26,791 results match your criteria bacterial communities

Cd immobilization and soil quality under Fe-modified biochar in weakly alkaline soil.

Chemosphere 2021 Apr 29;280:130606. Epub 2021 Apr 29.

Rural Energy & Environment Agency, MARA, Beijing, 100125, China. Electronic address:

Cost-effective and environment-friendly implementation techniques are critical to the success of remediation in large-scale cadmium (Cd) contaminated agricultural soil. Field experiments were conducted to investigate the effect of Fe-modified biochar on Cd bioavailability in soils and uptake by maize (Zea mays L.), soil aggregate distribution and stability, and microbial community composition in weakly alkaline Cd-contaminated soil. Read More

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Influence of hydrological factors on bacterial community structure in a tropical monsoonal estuary in India.

Environ Sci Pollut Res Int 2021 May 8. Epub 2021 May 8.

GenePath Dx, Shivajinagar, Pune, Maharashtra, 411004, India.

In the present study, we analyzed variations in bacterial community structure along a salinity gradient in a tropical monsoonal estuary (Cochin estuary [CE]), on the southwest coast of India, using Illumina next-generation sequencing (NGS). Water samples were collected from eight different locations thrice a year to assess the variability in the bacterial community structure and to determine the physico-chemical factors influencing the bacterial diversity. Proteobacteria was the most dominant phyla in the estuary followed by Bacteroidetes, Cyanobacteria, Actinobacteria, and Firmicutes. Read More

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In Vitro Antimicrobial Susceptibility Testing of Biofilm-Growing Bacteria: Current and Emerging Methods.

Adv Exp Med Biol 2021 May 8. Epub 2021 May 8.

Department of Medical, Oral and Biotechnological Sciences, and Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.

The antibiotic susceptibility of bacterial pathogens is typically determined based on planktonic cells, as recommended by several international guidelines. However, most of chronic infections - such as those established in wounds, cystic fibrosis lung, and onto indwelling devices - are associated to the formation of biofilms, communities of clustered bacteria attached onto a surface, abiotic or biotic, and embedded in an extracellular matrix produced by the bacteria and complexed with molecules from the host. Sessile microorganisms show significantly increased tolerance/resistance to antibiotics compared with planktonic counterparts. Read More

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Effects of thorium on bacterial, microalgal and micromeiofaunal community structures in a periphytic biofilm.

Ecotoxicol Environ Saf 2021 May 4;218:112276. Epub 2021 May 4.

Institut national de la recherche scientifique, 490 rue de la Couronne, G1K 9A9 Quebec City, QC, Canada. Electronic address:

Few ecotoxicity studies are available on thorium (Th) which hinders the ability to evaluate its ecotoxicological risk. Its release in the environment is often associated with the extraction of rare earth elements and uranium, as well as the field applications of phosphate fertilizers. This study investigates the effects of Th on microbial communities of periphytic biofilms. Read More

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A method for achieving complete microbial genomes and improving bins from metagenomics data.

PLoS Comput Biol 2021 May 7;17(5):e1008972. Epub 2021 May 7.

Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America.

Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes and often focus on species with circular genomes so they can help confirm completeness with circularity. Read More

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Host Trait Prediction from High-Resolution Microbial Features.

Giovanni Bacci

Methods Mol Biol 2021 ;2242:185-202

Department of Biology, University of Florence, Sesto Fiorentino, Italy.

Predicting host traits from metagenomes presents new challenges that can be difficult to overcome for researchers without a strong background in bioinformatics and/or statistics. Profiling bacterial communities using shotgun metagenomics often leads to the generation of a large amount of data that cannot be used directly for training a model. In this chapter we provide a detailed description of how to build a working machine learning model based on taxonomic and functional features of bacterial communities inhabiting the lungs of cystic fibrosis patients. Read More

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January 2021

Bacterial and archaeal lipids trace chemo(auto)trophy along the redoxcline in Vancouver Island fjords.

Geobiology 2021 May 7. Epub 2021 May 7.

Department of Geological Sciences and Institute of Arctic and Alpine Research (INSTAAR), University of Colorado Boulder, Boulder, CO, USA.

Marine oxygen minimum zones play a crucial role in the global oceanic carbon, nitrogen, and sulfur cycles as they harbor microbial communities that are adapted to the water column chemistry and redox zonation, and in turn control the water column chemistry and greenhouse gas release. These micro-organisms have metabolisms that rely on terminal electron acceptors other than O and often benefit from syntrophic relationships (metabolic coupling). Here, we study chemo(auto)trophy along the redoxcline in two stratified fjords on Vancouver Island (Canada) using bacterial bacteriohopanepolyols and archaeal ether lipids. Read More

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Diversity patterns and drivers of soil microbial communities in urban and suburban park soils of Shanghai, China.

PeerJ 2021 15;9:e11231. Epub 2021 Apr 15.

Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, China.

Background: The rapid expansion of urbanization leads to significant losses of soil ecological functions. Microbes directly participate in key soil processes and play crucial roles in maintaining soil functions. However, we still have a limited understanding of underlying mechanisms shaping microbial communities and the interactions among microbial taxa in park soils. Read More

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Inter-Individual Diversity Scaling Analysis of the Human Virome With Classic Diversity-Area Relationship (DAR) Modeling.

Front Genet 2021 20;12:627128. Epub 2021 Apr 20.

Computational Biology and Medical Ecology Laboratory, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.

The human virome is a critical component of the human microbiome, and it is believed to hold the richest diversity within human microbiomes. Yet, the inter-individual scaling (changes) of the human virome has not been formally investigated to the best of our knowledge. Here we fill the gap by applying diversity-area relationship (DAR) modeling (a recent extension to the classic species-area law in biodiversity and biogeography research) for analyzing four large datasets of the human virome with three DAR profiles: DAR scaling ()-measuring the inter-individual heterogeneity in virome diversity, (maximal accrual diversity: ) and ratio (ratio of local diversity to global diversity)-measuring the percentage of individual to population level diversity. Read More

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Resistance, Resilience, and Recovery of Dryland Soil Bacterial Communities Across Multiple Disturbances.

Front Microbiol 2021 20;12:648455. Epub 2021 Apr 20.

United States Geological Survey, Southwest Biological Science Center, Moab, UT, United States.

Dryland ecosystems are sensitive to perturbations and generally slow to recover post disturbance. The microorganisms residing in dryland soils are especially important as they contribute to soil structure and nutrient cycling. Disturbance can have particularly strong effects on dryland soil structure and function, yet the natural resistance and recovery of the microbial components of dryland soils has not been well documented. Read More

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Bioaugmented Phytoremediation of Metal-Contaminated Soils and Sediments by Hemp and Giant Reed.

Front Microbiol 2021 20;12:645893. Epub 2021 Apr 20.

Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy.

We assessed the effects of EDTA and selected plant growth-promoting rhizobacteria (PGPR) on the phytoremediation of soils and sediments historically contaminated by Cr, Ni, and Cu. A total of 42 bacterial strains resistant to these heavy metals (HMs) were isolated and screened for PGP traits and metal bioaccumulation, and two spp. strains were finally selected. Read More

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Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces.

BMC Genomics 2021 May 6;22(1):330. Epub 2021 May 6.

Molecular Genetics Veterinary Service (SVGM), Veterinary School, Universitat Autònoma de Barcelona, Barcelona, Spain.

Background: Long-read sequencing in metagenomics facilitates the assembly of complete genomes out of complex microbial communities. These genomes include essential biologic information such as the ribosomal genes or the mobile genetic elements, which are usually missed with short-reads. We applied long-read metagenomics with Nanopore sequencing to retrieve high-quality metagenome-assembled genomes (HQ MAGs) from a dog fecal sample. Read More

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Enhanced diversity and rock-weathering potential of bacterial communities inhabiting potash trachyte surface beneath mosses and lichens - A case study in Nanjing, China.

Sci Total Environ 2021 Apr 26;785:147357. Epub 2021 Apr 26.

Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China.

Mosses and lichens have been shown to play an important role in enhancing global chemical weathering of the surface rock. However, there are no studies concerning the effects of mosses and lichens on the microbial communities inhabiting rock surfaces. In this study, culture-dependent and culture-independent analyses were employed to compare the diversity, composition, and rock-weathering activity of bacterial communities inhabiting potash trachyte surfaces covered by mosses (MR) and lichens (LR) with those inhabiting surrounding bare rock surfaces (BR). Read More

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Detection of blaNDM-1 gene in ESBL producing Escherichia coli and Klebsiella pneumoniae isolated from urine samples.

J Infect Dev Ctries 2021 Apr 30;15(4):516-522. Epub 2021 Apr 30.

Department of Animal Health, University of Agriculture, Peshawar, Pakistan.

Introduction: Enterobacteriaceae such as Escherichia coli and Klebsiella pneumoniae are the most prominent bacterial species resistant to almost all commonly used antibiotics. Carbapenem is one of the last resort drugs for treating such emerging multidrug-resistant bacteria. This study aimed to detect carbapenem-resistant blaNDM-1 gene in ESBL producing E. Read More

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Contrasting Patterns of the Resident and Active Rhizosphere Bacterial Communities of Phragmites Australis.

Microb Ecol 2021 May 6. Epub 2021 May 6.

State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China.

Rhizosphere microbes play a key role in maintaining plant health and regulating biogeochemical cycles. The active bacterial community (ABC) in rhizosphere, as a small fraction of the rhizosphere resident bacterial community (RBC), has the potential to actively participate in nutrient cycling processes at the root-sediment interface. Here, we investigated the ABC and RBC within the rhizosphere of Phragmites australis (P. Read More

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Reproductive Diseases and Disorders of Female Camels: An Assessment and Pathological and Bacteriological Study in Eastern Ethiopia.

Vet Med Int 2021 13;2021:6641361. Epub 2021 Feb 13.

Haramaya University College of Veterinary Medicine, P.O. Box 138, Dire Dawa, Ethiopia.

Camels are the most efficient domesticated animals in arid and semiarid areas of the world. In Ethiopia, they are the main livestock kept to sustain the livelihoods of pastoralists, as camels are used for milk and meat production and also for transportation. However, she-camel reproductive diseases are one of the major constraints for camel-producing communities. Read More

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February 2021

Isotopic tracing reveals single-cell assimilation of a macroalgal polysaccharide by a few marine Flavobacteria and Gammaproteobacteria.

ISME J 2021 May 5. Epub 2021 May 5.

Institut Curie, Université Paris-Saclay, Paris, France.

Algal polysaccharides constitute a diverse and abundant reservoir of organic matter for marine heterotrophic bacteria, central to the oceanic carbon cycle. We investigated the uptake of alginate, a major brown macroalgal polysaccharide, by microbial communities from kelp-dominated coastal habitats. Congruent with cell growth and rapid substrate utilization, alginate amendments induced a decrease in bacterial diversity and a marked compositional shift towards copiotrophic bacteria. Read More

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Spatial segregation and cooperation in radially expanding microbial colonies under antibiotic stress.

ISME J 2021 May 5. Epub 2021 May 5.

Department of Biophysics, University of Michigan, Ann Arbor, USA.

Antibiotic resistance in microbial communities reflects a combination of processes operating at different scales. In this work, we investigate the spatiotemporal dynamics of bacterial colonies comprised of drug-resistant and drug-sensitive cells undergoing range expansion under antibiotic stress. Using the opportunistic pathogen Enterococcus faecalis with plasmid-encoded β-lactamase, we track colony expansion dynamics and visualize spatial patterns in fluorescently labeled populations exposed to antibiotics. Read More

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Clearance of Clostridioides difficile Colonization Is Associated with Antibiotic-Specific Bacterial Changes.

mSphere 2021 May 5;6(3). Epub 2021 May 5.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA

The gut bacterial community prevents many pathogens from colonizing the intestine. Previous studies have associated specific bacteria with clearing colonization across different community perturbations. However, those bacteria alone have been unable to clear colonization. Read More

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Whole lung tissue is the preferred sampling method for amplicon-based characterization of murine lung microbiota.

Microbiome 2021 May 5;9(1):99. Epub 2021 May 5.

Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.

Background: Low-biomass microbiome studies (such as those of the lungs, placenta, and skin) are vulnerable to contamination and sequencing stochasticity, which obscure legitimate microbial signal. While human lung microbiome studies have rigorously identified sampling strategies that reliably capture microbial signal from these low-biomass microbial communities, the optimal sampling strategy for characterizing murine lung microbiota has not been empirically determined. Performing accurate, reliable characterization of murine lung microbiota and distinguishing true microbial signal from noise in these samples will be critical for further mechanistic microbiome studies in mice. Read More

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A MicroRNA Gene Panel Predicts the Vaginal Microbiota Composition.

mSystems 2021 May 4;6(3). Epub 2021 May 4.

Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden

The vaginal microbiota plays an essential role in vaginal health. The vaginas of many reproductive-age women are dominated by one of the species. However, the vaginas of a large number of women are characterized by the colonization of several other anaerobes. Read More

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Predicted Metabolic Function of the Gut Microbiota of Drosophila melanogaster.

mSystems 2021 May 4;6(3). Epub 2021 May 4.

Department of Entomology, Cornell University, Ithaca, New York, USA.

An important goal for many nutrition-based microbiome studies is to identify the metabolic function of microbes in complex microbial communities and their impact on host physiology. This research can be confounded by poorly understood effects of community composition and host diet on the metabolic traits of individual taxa. Here, we investigated these multiway interactions by constructing and analyzing metabolic models comprising every combination of five bacterial members of the gut microbiome (from single taxa to the five-member community of and species) under three nutrient regimes. Read More

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Bacterial Communities in Concrete Reflect Its Composite Nature and Change with Weathering.

mSystems 2021 May 4;6(3). Epub 2021 May 4.

Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA

Concrete is an extreme but common environment and is home to microbial communities adapted to alkaline, saline, and oligotrophic conditions. Microbes inside the concrete that makes up buildings or roads have received little attention despite their ubiquity and capacity to interact with the concrete. Because concrete is a composite of materials which have their own microbial communities, we hypothesized that the microbial communities of concrete reflect those of the concrete components and that these communities change as the concrete ages. Read More

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Shift of Dominant Species in Plant Community and Soil Chemical Properties Shape Soil Bacterial Community Characteristics and Putative Functions: A Case Study on Topographic Variation in a Mountain Pasture.

Microorganisms 2021 Apr 29;9(5). Epub 2021 Apr 29.

National Institute of Agricultural Sciences, RDA, Wanju 55365, Korea.

Reducing management intensity according to the topography of pastures can change the dominant plant species from sown forages to weeds. It is unclear how changes in species dominance in plant community drive spatial variation in soil bacterial community characteristics and functions in association with edaphic condition. Analysing separately the effects of both plant communities and soil chemical properties on bacterial community is crucial for understanding the biogeographic process at a small scale. Read More

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The Responses to Long-Term Water Addition of Soil Bacterial, Archaeal, and Fungal Communities in A Desert Ecosystem.

Microorganisms 2021 Apr 30;9(5). Epub 2021 Apr 30.

Institute of Desertification Studies, Chinese Academy of Forestry, Beijing 100091, China.

The response of microbial communities to continual and prolonged water exposure provides useful insight when facing global climate changes that cause increased and uneven precipitation and extreme rainfall events. In this study, we investigated an in situ manipulative experiment with four levels of water exposure (ambient precipitation +0%, +25%, +50%, and +100% of local annual mean precipitation) in a desert ecosystem of China. After 9 years of water addition, Illumina sequencing was used to analyze taxonomic compositions of the soil bacterial, archaeal, and fungal communities. Read More

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Microbiota Associated with Different Developmental Stages of the Dry Rot Fungus .

J Fungi (Basel) 2021 Apr 30;7(5). Epub 2021 Apr 30.

Department of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria.

The dry rot fungus causes significant structural damage by decaying construction timber, resulting in costly restoration procedures. Dry rot fungi decompose cellulose and hemicellulose and are often accompanied by a succession of bacteria and other fungi. Bacterial-fungal interactions (BFI) have a considerable impact on all the partners, ranging from antagonistic to beneficial relationships. Read More

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Dead or alive: microbial viability treatment reveals both active and inactive bacterial constituents in the fish gut microbiota.

J Appl Microbiol 2021 May 4. Epub 2021 May 4.

Faculty of Science Engineering and Built Environment, School of Life and Environmental Sciences, Deakin University, Geelong, Vic., Australia.

Aims: This study evaluated the microbial viability of fish gut microbiota in both digesta (faecal) and mucosal samples using a modified propidium monoazide (PMA) protocol, followed by 16S ribosomal RNA (rRNA) gene sequencing.

Methods And Results: Digesta and gut mucosal samples from farmed yellowtail kingfish (Seriola lalandi) were collected and a modified PMA treatment was applied prior to DNA extraction to differentiate both active and nonviable microbial cells in the samples. All samples were then sequenced using a standard 16S rRNA approach. Read More

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Antibiotic resistance, antimicrobial residues and bacterial community diversity in pasture-raised poultry, swine and beef cattle manures.

J Anim Sci 2021 May 4. Epub 2021 May 4.

University of Pennsylvania, School of Veterinary Medicine, Kennett Square, PA , USA.

Animal manure can be a source of antibiotic resistant genes (ARG) and pharmaceutical residues; however, few studies have evaluated the presence of ARG in pasture-raised animal production systems. The objective of this study was to examine changes in microbiome diversity and the presence of antibiotic residues (ABR) on three farms that contained a diverse range of animal species: pasture-raised poultry (broiler and layer), swine and beef cattle. Total bacterial communities were determined using 16S rRNA microbiome analysis, while specific ARG (sulfonamide [Sul; Sul1] and tetracycline [Tet; TetA]) were enumerated by qPCR. Read More

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Heterogeneity of the white truffle Tuber magnatum in a limited geographic area of Central-Southern Italy.

Environ Microbiol Rep 2021 May 4. Epub 2021 May 4.

Institute for Sustainable Plant Protection (IPSP), Turin Unit, National Research Council, Viale P.A. Mattioli 25, Turin, 10125, Italy.

Molise region (Central-Southern Italy) is one of the Italian richest areas of truffles and contributes significantly to the national production of the precious Tuber magnatum. Nevertheless, Molise truffle has received little scientific attention. Accordingly, in the present study, two T. Read More

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Microbial species performance responses to environmental changes: genomic traits and nutrient availability.

Ecology 2021 May 3:e03382. Epub 2021 May 3.

State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.

How microbial species performance such as growth rate and carbon assimilation rate responds to environmental changes is a challenging question, especially for complex communities. This limits our ability to understand how species performance responses to environmental changes (that is, species environmental responses) of microbes could be linked to genomic traits and nutrient availability. Based on stable isotope labelling of DNA, we propose a new approach with effect size metrics to quantify the species environmental responses of microbes by comparing the species performance between defined control and treatment groups. Read More

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