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Shotgun metagenomics assessment of the resistome, mobilome, pathogen dynamics and their ecological control modes in full-scale urban wastewater treatment plants.

J Hazard Mater 2021 Jun 11;418:126387. Epub 2021 Jun 11.

Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, Nicosia, CY 1678, Cyprus; Department of Civil and Environmental Engineering, University of Cyprus, P.O. Box 20537, Nicosia, CY 1678, Cyprus. Electronic address:

The conventional activated sludge (CAS) process has limited capacity to remove pathogenic microorganisms and antibiotic resistance genes (ARGs), compared to membrane bioreactors (MBRs). However, the full extent of pathogenic microbial fraction, resistome (antibiotic and biocide resistance genes, ARGs and BRGs) and mobilome (mobile genetic elements, MGE) of urban wastewater treatment plant (UWTP) influents and effluents remains unknown. Thus, the fate of putative pathogenic bacteria, ARGs and potential co-occurrence patterns with BRGs, MGEs and bacterial-predatory microorganisms was determined in two full-scale UWTPs, a MBR and a CAS system, using shotgun metagenomics. Read More

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Variation of the mangrove sediment microbiomes and their phenanthrene biodegradation rates during the dry and wet seasons.

Environ Pollut 2021 Jul 26;289:117849. Epub 2021 Jul 26.

Department of Biology, Faculty of Science, Mahidol University, 272 Rama VI Road, Rachadhavi, Bangkok, 10400, Thailand. Electronic address:

Mangrove sediment is a major sink for phenanthrene in natural environments. Consequently, this study investigated the effects of seasonal variation on the biodegradation rates of low (150 mg kg), moderate (600 mg kg), and high (1200 mg kg) phenanthrene-contaminated mangrove sediments using a microcosm study and identified potential key phenanthrene-degrading bacteria using high throughput sequencing of 16 S rRNA gene and quantitative-PCR of the PAH-ring hydroxylating dioxygenase (PAH-RHD) genes. The biodegradation rates of phenanthrene in all treatments were higher in the wet-season sediments (11. Read More

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Stabilising role of seed banks and the maintenance of bacterial diversity.

Ecol Lett 2021 Jul 28. Epub 2021 Jul 28.

Department of Biology, Indiana University, Bloomington, Indiana, USA.

Coexisting species often exhibit negative frequency dependence due to mechanisms that promote population growth and persistence when rare. These stabilising mechanisms can maintain diversity through interspecific niche differences, but also through life-history strategies like dormancy that buffer populations in fluctuating environments. However, there are few tests demonstrating how seed banks contribute to long-term community dynamics and the maintenance of diversity. Read More

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Differential structure and functional gene response to geochemistry associated with the suspended and attached shallow aquifer microbiomes from the Illinois Basin, IL.

Water Res 2021 Jul 14;202:117431. Epub 2021 Jul 14.

Illinois State Geological Survey, IL, USA. Electronic address:

Despite the clear ecological significance of the microbiomes inhabiting groundwater and connected ecosystems, our current understanding of their habitats, functionality, and the ecological processes controlling their assembly have been limited. In this study, an efficient pipeline combining geochemistry, high-throughput Fluidigm functional gene amplification and sequencing was developed to analyze the suspended and attached microbial communities inhabiting five groundwater monitoring wells in the Illinois Basin, USA. The dominant taxa in the suspended and the attached microbial communities exhibited significantly different spatial and temporal changes in both alpha- and beta-diversity. Read More

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Response of Root-Associated Bacterial Communities to Different Degrees of Soft Rot Damage in Under a Plantation.

Authors:
Fei He

Front Microbiol 2021 8;12:652758. Epub 2021 Jul 8.

School of Modern Agriculture and Biotechnology, Ankang University, Ankang, China.

Bacterial soft rot is a destructive disease that restricts the development of the konjac ( K. Koch ex N.E. Read More

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Eight metagenome-assembled genomes provide evidence for microbial adaptation in 20,000 to 1,000,000-year-old Siberian permafrost.

Appl Environ Microbiol 2021 Jul 21:AEM0097221. Epub 2021 Jul 21.

University of Tennessee, Knoxville Tennessee 37996 USA.

Permafrost microbes may be metabolically active in microscopic layers of liquid brines, even in ancient soil. Metagenomics can help discern whether permafrost microbes show adaptations to this environment. Thirty-three metagenome-assembled genomes (MAGs) were obtained from six depths (3. Read More

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D- and l-amino acid concentrations in culture broth of are highly dependent on the phylogenetic group of .

Biochem Biophys Rep 2021 Sep 8;27:101073. Epub 2021 Jul 8.

Core Technology Laboratories, Asahi Quality & Innovations, Ltd., 1-21, Midori 1-Chome, Moriya-Shi, Ibaraki, 302-0106, Japan.

d-amino acids produced by are thought to contribute to the taste quality and health functions; however, no studies have comprehensively evaluated the concentrations of the D- and L-forms of amino acids separately in individual strains. To gain insight into amino acid concentrations in , we evaluated amino acid concentrations in culture broth of separately for the D- and L-forms. strains were cultured in culture broth, and the amino acid concentrations in supernatant were assessed. Read More

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September 2021

Dark-pigmented biodeteriogenic fungi in etruscan hypogeal tombs: New data on their culture-dependent diversity, favouring conditions, and resistance to biocidal treatments.

Fungal Biol 2021 Aug 29;125(8):609-620. Epub 2021 Mar 29.

Dipartimento di Scienze, Università 'Roma Tre', Viale G. Marconi 446 - 00146, Rome, Italy.

Subterranean Cultural Heritage sites are frequently subject to biological colonization due to the high levels of humidity, even in conditions of low irradiance and oligotrophy. Here microorganisms form complex communities that may be dangerous through mineral precipitation, through the softening of materials or causing frequent surface discolorations. A reduction of contamination's sources along with the control of microclimatic conditions and biocide treatments (overall performed with benzalkonium chloride) are necessary to reduce microbial growths. Read More

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Chronic Intermittent Hypoxia Participates in the Pathogenesis of Atherosclerosis and Perturbs the Formation of Intestinal Microbiota.

Front Cell Infect Microbiol 2021 1;11:560201. Epub 2021 Jul 1.

Key Laboratory of Upper Airway Dysfunction-related Cardiovascular Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, China.

Chronic intermittent hypoxia (CIH) is the prominent signature of highly prevalent obstructive sleep apnea (OSA) pathophysiology, which leads to increased risk and aggravation of atherosclerotic cardiovascular diseases. However, whether intestinal microbiota is implicated in the mechanisms linking CIH to arteriosclerosis (AS) pathogenesis remains unclear. The association of CIH with the development of altered gut microbiota (GM) may provide the opportunity to develop preventive strategies for atherosclerotic cardiovascular risk reduction. Read More

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Synergistic Effects Of Exercise And Catalase-Overexpression On Gut Microbiome.

Environ Microbiol 2021 Jul 16. Epub 2021 Jul 16.

Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, USA.

Exercise influences metabolic parameters in part by modulating redox stress and as recently suggested, by affecting gut microbiome. However, whether excess endogenous antioxidant potentiates or interferes with the beneficial effects of exercise on gut microbiome is not known. A comparison of the gut microbiome of C57Bl6 (C57/WT) mice to the "stress-less" catalase overexpressing mice models ([Tg(CAT) ] and Bob-Cat), that were either exercised or remained sedentary, showed differences in both alpha and beta diversity. Read More

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Interrogation of the perturbed gut microbiota in gouty arthritis patients through in silico metabolic modeling.

Authors:
Michael A Henson

Eng Life Sci 2021 Jul 9;21(7):489-501. Epub 2021 Jun 9.

Department of Chemical Engineering and the Institute for Applied Life Sciences University of Massachusetts Amherst MA USA.

Recent studies have shown perturbed gut microbiota associated with gouty arthritis, a metabolic disease characterized by an imbalance between uric acid production and excretion. To mechanistically investigate altered microbiota metabolism associated with gout disease, 16S rRNA gene amplicon sequence data from stool samples of gout patients and healthy controls were computationally analyzed through bacterial community metabolic models. Patient-specific community models constructed with the metagenomics modeling pipeline, mgPipe, were used to perform k-means clustering of samples according to their metabolic capabilities. Read More

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Reconstructing Dipsacales phylogeny using Angiosperms353: issues and insights.

Am J Bot 2021 Jul 13;108(7):1122-1142. Epub 2021 Jul 13.

Department of Biology, The College of New Jersey, Ewing, NJ, 08628, USA.

Premise: Phylogenetic relationships within major angiosperm clades are increasingly well resolved, but largely informed by plastid data. Areas of poor resolution persist within the Dipsacales, including placement of Heptacodium and Zabelia, and relationships within the Caprifolieae and Linnaeeae, hindering our interpretation of morphological evolution. Here, we sampled a significant number of nuclear loci using a Hyb-Seq approach and used these data to infer the Dipsacales phylogeny and estimate divergence times. Read More

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Changes in rumen fermentation and bacterial community in lactating dairy cows with subacute rumen acidosis following rumen content transplantation.

J Dairy Sci 2021 Jul 9. Epub 2021 Jul 9.

Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Centre for Ruminant Nutrition and Feed Engineering Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China. Electronic address:

Rumen microbiota intervention has long been used to cure ruminal indigestion in production and has recently become a research hotspot. However, how it controls the remodeling of rumen bacterial homeostasis and the restoration of rumen fermentation in cows of subacute ruminal acidosis (SARA) remains poorly understood. This study explored changes in rumen fermentation and bacterial communities in SARA cows following rumen content transplantation (RCT). Read More

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Gut Microbiota Signature Among Asian Post-gestational Diabetes Women Linked to Macronutrient Intakes and Metabolic Phenotypes.

Front Microbiol 2021 25;12:680622. Epub 2021 Jun 25.

Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.

Aberrant gut microbiota dysbiosis in women with a previous history of gestational diabetes mellitus (post-GDM) was comparable to that in adults with type 2 diabetes mellitus (T2DM). Nonetheless, potential relationships between diet, gut microbiota, and metabolic phenotypes in post-GDM women after delivery are yet to be discovered. In this research, we assessed the relationship of the macronutrient intakes, gut microbiota composition, and metabolic phenotypes (i. Read More

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Microbial Community Succession and Metabolite Changes During Fermentation of BS Sufu, the Fermented Black Soybean Curd by , , and .

Front Microbiol 2021 25;12:665826. Epub 2021 Jun 25.

College of Food Science and Engineering, Heilongjiang Bayi Agricultural University, Daqing, China.

BS Sufu is a fermented food that is made by mixed black soybeans and soybeans. Microbial communities and metabolites play an important role for the final product. We characterized microbial diversity of BS Sufu during fermentation by high-throughput DNA sequencing. Read More

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Changes in Intraspecific Diversity of the Arbuscular Mycorrhizal Community Involved in Plant-Plant Interactions Between Sporobolus robustus Kunth and Prosopis juliflora (Swartz) DC Along an Environmental Gradient.

Microb Ecol 2021 Jul 10. Epub 2021 Jul 10.

Laboratoire de Biologie Et Physiologie Végétales, Université Des Antilles, Guadeloupe, France.

The intensification of biological processes coping with salt stress became a major issue to mitigate land degradation. The Sine-Saloum Delta in Senegal is characterized by salt-affected soils with vegetation dominated by salt-tolerant grass Sporobolus robustus and shrubs like Prosopis juliflora. Plant experiments in controlled conditions suggested that arbuscular mycorrhizal (AM) fungi might be the key actors of facilitation process observed between S. Read More

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Convex hull estimation of mammalian body segment parameters.

R Soc Open Sci 2021 Jun 30;8(6):210836. Epub 2021 Jun 30.

School of Biological Sciences, University of Reading, Reading RG6 6BX, UK.

Obtaining accurate values for body segment parameters (BSPs) is fundamental in many biomechanical studies, particularly for gait analysis. Convex hulling, where the smallest-possible convex object that surrounds a set of points is calculated, has been suggested as an effective and time-efficient method to estimate these parameters in extinct animals, where soft tissues are rarely preserved. We investigated the effectiveness of convex hull BSP estimation in a range of extant mammals, to inform the potential future usage of this technique with extinct taxa. Read More

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Growth and miniaturization among alvarezsauroid dinosaurs.

Curr Biol 2021 Jun 30. Epub 2021 Jun 30.

Key Laboratory for the Evolutionary Systematics of Vertebrates, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; CAS Center of Excellence in Life and Paleoenvironment, Beijing 100044, China. Electronic address:

Sustained miniaturization, here defined as a drop in body size of at least two orders of magnitude from ancestors to descendants, is a widespread and important phenomenon in animals, but among dinosaurs, miniaturization occurred only rarely, once in the lineage leading to birds and once in the Alvarezsauroidea, one of the most bizarre theropod groups. Miniaturization and powered flight are intimately linked in avialan theropods, but the causes and patterns of body size reduction are less clear in the non-volant Alvarezsauroidea. Here, we present results from analyses on a comprehensive dataset, which not only includes new data from early-branching alvarezsauroids but also considers the ontogenetic effect based on histological data. Read More

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Hidden diversity of Ctenophora revealed by new mitochondrial COI primers and sequences.

Mol Ecol Resour 2021 Jul 5. Epub 2021 Jul 5.

Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.

The mitochondrial gene cytochrome-c-oxidase subunit 1 (COI) is useful in many taxa for phylogenetics, population genetics, metabarcoding, and rapid species identifications. However, the phylum Ctenophora (comb jellies) has historically been difficult to study due to divergent mitochondrial sequences and the corresponding inability to amplify COI with degenerate and standard COI "barcoding" primers. As a result, there are very few COI sequences available for ctenophores, despite over 200 described species in the phylum. Read More

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Leaf metabolic influence of glyphosate and nanotubes on the Arabidopsis thaliana phyllosphere.

J Environ Sci (China) 2021 Aug 27;106:66-75. Epub 2021 Jan 27.

College of Environment, Zhejiang University of Technology, Hangzhou 310032, China. Electronic address:

Chemical exposure can indirectly affect leaf microbiota communities, but the mechanism driving this phenomenon remains largely unknown. Results revealed that the co-exposure of glyphosate and multi-carbon nanotubes (CNTs) caused a synergistic inhibitory effect on the growth and metabolism of Arabidopsis thaliana shoots. However, only a slight inhibitory effect was induced by nanotubes or glyphosate alone at the tested concentrations. Read More

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Synthetic and Natural Insecticides: Gas, Liquid, Gel and Solid Formulations for Stored-Product and Food-Industry Pest Control.

Insects 2021 Jun 29;12(7). Epub 2021 Jun 29.

Laboratory of Entomology and Agricultural Zoology, Department of Agriculture, Crop Production and Rural Environment, University of Thessaly, Phytokou Str., 38446 Nea Ionia, Greece.

The selective application of insecticides is one of the cornerstones of integrated pest management (IPM) and management strategies for pest resistance to insecticides. The present work provides a comprehensive overview of the traditional and new methods for the application of gas, liquid, gel, and solid physical insecticide formulations to control stored-product and food industry urban pests from the taxa Acarina, Blattodea, Coleoptera, Diptera, Hymenoptera, Lepidoptera, Psocoptera, and Zygentoma. Various definitions and concepts historically and currently used for various pesticide application formulations and methods are also described. Read More

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Salivary Microbiome Diversity in Kuwaiti Adolescents with Varied Body Mass Index-A Pilot Study.

Microorganisms 2021 Jun 4;9(6). Epub 2021 Jun 4.

Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman 15462, Kuwait.

The potential role of the salivary microbiome in human diseases has increasingly been explored. The salivary microbiome has been characterized in several global populations, except the Arabian Gulf region. Hence, in this pilot study, we profiled the salivary microbiome of Kuwaiti adolescents with varied body mass indexes (BMI). Read More

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A taxonomist's nightmare - Cryptic diversity in Caribbean intertidal arthropods (Arachnida, Acari, Oribatida).

Mol Phylogenet Evol 2021 Jun 29;163:107240. Epub 2021 Jun 29.

Institute of Biology, University of Graz, Universitaetsplatz 2, 8010 Graz, Austria.

There has been a long controversy about what defines a species and how to delimitate them which resulted in the existence of more than two dozen different species concepts. Recent research on so-called "cryptic species" heated up this debate as some scientists argue that these cryptic species are only a result of incompatible species concepts. While this may be true, we should keep in mind that all concepts are nothing more than human constructs and that the phenomenon of high phenotypic similarity despite reproductive isolation is real. Read More

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The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces.

PLoS One 2021 30;16(6):e0253772. Epub 2021 Jun 30.

School of Sciences, University of Southern Queensland, Toowoomba, Queensland, Australia.

Many fungi require specific growth conditions before they can be identified. Direct environmental DNA sequencing is advantageous, although for some taxa, specific primers need to be used for successful amplification of molecular markers. The internal transcribed spacer region is the preferred DNA barcode for fungi. Read More

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Biochemical parameters and antioxidant property of three Salvia L. taxa endemic in Turkey.

Authors:
I Emre M Kursat

Braz J Biol 2021 28;82:e239539. Epub 2021 Jun 28.

Bitlis Eren University, Faculty of Science and Arts, Department of Biology, Bitlis, Turkey.

The aim of the present study was to determine and compare the fatty acids, lipid soluble vitamins, sterols, phenolics, and antioxidant capacities of three endemic Salvia L. taxa (S. euphratica var. Read More

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High diversity of basal fungal lineages and stochastic processes controlled fungal community assembly in mangrove sediments.

Appl Environ Microbiol 2021 Jun 30:AEM0092821. Epub 2021 Jun 30.

Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518061, Shenzhen, China.

Fungi are key components of microbial community in mangrove wetlands, with important roles in the transformation of nutrients and energy. However, existing studies typically focus on cultivable fungi, and seldomly on the structure and driving factors of the entire fungal communities. The compositions, community assembly and interaction patterns of mangrove fungal community on large scale remain elusive. Read More

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Niche partitioning of bacterial communities along the stratified water column in the Black Sea.

Microbiologyopen 2021 Jun;10(3):e1195

National Institute for Marine Research and Development "Grigore Antipa", Constanta, Romania.

The Black Sea is the largest semi-closed permanently anoxic basin on our planet with long-term stratification. The study aimed at describing the Black Sea microbial community taxonomic and functional composition within the range of depths spanning across oxic/anoxic interface, and to uncover the factors behind both their vertical and regional differentiation. 16S rRNA gene MiSeq sequencing was applied to get the data on microbial community taxonomy, and the PICRUSt pipeline was used to infer their functional profile. Read More

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Impact of Antibiotic-Induced Depletion of Gut Microbiota and Selenium Supplementation on Plasma Selenoproteome and Metal Homeostasis in a Mice Model.

J Agric Food Chem 2021 Jul 25;69(27):7652-7662. Epub 2021 Jun 25.

Research Center of Natural Resources, Health and the Environment (RENSMA), Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Fuerzas Armadas Avenue, 21007 Huelva, Spain.

Selenium (Se) is a micronutrient involved in important health functions and it has been suggested to shape gut microbiota. Limited information on Se assimilation by gut microbes and the possible link with selenoproteins are available. For this purpose, conventional and gut microbiota-depleted BALB/c mice were fed a Se-supplemented diet. Read More

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Characterization and Host-Feeding Patterns of s.l. Taxa in a West Nile Virus-Endemic Area in Southeastern Romania.

Vector Borne Zoonotic Dis 2021 Jun 22. Epub 2021 Jun 22.

Cantacuzino National Medico-Military Institute for Research and Development, Bucharest, Romania.

sensu lato has been documented as West Nile virus (WNV) vector in southeastern Romania. Bucharest, the densely populated capital city of Romania, and the surrounding Ilfov county are WNV hotspots. In this area, the morphologically indistinguishable biotypes of namely and , are usually differentiated by their behavioral and physiological traits. Read More

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Limitation of microbial processes at saturation-level salinities in a microbial mat covering a coastal saltflat.

Appl Environ Microbiol 2021 Jun 23:AEM0069821. Epub 2021 Jun 23.

Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany.

Hypersaline microbial mats are dense microbial ecosystems capable of performing complete element cycling and are considered analogs of Early Earth and hypothetical extraterrestrial ecosystems. We studied the functionality and limits of key biogeochemical processes, such as photosynthesis, aerobic respiration, and sulfur cycling in salt crust-covered microbial mats from a tidal flat at the coast of Oman. We measured light, oxygen, and sulfide microprofiles as well as sulfate-reduction rates at salt saturation and in flood conditions and determined fine-scale stratification of pigments, biomass, and microbial taxa in the resident microbial community. Read More

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