Marine heterotrophic prokaryotes (HP) play a key role in organic matter processing in the ocean; however, the view of HP as dissolved organic matter (DOM) sources remains underexplored. In this study, we quantified and optically characterized the DOM produced by two single marine bacterial strains. We then tested the availability of these DOM sources to in situ Mediterranean Sea HP communities. Two

The photolyases PHR1 and PHR2 enable photorepair of fungal DNA lesions in the forms of UV‐induced cyclobutane pyrimidine dimer (CPD) and (6‐4)‐pyrimidine‐pyrimidone (6‐4PP) photoproducts, but their regulation remains mechanistically elusive. Here, we report that the white collar proteins WC1 and WC2 mutually interacting to form a light‐responsive transcription factor regulate photolyase expression

Genomic data have identified a class of fungal specific transcription factors (FsTFs) that are thought to regulate unique aspects of fungal gene expression, although the functions of many of these proteins remain unknown. Here, a novel FsTF (BbStf1), which features a leucine zipper dimerization domain and a fungal transcription factor regulatory middle homology region, was characterized in Beauveria

While the environment is considered the primary origin of the plant microbiome, the potential role of seeds as a source of transmitting microorganisms has not received much attention. Here we tested the hypothesis that the plant microbiome is partially inherited through vertical transmission. An experimental culturing device was constructed to grow oak seedlings in a microbe‐free environment while

Kombucha is a multispecies microbial ecosystem mainly composed by acetic acid bacteria and osmophilic acid‐tolerant yeasts, which is used to produce a probiotic drink. Furthermore, Kombucha Mutualistic Community (KMC) has been recently proposed to be used during long space missions as both a living functional fermented product to improve astronauts’ health and an efficient source of bacterial nanocellulose

Dimethylsulfoniopropionate (DMSP) is an important organic carbon and sulfur source in the surface ocean that fuels microbial activity and significantly impacts Earth's climate. After three decades of research, the cellular role(s) of DMSP and environmental drivers of production remain enigmatic. Recent work suggests that cellular DMSP concentrations, and changes in these concentrations in response

Symbiotic association is universal in nature, and an array of symbionts play a crucial part in host life history. Aphids and their diverse symbionts have become a good model system to study insect‐symbiont interactions. Previous symbiotic diversity surveys have mainly focused on a few aphid clades, and the relative importance of different factors regulating microbial community structure is not well

Citrobacter spp., Enterobacter hormaechei subsp., Klebsiella variicola and Proteae tribe members are rarely isolated Enterobacterales increasingly implicated in nosocomial infections. Herein, we show that these species contain multiple genes encoding resistance to important antibiotics and are widely and globally distributed, being isolated from human, animal, plant, and environmental sources in 67

Members of the bacterial order Rickettsiales are obligatorily associated with a wide range of eukaryotic hosts. Their evolutionary trajectories, in particular concerning the origin of shared or differential traits among distant sub‐lineages, are still poorly understood. Here we characterised a novel Rickettsiales bacterium associated with the ciliate Paramecium tredecaurelia, and phylogenetically related

Microbial communities are essential for a healthy soil ecosystem. Metals and radionuclides can exert a persistent pressure on the soil microbial community. However, little is known on the effect of long‐term co‐contamination of metals and radionuclides on the microbial community structure and functionality. We investigated the impact of historical discharges of the phosphate and nuclear industry on

Our lower gastrointestinal tract plays host to a vast consortium of microbes, known as the human gut microbiota (HGM). The HGM thrives on a complex and diverse range of glycan structures from both dietary and host sources, the breakdown of which requires the concerted action of cohorts of carbohydrate‐active enzymes (CAZymes), carbohydrate‐binding proteins, and transporters. The glycan utilization

Geobacter sulfurreducens is a model bacterium to study the degradation of organic compounds coupled to the reduction of Fe(III). The response of G. sulfurreducens to the electron donors acetate, formate, hydrogen and a mixture of all three with Fe(III) citrate as electron acceptor was studied using comparative physiological and proteomic approaches. Variations in the supplied electron donors resulted

Bacteria and fungi are of uttermost importance in determining environmental and host functioning. Despite close interactions between animals, plants, their associated microbiomes, and the environment they inhabit, the distribution and role of bacteria and especially fungi across host and environments as well as the cross‐habitat determinants of their community compositions remain little investigated

Microbial taxon–taxon co‐occurrences may directly or indirectly reflect the potential relationships between the members within a microbial community. However, to what extent and the specificity by which these co‐occurrences are influenced by environmental factors remains unclear. In this report, we evaluated how the dynamics of microbial taxon–taxon co‐occurrence is associated with the changes of environmental

Recent discoveries of mcr and mcr‐like genes in genomes from diverse archaeal lineages suggest that methane metabolism is an ancient pathway with a complicated evolutionary history. One conventional view is that methanogenesis is an ancestral metabolism of the class Thermoplasmata. Through comparative genomic analysis of 12 Thermoplasmata metagenome‐assembled genomes (MAGs) basal to the Methanomassiliicoccales

Understanding the processes guiding microbial community assembly in soils is essential for predicting microbiome structure and function following soil disturbance events like agricultural soil fumigation. However, assembly outcomes are complex and variable, being affected by both selective abiotic forces and by the history of colonizing microorganisms. To untangle the interactions between these factors

High‐quality microbiome research relies on the integrity, management and quality of supporting data. Currently biobanks and culture collections have different formats and approaches to data management. This necessitates a standard data format to underpin research, particularly in line with the FAIR data standards of findability, accessibility, interoperability and reusability. We address the importance

Cyanobacteria are globally important primary producers and nitrogen fixers with high iron demands. Low ambient dissolved iron concentrations in many aquatic environments mean that these organisms must maintain sufficient and selective transport of iron into the cell. However, the nature of iron transport pathways through the cyanobacterial outer membrane remains obscure. Here we present multiple lines

Ecological assembly processes, by influencing community composition, determine ecosystem functions of microbiomes. However, debate remains on how stochastic versus deterministic assembly processes influence ecosystem functions such as carbon and nutrient cycling. Towards a better understanding, we investigated three types of agroecosystems (the upland, paddy, and flooded) that represent a gradient

Raphidiopsis raciborskii is an invasive bloom‐forming cyanobacteria with the flexibility to utilize atmospheric and fixed nitrogen. Since nitrogen‐fixation has a high requirement for iron as an ezyme cofactor, we hypothesize that iron availability would determine the success of the species under nitrogen‐fixing conditions. This study compares the proteomic response of cylindrospermopsin‐producing and

Cu(II)‐enhanced microbial Cr(VI) reduction is common in the environment, yet its mechanism is unknown. The specific activity of chromate reductase, NfoR, from Staphylococcus aureus sp. LZ‐01 was augmented 1.5‐fold by Cu(II). Isothermal titration calorimetry and spectral data show that Cu(II) binds to NfoR nonspecifically. Further, Cu(II) stimulates the nitrobenzene reduction of NfoR, indicating that

Gut microbiota could facilitate host to defense diseases, but fish–microbiota interactions during viral infection and the underlying mechanism are poorly understood. We examined interactions and responses of gut microbiota to grass carp reovirus (GCRV) infection in Ctenopharyngodon idellus, which is the most important aquaculture fish worldwide. We found that GCRV infection group with serious haemorrhagic

Microbial communities have important functions during spring phytoplankton blooms, regulating bloom dynamics and processing organic matter. Despite extensive research into such processes, an in‐depth assessment of the fungal component is missing, especially for the smaller size fractions. We investigated the dynamics of unicellular mycoplankton during a spring phytoplankton bloom in the North Sea by

Soil functions and processes are driven by complex microbial interactions. It is, therefore, critical to understand the coexistence patterns of soil microbiota, especially in fragile alpine ecosystems. We identified biogeographic patterns in the network‐level topological features of the soil microbial co‐occurrence network in the Tibetan alpine grasslands, based on high‐throughput sequencing. We verified

Assessing the extent of parasite diversity requires the application of appropriate molecular tools, especially given the growing evidence of multiple parasite co‐occurrence. Here, we compared the performance of a next‐generation sequencing technology (Ion PGM ™ System) in 12 Bombus terrestris specimens that were PCR‐identified as positive for trypanosomatids (Leishmaniinae) in a previous study. These

The heterogeneous nature of lotic habitats plays an important role in the complex ecological and evolutionary processes that structure the microbial communities within them. Due to such complexity, our understanding of lotic microbial ecology still lacks conceptual frameworks for the ecological processes that shape these communities. We explored how bacterial community composition and underlying ecological

Acetobacterium woodii utilizes the Wood‐Ljungdahl pathway for reductive synthesis of acetate from carbon dioxide. However, A. woodii can also perform non‐acetogenic growth on 1,2‐propanediol (1,2‐PD) where instead of acetate, equal amounts of propionate and propanol are produced as metabolic end products. Metabolism of 1,2‐PD occurs via encapsulated metabolic enzymes within large proteinaceous bodies

Natural chromosomal transformation (CT) plays a major role in prokaryote evolution, yet factors that govern the integration of DNA from related species remain poorly understood. We show that in naturally competent Bacillus subtilis cells the acquisition of homeologous sequences is governed by sequence divergence (SD). Integration initiates in a minimal efficient processing segment via homology‐directed

Bradyrhizobia are common members of soil microbiomes and known as N2‐fixing symbionts of economically important legumes. Many are also denitrifiers, which can act as sinks or sources for N2O. Inoculation with compatible rhizobia is often needed for optimal N2‐fixation, but the choice of inoculant may have consequences for N2O emission. Here, we determined the phylogeny and denitrification capacity

Geoactive fungi play a significant role in bioweathering of rock and mineral substrates. Monazite is a phosphate mineral containing the rare earth elements (REE) cerium, lanthanum and neodymium. Little is known about geomicrobial transformations of REE‐bearing minerals which are also relevant to REE biorecovery from terrestrial and extra‐terrestrial reserves. The geoactive soil fungus Aspergillus niger

As a young bacteriologist just launching my career during the early days of the “microbial revolution” in the 1980s, I was fortunate to participate and collaborate in some early discoveries, and the development of cross‐disciplinary methodological approaches. These are facilitating engagement in more holistic studies more linking reductionist laboratory studies with more holistic observational studies

Plant pathogens usually originate and diversify in geographical regions where hosts and pathogens co‐evolve. Erysiphe necator, the causal agent of grape powdery mildew, is a destructive pathogen of grapevines worldwide. Although Eastern US is considered the center of origin and diversity of E. necator, previous reports on resistant native wild and domesticated Asian grapevines suggest Asia as another

Inefficient syntrophic propionate degradation causes severe operating disturbances and reduces biogas productivity in many high‐ammonia anaerobic digesters, but propionate‐degrading microorganisms in these systems remain unknown. Here, we identified candidate ammonia‐tolerant syntrophic propionate‐oxidising bacteria using propionate enrichment at high ammonia levels (0.7–0.8 g NH3 L−1) in continuously‐fed

Metagenomics and single‐cell genomics have enabled the discovery of relevant uncultured microbes. Recently, single‐virus genomics (SVG), although still in an incipient stage, has opened new avenues in viral ecology by allowing the sequencing of one single virus at a time. The investigation of methodological alternatives and optimization of existing procedures for SVG is paramount to deliver high‐quality

Iron is an essential nutrient for bacterial growth and the cause of a fierce battle between the pathogen and host during infection. Bacteria have developed several strategies to access iron from the host, the most common being the production of siderophores, small iron‐chelating molecules secreted into the bacterial environment. The opportunist pathogen Pseudomonas aeruginosa produces two siderophores

Despite its environmental robustness Pseudomonas putida strain KT2440 is very sensitive to DNA damage and displays poor homologous recombination efficiencies. To gain an insight into this deficiency isogenic ∆recA and ∆lexA1 derivatives of prophage‐free strain P. putida EM173 were generated and responses of the recA and lexA1 promoters to DNA damage tested with GFP reporter technology. Basal expression

Glutamine synthetase (GS), a central nitrogen metabolic enzyme, plays important roles in the nitrogen regulation network and secondary metabolism in fungi. However, the mechanisms by which external nitrogen sources regulate fungal GS activity have not been determined. Here, we found that GS activity was inhibited under nitrate conditions in Ganoderma lucidum. By constructing gs‐silenced strains and

Fusarium graminearum is an important worldwide pathogen that causes Fusarium head blight (FHB) in wheat, barley, maize, and other grains. LncRNAs play important roles in many biological processes, but little is known about their functions and mechanisms in filamentous fungi. Here, we report that a natural antisense RNA, GzmetE‐AS, is transcribed from the opposite strand of GzmetE. GzmetE encodes a

Current method for obtaining microbial colonies still relies on traditional dilution and spreading plate (DSP) procedures, which is labor‐intensive, skill‐dependent, low‐throughput and inevitably causing dilution‐to‐extinction of rare microorganisms. Herein, we proposed a novel ultrasonic spraying inoculation (USI) method that disperses microbial suspensions into millions of aerosols containing single

Secreted proteins are key players in fungal physiology and cell protection against external stressing agents and antifungals. Oak stress‐induced protein 1 (OSIP1) is a fungal‐specific protein with unknown function. By using Podospora anserina and Phanerochaete chrysosporium as models, we combined both in vivo functional approaches and biophysical characterization of OSIP1 recombinant protein. The P

Due to climate warming, alpine ecosystems are changing rapidly. Ongoing upward migrations of plants and thus an increase of easily decomposable substrates will strongly affect the soil microbiome. To understand how belowground communities will respond to such changes, we set up an incubation experiment with permafrost and active soil layers from northern (NW) and southern (SE) slopes of a mountain

A diverse set of bacteria live on the above‐ground parts of plants, composing the phyllosphere, and play important roles for plant health. Phyllosphere microbial communities assemble in a predictable manner and diverge from communities colonizing other plant organs or the soil. However, how these communities differ functionally remains obscure. We assembled a collection of 258 bacterial isolates representative

Fungi represent a group of eukaryotic microorganisms that are an important part of the plant microbiome. They produce a vast array of metabolites, including fungal volatile organic compounds (fVOCs). However, the diversity and biological activities of fVOCs emitted by the mycobiota of plants native to arid and semi‐arid environments remains under‐explored.

Waterbodies such as lakes and ponds are fragile environments affected by human influences. Suitable conditions can result in massive growth of phototrophs, commonly referred to as phytoplankton blooms. Such events benefit heterotrophic bacteria able to use compounds secreted by phototrophs or their biomass as major nutrient source. One example of such bacteria are Planctomycetes, which are abundant

Crop plants carry an enormous diversity of microbiota that provide massive benefits to hosts. Protists, as the main microbial consumers and a pivotal driver of biogeochemical cycling processes, remain largely understudied in the plant microbiome. Here, we characterized the diversity and composition of protists in sorghum leaf phyllosphere, and rhizosphere and bulk soils, collected from an 8‐year field

Type IV pili (T4P) are bacterial surface‐exposed appendages that have been extensively studied in Gram‐negative pathogenic bacteria. Despite recent sequencing efforts, little is known regarding these structures in non‐pathogenic anaerobic Gram‐positive species, particularly commensals of the mammalian gut. Early studies revealed that T4P in two ruminal Gram‐positive species are associated with growth

A substantial amount of below‐ground carbon (C) is suggested to be associated with fungi, which may significantly affect the soil C balance in forested ecosystems. Ergosterol from in‐growth mesh bags and litterbags was used to estimate fungal biomass production and community composition in drained peatland forests with differing fertility. Extramatrical mycelia (EMM) biomass production was generally

Subseafloor oceanic crust is a vast yet poorly sampled habitat for life. Recent studies suggest that microbial composition in crustal habitats is variable in space and time, but biogeographic patterns are difficult to determine due to a paucity of data. To address this, we deployed hundreds of mineral colonization experiments at and below the seafloor for 4–6 years at North Pond, a borehole observatory

Laccases are widely present in bacteria, fungi, plants and invertebrates and involved in a variety of physiological functions. Here, we report that Beauveria bassiana, an economic important entomopathogenic fungus, secretes a laccase 2 (BbLac2) during infection that detoxifies insect immune response‐generated reactive oxygen species (ROS) and interferes with host immune phenoloxidase (PO) activation

During the COVID‐19 pandemic, governments face difficult decisions when being confronted with public health threats and economic needs. Decision making is further complicated by the different perception of the pandemic by the public. Politicians as well as the public need objective facts for guidance and numbers play here a crucial role. The current contribution compiles numbers for infections, cases

Kelps are dominant primary producers in temperate coastal ecosystems. Large amounts of kelp biomass can be exported to the seafloor during the algal growth cycle or following storms, creating new ecological niches for the associated microbiota. Here, we investigated the bacterial community associated with the kelp Laminaria hyperborea during its accumulation and degradation on the seafloor. Kelp tissue

Planktonic microorganisms play a key role in the biogeochemical processes of the aquatic system, and they may be affected by many factors. High‐throughput sequencing technology was used in this study to investigate and study the bacterioplankton community of water bodies in the upper reaches of the Heihe River Basin in Qinghai Plateau. Results showed that Proteobacteria, Firmicutes, Bacteroidetes and

The advances in synthetic biology bring exciting new opportunities to reprogram microorganisms with novel functionalities for environmental applications. For real‐world applications, a genetic tool that enables genetic engineering in a stably genomic inherited manner is greatly desired. In this work, we design a novel genetic device for rapid and efficient genome engineering based on the intron‐encoded

Alphaproteobacteria are typically characterized by a multipartite genome organization with a chromosome, stable chromids and accessory plasmids. Extrachromosomal elements determine the lifestyle of roseobacters and their horizontal transfer was previously correlated with rapid adaptations to novel ecological niches. We characterized the distribution and biology of a novel Rhodobacteraceae‐specific

Geothermal springs are essentially unaffected by environmental conditions aboveground as they are continuously supplied with subsurface water with little variability in chemistry. Therefore, changes in their microbial community composition and function, especially over a long period, are expected to be limited but this assumption has not yet been rigorously tested. Toward closing this knowledge gap

Cobalamin (B12) is an essential cofactor that is exclusively synthesized by some prokaryotes while many prokaryotes and eukaryotes require an external supply of B12. The spatial and temporal availability of B12 is poorly understood in marine ecosystems. Field measurements of B12 along with a large set of ancillary biotic and abiotic factors were obtained during three oceanographic cruises in the NW

Recent studies have identified key genes that control the symbiotic interaction between Epichloë festucae and Lolium perenne. Here we report on the identification of specific E. festucae genes that control host infection. Deletion of setB, which encodes a homologue of the H3K36 histone methyltransferase Set2/KMT3, reduced histone H3K36 trimethylation and led to severe defects in colony growth and hyphal

Type II toxin‐antitoxin (TA) systems modulate many essential cellular processes in prokaryotic organisms. Recent studies indicate certain type II antitoxins also transcriptionally regulate other genes, besides neutralizing toxin activity. Herein, we investigated the diverse transcriptional repression properties of type II TA antitoxin PaHigA from Pseudomonas aeruginosa. Biochemical and functional analyses