Soil biomes are vast, exceptionally diverse and crucial to the health of ecosystems and societies. Soils also contain an appreciable, but understudied, diversity of opportunistic human pathogens. With climate change and other forms of environmental degradation potentially increasing exposure risks to soilborne pathogens, it is necessary to gain a better understanding of their ecological drivers. Here

The filamentous chlorophyte Ostreobium sp. dominates shallow marine carbonate microboring communities, and is one of the major agents of reef bioerosion. While its large genetic diversity has emerged, its physiology remains little known, with unexplored relationship between genotypes and phenotypes (endolithic versus free‐living growth forms). Here, we isolated 9 strains affiliated to 2 lineages of

The common polysaccharide antigen (CPA) of the lipopolysaccharide (LPS) from Pseudomonas syringae is highly variable, but the genetic basis for this is poorly understood. We have characterised the CPA locus from P. syringae pv. actinidiae (Psa). This locus has genes for L‐ and D‐rhamnose biosynthesis and an operon coding for ABC transporter subunits, a bifunctional glycosyltransferase and an O‐methyltransferase

An unusually high lipid content and a complex lipid profile are the most distinctive features of the mycobacterial cell envelope. However, our understanding of the regulatory mechanism underlying mycobacterial lipid metabolism is limited, and the major regulators responsible for lipid homeostasis remain to be characterized. Here, we identified MmbR as a novel master regulator that is essential for

Among the mechanisms by which yeast overcomes multiple stresses is the expression of genes encoding ATP‐binding cassette (ABC) transporters required for resistance to a wide range of toxic compounds. These substrates may include weak acids, alcohols, agricultural pesticides, polyamines, metal cations, as in the case of Pdr18. This pleotropic drug resistance transporter was previously proposed to transport

Filamentous fungi are known as producers of a large array of diverse secondary metabolites (SMs) that aid in securing their environmental niche. Here, we demonstrated that the SMs have an additional role in fungal defence against other fungi: Trichoderma guizhouense, a mycoparasite, is able to antagonize Fusarium oxysporum f. sp. cubense race 4 (Foc4) by forming aerial hyphae that kill the host with

Microbialites are usually carbonate‐rich sedimentary rocks formed by the interplay of phylogenetically and metabolically complex microbial communities with their physicochemical environment. Yet, the biotic and abiotic determinants of microbialite formation remain poorly constrained. Here, we analyzed the structure of prokaryotic and eukaryotic communities associated with microbialites occurring in

Plants quickly accumulate reactive oxygen species (ROS) to resist against pathogen invasion, while pathogens strive to escape host immune surveillance by degrading ROS. However, the nature of the strategies that fungal pathogens adopt to counteract host‐derived oxidative stress is manifold, and requires deep investigation. In this study, a superoxide dismutase (SOD) from Puccinia striiformis f. sp

Magnetotactic bacteria (MTB) are diverse prokaryotes that produce magnetic nanocrystals within intracellular membranes (magnetosomes). Here, we present a large‐scale analysis of diversity and magnetosome biomineralization in modern magnetotactic cocci, which are the most abundant MTB morphotypes in nature. Nineteen novel magnetotactic cocci species are identified phylogenetically and structurally at

Uncultivable microbial communities provide enormous reservoirs of enzymes, but their experimental identification by functional metagenomics is challenging, mainly due to the difficulty of screening enormous metagenomic libraries. Here, we propose a reliable and convenient ultrahigh‐throughput screening platform based on flow cytometric droplet sorting (FCDS). The FCDS platform employs water‐in‐oil‐in‐water

It remains unknown whether and to what extent marine prokaryotic communities are capable of degrading plastic in the ocean. To address this knowledge gap, we combined enrichment experiments employing low‐density polyethylene (LDPE) as the sole carbon source with a comparison of bacterial communities on plastic debris in the Pacific, the North Atlantic and the northern Adriatic Sea. A total of 35 operational

To many scientists and political authorities, the development of a vaccine against Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) will be the way to restore normality to civil life in this time of a devastating pandemic. Expectations for a vaccine are high while the case numbers continue to rise. As of mid‐August 2020, more than 20 million people have been infected and more than 760 000

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 that target EcLamB. Here, we developed a simple method for isolating novel environmental phages in a predictable way, i.e. isolating phages that target a

Holobiont phenotype results from a combination of host and symbiont genotypes as well as from prevailing environmental conditions that alter the relationships among symbiotic members. Corals exemplify this concept, where shifts in the algal symbiont community can lead to some corals becoming more or less thermally tolerant. Despite linkage between coral bleaching and disease, the roles of symbiotic

Under ocean warming and acidification, diatoms use a unique acclimation and adaptation strategy by saving energy and utilizing it for other cellular processes. However, the molecular mechanisms that underlie this reprogramming of energy utilization are currently unknown. Here, we investigate the metabolic reprogramming of the ecologically important diatom Skeletonema dohrnii grown under two different

Sulfurimonas species (class Campylobacteria, phylum Campylobacterota) were globally distributed and especially predominant in deep‐sea hydrothermal environments. They were previously identified as chemolithoautotrophic sulfur‐oxidizing bacteria (SOB), whereas little is known about their potential in sulfur reduction. In this report, we found that the elemental sulfur reduction is quite common in different

Motivated to find options for prevention or intervention, molecular epidemiology aims to identify the host and microbial factors that determine the transmission, manifestation and progression of infectious disease. The genotyping of cultivatable bacterial strains is performed by either anonymous fingerprinting techniques or sequence‐based exploration of variable genomic sites. Multilocus sequence typing

Nanoparticles are ubiquitous and co‐occur with microbial life in every environment on Earth. Interactions between microbes and nanoparticles impact the biogeochemical cycles via accelerating various reaction rates and enabling biological processes at the smallest scales. Distinct from microbe‐mineral interactions at large, microbe‐nanoparticle interactions may involve higher levels of active recognition

The acquisition of the infant gut microbiota is key to establishing a host‐microbiota symbiosis. Microbially produced metabolites tightly interact with the immune system, and the fermentation‐derived short‐chain fatty acid butyrate is considered an important mediator linked to chronic diseases later in life. The intestinal butyrate‐forming bacterial population is taxonomically and functionally diverse

Phasin PhaF, a multifunctional protein associated with the surface of polyhydroxyalkanoate (PHA) granules that also interacts with the nucleoid, contributes significantly to PHA biogenesis in pseudomonads. As a protein present on the surface of PHA granules, PhaF participates in granule stabilization and segregation, whereas its deletion has a notable impact on overall transcriptome, PHA accumulation

The Gram‐positive bacterium Bacillus subtilis uses serine not only as a building block for proteins but also as an important precursor in many anabolic reactions. Moreover, a lack of serine results in the initiation of biofilm formation. However, excess serine inhibits the growth of B. subtilis. To unravel the underlying mechanisms, we isolated suppressor mutants that can tolerate toxic serine concentrations

The lithified oceanic crust, lower crust gabbros in particular, has remained largely unexplored by microbiologists. Recently, evidence for heterogeneously distributed viable and transcriptionally active autotrophic and heterotrophic microbial populations within low‐biomass communities was found down to 750 m below the seafloor at the Atlantis Bank Gabbro Massif, Indian Ocean. Here, we report on the

The Southern Ocean remains one of the least explored marine environments. The investigation of temporal microbial dynamics has thus far been hampered by the limited access to this remote ocean. We present here high‐resolution seasonal observations of the prokaryotic community composition during phytoplankton blooms induced by natural iron fertilization. A total of 18 seawater samples were collected

Marine sponge reefs usually comprise a complex array of taxonomically different sponge species, many of these hosting highly diverse microbial communities. The number of microbial species known to occupy a given sponge ranges from tens to thousands, bringing numerous challenges to their analysis. One way to deal with such complexity is to use a core microbiota approach, in which only prevalent and

Assembling microbial and viral genomes from metagenomes is a powerful and appealing method to understand structure–function relationships in complex environments. To compare the recovery of genomes from microorganisms and their viruses from groundwater, we generated shotgun metagenomes with Illumina sequencing accompanied by long reads derived from the Oxford Nanopore Technologies (ONT) sequencing

We analysed a widely used barcode, the V9 region of the 18S rRNA gene, to study the effect of environmental conditions on the distribution of two related heterotrophic protistan lineages in marine plankton, kinetoplastids and diplonemids. We relied on a major published dataset (Tara Oceans) where samples from the mesopelagic zone were available from just 32 of 123 locations, and both groups are most

Investigation of niche specialization in microbial communities is important in assessing consequences of environmental change for ecosystem processes. Ammonia oxidizing bacteria (AOB) and archaea (AOA) present a convenient model for studying niche specialization. They coexist in most soils and effects of soil characteristics on their relative abundances have been studied extensively. This study integrated

Adaptation of lipid membrane composition is an important component of archaeal homeostatic response. Historically, the number of cyclopentyl and cyclohexyl rings in the glycerol dibiphytanyl glycerol tetraether (GDGT) Archaeal lipids has been linked to variation in environmental temperature. However, recent work with GDGT‐making archaea highlight the roles of other factors, such as pH or energy availability

The aromatic hydrocarbon naphthalene, which occurs in coal and oil, can be degraded by aerobic or anaerobic microorganisms. A wide‐spread electron acceptor for the latter is sulfate. Evidence for in situ naphthalene degradation stems in particular from the detection of 2‐naphthoate and [5,6,7,8]‐tetrahydro‐2‐naphthoate in oil field samples. Because such intermediates are usually not detected in laboratory

Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Japanese deep freshwater lakes. However, their distribution and abundances in freshwater ecosystems remain unknown. We assessed abundance and diversity of diplonemids from several geographically distant deep

Like all macroorganisms, plants have to control bacterial biofilm formation on their surfaces. On the other hand, biofilms are highly tolerant against antimicrobial agents and other stresses. Consequently, biofilms are also involved in human chronic infectious diseases, which generates a strong demand for anti‐biofilm agents. Therefore, we systematically explored major plant flavonoids as putative

Serendipita vermifera ssp. bescii, hereafter referred to as S. bescii, is a root‐associated fungus that promotes plant growth in both its native switchgrass host, and a variety of monocots and dicots. Winter wheat (Triticum aestivum L.), a dual‐purpose crop, used for both forage and grain production, significantly contributes to the agricultural economies of the Southern Great Plains, USA. In this

Current studies show that multispecies forests are beneficial regarding biodiversity and ecosystem functionality. However, there are only little efforts to understand the ecological mechanisms behind these advantages of multispecies forests. Bacteria are among the key plant growth‐promoting microorganisms that support tree growth and fitness. Thus, we investigated links between bacterial communities

An anaerobic enrichment with CO from sediments of hypersaline soda lakes resulted in a methane‐forming binary culture, whereby CO was utilized by a bacterium and not the methanogenic partner. The bacterial isolate ANCO1 forms a deep‐branching phylogenetic lineage at the level of a new family within the class "Natranaerobiia". It is an extreme haloalkaliphilic and moderate thermophilic acetogen utilizing

The plant endosphere is colonized by complex microbial communities and microorganisms, which colonize the plant interior at least part of their lifetime and are termed endophytes. Their functions range from mutualism to pathogenicity. All plant organs and tissues are generally colonized by bacterial endophytes and their diversity and composition depend on the plant, the plant organ and its physiological

Chemoautotrophic bacteria from the SUP05 clade often dominate anoxic waters within marine oxygen minimum zones (OMZs) where they use energy gained from the oxidation of reduced sulfur to fuel carbon fixation. Some of these SUP05 bacteria are facultative aerobes that can use either nitrate or oxygen as a terminal electron acceptor making them ideally suited to thrive at the boundaries of OMZs where

Although studies of biogeography in soil bacterial communities have attracted considerable attention, the generality of these patterns along with assembly processes and underlying drivers is poorly understood in the inner tissues of plants. Plant tissues provide unique ecological habitats for microorganisms, which play an essential role in plant performance. Here, we compared core bacterial communities

Plant‐associated microbes influence plant performance and may also impact biotic and abiotic stress tolerance. The microbiome of mulberry trees planted for ecological restoration in the hydro‐fluctuation belt of the Three Gorges Reservoir Region, China, exhibited distinct patterns of localization. The endosphere exhibited lower α‐diversity relative to the rhizosphere, but was more closely related to

Zinc surplus in yeast cells has been previously investigated thanks to transcriptomic studies by using traditionally Saccharomyces cerevisiae as a model. However, proteome response under zinc‐replete conditions needs to be further studied in yeast. For that reason, eight yeast strains from seven different species were inoculated in zinc‐depleted and zinc‐replete media. The quantitative and qualitative

In vitro studies in plant, soil, and human systems have shown that microbial volatiles can mediate microbe–microbe or microbe–host interactions. These previous studies have often used artificially high concentrations of volatiles compared to in situ systems and have not demonstrated the roles volatiles play in mediating community‐level dynamics. We used the notoriously volatile cheese rind microbiome

Cyanophages encode host‐derived genes that may increase their fitness. We examined the relative abundance of 18 host‐derived cyanophages genes in metagenomes and viromes along depth profiles from the Eastern Tropical North Pacific Oxygen Deficient Zone (ETNP ODZ) where Prochlorococcus dominates a secondary chlorophyll maximum within the ODZ. Cyanophages at the oxic primary chlorophyll maximum encoded

Diverse communities of fungi and bacteria in deadwood mediate wood decay. While rates of decomposition vary greatly among woody species and spatially distinct habitats, the relative importance of these factors in structuring microbial communities and whether these shift over time remains largely unknown. We characterized fungal and bacterial diversity within pieces of deadwood that experienced 6.3–98

To assess the comparability between taxonomic identification methods for phytoplankton, multiple approaches were used to characterize phytoplankton community composition within the Neuse River Estuary (NRE), North Carolina. Small subunit 18S rRNA gene sequencing and accessory pigment analysis displayed similar trends, indicating chlorophytes were the dominant microalgal group during most of the year

Thermococcales has a strong adaptability to extreme environments, which is of profound interest in explaining how complex life forms emerge on earth. However, their gene composition, thermal stability and evolution in hyperthermal environments are still little known. Here, we characterized the pan‐genome architecture of 30 Thermococcales species to gain insight into their genetic properties, evolutionary

Direct electron uptake is emerging as a key process for electron transfer in anaerobic microbial communities, both between species and from extracellular sources, such as zero‐valent iron (Fe0) or cathodic surfaces. In this study, we investigated cathodic electron uptake by Fe0‐corroding Desulfovibrio ferrophilus IS5 and showed that electron uptake is dependent on direct cell contact via a biofilm

Cadmium (Cd) is a common toxic heavy metal in the environment, and bacteria have evolved different strategies against Cd‐toxicity. Here we found that marine bacterium Bacillus sp. 98 could significantly alleviate Cd‐toxicity by recruiting calcium (Ca) for reducing excessive intracellular nitric oxide (NO) and enhancing iron acquisition. To investigate the underlying mechanisms, mass spectrometry‐based

Interactions between phytoplankton and bacteria play major roles in global biogeochemical cycles and oceanic nutrient fluxes. These interactions occur in the microenvironment surrounding phytoplankton cells, known as the phycosphere. Bacteria in the phycosphere use either chemotaxis or attachment to benefit from algal excretions. Both processes are regulated by quorum sensing (QS), a cell–cell signalling

In the oceans, viruses that infect bacteria (phages) influence a variety of microbially‐mediated processes that drive global biogeochemical cycles. The nature of their influence is dependent upon infection mode, be it lytic or lysogenic. Temperate phages are predicted to be prevalent in marine systems where they are expected to execute both types of infection modes. Understanding the range and outcomes

Most microorganisms from deep terrestrial subsurface remain yet uncultured. Recent achievements in recovery of metagenome‐assembled genomes (MAG) provide clues for improving cultivation via metabolic reconstructions and other genomic characteristics. Here we report the isolation in pure culture of a thermophilic spirochete with the use of MAGs binned from metagenomes of the deep (>2 km) aquifers broached

The soils of the McMurdo Dry Valleys (MDV) of Antarctica are established models for understanding fundamental processes in soil ecosystem functioning (e.g. ecological tipping points, community structuring and nutrient cycling) because the extreme physical environment drastically reduces biodiversity and ecological complexity. Understanding the functioning of MDV soils requires in‐depth knowledge of

Acinetobacter baumannii is an opportunistic pathogen which has become a rising threat in healthcare facilities worldwide due to increasing antibiotic resistances and optimal adaptation to clinical environments and the human host. We reported in a former publication on the identification of three phopholipases of the phospholipase D (PLD) superfamily in A. baumannii ATCC 19606T acting in concerted manner

Healthcare and preventable disease The fundamental role of healthcare systems is minimisation of preventable morbidity and mortality in the population. Notwithstanding, despite their central role in promoting health and preserving and improving the well‐being of society, budgetary constraints limit accessibility and services provided to the population, resulting in preventable disease (OECD, 2015)

Coral reefs are facing increasing pressure from rising seawater temperatures and ocean acidification. Sponges have been proposed as possible winners in the face of climate change; however, little is known about the mechanisms underpinning their predicted tolerance. Here we assessed whether microbiome‐mediated cross‐generational acclimatization could enable the photosynthetic sponge Carteriospongia

Pseudoalteromonas luteoviolacea is a globally distributed marine bacterium that stimulates the metamorphosis of marine animal larvae, an important bacteria–animal interaction that can promote the recruitment of animals to benthic ecosystems. Recently, different P. luteoviolacea isolates have been shown to produce two stimulatory factors that can induce tubeworm and coral metamorphosis; Metamorphosis‐Associated

Plants and microbes have evolved sophisticated ways to communicate and coexist. The simplest interactions that occur in plant‐associated habitats, i.e., those involved in disease detection, depend on the production of microbial pathogenic and virulence factors and the host's evolved immunological response. In contrast, microbes can also be beneficial for their host plants in a number of ways, including

Oceanic oxygen minimum zones (OMZs) play a pivotal role in biogeochemical cycles due to extensive microbial activity. How OMZ microbial communities assemble and respond to environmental variation is therefore essential to understanding OMZ functioning and ocean biogeochemistry. Sampling along depth profiles at five stations in the eastern tropical North Pacific Ocean (ETNP), we captured systematic

Bacteria of the phylum Verrucomicrobia are ubiquitous in marine environments and can be found as free‐living organisms or as symbionts of eukaryotic hosts. Little is known about host‐associated Verrucomicrobia in the marine environment. Here we reconstructed two genomes of symbiotic Verrucomicrobia from bacterial metagenomes derived from the Atlanto‐Mediterranean sponge Petrosia ficiformis and three

Resistance Nodulation cell Division (RND) efflux pumps are known to contribute to the tolerance of Pseudomonas putida to aromatic hydrocarbons, but their role in antibiotic resistance has not been fully elucidated. In this study, two types of single‐step multidrug‐resistant (MDR) mutants were selected in vitro from reference strain KT2440. Mutants of the first type were more resistant to fluoroquinolones