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This document provides a list of web resources related to the topic of microbes and plastics in environmental microbiology. The resources cover various aspects such as the colonization and breakdown of plastics by microbial communities, the use of microbes for sustainable recycling, plastic biodegradation in cold regions and saltwater, plastic-eating enzymes, engineering plastic-degrading enzymes, machine learning for enzyme improvement, the impact of plastics on microbial growth in lakes, the potential link between microplastics and infectious diseases, and the study of plastic-microbe interactions in marine environments. These resources offer valuable information for researchers interested in understanding the role of microbes in plastic degradation and its environmental implications. [Extracted from the article]

This document provides a selection of World Wide Web sites that are relevant to the topic of plasmids in environmental microbes. The sites cover various aspects of plasmids, including their composition and distribution in different environments, plasmid transfer in microbial communities, plasmids in Pseudomonas, the role of plasmids in modulating their hosts, positive and negative selection for plasmids, plasmid stability without selection, plasmids for non-selection use, plasmids for delivering genes to microbiomes, mining environmental plasmids for engineering purposes, plasmid detection in genomic data, and databases of plasmid sequences. These resources can be valuable for researchers studying plasmids in environmental microbiology. [Extracted from the article]

This document provides a list of web resources related to the topic of microbes and iodine in environmental microbiology. The resources cover various aspects of iodine transformation and cycling by microbes, including its geochemical cycling, speciation in nuclear waste storage areas, methylation by marine and terrestrial bacteria, and formation of organic iodine compounds. The document also discusses the implications of methyl iodide formation, iodine-rich brine fields, and the use of iodate as an electron acceptor by certain bacteria. Additionally, it mentions the cytotoxic compound calicheamicin and its potential as an anti-tumor treatment. [Extracted from the article]

Acetogenesis pathways and proteins https://www.wikipathways.org/pathways/WP5019.html This WikiPathways page shows metabolite maps and has a linked table of metabolites and relevant proteins. Crystal structure of acetyl-CoA synthase, 1MJG https://www.rcsb.org/structure/1MJG This page of the Protein DataBank links to the crystal structure of the bifunctional carbon monoxide dehydrogenase, also known as acetyl-CoA synthase, from I Moorella thermoacetica i . Monomeric acetyl-CoA synthase https://www.rcsb.org/structure/7NYS This page of the Protein DataBank links to the crystal structure of the monomeric acetyl-CoA synthase, with carbon monoxide bound to the protein nickel atom. [Extracted from the article]

Microbe-insect chemical ecology https://www.ice.mpg.de/220415/chemistry-of-insect-microbe-interactions This page describes a research group and others working in the field of microbe-insect chemical ecology. Chemical ecology of microbes and coral reefs https://www.youtube.com/watch?app=desktop&v=ptbkGTLKmP0 This is a lecture recorded for a YouTube video on the chemical ecology of coral reef host-microbe interactions. Https://www.pnas.org/doi/10.1073/pnas.1902664116 This is a commentary on a study of chemical signaling between microbes and animals and the influence on both organisms. [Extracted from the article]

Solvent membrane stress https://pubs.rsc.org/en/content/articlelanding/2020/gc/d0gc01865a This article describes the disruptive effects of solvents on biological membranes using the techniques of small-angle scattering and molecular dynamics simulations. Mechanisms of solvent tolerance https://pubmed.ncbi.nlm.nih.gov/12142492/ This is a classic review article describing mechanisms of solvent tolerance in Gram-negative model bacteria, including I Escherichia coli i and I Pseudomonas putida i . Https://link.springer.com/chapter/10.1007/978-3-319-51686-8 9 This extensive review article examines a range of evolved mechanisms by which bacteria survive high levels of solvent stress. [Extracted from the article]

Acid and osmotic stress interaction https://www.nature.com/articles/s41467-017-02030-0 The stress transcription factor OmpR is shown to play a role in both osmotic and acid stress responses. Https://pubmed.ncbi.nlm.nih.gov/31773206/ This review deals with the mechanisms of microbial acid stress response in the context of better using microbes in industrial applications. Remodeling DNA under acid stress https://als.lbl.gov/how-proteins-remodel-dna-in-bacteria-under-stress/ This is an article describing the development of new methods to visualize protein-DNA interactions during the I E. coli i response to acid stress. [Extracted from the article]

Https://www.epa.gov/cyanohabs This site from the U.S. Environmental Protection Agency deals with cyanobacterial algal blooms, the toxic products made, monitoring efforts and research into the topic. Climate change and algal blooms https://pubs.acs.org/doi/10.1021/acs.est.7b01498 This paper presents a modeling framework that predicts the effect of climate change on cyanobacterial blooms in water bodies in and surrounding the United States. Blooms: Tastes and odors https://www.usgs.gov/centers/kansas-water-science-center/science/cyanobacterial-blue-green-algal-blooms-tastes-odors-and This site deals with some of the chemicals involved in toxic algal blooms and gives information about specific geographic locations that have been studied. [Extracted from the article]

Living at low substrate concentrations https://pubmed.ncbi.nlm.nih.gov/20688348/ This is a classic review article on how microbes grow at low substrate concentrations and with mixed substrates, conditions more likely in many environments. Ion homeostasis and starving bacteria https://www.biorxiv.org/content/10.1101/2021.11.22.469587v3.full The results obtained in this study suggest that starvation-induced cell death of I Escherichia coli i results from the loss of ion homeostasis, leading to membrane permeabilization and lysis. Modeling substrate limitation https://dspace.mit.edu/bitstream/handle/1721.1/133637/pcbi.1008140.pdf?sequence=2&isAllowed=y This strictly modeling study examined the course of I Escherichia coli i growth rate as a function of substrate availability. [Extracted from the article]

HGT and microbiome stability https://www.biorxiv.org/content/10.1101/2022.02.25.481914v1 This represents a modeling study that indicates HGT increases the stability of microbial communities. Https://www.nature.com/articles/s41579-021-00650-4 This paper contains a theoretical treatment of how positive selection operates on horizontal gene transfer (HGT) events to drive evolution. HGT and Bacillus evolution https://www.pnas.org/doi/10.1073/pnas.2007873118 In this study, the authors co-incubated two closely related I Bacillus subtilis i strains to examine how HGT could produce hybrid strains with different functional traits. [Extracted from the article]

OmcE nanowires from Geobacter sulfurreducens https://www.rcsb.org/structure/7TFS This page contains structural data from cryo-electron microscopy of the OmcE protein-type nanowires from I Geobacter sulfurreducens i . Accelerated conductivity if bacterially generated nanowires https://phys.org/news/2023-01-bacteria-generated-nanowires-soil-oceans.html This report highlights a recent peer-reviewed paper describing a dramatic increase in conductivity in microbial protein nanowires induced by light. OmcZ nanowires from Geobacter sulfurreducens https://www.rcsb.org/structure/8D9M This page contains structural data from cryo-electron microscopy of the OmcZ protein-type nanowires from I Geobacter sulfurreducens i . [Extracted from the article]

Https://www.epa.gov/P3/2021-p3-expo-biodegradation-microplastics-water-treatment This site has text, a poster and a video covering the biodegradation of microplastics in water treatment environments. Degradation of 28 chemicals in 4 classes https://www.frontiersin.org/articles/10.3389/fenvs.2021.700245/full This study looked at overall degradation, including photo-degradation and biodegradation. [Extracted from the article]

Adaptive evolution facilitated by horizontal gene transfer https://www.pnas.org/doi/10.1073/pnas.2007873118 This study used two closely related I Bacillus i strains and observed how positive and negative selective pressures led to gene transfers and adaption. Bottlenecks in adaptive evolution dynamics https://www.biorxiv.org/content/10.1101/2021.12.29.474457v1 This study used modelling and empirical experiments to examine the time of adaption as a function of different inoculum sizes in the transfer regime. Adaptive evolution of a Pseudomonas https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/1751-7915.13678 This study emphasized setting up conditions specific to a particular microorganism in adaptive evolution experiments. [Extracted from the article]

Metagenomics and wastewater treatment https://www.sciencedirect.com/science/article/abs/pii/S0048969721058150 This paper represents a general review of wastewater treatment system metagenomes. Https://www.nature.com/articles/s41598-020-65031-y This study used metagenomics and concluded that many antibiotic resistance genes are found in wastewater influent but are removed from wastewater effluent. Metagenomic-enabled antibiotic resistance https://www.frontiersin.org/articles/10.3389/fmicb.2021.657954/full This study did metagenomic sequencing after sampling to help standardize the analysis of wastewater treatment plants to evaluate patterns in indicators of antibiotic resistance. [Extracted from the article]

Universal free energy landscapes and electron bifurcation https://www.pnas.org/doi/10.1073/pnas.2010815117 This paper covers the theoretical aspects of electron bifurcation and how energy transfer can occur with little loss of energy. Energy conservation in microbes https://www.mikrobiologie-frankfurt.de/molecular-microbiology-bioenergetics/prof-dr-volker-müller/5-electron-bifurcation/ This researcher website links to research on electron bifurcation in microbes as a means of energy conservation. Electron-bifurcating hydrogenase in Desulfovibrio https://onlinelibrary.wiley.com/doi/10.1111/mmi.14881 The FeFe-hydrogenase Hnd in I Desulfovibrio fructosovorans i is involved in generating both NADH and reduced ferredoxin via electron bifurcation during ethanol production. [Extracted from the article]

Selection schemes from evolutionary computing https://dl.acm.org/doi/10.1145/3520304.3528900 This report describes parent strain selection algorithms to better carry out directed evolution of microbial populations and selecting for multiple traits simultaneously. Modeling bacterial toxin evolution https://www.nature.com/articles/s43588-022-00343-9 This report describes the modeling of the evolutionary trajectory of bacterial toxins. Metagenome assembly pipeline https://academic.oup.com/mbe/article/37/2/593/5601623 This report describes a computational framework that simplifies metagenome assembly and processing. [Extracted from the article]

Microbes as gatekeepers of methane clathrates https://theconversation.com/microbes-might-be-gatekeepers-of-the-planets-greatest-greenhouse-gas-reserves-149652 This article pertains to, at the time, yet to be peer-reviewed research suggesting that microbes stabilize methane clathrates in the oceans. Microbes in climate change and recycling https://microbiologysociety.org/our-work/75th-showcasing-why-microbiology-matters/microbes-and-where-to-find-them/role-of-microbes-in-climate-change-and-recycling.html This page by the Microbiology Society is accessible to all readers and highlight how microbes are important in greenhouse gases and recycling, hence central to climate change issues. Carbonate hosted seafloor microbes prolifically oxidize methane https://www.pnas.org/content/118/25/e2006857118 Deep ocean carbonate deposits may be hot spots of microbial methane oxidation. [Extracted from the article]

Oxygen requirements for microbial growth https://courses.lumenlearning.com/microbiology/chapter/oxygen-requirements-for-microbial-growth/ This site generally discusses microbial growth with respect to varying oxygen concentrations. Breaking the oxygen barrier https://schaechter.asmblog.org/schaechter/2017/05/breaking-the-oxygen-barrier-in-microbial-cultivation.html This blog from the American Society for Microbiology discusses oxygen effects and sensitivities in bacteria generally. Thioglycollate broth https://microbenotes.com/thioglycollate-broth/ Thioglycollate broth has traditionally been used to cultivate bacteria with different degrees of oxygen requirements and sensitivities, and has been used to isolate and cultivate microaerophiles. [Extracted from the article]

Cell-free DNA and antibiotic resistance genes https://pubs.acs.org/doi/10.1021/acs.est.7b04283 This report makes a key point that cell-free DNA is likely more important in conveying antibiotic resistance than previously considered. Https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061472/ This article presents a broad overview of extracellular DNA (eDNA) in the environment. EDNA Laboratories http://www.spygen.com/technologies/edna-laboratories/ This commercial website emphasizes the need to mitigate against DNA contamination when doing eDNA analysis. [Extracted from the article]

Metagenomes associated with plants https://www.ebi.ac.uk/metagenomics/browse?lineage=root:Host-associated:Plants#studies This page of the EMBL databases provides metadata and links to genomic data from a wide variety of plant microbiome genome projects. Microbe-microbe interactions on plant leaves https://www.nature.com/articles/s41396-020-0665-8 This paper focused on DNA sequencing of leaf microbiomes from 275 wild I Arabidopsis thaliana i plants. Https://science.sciencemag.org/content/371/6531/eaba6605?ijkey=0b633797998b09744af5cb9fcbb4e8aeabbb593d&keytype2=tf ipsecsha This recent paper in the journal I Science i focuses on the ancient nature of microbial-plant interactions, covering the time of the early proliferation of plants on land. [Extracted from the article]

Mathematical modelling of marine bacteriophage evolution https://royalsocietypublishing.org/doi/10.1098/rsos.171661 The goal of this study was to derive a relatively simple model of bacteriophage evolution. Bacteriophage evolution https://www.nature.com/articles/nmicrobiol2017112 This broad review of bacteriophages discusses phage evolution and also the impacts they have on bacterial functions and evolution. Bacteriophage experimental evolution https://en.wikipedia.org/wiki/Bacteriophage experimental evolution This Wikipedia entry is interesting because bacteriophages were important tools in early molecular evolution. [Extracted from the article]

Https://pubmed.ncbi.nlm.nih.gov/32630666/ A I Miceococcus luteus i strain was shown to carry out the transformation of the fatty acid oleic acid to -dodecalactone, a compound that has a peach and strawberry fragrance. -Lactone hydrolase from Rhodococcus https://pubmed.ncbi.nlm.nih.gov/11157238/ Cyclic ketones in the environment are often degraded via Baeyer-Villiger monooxygenases that produce lactones. Lactones to polyesters via Pseudomonas https://pubs.acs.org/doi/10.1021/ma1027627 This study examined the synthesis of bacterial copolyesters, modified lactones and -lactones, using I Pseudomonas oleovorans i . [Extracted from the article]

Https://www.frontiersin.org/research-topics/3843/atmospheric-microbiology This aeromicrobiology set of articles focuses on the interactions between microbes and the atmosphere within built environments. Aeromicrobiology https://microbewiki.kenyon.edu/index.php/Aeromicrobiology This page for the Microbe Wiki covers microbes in the general atmosphere, clouds, their microbial communities and the stresses of the atmospheric environment. Microbes and climate change FAQ series https://www.asmscience.org/content/99 This web fact sheet is put out by the American Society on Microbiology as part of their Frequently Asked Questions (FAQ) series on subjects relating to microbiology. [Extracted from the article]

Biodegradation of aromatic-aliphatic polyesters by a marine consortium https://www.nature.com/articles/s41467-020-19583-2 This very recent paper described a range of physic-chemical and biological methods to demonstrate plastics biodegradation by a mixed consortium from a marine environment. Plastics industry on additives and biodegradability https://www.plasticsindustry.org/sites/default/files/2018%20PLASTICS%20-%20Position%20Paper%20on%20Degradable%20Additives.pdf This web brochure from a plastic industry association discusses how additives, plasticizers and co-polymers can effect biodegradability. Biodegradation and photo-degradation of polylactic acid https://trace.tennessee.edu/cgi/viewcontent.cgi?article=3898&context=utk graddiss This is a thesis that describes polylactic acid (PLA) and its environmental fate. [Extracted from the article]

The article reviews several web sites related to environmental microbiology, including the web site located at https://en.wikipedia.org/wiki/Methylmercury; the site located at http://www.ncbi.nlm.nih.gov/pubmed/23393089, and the site located at http://www.ncbi.nlm.nih.gov/pubmed/26626101.

Https://enviroliteracy.org/air-climate-weather/biogeochemical-cycles/phosphorus-cycle/ This page deals with weathering, movement and bio-cycling of phosphorus-containing compounds in the environment. Microbial phosphite oxidation and global P cycling https://pubmed.ncbi.nlm.nih.gov/28189156/ This paper describes a bacterial metabolic process known as dissimilatory phosphite oxidation. Hypophosphite transporter X-ray structure https://www.rcsb.org/structure/5ME4 In many environments, phosphorus is a limiting nutrient for bacterial growth and so many bacteria can utilize phosphite and hypophosphite as alternative sources of phosphorus. [Extracted from the article]

Sulfur oxidations in the ocean https://academic.oup.com/femsre/article/33/6/999/510705 This review focuses on microbes, particularly marine, that rely on oxidation of sulfur compounds for their energy requirements. Methylphosphonate oxidation by Prochlorococcus https://aem.asm.org/content/85/13/e00289-19 Methylphosphonate can be metabolized by the bacterial enzyme C-P lyase to make methane, but this study showed that a I Prochlorococcus i strain would metabolize methylphosphonate oxygenatively to form formate and release phosphate. Marine microbial enzymes for biotechnology https://www.sciencedirect.com/science/article/pii/S1043452616300675 Enzymes from marine microorganisms are often different enough from their terrestrial counterparts that they have proven to be a useful resource to mine for industrial enzymes. [Extracted from the article]

Membrane vesicles review https://www.frontiersin.org/articles/10.3389/fmicb.2019.03026/full This mini-review focuses on the chemical composition and physical properties of bacterial membrane vesicles. Membrane vesicles https://www.sciencedirect.com/topics/medicine-and-dentistry/membrane-vesicle This publishers site contains abstracts and links to numerous articles on membrane vesicles that are found on both bacteria and archaea. Atomic force microscopic imaging of vesicles https://pubs.rsc.org/en/content/articlelanding/2020/nr/c9nr10850e#!divAbstract Atomic force microscopy is a new method to be applied to studies of extracellular membrane vesicles and may allow for single-vesicle analysis in the future. [Extracted from the article]

This novel study examines gut microbiome in an insect host harboring a parasite. This study demonstrated how plant defenses against infecting insects can modulate the gut microflora of the insect to enhance their defensive measures. This research described the genetic engineering of symbiotic honey bee gut bacteria to help the insects ward off Varroa mites and a specfic virus, both of which are thought to contribute significantly to honey bee colony collapse. [Extracted from the article]