 03:19
A multidisciplinary approach was carried out in order to study the biodeterioration and the associated microbiome of a XVIII Century wax seal coloured with minium. A small wax seal fragment was observed by scanning electron microscopy combined with energy dispersive spectroscopy in non‐destructive mode. The same object was analysed by Raman and Fourier‐transform infrared spectroscopy. The...
Tue, 09/24/2019 - 03:19
This study determines the natural product biosynthesis and full coding potential within the bacterial genus Aquimarina. Using comprehensive phylogenomics and functional genomics, we reveal that phylogeny instead of isolation source [host‐associated (HA) vs. free‐living (FL) habitats] primarily shape the inferred metabolism of Aquimarina species. These can be coherently organized into three major...
Tue, 09/24/2019 - 03:19
While the dynamics of microbial community assembly driven by environmental perturbations have been extensively studied, our understanding is far from complete, particularly for light‐induced perturbations. Extremely halophilic communities thriving in coastal solar salterns are mainly influenced by two environmental factors ‐ salt concentrations and high sunlight irradiation. By experimentally...
Wed, 09/11/2019 - 11:50
Summary Within streptophyte green algae Zygnematophyceae are the sister group to the land plants that inherited several traits conferring stress protection. Zygnema sp., a mat‐forming alga thriving in extreme habitats, was collected from a field site in Svalbard, where the bottom layers are protected by the top layers. The two layers were investigated by a metatranscriptomic approach and GC–MS‐...
Thu, 08/15/2019 - 08:38
Summary In marine ecosystems, dinoflagellates can become highly abundant and even dominant at times, despite their comparatively slow growth. Their ecological success may be related to their production of complex toxic polyketide compounds. Ostreopsis species produce potent palytoxin‐like compounds (PLTX), which are associated with human skin and eye irritations, and illnesses through the...
Thu, 08/15/2019 - 05:50
Summary Although many typical outer‐membrane proteins (OMPs) have been well characterized, the biological functions of many OMPs remain largely elusive. In this study, we successfully constructed 29 OMP knockout strains in the pathogen Aeromonas hydrophila, which account for about 50% of all predicted OMPs in this bacterial species. We then further validated the antibiotics' susceptibility...
Mon, 08/05/2019 - 12:34
Summary The use of antimicrobials in human and veterinary medicine has coincided with a rise in antimicrobial resistance (AMR) in the food‐borne pathogens Campylobacter jejuni and Campylobacter coli. Faecal contamination from the main reservoir hosts (livestock, especially poultry) is the principal route of human infection but little is known about the spread of AMR among source and sink...
Mon, 08/05/2019 - 06:10
Summary Nearly 1400 Bacillus strains growing in the plant rhizosphere were sampled from different sites on the Qinghai–Tibetan Plateau. Forty‐five of the isolates, selected due to their biocontrol activity, were genome‐sequenced and their taxonomic identification revealed that they were representatives of the Bacillus subtilis species complex (20) and the Bacillus cereus group (9). Majority of...

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