The ecological functions of core and non-core bacteria are being gradually identified, yet little is known about their responses to environmental changes and assembly processes, especially in urban river ecosystems. Here, we investigated bacterioplankton communities over one year in an urban section of the Ganjiang River, China. The results revealed that the alpha- and beta-diversity of bacterioplankton

The Allchar mineral mine is one of the oldest arsenic-antimony mines in the Republic of North Macedonia. The mine is a well-known reservoir of the worldwide purest source of the thallium-bearing mineral, lorandite (TlAsS2). The current study evaluated the bacterial and fungal diversity of three As- and Tl-contaminated sites in Allchar mineral mine. We used a combination of high-throughput sequencing

Plant growth promoting bacteria (PGPB) are an efficient and sustainable alternative to mitigate biotic and abiotic stresses in maize. This work aimed to sequence the genome of two Bacillus strains (B116 and B119) and to evaluate their plant growth-promoting (PGP) potential in vitro and their capacity to trigger specific responses in different maize genotypes. Analysis of the genomic sequences revealed

Mountains have a long history in the study of diversity. Like macroscopic taxa, soil microbes are hypothesized to be strongly structured by montane gradients, and recently there has been important progress in understanding how microbes are shaped by these conditions. Here we summarize this literature and synthesize patterns of microbial diversity on mountains. Unlike for flora and fauna which often

The sensitivity and spatial recovery of river sediment biofilms along 1 km after the input of two wastewater treatment plants (WWTPs) located in two river reaches with different degrees of anthropogenic influence were investigated. First, at the upper reach, we observed an inhibition of some microbial functions (microbial respiration and extracellular enzyme activities) and strong shifts in bacterial

Bacillus sp. Abq, belonging to Bacillus cereus sensu lato, was isolated from an aquifer in New Mexico, USA and phylogenetically classified. The isolate possesses the unusual property of precipitating Pb(II) by using cysteine, which is degraded intracellularly to hydrogen sulfide (H2S). H2S is then exported to the extracellular environment to react with Pb(II), yielding PbS (galena). Biochemical and

Table S1, which was missing in the initially published supplementary material, has now been added to the supplementary data.

Bacterioplankton communities play a critical role in biogeochemical cycling in freshwater environments, but how the hydrological regime impacts the assembly of bacterioplankton communities remains unclear. This study examined differences in bacterioplankton community structures between wet (July and September) and dry (October and November) seasons in two consecutive years (2016 and 2017) in Poyang

Bovine respiratory microbiota plays a significant role in bovine respiratory health. We conducted a meta-analysis using publicly available 16S rRNA gene datasets from the respiratory tract to characterize respiratory microbiota in feedlot cattle. Our aims were to determine the factors that influence microbiota development and to assess the differences in microbiota composition and diversity between

Microbial communities associated to plants are greatly influenced by water availability in soil. In flooded crops, such as rice, the impact of water management on microbial dynamics is not fully understood. Here, we present a comprehensive study of the rice microbiota investigated in an experimental field located in one of the most productive area of North Italy. The microbiota associated to paddy

We assessed the impacts of forest-to-pasture conversion on the dynamic of soil microbial communities, especially those involved in the N-cycle, and their potential functions, using DNA-metagenomic sequencing coupled with the quantification of marker genes for N-cycling. We also evaluated whether the community's dynamic was reestablished with secondary forest growth. In general, the microbial community

Due to climate-warming, tannin-rich Rhizophora mangle migrates into tannin-poor salt marshes, where the tannins interfere with the biogeochemistry in the soil. Changes in biogeochemistry are likely associated with changes in microbial communities. This was studied in microcosms filled with salt marsh soil and amended with leaf powder, crude condensed tannins, purified condensed tannins (PCT), all from

Bacterial endophytes are found in the internal tissues of plants and have intimate associations with their host. However, little is known about the diversity of medicinal plant endophytes (ME) or their capability to produce specialised metabolites that may contribute to therapeutic properties. We isolated 75 bacterial ME from 24 plant species of the Western Ghats, India. Molecular identification by

The 8th biennial Polar and Alpine Microbiology (PAM 2019 –www.confer.nz/pam2019) conference was held for the first time in the southern hemisphere at the University of Waikato, Hamilton, New Zealand on Feb 4–9th 2019. The conference attracted close to 100 attendees representing over 20 countries. Of these attendees over one third were early career researchers. The conference was hosted at the university

The gut microbial communities of beetles play crucial roles in their adaptive capacities. Environmental factors such as temperature or nutrition naturally affect the insect microbiome, but a shift in local conditions like the population density on a host tree could also lead to changes in the microbiota. The emerald ash borer (EAB), Agrilus planipennis Fairmaire, is an exotic wood borer that causes

The mechanisms underlying nitrogen (N)-regulated plant-fungi interactions are not well understood. N application modulates plant carbohydrate (C) sinks and is involved in the overall plant-fungal association. We hypothesized that N regulates plant-fungi interactions by influencing the carbohydrate metabolism. The mutualistic fungus Phomopsis liquidambaris was found to prioritize host hexose resources

Xanthomonas citri subsp. citri (Xcc) is the bacteria responsible for citrus canker. During its life cycle Xcc is found on leaves as epiphyte, where desiccation conditions may occur. In this work, two Xcc genes, XAC0100 and XAC4007, predicted in silico to be involved in general stress response, were studied under salt, osmotic, desiccation, oxidative and freezing stress, and during plant-pathogen interaction

This study aimed to determine the environmental and ecological factors influencing the planktonic prokaryotic community profiles in the composite ecosystem comprising Taihu Lake, Taipu River and Jinze Reservoir in the Taihu Watershed in China. A total of 42 water samples were intermittently collected from different sites in 6 months across four seasons. Physicochemical characteristics of the ecosystem

Discovering widespread microbial processes that create variation in soil carbon (C) cycling within ecosystems may improve soil C modeling. Toward this end, we screened 206 soil communities decomposing plant litter in a common garden microcosm environment and examined features linked to divergent patterns of C flow. C flow was measured as carbon dioxide (CO2) and dissolved organic carbon (DOC) from

Human gut microbiome could translocate to other tissues, and the relocation triggered by HIV/SIV infection has received increasing attention. However, the underlying mode of this translocation, whether it is deterministic or random (passive) process, is not clear, not to mention quantitative estimation of the relocation probability and rates. Using multi-tissue microbiome datasets collected from SIV-infected

Seagrasses are vital coastal ecosystem engineers, which are mutualistically associated with microbial communities that contribute to the ecosystem services provided by meadows. The seagrass microbiome and sediment microbiota play vital roles in belowground biogeochemical and carbon cycling. These activities are influenced by nutrient, carbon and oxygen availability, all of which are modulated by environmental

The rhizosphere provides several benefits to the plant host being a strong determinant for its health, growth and productivity. Nonetheless, the factors behind the assembly of the microbial communities associated with the rhizosphere such as the role of plant genotypes are not completely understood. In this study, we tested the role that intraspecific genetic variation has in rhizospheric microbial

There is interest in understanding how cultivation, plant genotype, climate, and soil conditions influence the biogeography of root nodule bacterial communities of legumes. For crops from regions with relict wild populations, this is of even greater interest because the effects of cultivation on symbiont communities can be revealed, which is of particular interest for bacteria such as rhizobia. Here

An animal's gut microbiota (GM) is shaped by a range of environmental factors affecting the bacterial sources invading the host. At the same time, animal hosts are equipped with intrinsic mechanisms enabling regulation of GM. However, there is limited knowledge on the relative importance of these forces. To assess the significance of host-intrinsic vs. environmental factors, we studied GM in nestlings

A sustainable future increasing depends on our capacity to utilize beneficial plant microbiomes to meet our growing needs. Plant microbiome symbiosis is a hallmark of the beneficial interactions between bacteria and their host. Specifically, colonization of plant roots by biocontrol agents and plant growth-promoting bacteria can play an important role in maintaining the optimal rhizosphere environment

Editors: Tong Zhang, Keiji Fukuda, Edward Topp, Yong-Guan Zhu, Kornelia Smalla, James Tiedje and D. G. Joakim Larsson

Climate warming in Greenland is facilitating the expansion of shrubs across wide areas of tundra. Given the close association between plants and soil microorganisms and the important role of soil bacteria in ecosystem functioning, it is of utmost importance to characterize microbial communities of arctic soil habitats and assess the influence of plant edaphic factors on their composition. We used 16S

Biochar (BC) has been shown to influence microbial denitrification and mitigate soil N2O emissions. However, it is unclear if BC is able to directly stimulate the microbial reduction of N2O to N2. We hypothesized that the ability of BC to lower N2O emissions could be related not only to its ability to store electrons, but to donate them to bacteria that enzymatically reduce N2O. Therefore, we carried

Terrestrial microbial communities may take advantage of running waters and runoff to enter rivers and mix with aquatic microorganisms. However, the environmental factors governing the interchange of the microbial community within a watercourse and its surrounding environment and the composition of the resulting community are often underestimated. The present study investigated the effect of flow rate

Niche is a fundamental concept in ecology. It integrates the sum of biotic and abiotic environmental requirements that determines a taxon's distribution. Microbiologists currently lack quantitative approaches to address niche-related hypotheses. We tested four approaches for the quantification of niche breadth and overlap of taxa in amplicon sequencing datasets, with the goal of determining generalists

The assembly of host-associated bacterial communities is influenced by a multitude of biotic and abiotic factors. It is essential to gain insight in the impact and relative strength of these factors if we want to be able to predict the effects of environmental change on the assembly of host-associated bacterial communities, or deliberately modify them. The environmental pool of bacteria, from which

Xenorhabdus bovienii strain jolietti (XBJ) is a Gram-negative bacterium that interacts with several organisms as a part of its life cycle. It is a beneficial symbiont of nematodes, a potent pathogen of a wide range of soil-dwelling insects and also has the ability to kill soil- and insect-associated microbes. Entomopathogenic Steinernema nematodes vector XBJ into insects, releasing the bacteria into

The leaf-colonizing bacterial microbiota was studied in a long-term warming experiment on a permanent grassland, which had been continuously exposed to increased surface temperature (+2°C) for more than six years. Two abundant plant species, Arrhenatherum elatius and Galium album, were studied. Surface warming reduced stomata opening and changed leaf metabolite profiles. Leaf surface colonization and

In coastal sediments, excess nitrogen is removed primarily by denitrification. However, losses in habitat diversity may reduce the functional diversity of microbial communities that drive this important filter function. We examined how habitat type and habitat diversity affects denitrification and the abundance and diversity of denitrifying and N2O reducing communities in illuminated shallow-water

Methane oxidizing bacteria (methanotrophs) within the genus Methylobacter constitute the biological filter for methane (CH4) in many Arctic soils. Multiple Methylobacter strains have been identified in these environments but we seldom know the ecological significance of the different strains. High Arctic peatlands in Svalbard are heavily influenced by herbivory, leading to reduced vascular plant and

Plant roots assemble in two distinct microbial compartments: the rhizosphere (microbes in soil surrounding roots) and the endosphere (microbes within roots). Our knowledge of fungal community assembly in these compartments is limited, especially in wetlands. We tested the hypothesis that biotic factors would have direct effects on rhizosphere and endosphere assembly, while abiotic factors would have

Microbes play an important role in plants and interact closely with their host starting from sprouting seeds, continuing during growth and after harvest. The discovery of their importance for plant and postharvest health initiated a biotechnological development of various antagonistic bacteria and fungi for disease control. Nevertheless, their application often showed inconsistent effects. Recently

Intermediate-level radioactive waste includes cellulosic materials, which under the hyperalkaline conditions expected in a cementitious geological disposal facility (GDF) will undergo abiotic hydrolysis forming a variety of soluble organic species. Isosaccharinic acid (ISA) is a notable hydrolysis product, being a strong metal complexant that may enhance the transport of radionuclides to the biosphere

Henry Lutz Ehrlich, emeritus professor of biological sciences at Rensselaer Polytechnic Institute (RPI) in Troy, N.Y., passed away on May 2, 2020 at the age of 94. Professor Ehrlich was born in Stettin Germany in 1925, but along with his family managed to flee the Nazi regime in 1940 and immigrate to the United States. Details of his life and contributions were published as a personal memoir some eight

The combination of flow cytometric sorting and high-throughput sequencing revealed the broad existence of photosynthetic picoeukaryote attached fungi (PPE-attached fungi) in Lake Chaohu. The relative sequence abundance of attached fungi was negatively correlated with that of the photosynthetic picoeukaryotes (PPEs). PPE-attached fungal communities were mainly composed of Basidiomycota, Chytridiomycota

Ectomycorrhizal (ECM) fungal communities show temporal dynamics. Such dynamics have been mainly assessed with 1 year of investigations and have been related to the seasonal changes in environment. Recent study in sub-tropical region has revealed that stochastic temporal-based process can affect ECM fungal community, making the community of the same season different between years. The different community

Among the natural halogenic compounds, the plant toxin fluoroacetate (FA) causes livestock fatalities in southern hemisphere countries. Here, we report on the isolation of a rumen bacterium, strain C12–8 that degrades FA under anaerobic conditions. 16S rRNA gene sequence analysis showed this bacterium belonged to the Pyramidobacter genus within the Synergistetes phylum and was 98% similar to Pyramidobacter

Microbial reduction of selenite [Se(IV)] and tellurite [Te(IV)] to Se(0) and Te(0) can function as a detoxification mechanism and serve in energy conservation. In this study, Bacillus sp. Y3 was isolated and demonstrated to have an ability of simultaneous reduction of Se(IV) and Te(IV) during aerobic cultivation, with reduction efficiencies of 100% and 90%, respectively. Proteomics analysis revealed

Urea is a cost-effective replacement for feed proteins in ruminant diets. However, its metabolism by the rumen microbiome is not fully understood. Here, rumen contents were collected from eighteen male sheep fed one of the following three treatments: a low N basal diet with no urea (UC, 0 g/kg dry matter (DM)), low urea (LU, 10 g/kg DM), and high urea (HU, 30 g/kg DM). Principal coordinate analysis

Biocrusts are the living skin of drylands, comprising diverse microbial communities that are essential to desert ecosystems. Despite extensive knowledge on biocrust ecosystem functions and lichen and moss biodiversity, little is known about factors structuring diversity among their microbial communities. We used amplicon-based metabarcode sequencing to survey microbial communities from biocrust surface

Undernutrition remains a public health problem in the developing world with an attributable under-five death proportion of 45%. Lower gut microbiota diversity and poor metabolic output are associated with undernutrition and new therapeutic paths may come from steering gut microbiota composition and functionality. Using a dynamic gut model, the Simulator of Human Intestinal Microbial Ecosystem (SHIME®)

Antimicrobial resistance is a major global challenge. Of particular concern are mobilizable elements that can transfer resistance genes between bacteria, leading to pathogens with new combinations of resistance. To date, mathematical models have largely focussed on transfer of resistance by plasmids, with fewer studies on transfer by bacteriophages. We aim to understand how best to model transfer of

The response to global change by soil microbes is set to affect important ecosystem processes. These impacts could be most immediate in transitional zones, such as the temperate-boreal forest ecotone, yet previous work in these forests has primarily focused on specific subsets of microbial taxa. Here, we examined how bacterial and fungal communities respond to simulated above- and below-ground warming

Iron (Fe) limitation is known to affect heterotrophic bacteria within the respiratory electron transport chain, therefore strongly impacting the overall intracellular energy production. We investigated whether the gene expression pattern of the light-sensitive proton pump, proteorhodopsin (PR), is influenced by varying light, carbon and Fe concentrations in the marine bacterium Photobacterium angustum

Plant growth-promoting bacteria (PGPB) have recently been demonstrated as a promising agent to improve wastewater treatment and biomass production efficiency of duckweed hydrocultures. With a view to their reliable use in aqueous environments, this study analysed the plant colonization dynamics of PGPB and the ecological consequences for the entire duckweed-associated bacterial community. A PGPB strain

Heterotrophic nanoflagellates (HNF) are considered as major planktonic bacterivores, however, larger HNF taxa can also be important predators of eukaryotes. To examine this trophic cascading, natural protistan communities from a freshwater reservoir were released from grazing pressure by zooplankton via filtration through 10-µm and 5-µm filters, yielding microbial food webs of different complexity

We examined how larvae of Culex restuans mosquito influences the bacterial abundance, composition and diversity in simulated container aquatic habitats. The microbiota of Cx. restuans larvae were also characterized and compared to those of their larval habitats. The presence of Cx. restuans larvae altered the bacterial community composition and reduced the bacterial abundance, diversity and richness

A bacterial consortium was enriched from gold particles that ‘experienced’ ca. 80 years of biotransformation within waste-rock piles (Australia). This bacterial consortium was exposed to 10 µM AuCl3 to obtain Au-tolerant bacteria. From these isolates, Serratia sp. and Stenotrophomonas sp. were the most Au-tolerant and reduced soluble Au as pure gold nanoparticles, indicating that passive mineralisation

Meloidogyne graminicola, also known as the rice root-knot nematode, is one of the most damaging plant-parasitic nematode, especially on rice. This obligate soilborne parasite induces the formation of galls that disturb the root morphology and physiology. Its impact on the root microbiome is still not well described. Here, we conducted a survey in Northern Vietnam where we collected infected (with galls)

There is little understanding about how soil water stress history and host genotype influence the response of wheat-associated microbiome under short-term decreases in soil moisture. To address this, we investigated how plant breeding history (four wheat genotypes; two with recognized drought resistance and two without) and soil water stress history (same wheat field soil from Saskatchewan with contrasting

Compared with the highly diverse microbiota of leaves, herbivorous insects exhibit impoverished gut microbial communities. Research to date has focused on the bacterial component of these gut microbiomes, neglecting the fungal component. As caterpillar gut bacterial microbiomes are derived strongly from their diet, we hypothesized that their mycobiomes would reflect the host leaf mycobiomes. Using

Auxotrophy, or an organism's requirement for an exogenous source of an organic molecule, is widespread throughout species and ecosystems. Auxotrophy can result in obligate interactions between organisms, influencing ecosystem structure and community composition. We explore how auxotrophy-induced interactions between aquatic microorganisms affect microbial community structure and stability. While some

Understanding the successional dynamics governing soil microbial community assembly following disturbance can aid in developing remediation strategies for disturbed land. However, the influences shaping microbial communities during succession following soil disturbance remain only partially understood. One example of a severe disturbance to soil is surface mining for natural resources, which displaces

Phenotypic plasticity or genetic adaptation in an organism provides phenotypic changes when exposed to the extreme environmental conditions. The resultant physiological and metabolic changes greatly enhance the organism's potential for its survival in such harsh environments. In the present novel approach, we tested the hypothesis whether acid-adapted microalgae, initially isolated from non-acidophilic

Due to the sequence homology between the bacterial 16S rRNA gene and plant chloroplast and mitochondrial DNA, the taxonomic characterization of plant microbiome using amplicon-based high throughput sequencing often results in the overwhelming presence of plant-affiliated reads, preventing the thorough description of plant-associated microbial communities. In this work we developed a PCR blocking primer