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On the hidden diversity and niche specialization of the microbial realm of subterranean estuaries Environ. Microbiol. (IF 5.476) Pub Date : 2022-08-15 E. Calvo-Martin, E. Teira, X. A. Álvarez-Salgado, C. Rocha, S. Jiang, M. Justel-Díez, J. S. P. Ibánhez
Subterranean estuaries (STEs) modulate the chemical composition of continental groundwater before it reaches the coast but their microbial community is poorly known. Here, we explored the microbial ecology of two neighbouring, yet contrasting STEs (Panxón and Ladeira STEs; Ría de Vigo, NW Iberian Peninsula). We investigated microbial composition (16S rRNA gene sequencing), abundance, heterotrophic
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Nectar resources affect bird-dispersed microbial metacommunities in suburban and rural gardens Environ. Microbiol. (IF 5.476) Pub Date : 2022-08-11 Marion L. Donald, Josie A. Galbraith, Daria A. Erastova, Anastasija Podolyan, Tom E. X. Miller, Manpreet K. Dhami
As cities expand, understanding how urbanization affects biodiversity is a key ecological goal. Yet, little is known about how host-associated microbial diversity responds to urbanization. We asked if communities of microbial (bacterial and fungal) species in floral nectar and sugar-water feeders and vectored by nectar-feeding birds – thus forming a metacommunity – differed in composition and diversity
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Antidepressants promote the spread of antibiotic resistance via horizontally conjugative gene transfer Environ. Microbiol. (IF 5.476) Pub Date : 2022-08-11 Pengbo Ding, Ji Lu, Yue Wang, Mark A. Schembri, Jianhua Guo
Antibiotic resistance is a global concern threatening public health. Horizontal gene transfer (HGT) between bacterial species contributes greatly to the dissemination of antibiotic resistance. Conjugation is one of the major HGT pathways responsible for the spread of antibiotic resistance genes (ARGs). Antidepressant drugs are commonly prescribed antipsychotics for major depressive disorders and are
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Plantaricin A reverses resistance to ciprofloxacin of multidrug-resistant Staphylococcus aureus by inhibiting efflux pumps Environ. Microbiol. (IF 5.476) Pub Date : 2022-08-12 Fanqiang Meng, Ting Nie, Yunbin Lyu, Fengxia Lyu, Xiaomei Bie, Yingjian Lu, Mingwen Zhao, Zhaoxin Lu
Overexpression of Staphylococcus aureus efflux pumps is commonly associated with antibiotic resistance, causing conventional antibiotics to be unsuccessful in combating multidrug-resistant bacterial infections. Reducing the activity of the efflux pump is an urgently required to tackle this problem. Here, we found that plantaricin A (PlnA), an antimicrobial peptide derived from Lactobacillus plantarum
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Transcriptional regulation of ergosterol biosynthesis genes in response to iron deficiency Environ. Microbiol. (IF 5.476) Pub Date : 2022-08-12 Tania Jordá, Marina Barba-Aliaga, Nicolas Rozès, Paula Alepuz, María Teresa Martínez-Pastor, Sergi Puig
Iron participates as an essential cofactor in the biosynthesis of critical cellular components, including DNA, proteins and lipids. The ergosterol biosynthetic pathway, which is an important target of antifungal treatments, depends on iron in four enzymatic steps. Our results in the model yeast Saccharomyces cerevisiae show that the expression of ergosterol biosynthesis (ERG) genes is tightly modulated
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Very early evolution from the perspective of microbial ecology Environ. Microbiol. (IF 5.476) Pub Date : 2022-08-09 Aaron D. Goldman, Betül Kaçar
The universal ancestor at the root of the species tree of life depicts a population of organisms with a surprising degree of complexity, posessing genomes and translation systems much like that of microbial life today. As the first life forms were most likely to have been simple replicators, considerable evolutionary change must have taken place prior to the last universal common ancestor. It is often
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Shared and contrasting associations in the dynamic nano- and picoplankton communities of two close but contrasting sites from the Bay of Biscay Environ. Microbiol. (IF 5.476) Pub Date : 2022-08-03 Leire Garate, Laura Alonso-Sáez, Marta Revilla, Ramiro Logares, Anders Lanzén
Pico- and nanoplankton are key players in the marine ecosystems due to their implication in the biogeochemical cycles, nutrient recycling and the pelagic food webs However, the specific dynamics and niches of most bacterial, archaeal and eukaryotic plankton remain unknown, as well as the interactions between them. Better characterisation of these is critical for understanding and predicting ecosystem
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‘Omics-guided prediction of the pathway for metabolism of isoprene by Variovorax sp. WS11 Environ. Microbiol. (IF 5.476) Pub Date : 2022-08-03 Robin A. Dawson, Gregory D. Rix, Andrew T. Crombie, J. Colin Murrell
Bacteria that inhabit soils and the leaves of trees partially mitigate the release of the abundant volatile organic compound, isoprene (2-methyl-1,3-butadiene). While the initial steps of isoprene metabolism were identified in Rhodococcus sp. AD45 two decades ago, the isoprene metabolic pathway still remains largely undefined. Limited understanding of the functions of isoG, isoJ and aldH and uncertainty
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Bacterial community dynamics explain carbon mineralization and assimilation in soils of different land-use history Environ. Microbiol. (IF 5.476) Pub Date : 2022-08-03 Samuel E. Barnett, Nicholas D. Youngblut, Daniel H. Buckley
Soil dwelling microorganisms are key players in the terrestrial carbon cycle, driving both the degradation and stabilization of soil organic matter. Bacterial community structure and function vary with respect to land use; yet the ecological drivers of this variation remain poorly described and difficult to predict. We conducted a multi-substrate DNA-stable isotope probing experiment across cropland
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Genetic diversity of honeybee colonies predicts gut bacterial diversity of individual colony members Environ. Microbiol. (IF 5.476) Pub Date : 2022-08-03 Calum Bridson, Latha Vellaniparambil, Rachel E. Antwis, Werner Müller, R. Tucker Gilman, Jennifer K. Rowntree
The gut microbiota of social bees is relatively simple and dominated by a set of core taxa found consistently in individuals around the world. Yet, variation remains and can affect host health. We characterized individual- and regional-scale variation in honeybee (Apis mellifera) gut microbiota from 64 colonies in North-West England by sequencing the V4 region of the 16S rRNA gene and asked whether
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Rhizobium leguminosarum symbiovar viciae strains are natural wheat endophytes that can stimulate root development Environ. Microbiol. (IF 5.476) Pub Date : 2022-08-03 Claudia Bartoli, Stéphane Boivin, Marta Marchetti, Carine Gris, Virginie Gasciolli, Mégane Gaston, Marie-Christine Auriac, Frédéric Debellé, Ludovic Cottret, Aurélien Carlier, Catherine Masson-Boivin, Marc Lepetit, Benoit Lefebvre
Although rhizobia that establish a nitrogen-fixing symbiosis with legumes are also known to promote growth in non-legumes, studies on rhizobial associations with wheat roots are scarce. We searched for Rhizobium leguminosarum symbiovar viciae (Rlv) strains naturally competent to endophytically colonize wheat roots. We isolated 20 strains from surface-sterilized wheat roots and found a low diversity
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Saliva for molecular detection of SARS-CoV-2 in pre-school and school-age children Environ. Microbiol. (IF 5.476) Pub Date : 2022-08-03 Agnes Delaunay-Moisan, Tiffany Guilleminot, Michaela Semeraro, Nelly Briand, Brigitte Bader-Meunier, Romain Berthaud, Guillaume Morelle, Pierre Quartier, Caroline Galeotti, Romain Basmaci, Gregoire Benoist, Vincent Gajdos, Mathie Lorrot, Mahmoud Rifai, Matis Crespin, Zakary M'Sakni, Faheemah Padavia, Catherine Savetier-Leroy, Michelle Lorenzi, Caroline Maurin, Sylvie Behillil, Loic de Pontual, Narcisse
SARS-CoV-2 diagnosis is a cornerstone for the management of coronavirus disease 2019 (COVID-19). Numerous studies have assessed saliva performance over nasopharyngeal sampling (NPS), but data in young children are still rare. We explored saliva performance for SARS-CoV-2 detection by RT-PCR according to the time interval from initial symptoms or patient serological status. We collected 509 NPS and
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Perchlorate-specific proteomic stress responses of Debaryomyces hansenii could enable microbial survival in Martian brines Environ. Microbiol. (IF 5.476) Pub Date : 2022-08-03 Jacob Heinz, Joerg Doellinger, Deborah Maus, Andy Schneider, Peter Lasch, Hans-Peter Grossart, Dirk Schulze-Makuch
If life exists on Mars, it would face several challenges including the presence of perchlorates, which destabilize biomacromolecules by inducing chaotropic stress. However, little is known about perchlorate toxicity for microorganisms on the cellular level. Here, we present the first proteomic investigation on the perchlorate-specific stress responses of the halotolerant yeast Debaryomyces hansenii
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High prevalence and genetic diversity of a single ancestral origin azole-resistant Aspergillus fumigatus in indoor environments at Walailak University, Southern Thailand Environ. Microbiol. (IF 5.476) Pub Date : 2022-08-03 Monlaya Daloh, Sueptrakool Wisessombat, Nadthanan Pinchai, Sirijan Santajit, Phuangthip Bhoopong, Areeya Soaart, Kuntida Chueajeen, Anucha Jitlang, Imran Sama-ae
This study explored the prevalence, genetic diversity, and population structure of azole-resistant Aspergillus fumigatus (ARAf) at Walailak University in Southern Thailand. Three hundred samples were collected from dwellings and workplaces, screened for azole resistance, and tested for drug susceptibility. Molecular detection of alterations in the cyp51A gene and CSP1 typing was performed. Nucleotide
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A lipopolysaccharide-dependent phage infects a pseudomonad phytopathogen and can evolve to evade phage resistance Environ. Microbiol. (IF 5.476) Pub Date : 2022-08-01 Suzanne L. Warring, Lucia M. Malone, Jay Jayaraman, Richard A. Easingwood, Luciano A. Rigano, Rebekah A. Frampton, Sandra B. Visnovsky, Shea M. Addison, Loreto Hernandez, Andrew R. Pitman, Elena Lopez Acedo, Torsten Kleffmann, Matthew D. Templeton, Mihnea Bostina, Peter C. Fineran
Bacterial pathogens are major causes of crop diseases, leading to significant production losses. For instance, kiwifruit canker, caused by the phytopathogen Pseudomonas syringae pv. actinidiae (Psa), has posed a global challenge to kiwifruit production. Treatment with copper and antibiotics, whilst initially effective, is leading to the rise of bacterial resistance, requiring new biocontrol approaches
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What are the options for treating infections by persister-forming pathogens? Environ. Microbiol. (IF 5.476) Pub Date : 2022-08-01 Laura Fernández-García, Joy M. Muthami, Maria Tomas, Thomas K. Wood
CONFLICT OF INTEREST Authors declare no conflicts of interest.
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What is the fate of the biofilm matrix? Environ. Microbiol. (IF 5.476) Pub Date : 2022-08-01 Joy M. Muthami, Laura Fernández-García, María Tomás, Thomas K. Wood
CONFLICT OF INTEREST Authors declare that there are no conflicts of interest and that all data are available.
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Daily dynamics of contrasting spring algal blooms in Santa Monica Bay (central Southern California Bight) Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-26 Gerid A. Ollison, Sarah K. Hu, Julie V. Hopper, Brittany P. Stewart, Jayme Smith, Jennifer L. Beatty, Laura K. Rink, David A. Caron
Protistan algae (phytoplankton) dominate coastal upwelling ecosystems where they form massive blooms that support the world's most important fisheries and constitute an important sink for atmospheric CO2. Bloom initiation is well understood, but the biotic and abiotic forces that shape short-term dynamics in community composition are still poorly characterized. Here, high-frequency (daily) changes
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Conversion of natural grassland to cropland alters microbial community assembly across northern China Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-26 Yongliang Chen, Xue Yang, Wei Fu, Baodong Chen, Hangwei Hu, Kai Feng, Stefan Geisen
To feed the growing human population, natural grasslands are being converted to agricultural use at a massive scale. This conversion may have negative consequences for soil biodiversity, but its impact on the community assembly of differentially microbial groups remains largely unknown. Here, we investigated the diversity and community compositions of bacteria, archaea, fungi and protists, using a
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Advances in the identification of signals and novel sensing mechanisms for signal transduction systems. Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-27 Miguel A Matilla,Elizabet Monteagudo-Cascales,Tino Krell
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Functional analysis, diversity, and distribution of carbendazim hydrolases MheI and CbmA, responsible for the initial step in carbendazim degradation Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-26 Mingliang Zhang, Xuekun Bai, Qian Li, Lu Zhang, Qian Zhu, Siyuan Gao, Zhijian Ke, Mingli Jiang, Junqiang Hu, Jiguo Qiu, Qing Hong
Strains Rhodococcus qingshengii djl-6 and Rhodococcus jialingiae djl-6-2 both harbour the typical carbendazim degradation pathway with the hydrolysis of carbendazim to 2-aminobenzimidazole (2-AB) as the initial step. However, the enzymes involved in this process are still unknown. In this study, the previous reported carbendazim hydrolase MheI was found in strain djl-6, but not in strain djl-6-2, then
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A PadR family transcriptional repressor controls transcription of a trivalent metalloid resistance operon of Azospirillum halopraeferens strain Au 4 Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-26 Jun Zhang, Yi-Fei Wu, Shi-Tong Tang, Jian Chen, Barry P. Rosen, Fang-Jie Zhao
Methylarsenite [MAs(III)] is a highly toxic arsenical produced by some microbes as an antibiotic. In this study, we demonstrate that a PadR family transcriptional regulator, PadRars, from Azospirillum halopraeferens strain Au 4 directly binds to the promoter region of the arsenic resistance (ars) operon (consisting of padRars, arsV, and arsW) and represses transcription of arsV and arsW genes involved
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Genetic redundancy of 4-hydroxybenzoate 3-hydroxylase genes ensures the catabolic safety of Pigmentiphaga sp. H8 in 3-bromo-4-hydroxybenzoate-contaminated habitats Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-25 Kai Chen, Xihui Xu, Muji Yang, Tairong Liu, Bin Liu, Jianchun Zhu, Baozhan Wang, Jiandong Jiang
Genetic redundancy is prevalent in organisms and plays important roles in the evolution of biodiversity and adaptation to environmental perturbation. However, selective advantages of genetic redundancy in overcoming metabolic disturbance due to structural analogues have received little attention. Here, functional divergence of the three 4-hydroxybenzoate 3-hydroxylase (PHBH) genes (phbh1~3) was found
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Investigating the microbial community of Cacopsylla spp. as potential factor in vector competence of phytoplasma Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-25 Hannes Schuler, Jessica Dittmer, Luigimaria Borruso, Jonas Galli, Stefanie Fischnaller, Gianfranco Anfora, Omar Rota-Stabelli, Tobias Weil, Katrin Janik
Phytoplasmas are obligatory intracellular bacteria that colonize the phloem of many plant species and cause hundreds of plant diseases worldwide. In nature, phytoplasmas are primarily transmitted by hemipteran vectors. While all phloem-feeding insects could in principle transmit phytoplasmas, only a limited number of species have been confirmed as vectors. Knowledge about factors that might determine
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Toward an accurate mechanistic understanding of Wolbachia-induced cytoplasmic incompatibility Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-20 Wei Wang, Wen Cui, Haitao Yang
Wolbachia are the most successful intracellular bacteria in arthropods. They can manipulate host reproduction to favour infected females, which transmit Wolbachia to their progeny and increase the presence of Wolbachia in the population. The reproductive alterations caused by Wolbachia include feminization, parthenogenesis, male killing and cytoplasmic incompatibility (CI), among which CI is the most
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Countrywide inter-epidemic region migration pattern suggests the role of southwestern population in wheat stripe rust epidemics in China Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-20 Muhammad Awais, Sajid Ali, Meng Ju, Wei Liu, Gensheng Zhang, Zedong Zhang, Zejian Li, Xinyao Ma, Lin Wang, Zhimin Du, Xiaxia Tian, Qingdong Zeng, Zhensheng Kang, Jie Zhao
Understanding countrywide pathogen population structure and inter-epidemic region spread is crucial for deciphering crop potential losses. Wheat stripe rust caused by Puccinia striiformis f. sp. tritici is a destructive disease that affects worldwide wheat production, widespread in China, representing largest epidemic region globally. This study aimed to understand the population structure and migration
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Long-term unsustainable patterns of development rather than recent deforestation caused the emergence of Orthocoronavirinae species Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-20 Sérvio P. Ribeiro, Debmalya Barh, Bruno Silva Andrade, Raner José Santana Silva, Diogo Henrique Costa-Rezende, Paula Luize Camargos Fonseca, Sandeep Tiwari, Marta Giovanetti, Luiz Carlos Junior Alcantara, Vasco Ariston Azevedo, Preetam Ghosh, José Alexandre F. Diniz-Filho, Rafael Loyola, Maria Fernanda Brito de Almeida, Aristóteles Góes-Neto
We investigated whether a set of phylogeographical tracked emergent events of Orthocoronavirinae were related to developed, urban and polluted environments worldwide. We explored coronavirus records in response to climate (rainfall parameters), population density, CO2 emission, Human Developmental Index (HDI) and deforestation. We contrasted environmental characteristics from regions with spillovers
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The importance of understanding the regulation of bacterial metabolism Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-20 Renata Moreno, Fernando Rojo
Many bacterial species have biotechnological applications, for example in the production of compounds of interest by fermentation or biotransformation, the handling of waste and the decontamination of polluted sites. The genetic manipulation of such bacteria may improve their suitability for these processes, and even allow them to synthesize or degrade new compounds. Obtaining good results usually
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Antarctic lake phytoplankton and bacteria from near-surface waters exhibit high sensitivity to climate-driven disturbance Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-20 Shasten Sherwell, Isha Kalra, Wei Li, Diane M. McKnight, John C. Priscu, Rachael M. Morgan-Kiss
The McMurdo Dry Valleys (MDVs), Antarctica, represent a cold, desert ecosystem poised on the threshold of melting and freezing water. The MDVs have experienced dramatic signs of climatic change, most notably a warm austral summer in 2001–2002 that caused widespread flooding, partial ice cover loss and lake level rise. To understand the impact of these climatic disturbances on lake microbial communities
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Biocrust diazotrophs and bacteria rather than fungi are sensitive to chronic low N deposition Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-18 Xiaoying Rong, Xiaobing Zhou, Xiangzhen Li, Minjie Yao, Yongxing Lu, Peng Xu, Benfeng Yin, Yonggang Li, Zachary T. Aanderud, Yuanming Zhang
Anthropogenic long-term nitrogen (N) deposition may dramatically impact biocrusts due to the overarching N limitation of soil biota in deserts. Even low levels of N may reach a critical loading threshold altering biocrust constituents and function. To identify the impact of chronic and continuous low levels of N deposition on biocrusts, we created a realistic gradient mirroring anthropogenic N addition
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Polaramycin B, and not physical interaction, is the signal that rewires fungal metabolism in the Streptomyces–Aspergillus interaction Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-18 Harald Berger, Markus Bacher, Roman Labuda, Isabel Maria Eppel, Florentina Bayer, Michael Sulyok, Erika Gasparotto, Franz Zehetbauer, Maria Doppler, Hannes Gratzl, Joseph Strauss
Co-culturing the bacterium Streptomyces rapamycinicus and the ascomycete Aspergillus nidulans has previously been shown to trigger the production of orsellinic acid (ORS) and its derivates in the fungal cells. Based on these studies it was assumed that direct physical contact is a prerequisite for the metabolic reaction that involves a fungal amino acid starvation response and activating chromatin
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Toward a molecular understanding of fluoride stress in a model Pseudomonas strain Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-18 Lawrence P. Wackett
Chemical and biological understanding of fluorine in its many forms has lagged behind that of the other halogens, but studies on fluorine have recently come to the forefront. Thousands of commercial fluorine-containing materials are now found throughout the fabric of society, prompting new concerns regarding their health and environmental impacts. The utility and fate of many fluorine-containing products
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Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics. Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-18 Vuong Quoc Hoang Ngo,François Enault,Cédric Midoux,Mahendra Mariadassou,Olivier Chapleur,Laurent Mazéas,Valentin Loux,Théodore Bouchez,Mart Krupovic,Ariane Bize
Diversity of viruses infecting non-extremophilic archaea has been grossly understudied. This is particularly the case for viruses infecting methanogenic archaea, key players in the global carbon biogeochemical cycle. Only a dozen of methanogenic archaeal viruses have been isolated so far. In the present study, we implemented an original coupling between stable isotope probing and complementary shotgun
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Reversible mutations in gliding motility and virulence genes: A flexible and efficient phage defence mechanism in Flavobacterium psychrophilum Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-15 Jóhanna Jørgensen, Krister Sundell, Daniel Castillo, Liv S. Dramshøj, Natasja B. Jørgensen, Susie B. Madsen, Lotta Landor, Tom Wiklund, Valentina L. Donati, Lone Madsen, Inger Dalsgaard, Mathias Middelboe
Flavobacteria are among the most important pathogens in freshwater salmonid aquaculture worldwide. Due to concerns regarding development of antibiotic resistance, phage therapy has been proposed as a solution to decrease pathogen load. However, application of phages is challenged by the development of phage resistance, and knowledge of the mechanisms and implications of phage resistance is therefore
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The roles of DmsEFAB and MtrCAB in extracellular reduction of iodate by Shewanella oneidensis MR-1 with lactate as the sole electron donor Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-15 Jinzhi Guo, Yongguang Jiang, Yidan Hu, Zhou Jiang, Yiran Dong, Liang Shi
To investigate their roles in extracellular reduction of iodate (IO3−) with lactate as an electron donor, the gene clusters of dmsEFAB, mtrCAB, mtrDEF and so4360-4357 in Shewanella oneidensis MR-1 were systematically deleted. Deletions of dmsEFAB and/or mtrCAB gene clusters diminished the bacterial ability to reduce IO3−. Furthermore, DmsEFAB and MtrCAB worked collaboratively to reduce IO3− of which
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Gene expression in the microbial consortia of colonial Microcystis aeruginosa-a potential buoyant particulate biofilm Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-15 Limei Shi, Yuanfeng Cai, Shengling Gao, Daoyan Fang, Yaping Lu, Pengfu Li, Qinglong L. Wu
Microcystis spp., notorious bloom-forming cyanobacteria, are often present in colony form in eutrophic lakes worldwide. Uncovering the mechanisms underlying Microcystis colony formation and maintenance is vital to controlling the blooms, but it has long been a challenge. Here, bacterial communities and gene expression patterns of colonial and unicellular forms of one non-axenic strain of Microcystis
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RsmA3 modulates RpoS through the RetS-Gac-Rsm signalling pathway in response to H2O2 stress in the phytopathogen Pseudomonas syringae Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-15 Xun Yu, Cui Meng, Xiaocheng Tan, Yuwei Su, Zhiping Cao, Tzann-Shun Hwang, Lin Li
Reactive oxygen species are a fatal challenge to the plant pathogenic bacterium Pseudomonas syringae. In this study, we reveal that the global regulatory protein RsmA3 from the RetS-Gac/Rsm signalling pathway modulates RpoS in the early-log growth phase in the P. syringae wild-type strain MB03, thereby regulating oxidative tolerance to H2O2 and ultimately affecting pathogenicity to the host plant.
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Infection-competent monkeypox virus contamination identified in domestic settings following an imported case of monkeypox into the UK Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-15 Barry Atkinson, Christopher Burton, Thomas Pottage, Katy-Anne Thompson, Didier Ngabo, Ant Crook, James Pitman, Sian Summers, Kuiama Lewandowski, Jenna Furneaux, Katherine Davies, Timothy Brooks, Allan M. Bennett, Kevin S. Richards
An imported case of monkeypox was diagnosed in December 2019 in a traveller returning from Nigeria to the UK. Subsequently, environmental sampling was performed at two adjoining single-room residences occupied by the patient and their sibling. Monkeypox virus DNA was identified in multiple locations throughout both properties, and monkeypox virus was isolated from several samples 3 days after the patient
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Wide distribution of the sad gene cluster for sub-terminal oxidation in alkane utilizers Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-15 Chao-Fan Yin, Ying Xu, Tao Li, Ning-Yi Zhou
Alkane constitutes major fractions of crude oils, and its microbial aerobic degradation dominantly follows the terminal oxidation and the sub-terminal pathways. However, the latter one received much less attention, especially since the related genes were yet to be fully defined. Here, we isolated a bacterium designated Acinetobacter sp. strain NyZ410, capable of growing on alkanes with a range of chain
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Hidden fairy rings and males—Genetic patterns of natural Burgundy truffle (Tuber aestivum Vittad.) populations reveal new insights into its life cycle Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-15 Florian Staubli, Lea Imola, Benjamin Dauphin, Virginie Molinier, Stephanie Pfister, Yasmine Piñuela, Laura Schürz, Ludger Sproll, Brian S. Steidinger, Uli Stobbe, Willy Tegel, Ulf Büntgen, Simon Egli, Martina Peter
Burgundy truffles are heterothallic ascomycetes that grow in symbiosis with trees. Despite their esteemed belowground fruitbodies, the species' complex lifecycle is still not fully understood. Here, we present the genetic patterns in three natural Burgundy truffle populations based on genotyped fruitbodies, ascospore extracts and ectomycorrhizal root tips using microsatellites and the mating-type locus
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Golgi-localized calcium/manganese transporters FgGdt1 and FgPmr1 regulate fungal development and virulence by maintaining Ca2+ and Mn2+ homeostasis in Fusarium graminearum Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-15 Congxian Wu, Zhongkun Guo, Meiru Zhang, Huilin Chen, Minghui Peng, Yakubu Saddeeq Abubakar, Huawei Zheng, Yingzi Yun, Wenhui Zheng, Zonghua Wang, Jie Zhou
Calcium and manganese transporters play important roles in regulating Ca2+ and Mn2+ homeostasis in cells, which is necessary for the normal physiological activities of eukaryotes. Gdt1 and Pmr1 function as calcium/manganese transporters in the Golgi apparatus. However, the functions of Gdt1 and Pmr1 have not been previously characterized in the plant pathogenic fungus Fusarium graminearum. Here, we
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Hierarchical phylogenetic community assembly of soil protists in a temperate agricultural field Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-15 Julien Roy, Florent Mazel, Kenneth Dumack, Michael Bonkowski, Matthias C. Rillig
Protists are abundant, diverse and perform essential functions in soils. Protistan community structure and its change across time or space are traditionally studied at the species level but the relative importance of the processes shaping these patterns depends on the taxon phylogenetic resolution. Using 18S rDNA amplicon data of the Cercozoa, a group of dominant soil protists, from an agricultural
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Membrane lipid renovation in Pseudomonas aeruginosa - implications for phage therapy? Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-15 Rhiannon Lyon, Rebekah A. Jones, Holly Shropshire, Isabel Aberdeen, David J. Scanlan, Andrew Millard, Yin Chen
Pseudomonas aeruginosa is an important Gram-negative pathogen with intrinsic resistance to many clinically used antibiotics. It is particularly troublesome in nosocomial infections, immunocompromised patients, and individuals with cystic fibrosis. Antimicrobial resistance (AMR) is a huge threat to global health, with a predicted 10 million people dying from resistant infections by 2050. A promising
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Responses of dinoflagellate cells to ultraviolet-C irradiation Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-15 Alvin Chun Man Kwok, Chongping Li, Wing Tai Lam, Joseph Tin Yum Wong
Dinoflagellates are important aquatic microbes and major harmful algal bloom (HAB) agents that form invasive species through ship ballast transfer. UV-C installations are recommended for ballast treatments and HAB controls, but there is a lack of knowledge in dinoflagellate responses to UV-C. We report here dose-dependent cell cycle delay and viability loss of dinoflagellate cells irradiated with UV-C
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Mycorrhiza-induced mycocypins of Laccaria bicolor are potent protease inhibitors with nematotoxic and collembola antifeedant activity Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-11 Jonathan M. Plett, Jerica Sabotič, Eva Vogt, Fridtjof Snijders, Annegret Kohler, Uffe N. Nielsen, Markus Künzler, Francis Martin, Claire Veneault-Fourrey
Fungivory of mycorrhizal hyphae has a significant impact on fungal fitness and, by extension, on nutrient transfer between fungi and host plants in natural ecosystems. Mycorrhizal fungi have therefore evolved an arsenal of chemical compounds that are hypothesized to protect the hyphal tissues from being eaten, such as the protease inhibitors mycocypins. The genome of the ectomycorrhizal fungus Laccaria
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Watershed-scale liming reveals the short- and long-term effects of pH on the forest soil microbiome and carbon cycling Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-07 Bhavya Sridhar, Gregory B. Lawrence, Spencer J. Debenport, Timothy J. Fahey, Daniel H. Buckley, Roland C. Wilhelm, Christine L. Goodale
Soil microbial community composition routinely correlates with pH, reflecting both direct pH effects on microbial physiology and long-term biogeochemical feedbacks. We used two watershed-scale liming experiments to identify short- (2 years) and long-term (25 years) changes in the structure and function of bacterial and fungal communities in organic horizons (Oe and Oa) of acid forest soils. Liming
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Response of potential activity, abundance and community composition of nitrite-dependent anaerobic methanotrophs to long-term fertilization in paddy soils Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-07 Yuling Yang, Lidong Shen, Yanan Bai, Xu Zhao, Shuwei Wang, Jiaqi Liu, Xin Liu, Maohui Tian, Wangting Yang, Jinghao Jin, Hechen Huang, Hongsheng Wu
The process of nitrite-dependent anaerobic methane oxidation (n-damo) catalysed by Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria is a novel pathway in regulating methane (CH4) emissions from paddy fields. Nitrogen fertilization is essential to improve rice yields and soil fertility; however, its effect on the n-damo process is largely unknown. Here, the potential n-damo activity, abundance
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Context-dependent costs and benefits of endosymbiotic interactions in a ciliate–algae system Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-07 Elena L. Horas, Sarah M. Metzger, Barbara Platzer, Joseph B. Kelly, Lutz Becks
Endosymbiosis, an interaction between two species where one lives within the other, has evolved multiple times independently, but the underlying mechanisms remain unclear. Evolutionary theory suggests that for an endosymbiotic interaction to remain stable over time, births of both partners should be higher than their deaths in symbiosis and deaths of both partners should be higher than their births
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Nutritional inter-dependencies and a carbazole-dioxygenase are key elements of a bacterial consortium relying on a Sphingomonas for the degradation of the fungicide thiabendazole Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-07 Sotirios Vasileiadis, Chiara Perruchon, Benjamin Scheer, Lorenz Adrian, Nicole Steinbach, Marco Trevisan, Patricia Plaza-Bolaños, Ana Agüera, Antonis Chatzinotas, Dimitrios G. Karpouzas
Thiabendazole (TBZ), is a persistent fungicide/anthelminthic and a serious environmental threat. We previously enriched a TBZ-degrading bacterial consortium and provided first evidence for a Sphingomonas involvement in TBZ transformation. Here, using a multi-omic approach combined with DNA-stable isotope probing (SIP) we verified the key degrading role of Sphingomonas and identify potential microbial
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Biogeographical variation in antimicrobial resistance in rivers is influenced by agriculture and is spread through bacteriophages Environ. Microbiol. (IF 5.476) Pub Date : 2022-07-07 Tilde Andersson, Aiko D. Adell, Andrea I. Moreno-Switt, Peter Spégel, Charlotta Turner, Søren Overballe-Petersen, Kurt Fuursted, Rolf Lood
Antibiotic resistance is currently an extensive medical challenge worldwide, with global numbers increasing steadily. Recent data have highlighted wastewater treatment plants as a reservoir of resistance genes. The impact of these findings for human health can best be summarized using a One Health concept. However, the molecular mechanisms impacting resistance spread have not been carefully evaluated
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Genetic characterization of the cyclohexane carboxylate degradation pathway in the denitrifying bacterium Aromatoleum sp. CIB Environ. Microbiol. (IF 5.476) Pub Date : 2022-06-29 David Sanz, Eduardo Díaz
The alicyclic compound cyclohexane carboxylate (CHC) is anaerobically degraded through a peripheral pathway that converges with the central benzoyl-CoA degradation pathway of aromatic compounds in Rhodopseudomonas palustris (bad pathway) and some strictly anaerobic bacteria. Here we show that in denitrifying bacteria, e.g. Aromatoleum sp. CIB strain, CHC is degraded through a bad-ali pathway similar
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Climate dictates microbial community composition and diversity in Australian biological soil crusts (biocrusts) Environ. Microbiol. (IF 5.476) Pub Date : 2022-06-29 Angela M. Chilton, Suong T. T. Nguyen, Tiffanie M. Nelson, Leanne A. Pearson, Brett A. Neilan
The soil surface of drylands can typically be colonized by cyanobacteria and other microbes, forming biological soil crusts or ‘biocrusts’. Biocrusts provide critical benefits to ecosystems and are a common component of the largely arid and semi-arid Australian continent. Yet, their distribution and the parameters that shape their microbial composition have not been investigated. We present here the
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Late Pleistocene-dated divergence between South Hemisphere populations of the non-conventional yeast L. cidri Environ. Microbiol. (IF 5.476) Pub Date : 2022-06-29 Pablo Villarreal, Carlos A. Villarroel, Sam O'Donnell, Nicolas Agier, Julian F. Quintero-Galvis, Tomas A. Peña, Roberto F. Nespolo, Gilles Fischer, Cristian Varela, Francisco A. Cubillos
Most organisms belonging to the Saccharomycotina subphylum have high genetic diversity and a vast repertoire of metabolisms and lifestyles. Lachancea cidri is an ideal yeast model for exploring the interplay between genetics, ecological function and evolution. Lachancea cidri diverged from the Saccharomyces lineage before the whole-genome duplication and is distributed across the South Hemisphere,
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High diversity of pathogenic Escherichia coli clones carrying mcr-1 among gulls underlines the need for strategies at the environment–livestock–human interface Environ. Microbiol. (IF 5.476) Pub Date : 2022-06-21 Marisa Ribeiro-Almeida, Joana Mourão, Ângela Novais, Sofia Pereira, Joana Freitas-Silva, Sofia Ribeiro, Paulo Martins da Costa, Luísa Peixe, Patrícia Antunes
The expansion of mcr-carrying bacteria is a well-recognized public health problem. Measures to contain mcr spread have mainly been focused on the food–animal production sector. Nevertheless, the spread of MCR producers at the environmental interface particularly driven by the increasing population of gulls in coastal cities has been less explored. Occurrence of mcr-carrying Escherichia coli in gull's
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Identification of sulfate-reducing magnetotactic bacteria via a group-specific 16S rDNA primer and correlative fluorescence and electron microscopy: Strategy for culture-independent study Environ. Microbiol. (IF 5.476) Pub Date : 2022-06-21 Jinhua Li, Peiyu Liu, Nicolas Menguy, Karim Benzerara, Jinling Bai, Xiang Zhao, Eric Leroy, Chaoqun Zhang, Heng Zhang, Jiawei Liu, Rongrong Zhang, Kelei Zhu, Andrew P. Roberts, Yongxin Pan
Magnetotactic bacteria (MTB) biomineralize intracellular magnetic nanocrystals and swim along geomagnetic field lines. While few axenic MTB cultures exist, living cells can be separated magnetically from natural environments for analysis. The bacterial universal 27F/1492R primer pair has been used widely to amplify nearly full-length 16S rRNA genes and to provide phylogenetic portraits of MTB communities
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Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride Environ. Microbiol. (IF 5.476) Pub Date : 2022-06-21 Patricia Calero, Nicolás Gurdo, Pablo I. Nikel
The presence of mineral fluoride (F−) in the environment has both a geogenic and anthropogenic origin, and the halide has been described to be toxic in virtually all living organisms. While the evidence gathered in different microbial species supports this notion, a systematic exploration of the effects of F− salts on the metabolism and physiology of environmental bacteria remained underexplored thus
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Ecology of Methanonatronarchaeia Environ. Microbiol. (IF 5.476) Pub Date : 2022-06-21 Dimitry Y. Sorokin, Alexander Y. Merkel, Ben Abbas
Methanonatronarchaeia represents a deep-branching phylogenetic lineage of extremely halo(alkali)philic and moderately thermophilic methyl-reducing methanogens belonging to the phylum Halobacteriota. It includes two genera, the alkaliphilic Methanonatronarchaeum and the neutrophilic Ca. Methanohalarchaeum. The former is represented by multiple closely related pure culture isolates from hypersaline soda
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Polar flagellar wrapping and lateral flagella jointly contribute to Shewanella putrefaciens environmental spreading Environ. Microbiol. (IF 5.476) Pub Date : 2022-06-20 Marco J. Kühn, Daniel B. Edelmann, Kai M. Thormann
Flagella enable bacteria to actively spread within the environment. A number of species possess two separate flagellar systems, where in most cases a primary polar flagellar system is supported by distinct secondary lateral flagella under appropriate conditions. Using functional fluorescence tagging on one of these species, Shewanella putrefaciens, as a model system, we explored how two different flagellar
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Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables Environ. Microbiol. (IF 5.476) Pub Date : 2022-06-17 Jessica L. Gronniger, Zhao Wang, Genevieve R. Brandt, Christopher S. Ward, Despina Tsementzi, Han Mu, Junyao Gu, Zackary I. Johnson, Konstantinos T. Konstantinidis, Dana E. Hunt
Disturbances, here defined as events that directly alter microbial community composition, are commonly studied in host-associated and engineered systems. In spite of global change both altering environmental averages and increasing extreme events, there has been relatively little research into the causes, persistence and population-level impacts of disturbance in the dynamic coastal ocean. Here, we
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Bacterioplankton communities reveal horizontal and vertical influence of an Island Mass Effect Environ. Microbiol. (IF 5.476) Pub Date : 2022-06-12 Jacqueline Comstock, Craig E. Nelson, Anna James, Emma Wear, Nicholas Baetge, Kristina Remple, Amethyst Juknavorian, Craig A. Carlson
Coral reefs are highly productive ecosystems with distinct biogeochemistry and biology nestled within unproductive oligotrophic gyres. Coral reef islands have often been associated with a nearshore enhancement in phytoplankton, a phenomenon known as the Island Mass Effect (IME). Despite being documented more than 60 years ago, much remains unknown about the extent and drivers of IMEs. Here we utilized