The Stenotrophomonas maltophilia complex (Smc) comprises opportunistic environmental Gram-negative bacilli responsible for a variety of infections in both humans and animals. Beyond its large genetic diversity, its genetic organization in genogroups was recently confirmed through the whole-genome sequencing of human and environmental strains. As they are poorly represented in these analyses, we sequenced the whole genomes of 93 animal strains to determine their genetic background and characteristics. Combining these data with 81 newly sequenced human strains and the genomes available from RefSeq, we performed a genomic analysis that included 375 nonduplicated genomes with various origins (animal, 104; human, 226; environment, 30; unknown, 15). Phylogenetic analysis and clustering based on genome-wide average nucleotide identity confirmed and specified the genetic organization of Smc in at least 20 genogroups. Two new genogroups were identified, and two previously described groups were further divided into two subgroups each. Comparing the strains isolated from different host types and their genogroup affiliation, we observed a clear disequilibrium in certain groups. Surprisingly, some antimicrobial resistance genes, integrons, and/or clusters of attC sites lacking integron-integrase (CALIN) sequences targeting antimicrobial compounds extensively used in animals were mainly identified in animal strains. We also identified genes commonly found in animal strains coding for efflux systems. The result of a large whole-genome analysis performed by us supports the hypothesis of the putative contribution of animals as a reservoir of Stenotrophomonas maltophilia complex strains and/or resistance genes for strains in humans.

IMPORTANCE Given its naturally large antimicrobial resistance profile, the Stenotrophomonas maltophilia complex (Smc) is a set of emerging pathogens of immunosuppressed and cystic fibrosis patients. As it is group of environmental microorganisms, this adaptation to humans is an opportunity to understand the genetic and metabolic selective mechanisms involved in this process. The previously reported genomic organization was incomplete, as data from animal strains were underrepresented. We added the missing piece of the puzzle with whole-genome sequencing of 93 strains of animal origin. Beyond describing the phylogenetic organization, we confirmed the genetic diversity of the Smc, which could not be estimated through routine phenotype- or matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF)-based laboratory tests. Animals strains seem to play a key role in the diversity of Smc and could act as a reservoir for mobile resistance genes. Some genogroups seem to be associated with particular hosts; the genetic support of this association and the role of the determinants/corresponding genes need to be explored.

In Lysobacter enzymogenes OH11, RpfB1 and RpfB2 were predicted to encode acyl coenzyme A (CoA) ligases. RpfB1 is located in the Rpf gene cluster. Interestingly, we found an RpfB1 homolog (RpfB2) outside this canonical gene cluster, and nothing is known about its functionality or mechanism. Here, we report that rpfB1 and rpfB2 can functionally replace EcFadD in the Escherichia coli fadD mutant JW1794. RpfB activates long-chain fatty acids (n-C_16:0 and n-C_18:0) for the corresponding fatty acyl-CoA ligase (FCL) activity in vitro, and Glu-361 plays critical roles in the catalytic mechanism of RpfB1 and RpfB2. Deletion of rpfB1 and rpfB2 resulted in significantly increased heat-stable antifungal factor (HSAF) production, and overexpression of rpfB1 or rpfB2 completely suppressed HSAF production. Deletion of rpfB1 and rpfB2 resulted in increased L. enzymogenes diffusible signaling factor 3 (LeDSF3) synthesis in L. enzymogenes. Overall, our results showed that changes in intracellular free fatty acid levels significantly altered HSAF production. Our report shows that intracellular free fatty acids are required for HSAF production and that RpfB affects HSAF production via FCL activity. The global transcriptional regulator Clp directly regulated the expression of rpfB1 and rpfB2. In conclusion, these findings reveal new roles of RpfB in antibiotic biosynthesis in L. enzymogenes.

IMPORTANCE Understanding the biosynthetic and regulatory mechanisms of heat-stable antifungal factor (HSAF) could improve the yield in Lysobacter enzymogenes. Here, we report that RpfB1 and RpfB2 encode acyl coenzyme A (CoA) ligases. Our research shows that RpfB1 and RpfB2 affect free fatty acid metabolism via fatty acyl-CoA ligase (FCL) activity to reduce the substrate for HSAF synthesis and, thereby, block HSAF production in L. enzymogenes. Furthermore, these findings reveal new roles for the fatty acyl-CoA ligases RpfB1 and RpfB2 in antibiotic biosynthesis in L. enzymogenes. Importantly, the novelty of this work is the finding that RpfB2 lies outside the Rpf gene cluster and plays a key role in HSAF production, which has not been reported in other diffusible signaling factor (DSF)/Rpf-producing bacteria.

Most freshwater bacterial communities are characterized by a few dominant taxa that are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic diversity within these taxonomic groups is limited to a subset of taxa. Here, we investigated the genomic diversity that enables Limnohabitans, a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight putative Limnohabitans metagenome-assembled genomes (MAGs) from stations located along broad environmental gradients existing in Lake Michigan, part of Earth’s largest surface freshwater system. De novo strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with cooccurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust in situ strain delineation had not previously been achieved. Our data show that temperature and nutrient levels may be important environmental parameters associated with microdiversification within the Limnohabitans genus. In addition, strains predominant in low- and high-phosphorus conditions had larger genomic divergence than strains abundant under different temperatures. Comparative genomics and gene expression analysis yielded evidence for the ability of LimB populations to exhibit cellular motility and chemotaxis, a phenotype not yet associated with available Limnohabitans isolates. Our findings broaden historical marker gene-based surveys of Limnohabitans microdiversification and provide in situ evidence of genome diversity and its functional implications across freshwater gradients.

IMPORTANCE Limnohabitans is an important bacterial taxonomic group for cycling carbon in freshwater ecosystems worldwide. Here, we examined the genomic diversity of different Limnohabitans lineages. We focused on the LimB lineage of this genus, which is globally distributed and often abundant, and its abundance has shown to be largely invariant to environmental change. Our data show that the LimB lineage is actually comprised of multiple cooccurring populations for which the composition and genomic characteristics are associated with variations in temperature and nutrient levels. The gene expression profiles of this lineage suggest the importance of chemotaxis and motility, traits that had not yet been associated with the Limnohabitans genus, in adapting to environmental conditions.

Tigecycline serves as one of the antibiotics of last resort to treat multidrug-resistant (including carbapenem-resistant) pathogens. However, the recently emerged plasmid-mediated tigecycline resistance mechanism, Tet(X), challenges the clinical efficacy of this class of antibiotics. In this study, we detected 180 tet(X)-harboring Acinetobacter isolates (8.9%, n = 180) from 2,018 samples collected from avian farms and adjacent environments in China. Eighteen tet(X)-harboring isolates (10.0%) were found to cocarry the carbapenemase gene bla_NDM-1, mostly from waterfowl samples (94.4%, 17/18). Interestingly, among six Acinetobacter strains, tet(X) and bla_NDM-1 were found to colocalize on the same plasmids. Moreover, whole-genome sequencing (WGS) revealed a novel orthologue of tet(X) in the six isolates coharboring tet(X) and bla_NDM-1. Inverse PCR suggested that the two tet(X) genes form a single transposable unit and may be cotransferred. Sequence comparison between six tet(X)- and bla_NDM-1-coharboring plasmids showed that they shared a highly homologous plasmid backbone even though they were isolated from different Acinetobacter species (three from Acinetobacter indicus, two from Acinetobacter schindleri, and one from Acinetobacter lwoffii) from various sources and from different geological regions, suggesting the horizontal genetic transfer of a common tet(X)- and bla_NDM-1-coharboring plasmid among Acinetobacter species in China. Emergence and spread of such plasmids and strains are of great clinical concern, and measures must be implemented to avoid their dissemination.

Bacterial persisters are phenotypic variants that temporarily demonstrate an extraordinary tolerance toward antibiotics. Persisters have been linked to the recalcitrance of biofilm-related infections; hence, a complete understanding of their physiology can lead to improvement of therapeutic strategies for such infections. Mechanisms pertaining to persister formation are thought to be associated with stress response pathways triggered by intra- or extracellular stress factors. Unfortunately, studies demonstrating the effects of osmolyte- and/or pH-induced stresses on bacterial persistence are largely missing. To fill this knowledge gap within the field, we studied the effects of various osmolytes and pH conditions on Escherichia coli persistence with the use of phenotype microarrays and antibiotic tolerance assays. Although we found that a number of chemicals and pH environments, including urea, sodium nitrite, and acidic pH, significantly reduced persister formation in E. coli compared to no-osmolyte/no-buffer controls, this reduction in persister levels was less pronounced in late-stationary-phase cultures. Our results further demonstrated a positive correlation between cell growth and persister formation, which challenges the general notion in the field that slow-growing cultures have more persister cells than fast-growing cultures.

The poor prognosis for patients with pancreatic ductal adenocarcinoma (PDAC) impels an improved understanding of disease biology to facilitate the development of better therapies. PDAC typically features a remarkably dense stromal reaction, featuring and established by a prominent population of cancer-associated fibroblasts (CAF). Genetically engineered mouse models and increasingly sophisticated cell culture techniques have demonstrated important roles for fibroblasts in PDAC progression and therapy response, but these roles are complex, with strong evidence for both tumor-supportive and tumor-suppressive or homeostatic functions. Here, we review the recent literature that has improved our understanding of heterogeneity in fibroblast fate and function in this disease including the existence of distinct fibroblast populations, and highlight important avenues for future study.

T-cell immunoglobulin and mucin domain–containing molecule 3 (TIM-3), a potential immunotherapeutic target for cancer, has been shown to display diverse characteristics in a context-dependent manner. Thus, it would be useful to delineate the precise functional features of TIM-3 in a given situation. Here, we report that glial TIM-3 shows distinctive properties in the brain tumor microenvironment. TIM-3 was expressed on both growing tumor cells and their surrounding cells including glia and T cells in an orthotopic mouse glioma model. The expression pattern of TIM-3 was distinct from those of other immune checkpoint molecules in tumor-exposed and tumor-infiltrating glia. Comparison of cells from tumor-bearing and contralateral hemispheres of a glioma model showed that TIM-3 expression was lower in tumor-infiltrating CD11b+CD45mid glial cells but higher in tumor-infiltrating CD8+ T cells. In TIM-3 mutant mice with intracellular signaling defects and Cre-inducible TIM-3 mice, TIM-3 affected the expression of several immune-associated molecules including iNOS and PD-L1 in primary glia-exposed conditioned media (CM) from brain tumors. Further, TIM-3 was cross-regulated by TLR2, but not by TLR4, in brain tumor CM- or Pam3CSK4-exposed glia. In addition, following exposure to tumor CM, IFNγ production was lower in T cells cocultured with TIM-3–defective glia than with normal glia. Collectively, these findings suggest that glial TIM-3 actively and distinctively responds to brain tumor, and plays specific intracellular and intercellular immunoregulatory roles that might be different from TIM-3 on T cells in the brain tumor microenvironment.Significance:TIM-3 is typically thought of as a T-cell checkpoint receptor. This study demonstrates a role for TIM-3 in mediating myeloid cell responses in glioblastoma.

Carcinoma-associated fibroblasts (CAF) are a potential therapeutic target for both direct and indirect regulation of cancer progression and therapy response. In this issue of Cancer Research, Ford and colleagues investigate the influence of CAF on the immune environment of tumors, specifically focusing on the regulation of CD8+ T cells, required for immune therapy response. Their work suggests a role for stromally expressed NADPH oxidase 4 (NOX4) as a modulator of reactive oxygen species that in turn can reduce the number of CD8+ T cells locally. Inhibition of NOX4 increased CD8+ T cells and restored responsiveness to immune therapy, suggesting an indirect stromally targeted avenue for therapy resensitization.See related article by Ford et al., p. 1846

Prof. Jason Pomeroy talks about the rise of the digital economy and its impact on the workplace.

Study highlights industry failures and calls for shift in consumer attitudes

The fashion industry needs to fundamentally change in order to mitigate the environmental impact of fast fashion, experts have said.

Clothes rental, better recycling processes, pollution control technology and the innovative use of offcuts are among measures that could help, they said.

Nation replaces Brazil for first time in annual list of murders compiled by Global Witness

The Philippines has replaced Brazil as the most murderous country in the world for people defending their land and environment, according to research that puts a spotlight on the administration of President Rodrigo Duterte.

More than three defenders were killed across the world every week in 2018, according to the annual toll by the independent watchdog Global Witness, highlighting the continued dangers facing those who stand up to miners, loggers, farmers, poachers and other extractive industries.

Planet of the Humans film has had 5m views on YouTube and has enraged renewable energy experts who are demanding an apology

Planet of the Humans is an environmental documentary that has enraged renewable energy experts and environmentalists, with some calling for its high-profile executive producer, Michael Moore, to apologise.

It was released for free less than two weeks ago, and at the time of writing had had close to 5m views on YouTube.

Plan would help Trump administration advance projects held up over global heating concerns such as the Keystone XL oil pipeline

The Trump administration on Thursday unveiled a plan to speed permitting for major infrastructure projects like oil pipelines, road expansions and bridges.

Related: How the oil industry has spent billions to control the climate change conversation

The green-and-white banner from an Illinois high school recalls the first Earth Day 50 years ago

The Monte Conca cave system in Sicily is showing signs of being altered by pollution from above.

Regular processes in the environment improve our eyesight.

Read our live updates on coronavirus HERE Coronavirus: The symptoms

Drive-thru restaurants such as McDonald's are "made for social distancing", Environment Secretary George Eustice has said.

Nazareth, once thought to have been a small village, likely to have been a town of around 1,000 people, new evidence suggests

It's been 50 years since the first Earth Day, and while progress has been made in some areas, humanity still has had a major impact on the planet.

Exclusive: Documents show department has stopped recommending assessment of ‘key threatening processes’ affecting native wildlife

The federal government has stopped listing major threats to species under national environment laws, and plans to address listed threats are often years out of date or have not been done at all.

Environment department documents released under freedom of information laws show the government has stopped assessing what are known as “key threatening processes”, which are major threats to the survival of native wildlife.

The Once Upon a Time… In Hollywood star has praised teenage activists

Forget the food-porn images, Instagram is a source of inspiration for those looking to follow a no-waste lifestyle

Instagram can be a source of inspiration for those looking to follow a no-waste lifestyle

Regular processes in the environment improve our eyesight.

The Monte Conca cave system in Sicily is showing signs of being altered by pollution from above.

Human activities have destroyed more than 7.7 million hectares of threatened species habitat.

NSW Environment Minister Matt Kean says Australia must stop making climate change a matter of religion and instead make it a matter of science as unprecedented bushfires burn across the state.

As a new year of tertiary education gets underway and Australia recovers from a summer of bushfires, Australian universities have told SBS News there has been increasing interest in their environment courses. Here, three students share their motivations.

A company linked to Labor figures that bought a mine for just $1 enjoyed multi-million-dollar refunds from its environmental bond after concessions from the Palaszczuk Government, documents show.

SunRice says it will guarantee Australian-grown rice returns to supermarkets in April if the Murray-Darling Basin Plan is changed so environmental water can be used to grow rice.

Disposable cups are currently the only option for most cafe owners to provide takeaway coffee to customers, but environmentalists are worried about the consequences.

The highly distinctive and mostly endemic Australian land mammal fauna has suffered an extraordinary rate of extinction (>10% of the 273 endemic terrestrial species) over the last ∼200 y: in comparison, only one native land mammal from continental North America became extinct since European settlement. A further 21% of Australian...

By: Jacqueline Chan and Vanessa Fulton Consumers are increasingly demanding environmentally-friendly products and packaging.  Driven by this increased demand and desire to create positive environmental change, companies are working hard to shift to more sustainable materials and packaging and seeking to communicate such efforts to consumers through product labels and advertising.  “Recyclable.”  “Biodegradable.”  “Made of

The post It’s Not Always Easy Being Green – Lawsuit Related to “Recyclable” Claims Highlights Risks Related to Environmental Benefit Claims appeared first on Kleinfeld Kaplan & Becker LLP.

An employee of a Sewell, N.J., company that provided temporary electrical utilities pleaded guilty today to participating in a fraud conspiracy at an Environmental Protection Agency (EPA)-designated Superfund site in New Jersey.

Holy House Shipping AB, a Swedish corporation, was sentenced today in U.S. District Court in Camden, N.J., to pay a $1 million fine, a special assessment of $400,000 in community service payments and serve three years of probation for failing to maintain an accurate oil record book in an attempt to conceal illegal discharges of oil-contaminated waste directly into the ocean from one of its ships.

Invista will pay a $1.7 million civil penalty and spend up to an estimated $500 million to correct self-reported environmental violations discovered at facilities in seven states. The company disclosed more than 680 violations of water, air, hazardous waste, emergency planning and preparedness, and pesticide regulations to EPA after auditing 12 facilities it acquired from DuPont in 2004.

Texas Oil and Gathering Inc., its owner John Kessel and its operations manager Edgar Pettijohn pleaded guilty today in U.S. District Court in Houston to criminal violations related to the disposal of refinery wastes at an underground injection well in violation of the Safe Drinking Water Act.

Atlantic States Cast Iron Pipe Co. a Phillipsburg, N.J.-based division of McWane Inc. of Alabama was sentenced today to pay a fine of $8 million for violations of environmental and worker safety laws as well as obstructing the federal investigation of its conduct.

Alaska Gold Co. (Alaska Gold), and NovaGold Resources Inc. (NovaGold), the owners and operators of the Rock Creek Mine near Nome, Alaska, have agreed to pay a $883,628 civil penalty to resolve violations of a storm water discharge permit.

The co-owner of a Martinsville, N.J., landscaping company pleaded guilty to participating in a fraud conspiracy at the Environmental Protection Agency (EPA)-designated Superfund site, Federal Creosote, located in Manville, N.J. Frederick Landgraber pleaded guilty in the U.S. District Court of New Jersey today to one count of conspiracy to defraud the EPA from approximately March 2002 until approximately June 2005 at the Federal Creosote site.

A former executive of Bennett Environmental Inc. (BEI), a Canadian-based company that treats and disposes of contaminated soil, pleaded guilty to participating in a conspiracy to pay kickbacks and commit fraud at the U.S. Environmental Protection Agency (EPA)-designated Superfund site, Federal Creosote, located in Manville, N.J. The former executive also pleaded guilty to participating in a money laundering conspiracy and impeding a proceeding before the U.S. Securities and Exchange Commission.

The former and current owners and operators of a chemical facility in Addyston, Ohio, LANXESS Corp. and INEOS ABS USA Corp., have agreed to pay a $3.1 million civil penalty and INEOS will spend up to $2 million to install environmental controls and modify operating procedures to resolve violations of multiple environmental laws.

Five companies have agreed to compensate the United States and the Commonwealth of Pennsylvania nearly $21.4 million in cash and valuable property to address natural resource damages resulting from decades of zinc smelting operations at the Palmerton Zinc Pile Superfund site in northeast Pennsylvania.

A federal grand jury in Houston has returned an indictment charging two crewmembers of the oil tanker Georgios M with making false statements, violating federal law designed to prevent pollution from ships and obstruction of justice.

The vice president of a Missouri pesticide company, HPI Products Inc., pleaded guilty today in federal court in Kansas City, Mo., for violating a federal pesticides law designed to provide proper regulatory oversight and prevent improper storage of pesticides.

William Garvey, the president of HPI Products Inc., a pesticide company based in St. Joseph, Mo., was sentenced today in federal court in Kansas City, Mo., for violations of the Clean Water Act and hazardous waste storage laws related to the company’s pesticide production.

A Newark grand jury indicted three individuals for their participation in fraud and kickback conspiracies related to contracts at a U.S. Environmental Protection Agency (EPA)-designated Superfund site, Federal Creosote, located in Manville, N.J.

Gary Fillers pleaded guilty to one criminal felony count for conspiring to violate the Clean Air Act’s “work practice standards” related to the proper stripping, bagging, removal and disposal of asbestos.

Panagiotis Lekkas, the captain of the cargo ship, M/V Theotokos, was sentenced today in federal court in New Orleans to 10 months confinement.