Plant roots form associations with beneficial and pathogenic soil microorganisms. Although members of the rhizosphere microbiome can protect against pathogens, the mechanisms are poorly understood. We hypothesized that the ability to form a biofilm on the root surface is necessary for the exclusion of pathogens; however, it is not known if the same biofilm formation components required in vitro are

Analyzing the nitrogen (15ε) and oxygen (18ε) isotope effects of anaerobic ammonium oxidation (anammox) is essential for accurately assessing its potential contribution to fixed-N losses in the ocean, yet the 18ε of anammox remains unexplored. Here, we determined the previously unexplored 18ε of anammox using a highly enriched culture of the marine anammox species “Ca. Scalindua sp”. Because Scalindua

Electroactive microorganisms influence environmental and host-associated ecosystems through their ability to mediate extracellular electron transfer. This review explores parallels between EAM-driven microbiologically influenced corrosion systems and the human gut microbiome. In corrosion, EAMs contribute to biofilm formation, redox cycling, and material degradation through mechanisms such as direct

Microbial consortia play pivotal roles in nutrient cycling across diverse ecosystems, where the functionality and composition of microbial communities are shaped by metabolic interactions. Despite the critical importance of understanding these interactions, accurately mapping and manipulating microbial interaction networks to achieve specific outcomes remains challenging. Genome-scale metabolic models

Marine sponge holobionts are important contributors to numerous biogeochemical cycles, including the natural organohalogen cycle. Sponges produce diverse brominated secondary metabolites, which select for a population of anaerobic debrominating bacteria within the sponge body. Sponge microbiomes can be host-specific, but the selection and host-specificity of debrominating bacteria are unknown currently

Methane mitigation is regarded as a critical strategy to combat the scale of global warming. Currently, about 40% of methane emissions originate from microbial sources, which is causing strategies to suppress methanogens—either through direct toxic effects or by diverting their substrates and energy—to gain traction. Problematically, current microbial methane mitigation knowledge lacks detailed microbiome-centered

From the perspective of a marine copiotrophic bacterium, the surface ocean is a mosaic of exploitable hotspots of organic matter released from living and senescing phytoplankton. Bacterial success in exploiting this patchy microscale environment relies on sensing and swimming towards the hotspots, and upon arrival, growing on available substrates. However, the combined effect of chemotaxis and growth

Mesoscale eddies, horizontally rotating currents sometimes referred to as “ocean weather,” influence open ocean macronutrient distributions, primary production, and microbial community structure. Such eddies impact ecosystems like the North Pacific Subtropical Gyre, where year-round thermal stratification limits the mixing of subsurface macronutrients with surface waters. Populations of the dominant

For over a century, bacterial infections have been studied through the lens of the one-microbe, one-disease paradigm. However, it is now clear that multi-pathogen infections are common, and many infectious diseases are inherently polymicrobial. These complex infections can involve a variety of pathogens, including viruses, bacteria, fungi, and parasites, with polyviral and viral-bacterial interactions

Evolution is defined as the change in allele frequency over time as a result of either neutral processes, such as genetic drift, or as an adaptive process in response to selection. In contrast, ecological dynamics describe changes in population densities, species distributions, species interactions, and/or relative abundances within communities, all of which can also be the result of either stochastic

Methanogens are methane-producing, hydrogen-oxidizing (i.e., hydrogenotrophic) archaea. Numerous studies have associated methanogens with obesity, but these results have been inconsistent. One link to metabolism may be methanogens’ hydrogen-oxidizing ability, thus reducing hydrogen partial pressure and thermodynamically enhancing fermentation of sugars to short-chain fatty acids that the host can absorb

Carbon flux to the deep sea can be dictated by surface ocean phytoplankton community composition, but translating surface ocean observations into quantitative predictions of carbon export requires additional consideration of the underlying ecosystem drivers. Here, we used genetic tracers of phytoplankton detected in surface seawater and within sinking particles collected in the mesopelagic ocean to

Mycorrhizal phenotypes arise from interactions among plants, soil biota, and environmental factors, but disentangling these drivers remains a key challenge in ecology. Understanding how these interactions shape mycorrhizal community assembly and stability is essential for predicting and managing these relationships in both natural and agricultural ecosystems. Here, we designed a fully factorial experiment

β-1,3-xylan, typically found in marine algae as a major cell wall polysaccharide, represents an overlooked pool of organic carbon in global oceans. Whilst our understanding of microbial catabolism of xylans has improved significantly, particularly from biotransformations of terrestrial plant biomass that are typically composed of β-1,4-xylans, knowledge on how microbes utilize β-1,3-xylan remains limited

Nucleocytoplasmic large DNA viruses, or “giant viruses,” are prevalent in marine environments, infecting diverse eukaryotic lineages and influencing the marine carbon cycle. Their genomes harbor wide range of auxiliary metabolic genes that influence biogeochemical processes. This study integrates planktonic (5–4000 m) and particle-associated (4000 m) metagenomic samples in the North Pacific Subtropical

The legume-rhizobia symbiosis possesses great potential for sustainable agriculture because of its ability to fix atmospheric nitrogen, reducing crop dependence on nitrogen fertilizers. Rhizobia recognize the host legume through flavonoids released by the roots. These signals are detected by bacteria typically over a few millimeters. Recent research has shown that arbuscular mycorrhizal fungi extend

Global warming is causing sea ice retreat and intensifying algal blooms in the Arctic Ocean, in turn increasing nitrogen limitation in surface waters. Dinitrogen fixation by diazotrophic microorganisms, usually favored in low reactive nitrogen systems, may become an increasingly important source of nitrogen in the Arctic. Previous studies have shown that non-cyanobacterial diazotrophs are dominant

The availability of the micronutrient iron is important in regulating phytoplankton growth across much of the world’s oceans, particularly in the high-nutrient, low-chlorophyll regions. Compared to known mechanisms of iron acquisition and conservation in autotrophic protists (e.g., diatoms), those of dinoflagellates remain unclear, despite their frequent presence in offshore iron-limited waters. Here

Phytoplankton account for nearly half of global photosynthetic carbon fixation, and the fate of that carbon is regulated in large part by microbial food web processing. We currently lack a mechanistic understanding of how interactions among heterotrophic bacteria impact the fate of photosynthetically fixed carbon. Here, we used a set of bacterial isolates capable of growing on exudates from the diatom

Extracellular electron transfer plays a role in the biogeochemical cycling of carbon, metals, sulfur, and nitrogen, and has wide-ranging biotechnological applications. The metal-reducing (Mtr), outer-membrane cytochrome (Omc), and porin-cytochrome (Pcc) pathways facilitate electron transfer to insoluble electron acceptors via trans-outer membrane cytochrome complexes. Although these pathways perform

Existing data and models suggest increasing prominence of dinoflagellates and their blooms in future warmer ocean but supporting long-term data are sparse. Here, we used 18S rRNA gene sequencing to investigate sedimentary ancient dinoflagellate communities in northern South China Sea and compared them with contemporary dinoflagellate data from global oceans (TARA Oceans data) and 40 years of dinoflagellate

Organisms are facing multiple, potentially interacting stressors in natural populations. The ability of populations coping with combined stressors depends on their tolerance to individual stressors and how stressors interact, which may not be correctly captured in controlled laboratory settings. One reason for this is that the microbial communities in laboratory settings often differ from the natural

Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, is driving an unprecedented increase in the emission of nitrous oxide (N2O), a potent greenhouse gas and an ozone depleting substance, causing urgency in identifying the sources and sinks of N2O. Microbial denitrification is a primary contributor to biotic production of N2O in anoxic regions of soil,

Plasmids are a ubiquitous feature of bacterial genomes, but the forces driving genes and phenotypes to become associated with plasmids are poorly understood. To address this problem, we compared the fitness effects of chromosomal and plasmid genes in the plant symbiont Rhizobium leguminosarum. The relative abundance of beneficial genes on plasmids was very low compared to the chromosome across niches

Microbes inhabit natural environments that are remarkably dynamic. Therefore, microbes harbor regulated genetic mechanisms to sense shifts in conditions and induce the appropriate responses. Recent studies suggest that the initial evolution of microbes occupying new niches favors mutations in regulatory pathways. However, it is not clear how this evolution is affected by how quickly conditions change

Wetlands can be a significant source of N2O under current global climate change regime with the soil-water interface representing a biogeochemical hotspot for microbial activity. However, the role of soil-water interface in controlling N2O emissions remains poorly understood. We hypothesized that the millimeter-scale redox gradient across the soil-water interface generates corresponding distinct niche

Studies of microbial interactions often emphasize interactions with large, easily measurable growth differences and short-term ecological outcomes spanning just a few generations. However, more subtle interactions, such as those without obvious phenotypes, may play a significant role in shaping both the short-term ecological dynamics and the long-term evolutionary trajectories of microbial species

The presence of fungi in the coral microbiome is increasingly recognized, yet their potential impact on the holobiont’s health, particularly under stress conditions, remains underexplored. To address this gap, we isolated over 200 strains (predominantly Ascomycota) from the common scleractinian Red Sea coral, Stylophora pistillata. Using conidia from a rare (Stachybotrys chlorohalonata) and a common

Sea cucumbers have been overharvested world-wide, making assessments of their ecological effects challenging, but recent research demonstrated that sea cucumbers increase coral survival via disease suppression and were therefore important for facilitating reef health. The mechanisms underpinning the sea cucumber-coral interaction therefore are not well understood but are likely mediated through sea

Despite abundant literature on pathogenicity and virulence of the opportunistic pathogen Escherichia coli, much less is known about its ecological and evolutionary dynamics as a commensal. Based on two detailed longitudinal datasets on the gut microbiota of healthy adults followed for months to years in France and the USA, we identified a robust trade-off between the ability to establish in a new host

SAR11 bacteria (order Pelagibacterales) are oligotrophs and often the most abundant bacterioplankton in aquatic environments. A subset of sequenced SAR11 genomes, predominantly in the brackish and freshwater SAR11 subclades, contain homologs of pha genes, which in other organisms confer the ability to store carbon and energy via polyhydroxyalkanoate polymers. Here, we investigated the relevance of

Host-associated microbiomes often promote host health, yet the key drivers of microbiome assembly and its consequences for host fitness remain unclear. We aimed to determine the relative roles of host identity versus the environment in driving host-microbiome assembly and the consequences of this variation in assembly for host fitness, which may help predict the resilience of host-associated microbiomes

Unicellular plankton form the foundation of the marine food web, driving carbon fixation and cycling essential biogeochemical elements in marine ecosystems. Carbon biomass, often measured as a bulk property, serves as a common “currency” for ecologists. The increasing availability of metatranscriptomic data presents an opportunity to add taxonomic and functional resolution to ecological models and

The development of ecologically based in vivo microecological formulations for treating Clostridioides difficile infection (CDI) is a current research focus. Here, we selected three microorganisms—Akkermansia muciniphila (AM), Bacteroides ovatus (BO), and Bifidobacterium breve (BB)—to formulate a mixed bacterial formulation (ABB). Subsequently, we evaluated the ecological interactions among these three

Dysbiosis of gut microbiota plays a crucial role in acute radiation-induced intestinal injury. However, studies on the influence of gut microbiota on acute radiation-induced intestinal injury are inconsistent. In this study, we established an acute radiation-induced intestinal injury mouse model and performed fecal microbiota transplantation to explore the role of the gut microbiota in acute radiation-induced

Corals (Cnidaria; Anthozoa) play critical roles as habitat-forming species with a wide range, from warm shallow-water tropical coral reefs to cold-water ecosystems. They also represent a complex ecosystem as intricate holobionts made up of microbes from all domains of the Tree of Life that can play significant roles in host health and fitness. The corallicolids are a clade of apicomplexans that infect

Applying synthetic microbial communities to manipulate the gut microbiota is a promising manner for reshaping the chicken gut microbial community. However, it remains elusive the role of a designed microbial community in chicken physiological metabolism and immune responses. In this study, we constructed a ten-member synthetic microbial community (SynComBac10) that recapitulated the phylogenetic diversity

Antibiotic-manufacturing wastewater treatment plants primarily target chemical pollutants, but their processes may select for antibiotic-resistant pathogens and antibiotic resistance genes. Here, leveraging the combined strengths of deep metagenomic sequencing, 16S rRNA gene sequencing, qPCR, and bacterial culturing, we investigated bacterial communities and antibiotic resistomes across eleven treatment

The susceptibility of corals to environmental stress is determined by complex interactions between host genetic variation and the Symbiodiniaceae family community. We exposed genotypes of Montipora capitata hosting primarily Cladocopium or Durusdinium symbionts to ambient conditions and an eight-day heat stress. Symbionts’ cell surface glycan composition differed between genera and was significantly

Soil drying challenges microbial viability and survival, with bacteria employing various mechanisms to respond to shifts in osmolarity, including dormancy or metabolic upregulation of osmoprotectants. However, the extent to which these responses are shaped by an organism’s phylogeny, or the climate history of a given environment is poorly understood. This study examines the responses of phylogenetically

Insufficient dietary fiber intake is associated with dysbiosis and compromised colonization resistance to enteric infections. However, a detailed understanding of the relationship between dietary fiber insufficiency and colonization resistance remains elusive. Our study aimed to delineate the impact of fiber deprivation on gut microbiome and colonization resistance in a murine model with Salmonella

Soils can potentially be turned into net carbon sinks for atmospheric carbon to offset anthropogenic greenhouse gas emissions. Occlusion of soil organic carbon (SOC) in soil aggregates is a key mechanism which temporarily protects it from decomposition by soil organisms. Filamentous fungi are recognized for their positive role in the formation and stabilization of aggregates. In this review we assess

Surveys of microbial communities (metagenomics) or isolate genomes have revealed sequence-discrete species. That is, members of the same species show >95% Average Nucleotide Identity (ANI) of shared genes among themselves vs. <83% ANI to members of other species while genome pairs showing between 83-95% ANI are comparatively rare. In these surveys, aquatic bacteria of the ubiquitous SAR11 clade (Class

Pathogens newly invading a host must compete with resident microbiota. This. within-host microbial warfare could lead to more severe disease outcomes or constrain the evolution of virulence. By passaging a widespread pathogen (Staphylococcus aureus) and a native microbiota community across populations of nematode hosts, we show that the pathogen displaced microbiota and reduced species richness, but

Protozoan predation is increasingly understood to be one of the main environmental factors driving bacterial virulence evolution and adaptation strategies. In this study, we reveal the adaptive evolution of Salmonella Enteritidis in phenotypic and genomic traits after passage through Tetrahymena thermophila. We identified a beneficial and fixed mutation that occurs at the coding region of rfbP, encoding

Viruses are ubiquitous in aquatic environments with total densities of virus-like particles often exceeding 107/ml in surface marine oligotrophic waters. Hypersaline environments harbor elevated prokaryotic population densities of 108/ml that coexist with viruses at even higher densities, approaching 1010/ml. The presence of high densities of microbial populations and viruses challenge traditional

Plant genetic and metabolic cues are involved in assembling their “core microbiome” under normal growth conditions. However, whether there is a core “stress responsive microbiome” among natural plant ecotypes remains elusive. Drought is the most significant abiotic stress worldwide. Characterizing conserved core root microbiome changes upon drought stress has the potential to increase plant resistance

Microbes adopt a diversity of strategies to successfully compete with coexisting strains for space and resources. One common strategy is the production of toxic compounds to inhibit competitors, but the strength and direction of selection for this strategy varies depending on the environment. Existing theoretical and experimental evidence suggests growth in spatially structured environments makes toxin

SAR202 bacteria are a diverse group of bacteria in the ocean. The SAR202 lineages dominate the bacterial community and evolve specialized metabolisms for oxidizing recalcitrant organic compounds in the dark ocean. SAR202 bacteria are also present in the euphotic oceans; however, their ecological roles and metabolic potential remain poorly understood. In this study, we collected 392 non-redundant metagenome-assembled

Virulent bacteriophages (or phages) are viruses that specifically infect and lyse a bacterial host. When multiple phages co-infect a bacterial host, the extent of lysis, dynamics of bacteria-phage and phage-phage interactions are expected to vary. The objective of this study is to identify the factors influencing the interaction of two virulent phages with different Pseudomonas aeruginosa growth states

With extreme nutritional substrate deficiency, the adaptive responses of the gastrointestinal microbiota and host metabolism are largely unknown. Here, we successfully established a microbial substrate deficiency model in the rumen without solid diet introduction in neonatal lambs. In the absence of solid diet, we observed a reduction in the Simpson Index of rumen bacteria, along with a marked decline

The host range of a bacteriophage—the diversity of hosts it can infect—is central to understanding phage ecology and applications. Whereas most well-characterized phages have narrow host ranges, broad-host-range phages represent an intriguing component of marine ecosystems. The genetic and evolutionary mechanisms driving their generalism remain poorly understood. In this study, we analyzed Schizotequatroviruses

Activated sludge is a large reservoir of novel microorganisms and microbial genetic diversity. While much attention has been given to the profile and functions of prokaryotes, the eukaryotic diversity remains largely unexplored. In this study, we analyzed longitudinal activated sludge samples spanning 13 years from the largest secondary wastewater treatment plants in Hong Kong, unveiling a wealth of

Microbial community coalescence refers to the mixing of entire microbial communities and their environments. Despite conceptually analogous to a multispecies invasion, the ecological processes driving this phenomenon remain poorly understood. Here, we developed and implemented a beta-diversity–based statistical framework to quantify the contribution of distinct donor communities to community reassembly

Bacteria in the genus Endozoicomonas are well-known coral symbionts commonly found as clusters within tissues of several coral species. Mapping the spatial distribution of these microbial communities is critical to gaining a holistic understanding of the potential role they may play within the coral host. This study focuses on characterizing bacterial aggregates associated with the common reef-building

To date, the only known Lanthanide (Ln)-dependent enzymes are pyrroloquinoline quinone-dependent alcohol dehydrogenases. When compared to their Ca dependent counterparts, there is an emerging picture that Ln-dependent versions of these enzymes are generally more efficient, are preferentially upregulated in the presence of Ln when there is functional redundancy, and may even be evolutionarily older

The source of protein in a person's diet affects their total life expectancy. However, the mechanisms by which dietary protein sources differentially impact human health and life expectancy are poorly understood. Dietary choices impact the composition and function of the intestinal microbiota that ultimately modulate host health. This raises the possibility that health outcomes based on dietary protein

Antibiotic residues are commonly found in food. The effect of dietary exposure to veterinary antibiotics on the transmission of antibiotic resistant bacteria and antibiotic resistance genes from food to humans is unknown. We found that dietary exposure to enrofloxacin reduced microbial diversity, interactions and the immune responses, weakened the colonization resistance of the resident microbiota

Microbial symbioses are essential for many animals, but their outcomes are often context dependent. For example, rising temperatures can disrupt symbioses by eliminating thermally sensitive symbionts. The temperature tolerance of a symbiont may therefore limit the temperature range of its host, but switching to a more thermally tolerant partner could expand this range. Eastern leaf footed bugs (Leptoglossus

Poorly understood microorganisms “short-circuit” the nitrogen cycle via the dissimilatory nitrate reduction to ammonium to retain the element in agricultural lands and stimulate crop productivity. The prevalence of Geobacterales closely related to Trichlorobacter lovleyi in nitrate ammonification hotspots motivated us to investigate adaptive responses contributing to ammonification rates in the laboratory