Strictly lytic phages are considered powerful tools for biocontrol of foodborne pathogens. Safety issues needed to be addressed for the biocontrol of Shiga toxin-producing Escherichia coli (STEC) include: lysogenic conversion, Shiga toxin production through phage induction, and emergence/proliferation of bacteriophage insensitive mutants (BIMs). To address these issues, two new lytic phages, vB_EcoS_Ace

The prevalence of antibiotic-resistant bacteria in surface water in Lebanon is a growing concern and understanding the mechanisms of the spread of resistance determinants is essential. We aimed at studying the occurrence of resistant bacteria and determinants in surface water sources in Lebanon and understanding their mobilization and transmission. Water samples were collected from five major rivers

Long-term survivability is well-known for microorganisms in nutrient-depleted environments, but the damage accrued by proteins and the associated repair processes during the starvation and recovery phase of microbial life still remain enigmatic. We focused on aspartic acid (Asp) racemization and repair in the survival of Pyrococcus furiosus and Thermococcus litoralis under starvation conditions at

A recently introduced quantitative framework for gut microbiota analysis indicated that microbial load alterations can be linked to various diseases, making it essential to pinpoint its determinants. We identified nutrient load as a main driver of the quantitative microbial community composition and functionality in vitro by stepwise decreasing standardised feed concentrations from 100% to 33, 20 and

Deep-sea carbonate mounds can harbor a wide variety of heterotrophic and chemosynthetic microbial communities, providing biodiversity hotspots among the deep-sea benthic ecosystems. This study examined the bacterial and archaeal diversity and community structure in the water column and sediments associated to a recently described giant carbonate mound named Alpha Crucis Carbonate Ridge (ACCR), Southwestern

Sand dunes of the Mediterranean region constitute drought-stressed, low-fertility ecosystems. Arbuscular mycorrhizal fungi (AMF) are regarded as key components of their biota, that contribute to plant host adaptation and fitness. However, AMF community assembly rules in the roots of the psammophilous plants of coastal sand dunes have not been investigated. We studied the root colonizing AMF communities

ABSTRACTAt the spring, goat and sheep herds are transferred to planted forests, in a semi-arid region in the northern Negev Desert, Israel, to reduce herbaceous biomass and, fire risk. The herds are held overnight in corrals for about 4 months, enriching the soil with organic matter and nitrogen. This research examined the effect of these enrichments on soil bacterial community structure (BCS) and

ABSTRACTFilamentous cyanobacteria belonging to the ‘marine Geitlerinema’ cluster are spread worldwide in saline environments and considered to play an important ecological role. However, the taxonomy of this group remains unclear. Here, we analyzed the phylogeny, ecology and biogeography of the ‘marine Geitlerinema’ cluster representatives and revealed two subclusters: (1) an ‘oceanic’ subcluster containing

Wild berries are interesting research subjects due to their rich sources of health-beneficial phenolic compounds. However, the internal microbial communities, endophytes, associated with the wild berry fruits are currently unknown. Endophytes are bacteria or fungi inhabiting inside plant tissues, and their functions vary depending on the host species and environmental parameters. The present study

Short chain fatty acids (SCFAs) derived from the human gut microbiota, and in particular propionate, may beneficially influence metabolic processes such as appetite regulation. Development of prebiotics that induce high propionate levels during fermentation is desirable. A total of 11 candidate prebiotics were screened to investigate their fermentation characteristics, with a focus on propionate production

The spatial dynamics of picophytoplankton were investigated by flow cytometry and high-throughput sequencing in Lake Hongze, a large river-connecting lake. Picophytoplankton were mainly composed of phycocyanin-rich picocyanobacteria (PCY) and photosynthetic picoeukaryotes (PPEs). Picocyanobacteria was the dominant picophytoplankton group since the contribution of PPEs to total picophytoplankton was

The seafloor sulfide structures of inactive vents are known to host abundant and diverse microorganisms potentially supported by mineralogy of sulfides. However, little is known about the diversity and distribution of microbial functions. Here, we used genome-resolved metagenomics to predict microbial metabolic functions and the contribution of horizontal gene transfer to the functionality of microorganisms

The microbial communities associated to the rhizosphere (the rhizomicrobiome) have a substantial impact on plant growth and yield. Understanding the effects of agricultural management on the rhizomicrobiome is very important for selecting efficient practices. By sequencing the V4 region of 16S rRNA for bacteria and the ITS1 regions and fungi, we investigated the influences of agronomic practices, including

Thousands of microbial taxa in the soil form symbioses with host plants, and due to their contribution to plant performance, these microbes are often considered an extension of the host genome. Given microbial effects on host performance, it is important to understand factors that govern microbial community assembly. Host developmental stage could affect rhizosphere microbial diversity while, alternatively

Consistent with the concept of ecosystem sustainability—defined as ‘the ability of an ecosystem to maintain its potential for self-regulation in the long term’ (Bender, Wagg and van der Heijden 2016)—sustainable agricultural production aims to meet future food, feed and fibre demands with the given natural resources and without adverse environmental impact or greater land consumption. However, intensification

ABSTRACTOyster microbiomes are integral to healthy function and can be altered by climate change conditions. Genetic variation among oysters is known to influence the response of oysters to climate change and may ameliorate any adverse effects on oyster microbiome; however, this remains unstudied. Nine full-sibling selected breeding lines of the Sydney rock oyster (Saccostrea glomerata) were exposed

Bacterial species in the human gut predominantly exist in the form of mixed-species biofilms on mucosal surfaces. In this study, the biofilm-forming ability of many human gut bacterial strains (133 strains recovered from human faeces) on mucin-coated and non-coated polystyrene surfaces was determined. A significant variation (P < 0.05) in the biofilm-forming ability of many bacterial species on both

Animals are an essential part of the ecosystem, and their carcasses are the nutrient patches or hotspots where nutrients accumulate for a long time. After death, the physical and chemical properties undergo alterations inside the carcass. The animal carcass is decomposed by many decomposers such as bacteria, fungi, microeukaryotes and insects. The role of microbial symbionts in living organisms is

ABSTRACTDisease has become an increasingly recognised problem in the marine environment, but our understanding of the factors that drive disease or our ability to predict its occurrence is limited. Marine sponges are known for their close associations with microorganisms, which are generally accepted to underpin sponge health and function. The aim of this study is to explore whether the microbial community

The ‘principle of microbial infallibility’ was a mainstay of microbial physiology and environmental microbiology in earlier decades. This principle asserts that wherever there is an energetic gain to be made from environmental resources, microorganisms will find a way to take advantage of the situation. Although previously disputed, this claim was revived with the discovery of anammox bacteria and

Relatively little is known about the diversity of fungi in deep-sea, hydrothermal sediments. Less thoroughly explored environments are likely untapped reservoirs of unique biodiversity with the potential to augment our current arsenal of microbial compounds with biomedical and/or industrial applications. In this study, we applied traditional culture-based methods to examine a subset of the morphological

Soil microorganisms play a key role in driving major biogeochemical cycles and in global responses to climate change. However, understanding and predicting the behavior and function of these microorganisms remains a grand challenge for soil ecology due in part to the microscale complexity of soils. It is becoming increasingly clear that understanding the microbial perspective is vital to accurately

ABSTRACTOur understanding of the pathogenic yeasts Cryptococcus neoformans and Cryptococcus gattii has been greatly enhanced by use of genome sequencing technologies. Found ubiquitously as saprotrophs in the environment, inhalation of infectious spores from these pathogens can lead to the disease cryptococcosis. Individuals with compromised immune systems are at particular risk, most notably those

AbstractEpiphytic microbial communities often have a close relationship with their eukaryotic host, assisting with defence, health, disease prevention and nutrient transfer. Shifts in the structure of microbial communities could therefore have negative effects on the individual host and indirectly impact the surrounding ecosystem, particularly for major habitat-forming hosts, such as kelps in temperate

ABSTRACTIce-free areas of Victoria Land, in Antarctica, are characterized by different terrestrial ecosystems, that are dominated by microorganisms supporting highly adapted communities. Despite the unique conditions of these ecosystems, reports on their bacterial diversity are still fragmentary. From this perspective, 60 samples from 14 localities were analyzed. These localities were distributed in

AbstractDefaunation including invertebrate decline is one of the major consequences of anthropogenic alterations of the environment. Despite recent reports of ubiquitous invertebrate decline, the ecosystem consequences have been rarely documented. We exposed standardized plant communities grown in the iDiv Ecotron to different levels of invertebrate numbers and biomass and tracked effects on the diversity

ABSTRACTThe microbiome of an aquifer contaminated by landfill leachate and undergoing intrinsic remediation was characterised using 16S rRNA metabarcoding. The archaeal/bacterial V3–V4 hypervariable region of the 16S rRNA gene was sequenced using Illumina MiSeq, and multivariate statistics were applied to make inferences. Results indicate that the aquifer recharge and aquifer sediment samples harbour

ABSTRACTThis study evaluated the effects of glutamine supplementation on nutrient digestibility, immunity, digestive enzyme activity, gut bacterial community and fermentation of growth-retarded yaks. A total of 16 growth-retarded yaks were randomly allocated to two groups: negative control (GRY) and glutamine supplementation group (GLN). Another eight growth-normal yaks were used as a positive control

ABSTRACTSerpentine soils are drought-prone and rich in heavy metals, and plants growing on serpentine soils host distinct microbial communities that may affect plant survival and phenotype. However, whether the rhizosphere communities of plants from different soil chemistries are initially distinct or diverge over time may help us understand drivers of microbial community structure and function in

ABSTRACTIt is of great interest to elucidate the biogeographic patterns of soil microorganisms and their driving forces, which is fundamental to predicting alterations in microbial-mediated functions arising from environment changes. Although dissolved organic matter (DOM) represents an important resource for soil microorganisms, knowledge of how its quality affects microbial biogeography is limited

AbstractAs major primary producers in aquatic systems, the diversity and community composition dynamics of photosynthetic picoeukaryotes (PPEs) have been investigated in recent years. Here, we explored the three-day diurnal succession of the PPE community in a highly eutrophic lake in early spring using a combination of flow cytometric sorting and high-throughput sequencing. Our results showed that

Douglas Channel and the adjacent Hecate Strait (British Columbia, Canada) are part of a proposed route to ship diluted bitumen (dilbit). This study presents how two types of dilbit naturally degrade in this environment by using an in situ microcosm design based on dilbit-coated beads. We show that dilbit-associated n-alkanes were microbially biodegraded with estimated half-lives of 57–69 days. n-Alkanes

Tree canopies are colonized by billions of highly specialized microorganisms that are well adapted to the highly variable microclimatic conditions, caused by diurnal fluctuations and seasonal changes. In this study, we investigated seasonality patterns of protists in the tree canopies of a temperate floodplain forest via high-throughput sequencing with group-specific primers for the phyla Cercozoa

Recent discovery of endophytic strains of Bacillus thuringiensis significantly improves the knowledge on its ecology. It also may be a new source for the isolation of insecticidal strains. This report shows the characterization of two endophytic, highly insecticidal strains of B. thuringiensis. Strains LBIT-1250L and LBIT-1251P were isolated from lavender and Poinsettia sap, respectively. Their parasporal

Freshwater picocyanobacteria (Pcy) are important yet understudied components of lake ecosystems. Most previous studies have relied on cell abundances to assess Pcy dynamics in largely oligotrophic lakes, while little is known about spatial diversity and dynamics across different lake types. In the present study we assessed the horizontal-spatial abundance and community structure of Pcy in two contrasting

Plantations of Norway spruce have been established well beyond its natural range in many parts of the world, potentially impacting native microbial ecosystems and the processes they mediate. In this study, we investigate how the establishment of spruce plantations in a landscape dominated by native birch forests in western Norway impacts soil properties and belowground fungal communities. Soil cores

milkmastitisone healthzoonosis

milkmastitismicrobiotaStaphylococcus aureusOne Health

Microbial communities can have dramatically different compositions even among similar environments. This might be due to the existence of multiple alternative stable states, yet there exists little experimental evidence supporting this possibility. Here, we gathered a large collection of absolute population abundances capturing population dynamics in one- to four-strain communities of soil bacteria

Lichens are classic models of symbiosis, and one of the most frequent nutritional modes among fungi. The ecologically and geographically widespread lichen-forming algal (LFA) genus Trebouxia is one of the best-studied groups of LFA and associates with over 7000 fungal species. Despite its importance, little is known about its diversification. We synthesized twenty years of publicly available data by

It is thought that modern wheat genotypes have lost their capacity to associate with soil microbes that would help them acquire nutrients from the soil. To test this hypothesis, ten ancestral and modern wheat genotypes were seeded in a field experiment under low fertilization conditions. The rhizosphere soil was collected, its DNA extracted and submitted to shotgun metagenomic sequencing. In contrast

ABSTRACTThe microbiota colonizing the rhizosphere contributes to plant growth, productivity, carbon sequestration and phytoremediation. Several studies address plant-associated bacteria; however, few studies analyze the effect of plant genotype on the eukaryotic community. Here, we analyzed the eukaryotic composition of maize rhizosphere from three different plant landraces and one inbred line grown

One of the challenges to implementing the modeling of the biological reductive dechlorination (RD) process is the evaluation of biological parameters that represent the abundance/activity levels of the microorganisms involved in the biodegradation of chloroethenes. Here we report a combined analysis of kinetic and specific biomass parameters conducted on three dechlorinating consortia enriched on PCE

Seed borne microorganisms play an important role in plant biology. Concerns have recently been raised about loss of seed microbial diversity by seed treatments, crop domestication and plant breeding. Information on the seed microbiomes of native plants growing in natural ecosystems is beneficial as they provide the best settings to detect indigenous plant microbe interactions. Here, we characterized

*Corresponding author: ppoeta@utad.pt

AbstractGammaproteobacteria from the family Endozoicomonadaceae have emerged as widespread associates of dense marine animal communities. Their abundance in coral reefs involves symbiotic relationships and possibly host nutrition. We explored functions encoded in the genome of an uncultured Endozoicomonadaceae ‘Candidatus Acestibacter aggregatus’ that lives inside gill cells of large Acesta excavata

Chloroethenes are common soil and groundwater pollutants. Their dechlorination is impacted by environmental factors, such as the presence of metal ions. We here investigated the effect of ferrous iron on bacterial reductive dechlorination of chloroethenes and on methanogen community. Reductive dechlorination of tetrachloroethene was assayed with a groundwater sample originally containing 6.3 × 103

ABSTRACTSymbiosis involving two (or more) prokaryotic and/or eukaryotic partners is extremely widespread in nature, and it has performed, and is still performing, a key role in the evolution of several biological systems. The interaction between symbiotic partners is based on the emission and perception of a plethora of molecules, including volatile organic compounds (VOCs), synthesized by both prokaryotic

Landfills are engineered, heterogeneously contaminated sites containing large reservoirs of paper waste. Cellulose degradation is an important process within landfill microbial ecology, and these anoxic, saturated environments are prime locations for discovery of cellulases that may offer improvements on industrial cellulose degradation efforts. We sampled leachate from three locations within a municipal

Microbial interconnections in soil are pivotal to ecosystem services and restoration. However, little is known about how soil microbial interconnections respond to slash-and-burn agriculture and to the subsequent ecosystem restoration after the practice. Here, we used amplicon sequencing and co-occurrence network analyses to explore the interconnections within soil bacterial and fungal communities

Functional, physiological traits are the underlying drivers of niche differentiation. A common framework related to niches occupied by terrestrial prokaryotes is based on copiotrophy or oligotrophy, where resource investment is primarily in either rapid growth or stress tolerance, respectively. A quantitative trait-based approach sought relationships between taxa, traits and niche in terrestrial prokaryotes

ABSTRACTFungi have a huge biodiversity and play important roles in soil biogeochemical cycling in island ecosystems. Although island biogeography has been widely studied for macroorganisms, fungal community assembly in true islands and its relationship with island area are less documented. We examined soil fungal communities in 18 oceanic islands of two types (eight non-coral islands and 10 coral islands)

ABSTRACTWe report on a study that aimed at establishing a large soil–fungal culture collection spanning a wide taxonomic diversity and systematically screening the collection for bacterial associations. Fungal cultures were isolated from soil samples obtained from a natural grassland in eastern Germany and bacterial associations were assessed by PCR-amplification and sequencing of bacterial 16S rRNA

ABSTRACTMethane is an important energy resource internationally, and a large proportion of this methane is produced by microbial communities living in coal seams. Despite the value of this resource for human energy security, our understanding of the metabolic roles played by specific taxa during the biodegradation of coal to methane in situ is quite limited. In order to develop a greater understanding

In aquatic systems, an interplay between bottom-up and top-down processes determines the dynamic of picocyanobacteria (Pcy) abundance and community structure. Here, we analyzed a 10-year time series (sampled fortnightly) from a hypereutrophic turbid shallow lake located within the Pampa Region of South America, generating the first long-term record of freshwater Pcy from the Southern Hemisphere. We

Microbes and metals are intricately linked in a complex relationship. Many microbial pathways rely on metals for functionality, including enzymatic machinery (co-factors in key enzymes), dissimilatory reduction in energy generation (as alternative electron acceptors in anaerobic respiration) and biomineralization. Some metals share very close physical–chemical properties, thus sensing and incorporating

Ocean acidification (OA) in estuaries is becoming a global concern, and may affect microbial characteristics in estuarine sediments. Bacterial communities in response to acidification in this habitat have been well discussed; however, knowledge about how fungal communities respond to OA remains poorly understood. Here, we explored the effects of acidification on bacterial and fungal activities, structures

Antimony (Sb), the analog of arsenic (As), is a toxic metalloid that poses risks to the environment and human health. Antimonite (Sb(III)) oxidation can decrease Sb toxicity, which contributes to the bioremediation of Sb contamination. Bacteria can oxidize Sb(III), but the current knowledge regarding Sb(III)-oxidizing bacteria (SbOB) is limited to pure culture studies, thus underestimating the diversity

The frequent exposure of agricultural soils to pesticides can lead to microbial adaptation, including the development of dedicated microbial populations that utilize the pesticide compound as a carbon and energy source. Soil from an agricultural field in Halen (Belgium) with a history of linuron exposure has been studied for its linuron-degrading bacterial populations at two time points over the past