ANME‐1 archaea subsist on the very low energy of anaerobic oxidation of methane (AOM). Most marine sediments shift from net AOM in the sulfate methane transition zone (SMTZ) to methanogenesis in the methane zone (MZ) below it. In White Oak River estuarine sediments, ANME‐1 comprised 99.5% of 16S rRNA genes from amplicons and 100% of 16S rRNA genes from metagenomes of the Methanomicrobia in the SMTZ

The combined biochemical impact of carbon, nitrogen and temperature on the biosynthesis of the antifungal volatile organic compounds (VOCs): ethanol, 2‐methyl‐1‐propanol, 3‐methyl‐1‐butanol and 2‐phenylethanol produced by Aureobasidium pullulans A1 and A3 was investigated using a Box–Behnken experimental design and response surface methodology (RSM). Normalized peak areas derived from solid phase micro

Carbon capture and storage technologies are crucial for reducing carbon emission from power plants as a response to global climate change. The CarbFix project (Iceland) aims at examining the geochemical response of injected CO2 into subsurface reservoirs. The potential role of the subsurface biosphere has been little investigated up to now. Here, we used Thiobacillus thioparus that became abundant

This work aimed at studying the unconfirmed hypothesis predicting the existence of a connection between coffee farm microbiome and the resulting spontaneous fermentation process. Using Illumina‐based amplicon sequencing, 360 prokaryotes and 397 eukaryotes were identified from coffee fruits and leaves, over‐ripe fruits, water used for coffee de‐pulping, depulped coffee beans, soil, and temporal fermentation

We examined factors shaping community assembly of the bull kelp (Nereocystis luetkeana) microbiome by comparing microbial biofilm formation on photosynthetic kelp blade tissues and artificial kelp substrates (‘agar substrates’) deployed into a kelp forest. New kelp blade tissues were colonized by markedly distinct microbial taxa relative to agar substrates during the same time interval, even when agar

Stromatolites are complex microbial mats that form lithified layers. Fossilized stromatolites are the oldest evidence of cellular life on Earth, dating back over 3.4 billion years. Modern stromatolites are relatively rare but may provide clues about the function and evolution of their ancient counterparts. In this study, we focus on peritidal stromatolites occurring at Cape Recife and Schoenmakerskop

Bacterial dormancy is a valuable strategy to endure unfavourable conditions. The term ‘persister’ has been coined for cells that tolerate antibiotic treatments due to reduced cellular activity. The type I toxin–antitoxin system tisB/istR‐1 is linked to persistence in Escherichia coli, because toxin TisB depolarizes the inner membrane and causes ATP depletion. Transcription of tisB is induced upon activation

Coxiellosis or Q fever is an important global occupational zoonotic disease caused by one of the most contagious bacterial pathogens – Coxiella burnetii, which ranks one among the 13 global priority zoonoses. The detection of C. burnetii infection is exhibiting an increasing trend in high‐risk personnel around the globe. It has increasingly been detected from foods of animal origin (including bulk

Soil bacteria play an essential role in functioning of ecosystems and maintaining of biogeochemical cycles. However, little is known about changes in the compositions and functional groups of soil bacterial communities during different restoration stages. The influences of aboveground vegetation and belowground soil properties on soil bacterial communities were also unclear during this process. Here

The in vitro growth of Bradyrhizobium diazoefficiens USDA 110 strain is inhibited by glyphosate. The herbicide affects 5‐enolpyruvylshikimic acid‐3‐phosphate synthase, a key enzyme for aromatic aminoacid synthesis. In this study, site‐directed mutagenesis was used to change only two nucleotides of the coding region of phosphoenolpyruvate binding site. This change improved the in vitro growth of B.

The environmental reservoirs of different serogroups of Vibrio cholerae causing cholera in the flowing freshwater bodies of the tribal areas of Odisha are not known. So the present study was conducted from June 2017 to March 2020 to find out the environmental reservoirs of V. cholerae serogroups in the water and plankton samples collected from the river, nala, stream and chua from Rayagada district

As we sit six feet apart in the San Francisco airport terminal, waiting for a flight to our field site, we hear an attendant's voice echoing, ‘All passengers must provide proof of a negative RT‐qPCR COVID‐19 test prior to boarding the airplane’. A year ago, we would have been hard‐pressed to hear such terminology on any loudspeaker in a major US airport. But a year ago, we were not mid‐pandemic. When

Although sulfate ions are the main form of sulfur in the ocean, there is limited knowledge on their use by living organisms. Stable isotope labelling and NanoSIMS analysis were used in this study to clarify how sulfate, in seawater, is assimilated by corals and zooxanthellae at the cellular level. Aposymbiotic and symbiotic coral juveniles from the genus Acropora were incubated for 2 days in filtered

In addition to their common planktonic lifestyle, bacteria frequently live in surface‐associated habitats. Surface motility is essential for exploring these habitats for food sources. However, many bacteria are found on surfaces, even though they lack features required for migrating along surfaces. How these canonical non‐motile bacteria adapt to the environmental fluctuations on surfaces remains unknown

Streptococcus mutans (S. mutans) effectively utilizes dietary sucrose for the exopolysaccharide productions, which are mostly synthesized by the effects of glucosyltransferases (Gtfs). In the present study, the acetylome of S. mutans was identified and quantitative acetylome analysis of the bacterial biofilm growth (SMB) was compared with that of planktonic growth (SMP). The dynamic changes of protein

We surveyed Spartina saltmarsh sediment rhizosphere fungal communities at three saltmarshes and two timepoints in coastal Nova Scotia. Based on ITS2 Illumina miSeq rDNA data and multivariate analysis, neither sediment zone nor collection period correlated with fungal ASV richness, but collection site did. However, Shannon diversity indicated that sediment zone played a significant role in fungal diversity

Halomethanes (e.g., CH3Cl, CH3Br, CH3I and CHBr3) are ozone‐depleting compounds that, in contrast to the human‐made chlorofluorocarbons, marine organisms synthesize naturally. Therefore, their production cannot be totally controlled by human action. However, identifying all their natural sources and understanding their synthesis regulation can help to predict their production rates and their impact

Sponges have co‐evolved for millions of years alongside several types of microorganisms, which aside from participating in the animal's diet, are mostly symbionts. Since most of the genetic repertoire in the holobiont genome is provided by microbes, it is expected that the host‐associated microbiome will be at least partially heritable. Sponges can therefore acquire their symbionts in different ways

The stint of the bacterial species is convoluting, but the new algorithms to calculate genome‐to‐genome distance (GGD) and DNA–DNA hybridization (DDH) for comparative genome analysis have rejuvenated the exploration of species and sub‐species characterization. The present study reports the first whole genome sequence of Exiguobacterium profundum PHM11. PHM11 genome consist of ~ 2.92 Mb comprising 48

Pseudomonas putida BIRD‐1 is a microorganism that inhabits the rhizosphere and solubilizes phosphate and iron and produces indolacetic acid [Roca, A., Pizarro‐Tobías, P., Udaondo, Z., Fernández, M., Matilla, M.A., Molina‐Henares, M.A., et al. (2013) Analysis of plant growth‐promoting properties encoded by the genome of the rhizobacterium Pseudomonas putida BIRD‐1. Environ Microbiol 15: 780–794]. In

With rates of community‐associated Clostridium difficile infection (CA‐CDI) increasing worldwide, potential reservoirs/sources of C. difficile in the community are being sought. Since C. difficile is found in animal manure and human biosolids, which are composted for agricultural purposes, composted products could be a source. In this study, the presence of C. difficile in composted products, and their

Foraminifera host diverse microbial communities that can shift in response to changing environmental conditions. To characterize climate change impacts on the foraminifera microbiome across life stages, we exposed adult Marginopora vertebralis (Large Benthic Foraminifera) to pCO2 and temperature scenarios representing present‐day, 2050 and 2100 levels and raised juveniles under present‐day and 2050

The phenomenon of resistance of Escherichia coli strains in free‐living animals has been constantly expanding in recent years. However, the data are still fragmented and, due to the growing threat to public health, there is a constant need to search for and analyse new reservoirs and indicate their role and importance in the circulation of resistance genes in the environment. Therefore, the target

Relationships fueled by sulfide between deep‐sea invertebrates and bacterial symbionts are well known, yet the diverse overlapping factors influencing symbiont specificity are complex. For animals that obtain their symbionts from the environment, both host identity and geographic location can impact the ultimate symbiont partner. Bacterial symbionts were analysed for three co‐occurring species each

Predicting the future of our field can be an exciting and valuable thought experiment. For this exercise to be more than just wishful thinking, we set out to discuss some areas in environmental microbiology where we think current evidence suggests a particularly rapid change is taking place. To this end, through three imagined conversations, we explore some anticipated impacts on the current state

Principal challenges in environmental microbiology include determining the functions of specific microorganisms, when and where those functions change, and why. Unveiling this information for creatures on the micron scale is exquisitely difficult, but culturing microorganisms offers a sturdy experimental foundation for such queries. Unfortunately, bringing microbes into culture presents its own set

Plasmids are extrachromosomal genetic elements commonly found in prokaryotic (and sometime eukaryotic) cells. Small plasmids are often considered cryptic and their effect on the host is elusive, while large plasmids may encode functions that are essential for the host lifestyle and attain a secondary chromosome status. Plasmids are thus an important source of raw material for microbial genome evolution

Microbes need resources for energy and cellular building material. They also need access to clement conditions with liquid water and a cellular damage rate that is lower than repair. When deprived of resources and clement conditions, microbes often enter some form of dormancy (e.g., by ceasing cell division, slowing metabolic rate, or forming an endospore) until they can grow again (Lennon and Jones

During the 2019 United Nations Summit on Climate Change held in Madrid, also known as COP25, the European Commission announced new support for projects to improve soil health and fight global warming through sustainable agriculture. Discussions at the summit laid the foundation for defining the steps and guidelines necessary to ensure that agriculture and forestry practices adopt more environmentally

Relationships between collective scientific knowledge and country's economic prosperity and competitiveness have been described. Hence, interaction between industry and academic institutions is seen as a way to valorize this knowledge at social and economic levels. The ability to translate scientific knowledge in social and economic benefits is now receiving most of the funding for public research

Freshwater bloom‐forming cyanobacteria densely grow in the aquatic environments, leading to an increase in the viral‐contact rate. They possess numerous antiviral genes, as well as cell differentiation‐ and physiological performance‐related genes, owing to genome expansion. Their genomic features and unique lifestyles suggest that they coexist with cyanoviruses in ways different from marine cyanobacteria

Antimicrobial resistance among isolates from wild animals is increasingly reported. Extended‐spectrum beta‐lactamase (ESBL)‐producing Enterobacteriaceae, and particularly Escherichia coli, have spread worldwide as one of the most common multidrug‐resistant organisms. The aim of this study was to determine the carriage rate of ESBL‐producing E. coli isolates and their genetic characteristics in wild

Shewanella sp., the progenitors of blaOXA‐48‐like genes are increasingly reported with the possession of different blaOXA‐48‐like variants. This study aims to characterize blaOXA‐731, a new variant of a blaOXA‐48‐like gene identified in Shewanella sp. isolated from the aquatic environment in Myanmar. Phylogenetic analysis of the blaOXA‐731 sequence with other blaOXA‐48‐like variants showed that it

Dual stable isotope probing has been used to infer rates of microbial biomass production and modes of carbon fixation. In order to validate this approach for assessing archaeal production, the methanogenic archaeon Methanosarcina barkeri was grown either with H2, acetate or methanol with D2O and 13C‐dissolved inorganic carbon (DIC). Our results revealed unexpectedly low D incorporation into lipids

Escherichia coli O157:H7, a causative agent of haemolytic uremic syndrome, can enter into a viable but non‐culturable (VBNC) state in response to harsh stress. Bacteria in this state can retain membrane integrity, metabolic activity and virulence expression, which may present health risks. However, virulence expression and resuscitation ability of the VBNC state are not well understood. Here, we induced

Ideonella sakaiensis produces an enzyme, PETase, that is capable of hydrolyzing polyethylene terephthalate (PET) plastic. We demonstrate that although I. sakaiensis can grow on amorphous plastic, it does not grow on highly crystalline plastic under otherwise identical conditions. Both amorphous film and amorphous plastic obtained from commercial food containers support the growth of the bacteria, whereas

Vibrio cholerae form biofilm, which is essential for their survival under harsh environmental conditions. The eDNA produced during biofilm formation and interaction with other components like vibrio polysaccharide is less studied in Vibrio cholerae despite its importance in biofilm structure and stability. In this study, we selected two strains of V. cholerae, which produced sufficient extracellular

Microbial biocathodes are gaining interest due to their low cost, environmental friendliness and sustainable nature. In this study, a microbial consortium was enriched from activated sludge obtained from a common textile effluent treatment plant in the absence of organic carbon source to produce an electroactive biofilm. Chronoamperometry method of enrichment was carried out for over 70 days to select

Many Gram‐negative bacteria communicate by using homoserine lactones (HSLs) as quorum sensing (QS) signals in a cell density‐dependent manner. In addition to fatty acyl‐HSL (acyl‐HSL) signals, certain strains, most of them associated with plants, produce non‐canonical aryl‐HSLs such as cinnamoyl‐HSL. However, the role of aryl‐HSL in endophytic associations remained elusive. Bradyrhizobium sp. strain

Resistance‐Nodulation‐Division (RND) efflux pumps are relevant determinants of Stenotrophomonas maltophilia multidrug resistance as they can extrude a broad range of antibiotics and compounds involved in virulence and physiological functions. S. maltophilia, an environmental bacterium, was shown to be associated with amoebae and able to multiply inside them. To explore whether S. maltophilia RND efflux

The genome is the blueprint for life. A genome sequence can be transcribed and translated by molecular machines to assemble an organism capable of replication, sensation, and response. Organisms respond to each other, forming intricate interaction webs that manifest as ecosystems, defining the world we live in and rely on. It all starts with a genome. And if we can build a genome, we can create worlds

Soil microbiome is one of the most heterogeneous biological systems. State‐of‐the‐art molecular approaches such as those based on single‐amplified genomes (SAGs) and metagenome assembled‐genomes (MAGs) are now improving our capacity for disentailing soil microbial‐mediated processes. Here, we analysed publicly available datasets of soil microbial genomes and MAG's reconstructed from the Amazon's tropical

Microbial enzymes often occur as distinct variants that share the same substrate but differ in substrate affinity, sensitivity to environmental conditions, or phylogenetic ancestry. Determining where variants occur in the environment helps identify thresholds that constrain microbial cycling of key chemicals, including the greenhouse gas nitrous oxide (N2O). To understand the enzymatic basis of N2O

Antigen 43 (Ag43) is a self‐recognizing outer membrane protein of Escherichia coli expressed during intracellular growth and biofilm formation, suggesting a role in infection. The expression of agn43 is under phase variation control, meaning that there are regulatory mechanisms adjusting the percentage of agn43‐expressing cells in the population, in addition to mechanisms modulating the transcriptional

Vibrio cholerae O1, a natural inhabitant of estuarine environments, is found in a dormant, viable but non‐culturable (VBNC) state during interepidemic periods. Although the individual roles of abiotic factors affecting VBNC formation have been extensively studied, their interplay in driving this phenomenon remains largely unaddressed. Here, we identified that major abiotic factors synergize with low

Microbial communities play important roles in the biogeochemical cycling of carbon in the Earth's deep subsurface. Previously, we demonstrated changes to the microbial community structure of a deep aquifer (1.4 km) receiving 150 tons of injected supercritical CO2 (scCO2) in a geosequestration experiment. The observed changes support a key role in the aquifer microbiome for the thermophilic CO‐utilizing

The dimethylsulfoxide (DMSO) reductase family of enzymes has many subfamilies catalysing unique biogeochemical reactions. It also has many uncharacterized subfamilies. Comparative genomics predicted one such subfamily to participate in a key step of the chlorine cycle because of a conserved genetic association with chlorite dismutase, implying they produce chlorite through chlorate or perchlorate reduction

Surveys of microbial systems indicate that in many situations taxonomy and function may constitute largely independent (‘decoupled’) axes of variation. However, this decoupling is rarely explicitly tested experimentally, partly because it is hard to directly induce taxonomic variation without affecting functional composition. Here we experimentally evaluate this paradigm using microcosms resembling

Photosynthetic bacteria are abundant in alkaline, terrestrial hot springs and there is a long history of research on phototrophs in Yellowstone National Park (YNP). Hot springs provide a framework to examine the ecophysiology of phototrophs in situ because they provide natural gradients of geochemistry, pH and temperature. Phototrophs within the Cyanobacteria and Chloroflexi groups are frequently observed

Soluble ligand‐bound Mn(III) can support anaerobic microbial respiration in diverse aquatic environments. Thus far, Mn(III) reduction has only been associated with certain Gammaproteobacteria. Here, we characterized microbial communities enriched from Mn‐replete sediments of Lake Matano, Indonesia. Our results provide the first evidence for the biological reduction of soluble Mn(III) outside the Gammaproteobacteria

Microbes drive the majority of the global carbon cycle. The effect of environmental conditions on selecting microbial functional diversity is well established, and recent studies have revealed the effects of geographic distances on selecting the functional components of marine microbial communities. Our study is the first attempt at establishing the effects of environmental factors on driving the marine

Reef‐building corals live in a mutualistic relationship with photosynthetic algae (family Symbiodiniaceae) that usually provide most of the energy required by the coral host. This relationship is sensitive to temperature stress; as little as a 1°C increase often leads to the collapse of the association. This sensitivity has led to an interest in the potential of more stress‐tolerant algae to supplement

The recent emergence of Vibrio infections at high latitudes represents a clear human health risk attributable to climate change. Here, we investigate the population dynamics of three Vibrio species: Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae within a British coastal estuarine site, with contrasting salinity and temperature regimes during an intense heatwave event. Water samples

The extraordinary desiccation resistance of the opportunistic human pathogen Acinetobacter baumannii is a key to its survival and spread in medical care units. The accumulation of compatible solute such as glutamate, mannitol and trehalose contributes to the desiccation resistance. Here, we have used osmolarity as a tool to study the response of cells to low water activities and studied the role of

Knowledge of biofilm formation on pollutants in the marine realm is expanding, but how communities respond to substrates during colonization remains poorly understood. Here, we assess community assembly and respiration in response to two different micropollutants, virgin high‐density polyethylene (HDPE) microbeads and textile fibres under different light settings. Raman characterization, high‐throughput

A new autotrophic hydrogen‐oxidizing Chromatiaceae bacterium, namely bacterium CTD079, was enriched from a water column sample at 1500 m water depth in the southern Pacific Ocean. Based on the phylogeny of 16S rRNA genes, it was closely related to a scaly snail endosymbiont (99.2% DNA sequence identity) whose host so far is only known to colonize hydrothermal vents along the Indian ridge. The average

Following the publication of the article by Bray et al. (2020), the authors alerted the Journal to the fact that, in Figure 1, the boxes for amino acids 24, 27, 32, 50, 51, and 57 are incorrectly aligned. The amended Figure is shown below. The Publisher apologises for the mistake. Figure 1 Open in figure viewerPowerPoint Basis for distinguishing e‐pilins from other pilins. Top: Alignment showing the