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Bacterial communities are more sensitive to ocean acidification than fungal communities in estuarine sediments FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-04-01 Xiaoxuan Su, Xiaoru Yang, Hu Li, Hongtao Wang, Yingmu Wang, Jianxin Xu, Kai Ding, Yong-guan Zhu
Ocean acidification (OA) in estuaries is becoming a global concern, and may affect microbial characteristics in estuarine sediments. Bacterial communities in response to acidification in this habitat have been well discussed; however, knowledge about how fungal communities respond to OA remains poorly understood. Here, we explored the effects of acidification on bacterial and fungal activities, structures
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Bacteria responsible for antimonite oxidation in antimony-contaminated soil revealed by DNA-SIP coupled to metagenomics FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-03-31 Miaomiao Zhang, Max Kolton, Zhe Li, Hanzhi Lin, Fangbai Li, Guimei Lu, Pin Gao, Xiaoxu Sun, Rui Xu, Fuqing Xu, Weimin Sun
Antimony (Sb), the analog of arsenic (As), is a toxic metalloid that poses risks to the environment and human health. Antimonite (Sb(III)) oxidation can decrease Sb toxicity, which contributes to the bioremediation of Sb contamination. Bacteria can oxidize Sb(III), but the current knowledge regarding Sb(III)-oxidizing bacteria (SbOB) is limited to pure culture studies, thus underestimating the diversity
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Aromatic compound-degrading taxa in an anoxic coal seam microbiome from the Surat Basin, Australia FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-03-31 Bronwyn C Campbell, Se Gong, Paul Greenfield, David J Midgley, Ian T Paulsen, Simon C George
Methane is an important energy resource internationally, and a large proportion of this methane is produced by microbial communities living in coal seams. Despite the value of this resource for human energy security, our understanding of the metabolic roles played by specific taxa during the biodegradation of coal to methane in situ is quite limited. In order to develop a greater understanding of microbial
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Responses of abundant and rare bacterioplankton to temporal change in a subtropical urban reservoir FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-03-31 Pascaline Nyirabuhoro, Xiaofei Gao, Jean Claude Ndayishimiye, Peng Xiao, Yuanyuan Mo, Hossein Ganjidoust, Jun Yang
Investigation of bacterial community dynamics across different time scales is important for understanding how environmental conditions drive community change over time. Bacterioplankton from the surface waters of a subtropical urban reservoir in southeast China were analyzed through high-frequency sampling over 13 months to compare patterns and ecological processes between short (0‒8 weeks), medium
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Gill microbiome structure and function in the chemosymbiotic coastal lucinid Stewartia floridana FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-03-11 Shen Jean Lim, Brenton Davis, Danielle Gill, John Swetenburg, Laurie C Anderson, Annette Summers Engel, Barbara J Campbell
Lucinid bivalves harbor environmentally acquired, chemosynthetic, gammaproteobacterial gill endosymbionts. Lucinid gill microbiomes, which may contain other gammaproteobacterial and/or spirochete taxa, remain under-sampled. To understand inter-host variability of the lucinid gill microbiome, specifically in the bacterial communities, we analyzed the microbiome content of Stewartia floridana collected
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Gut bacteria formation and influencing factors FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-03-11 Jing Yang, Jin'en Wu, Yating Li, Yong'e Zhang, William C Cho, Xianghong Ju, Evert M van Schothorst, Yadong Zheng
The gut microbiota plays an important role in human health. In modern life, with the improvement of living conditions, the intake of high-sugar and high-fat diets as well as the large-scale use of antibacterial drugs have an extensive impact on the gut microbiota, even leading to gut microbiota-orchestrating disorders. This review discusses the effects of various factors, including geographic location
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Enhancement of antibiotic production by co-cultivation of two antibiotic producing marine Vibrionaceae strains FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-03-09 Yannick Buijs, Sheng-Da Zhang, Karen Marie Jørgensen, Thomas Isbrandt, Thomas Ostenfeld Larsen, Lone Gram
Deciphering the cues that stimulate microorganisms to produce their full secondary metabolic potential promises to speed up the discovery of novel drugs. Ecology-relevant conditions, including carbon-source(s) and microbial interactions, are important effectors of secondary metabolite production. Vice versa secondary metabolites are important mediators in microbial interactions, although their exact
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Characterizing the culturable surface microbiomes of diverse marine animals FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-03-03 Abigail G Keller, Amy Apprill, Philippe Lebaron, Jooke Robbins, Tracy A Romano, Ellysia Overton, Yuying Rong, Ruiyi Yuan, Scott Pollara, Kristen E Whalen
Biofilm-forming bacteria have the potential to contribute to the health, physiology, behavior and ecology of the host and serve as its first line of defense against adverse conditions in the environment. While metabarcoding and metagenomic information furthers our understanding of microbiome composition, fewer studies use cultured samples to study the diverse interactions among the host and its microbiome
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Microbiome variation during culture growth of the European house dust mite, Dermatophagoides pteronyssinus FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-03-01 Marta Nesvorna, Stano Pekar, Elena Shcherbachenko, Vit Molva, Tomas Erban, Stefan J Green, Pavel B Klimov, Jan Hubert
In culture, the house dust mite, Dermatophagoides pteronyssinus, shows different growth patterns, but the composition and changes in the associated microbial community during mite culture growth are poorly known. In this study, we analyzed temporal changes in microbial communities including ‘internal’ communities (inside mites, ingested) and ‘environmental’ communities (from culture environment). Microbial
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Potato plant spheres and to a lesser extent the soil type influence the proportion and diversity of bacterial isolates with in vitro antagonistic activity towards Ralstonia solanacearum FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-03-01 Tarek R Elsayed, Rita Grosch, Kornelia Smalla
Ralstonia solanacearum biovar2-race3 (Rs r3b2) is an epidemic soil-borne bacterial phytopathogen causing brown rot disease in potato. In this study, we assessed how three soil types stored at the same field site influenced the proportion and diversity of bacterial isolates with in vitro antagonistic activity towards Rs in bulk soil and different potato plant spheres (rhizosphere, endorhiza and endocaulosphere;
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Bicarbonate uptake rates and diversity of RuBisCO genes in saline lake sediments FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-25 Beichen Wang, Jianrong Huang, Jian Yang, Hongchen Jiang, Haiyi Xiao, Jibin Han, Xiying Zhang
There is limited knowledge of microbial carbon fixation rate, and carbon-fixing microbial abundance and diversity in saline lakes. In this study, the inorganic carbon uptake rates and carbon-fixing microbial populations were investigated in the surface sediments of lakes with a full range of salinity from freshwater to salt saturation. The results showed that in the studied lakes light-dependent bicarbonate
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Sea foams are ephemeral hotspots for distinctive bacterial communities contrasting sea-surface microlayer and underlying surface water FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-24 Janina Rahlff, Christian Stolle, Helge-Ansgar Giebel, Nur Ili Hamizah Mustaffa, Oliver Wurl, Daniel P. R. Herlemann
The occurrence of foams at oceans’ surfaces is patchy and generally short-lived, but a detailed understanding of bacterial communities inhabiting sea foams is lacking. Here, we investigated how marine foams differ from the sea-surface microlayer (SML), a <1-mm-thick layer at the air–sea interface, and underlying water from 1 m depth. Samples of sea foams, SML and underlying water collected from the
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Soil microbial communities influencing organic phosphorus mineralization in a coastal dune chronosequence in New Zealand FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-20 Jonathan R Gaiero, Micaela Tosi, Elizabeth Bent, Gustavo Boitt, Kamini Khosla, Benjamin L Turner, Alan E Richardson, Leo M Condron, Kari E Dunfield
The Haast chronosequence in New Zealand is an ∼6500-year dune formation series, characterized by rapid podzol development, phosphorus (P) depletion and a decline in aboveground biomass. We examined bacterial and fungal community composition within mineral soil fractions using amplicon-based high-throughput sequencing (Illumina MiSeq). We targeted bacterial non-specific acid (class A, phoN/phoC) and
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Crop type exerts greater influence upon rhizosphere phosphohydrolase gene abundance and phylogenetic diversity than phosphorus fertilization FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-20 Andrew L. Neal, Timothy McLaren, Mariana Lourenço Campolino, David Hughes, Antônio Marcos Coelho, Ubiraci Gomes de Paula Lana, Eliane Aparecida Gomes, Sylvia Morais de Sousa
Rock phosphate is an alternative form of phosphorus (P) fertilizer; however, there is no information regarding the influence of P fertilizer sources in Brazilian Cerrado soils upon microbial genes coding for phosphohydrolase enzymes in crop rhizospheres. Here, we analyze a field experiment comparing maize and sorghum grown under different P fertilization (rock phosphate and triple superphosphate) upon
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Rickettsia increases its infection and spread in whitefly populations by manipulating the defense patterns of the host plant FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-19 Pei-Qiong Shi, Xin-Yi Chen, Xiao-Sheng Chen, Ning Lv, Yuan Liu, Bao-Li Qiu
The whitefly Bemisia tabaci is a destructive agricultural pest that frequently harbors various species of secondary symbionts including Rickettsia. Previous studies have revealed that the infection of Rickettsia can improve whitefly performance on food plants; however, to date, no evidence has shown, if, and how, Rickettsia manipulates the plant-insect interactions. In the current study, the effects
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Root exposure to apple replant disease soil triggers local defense response and rhizoplane microbiome dysbiosis FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-15 Balbín-Suárez A, Jacquiod S, Rohr A, et al.
ABSTRACTA soil column split-root experiment was designed to investigate the ability of apple replant disease (ARD)-causing agents to spread in soil. ‘M26’ apple rootstocks grew into a top layer of Control soil, followed by a barrier-free split-soil layer (Control soil/ARD soil). We observed a severely reduced root growth, concomitant with enhanced gene expression of phytoalexin biosynthetic genes and
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The first sequenced Sphaerotilus natans bacteriophage– characterization and potential to control its filamentous bacterium host FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-15 Ferreira R, Amado R, Padrão J, et al.
ABSTRACTBacteriophages (phages) are ubiquitous entities present in every conceivable habitat as a result of their bacterial parasitism. Their prevalence and impact in the ecology of bacterial communities and their ability to control pathogens make their characterization essential, particularly of new phages, improving knowledge and potential application. The isolation and characterization of a new
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Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-13 Lucas Dantas Lopes, Jingjie Hao, Daniel P Schachtman
Soil pH is a major factor shaping bulk soil microbial communities. However, it is unclear whether the belowground microbial habitats shaped by plants (e.g. rhizosphere and root endosphere) are also affected by soil pH. We investigated this question by comparing the microbial communities associated with plants growing in neutral and strongly alkaline soils in the Sandhills, which is the largest sand
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The proficiency of the original host species determines community-level plasmid dynamics FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-13 Anastasia Kottara, James P J Hall, Michael A Brockhurst
Plasmids are common in natural bacterial communities, facilitating bacterial evolution via horizontal gene transfer. Bacterial species vary in their proficiency to host plasmids: whereas plasmids are stably maintained in some species regardless of selection for plasmid-encoded genes, in other species, even beneficial plasmids are rapidly lost. It is, however, unclear how this variation in host proficiency
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Distinct rhizomicrobiota assemblages and plant performance in lettuce grown in soils with different agricultural management histories FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-11 Babin D, Sommermann L, Chowdhury S, et al.
ABSTRACTA better understanding of factors shaping the rhizosphere microbiota is important for sustainable crop production. We hypothesized that the effect of agricultural management on the soil microbiota is reflected in the assemblage of the rhizosphere microbiota with implications for plant performance. We designed a growth chamber experiment growing the model plant lettuce under controlled conditions
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Impacts of switching tillage to no-tillage and vice versa on soil structure, enzyme activities and prokaryotic community profiles in Argentinean semi-arid soils FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-11 Luciano A Gabbarini, Eva Figuerola, Juan P Frene, Natalia B Robledo, Federico M Ibarbalz, Doreen Babin, Kornelia Smalla, Leonardo Erijman, Luis G Wall
The effects of tillage on soil structure, physiology and microbiota structure were studied in a long-term field experiment, with side-to-side plots, established to compare effects of conventional tillage (CT) vs no-till (NT) agriculture. After 27 years, part of the field under CT was switched to NT and vice versa. Soil texture, soil enzymatic profiles and the prokaryotic community structure (16S rRNA
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Insights into the structure and role of seed-borne bacteriome during maize germination FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-11 Figueiredo dos Santos L, Fernandes Souta J, de Paula Soares C, et al.
ABSTRACTSeed germination events modulate microbial community composition, which ultimately influences seed-to-seedling growth performance. Here, we evaluate the germinated maize (variety SHS 5050) root bacterial community of disinfected seed (DS) and non-disinfected seed (NDS). Using a gnotobiotic system, sodium hypochlorite (1.25%; 30 min)-treated seeds showed a reduction of bacterial population size
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The dynamics of picocyanobacteria from a hypereutrophic shallow lake is affected by light-climate and small-bodied zooplankton: a ten-year cytometric time-series analysis FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-03-30 María Victoria Quiroga, Paula Huber, Juliana Ospina-Serna, Nadia Diovisalvi, Mariana Odriozola, Gerardo R Cueto, Leonardo Lagomarsino, Paulina Fermani, José Bustingorry, Roberto Escaray, Horacio Zagarese, Fernando Unrein
In aquatic systems, an interplay between bottom-up and top-down processes determines the dynamic of picocyanobacteria (Pcy) abundance and community structure. Here, we analyzed a 10-year time series (sampled fortnightly) from a hypereutrophic turbid shallow lake located within the Pampa Region of South America, generating the first long-term record of freshwater Pcy from the Southern Hemisphere. We
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DNA-SIP and repeated isolation corroborate Variovorax as a key organism in maintaining the genetic memory for linuron biodegradation in an agricultural soil FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-03-30 Harry Lerner, Başak Öztürk, Anja B Dohrmann, Joice Thomas, Kathleen Marchal, René De Mot, Wim Dehaen, Christoph C Tebbe, Dirk Springael
The frequent exposure of agricultural soils to pesticides can lead to microbial adaptation, including the development of dedicated microbial populations that utilize the pesticide compound as a carbon and energy source. Soil from an agricultural field in Halen (Belgium) with a history of linuron exposure has been studied for its linuron-degrading bacterial populations at two time points over the past
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Relative contributions of egg-associated and substrate-associated microorganisms to black soldier fly larval performance and microbiota FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-03-30 Stijn J J Schreven, Hugo de Vries, Gerben D A Hermes, Hauke Smidt, Marcel Dicke, Joop J A van Loon
Larvae of the black soldier fly (BSF) can be used to convert organic waste into insect biomass for animal feed. In this process, they interact with microorganisms originating from the substrate, the insect, and the environment. The substrate is the main determinant of the larval gut microbiota composition, but inoculation of the substrate with egg-associated bacteria can improve larval performance
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The association between the initial adhesion and cyanobacterial biofilm development FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-03-30 Sara I Faria, Rita Teixeira-Santos, João Morais, Vitor Vasconcelos, Filipe J Mergulhão
Although laboratory assays provide valuable information about the antifouling effectiveness of marine surfaces and the dynamics of biofilm formation, they may be laborious and time-consuming. This study aimed to determine the potential of short-time adhesion assays to estimate how biofilm development may proceed. The initial adhesion and cyanobacterial biofilm formation were evaluated using glass and
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Factors influencing biodiversity of three microbial groups within and among islands of the Baltic Sea FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-03-22 Anette Teittinen, Leena Virta, Mingjia Li, Jianjun Wang
Islands provide ideal model systems to examine the factors influencing biodiversity, yet knowledge of microbial biodiversity on islands remains scarce. We collected a dataset from 101 rock pools along a freshwater to brackish water transition on islands of the Baltic Sea and investigated the patterns and drivers of community composition and species richness of diatoms, cyanobacteria, and non-cyanobacteria
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Composition and structure of the skin microbiota of rorquals off the Eastern South Pacific FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-03-22 Frederick Toro, Jaime Alarcón, Sebastián Márquez, Juan Capella, Paulina Bahamonde, Fernando Esperón, Andrea Moreno-Switt, Eduardo Castro-Nallar
Recent advances in high-throughput sequencing have enabled the large-scale interrogation of microbiota in the most diverse environments, including host-associated microbiota. This has led to the recognition that the skin microbiota of rorquals is specific and structurally different from that of the ocean. This study reveals the skin microbiome of 85 wild individuals along the Chilean coast belonging
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Effects of the prey landscape on the fitness of the bacterial predators Bdellovibrio and like organisms FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-03-19 Rajesh Sathyamoorthy, Amit Huppert, Daniel E Kadouri, Edouard Jurkevitch
Bdellovibrio and like organisms (BALOs) are obligate predatory bacteria commonly encountered in the environment. In dual predator-prey cultures, prey accessibility ensures optimal feeding and replication and rapid BALO population growth. However, the environmental prey landscape is complex, as it also incorporates non-prey cells and other particles. These may act as decoys, generating unproductive
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Corrigendum to: Host genotype explains rhizospheric microbial community composition: the case of wild cotton metapopulations (Gossypium hirsutum L.) in Mexico FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-25
In the originally published version of this manuscript, errors were noted and listed in this corrigendum.
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Phylogeographic distribution of rhizobia nodulating common bean (Phaseolus vulgaris L.) in Ethiopia FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-03-16 A H Gunnabo, R Geurts, E Wolde-meskel, T Degefu, K E Giller, J van Heerwaarden
Rhizobia are soil borne bacteria that form symbiotic relations with legumes and fix atmospheric nitrogen. The nitrogen fixation potential depends on several factors such as the type of host and symbionts and on environmental factors that affect the distribution of rhizobia. We isolated bacteria nodulating common bean in Southern Ethiopia to evaluate their genetic diversity and phylogeography at nucleotide
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Are permafrost microorganisms as old as permafrost? FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-19 Abramov A, Vishnivetskaya T, Rivkina E.
ABSTRACTPermafrost describes the condition of earth material (sand, ground, organic matter, etc.) cemented by ice when its temperature remains at or below 0°C continuously for longer than 2 years. Evidently, permafrost is as old as the time passed from freezing of the earth material. Permafrost is a unique phenomenon and may preserve life forms it encloses. Therefore, in order to talk confidently about
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Democratization of fungal highway columns as a tool to investigate bacteria associated with soil fungi FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-01-13 Junier P, Cailleau G, Palmieri I, et al.
ABSTRACTBacteria–fungi interactions (BFIs) are essential in ecosystem functioning. These interactions are modulated not only by local nutritional conditions but also by the physicochemical constraints and 3D structure of the environmental niche. In soils, the unsaturated and complex nature of the substrate restricts the dispersal and activity of bacteria. Under unsaturated conditions, some bacteria
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Co-infecting pathogen lineages have additive effects on host bacterial communities FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-13 Daniel Medina, Sasha E Greenspan, Tamilie Carvalho, C Guilherme Becker, Luís Felipe Toledo
Amphibian skin bacteria may confer protection against the fungus Batrachochytrium dendrobatidis (Bd), but responses of skin bacteria to different Bd lineages are poorly understood. The global panzootic lineage (Bd-GPL) has caused amphibian declines and extinctions globally. However, other lineages are enzootic (Bd-Asia-2/Brazil). Increased contact rates between Bd-GPL and enzootic lineages via globalization
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Seemingly trivial secondary factors may determine microbial competition: a cautionary tale on the impact of iron supplementation through corrosion FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-01-11 Gerben R Stouten, Kelly Hamers, Rinke J van Tatenhove-Pel, Eline van der Knaap, Robbert Kleerebezem
Microbial community engineering aims for enrichment of a specific microbial trait by imposing specific cultivation conditions. This work demonstrates that things may be more complicated than typically presumed and that microbial competition can be affected by seemingly insignificant variables, like in this case the type of acid used for pH control. Aerobic bioreactors pulse fed with acetate operated
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Reduced tillage, cover crops and organic amendments affect soil microbiota and improve soil health in Uruguayan vegetable farming systems FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-06 Victoria Cerecetto, Kornelia Smalla, Joseph Nesme, Silvia Garaycochea, Pablo Fresia, Søren Johannes Sørensen, Doreen Babin, Carolina Leoni
Conventional tillage and mineral fertilization (CTMF) jeopardize soil health in conventional vegetable production systems. Using a field experiment established in Uruguay in 2012, we aimed to compare the soil restoration potential of organic fertilization (compost, poultry manure) combined with conventional tillage and cover crop incorporated into the soil (CTOF) or with reduced tillage and the use
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Soil depth matters: Shift in composition and inter-kingdom co-occurrence patterns of microorganisms in forest soils FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-06 Sunil Mundra, O Janne Kjønaas, Luis N Morgado, Anders Kristian Krabberød, Yngvild Ransedokken, Håvard Kauserud
Soil depth represents a strong physiochemical gradient that greatly affects soil-dwelling microorganisms. Fungal communities are typically structured by soil depth, but how other microorganisms are structured is less known. Here, we tested whether depth-dependent variation in soil chemistry affects the distribution and co-occurrence patterns of soil microbial communities. This was investigated by DNA
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Changes in the gut microbial community of the eastern newt (Notophthalmus viridescens) across its three distinct life stages FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-06 Samantha S Fontaine, Patrick M Mineo, Kevin D Kohl
Understanding the forces that shape vertebrate gut microbial community assembly and composition throughout development is a major focus of the microbiome field. Here, we utilize the complex life cycle of the eastern newt (Notophthalmus viridescens) as a natural wild model to compare the effects of host and environmental factors on gut microbiome development. We compared bacterial inventories of each
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Dust-borne microbes affect Ulva ohnoi’s growth and physiological state FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-05 Nimrod Krupnik, Dorin Theodora Asis, Natalia Belkin, Maxim Rubin-Blum, Álvaro Israel, Adina Paytan, David Meiri, Barak Herut, Eyal Rahav
The marine macroalgae Ulva sp. is considered an ecosystem engineer in rocky shores of temperate waters worldwide. Ulva sp. harbors a rich diversity of associated microbial epibionts, which are known to affect the algae's typical morphological development and ‘health’. We examined the interaction between airborne microbes derived from atmospheric aerosols and Ulva ohnoi growth and physiological state
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Tillage shapes the soil and rhizosphere microbiome of barley - but not its susceptibility towards Blumeria graminis f. sp. hordei FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-02-05 Nina Bziuk, Lorrie Maccario, Dimitar Douchkov, Stefanie Lueck, Doreen Babin, Søren J Sørensen, Adam Schikora, Kornelia Smalla
Long-term agricultural practices are assumed to shape the rhizosphere microbiome of crops with implications for plant health. In a long-term field experiment, we investigated the effect of different tillage and fertilization practices on soil and barley rhizosphere microbial communities by means of amplicon sequencing of 16S rRNA gene fragments from total community DNA. Differences in the microbial
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Limited carbon sources prevent sulfate remediation in circumneutral abandoned mine drainage FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-01-08 Michelle M Valkanas, Taylor Rosso, Jessica E Packard, Nancy J Trun
Passive remediation systems (PRS) use both biotic and abiotic processes to precipitate contaminants from abandoned mine drainage (AMD) so that the contaminants do not spread into local watersheds. PRS are efficient at removing heavy metals but sulfate remediation frequently does not occur. To understand the reasons for the lack of sulfate remediation, we studied four PRS that treat circumneutral AMD
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Occurrence of XoxF-type methanol dehydrogenases in bacteria inhabiting light lanthanide-rich shale rock FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2020-12-24 Paula Roszczenko-Jasińska, Tomasz Krucoń, Robert Stasiuk, Renata Matlakowska
This study analyzed the occurrence of lanthanide-dependent (XoxF type) methanol dehydrogenases in the bacterial community dominated by Proteobacteria inhabiting shale rock. In total, 22 sequence matches of XoxF were identified in the metaproteome of the community. This enzyme was produced by bacteria represented by orders such as Rhizobiales, Rhodobacterales, Rhodospiralles, Burkholderiales and Nitrosomonadales
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Utilization of low-molecular-weight organic compounds by the filterable fraction of a lotic microbiome FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2020-12-02 Lydia-Ann J Ghuneim, Marco A Distaso, Tatyana N Chernikova, Rafael Bargiela, Evgenii A Lunev, Aleksei A Korzhenkov, Stepan V Toshchakov, David Rojo, Coral Barbas, Manuel Ferrer, Olga V Golyshina, Peter N Golyshin, David L Jones
Filterable microorganisms participate in dissolved organic carbon (DOC) cycling in freshwater systems, however their exact functional role remains unknown. We determined the taxonomic identity and community dynamics of prokaryotic microbiomes in the 0.22 µm-filtered fraction and unfiltered freshwater from the Conwy River (North Wales, UK) in microcosms and, using targeted metabolomics and 14C-labelling
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Temperature management potentially affects carbon mineralization capacity and microbial community composition of a shallow aquifer FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2020-12-30 Metze D, Popp D, Schwab L, et al.
ABSTRACTHigh-temperature aquifer thermal energy storage (HT-ATES) is a promising technique to reduce the CO2 footprint of heat supply in the frame of transitioning to renewable energies. However, HT-ATES causes temperature fluctuations in groundwater ecosystems potentially affecting important microbial-mediated ecosystem services. Hence, assessing the impact of increasing temperatures on the structure
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Anoxygenic photo- and chemosynthesis of phototrophic sulfur bacteria from an alpine meromictic lake FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-01-29 Francesco Di Nezio, Clarisse Beney, Samuele Roman, Francesco Danza, Antoine Buetti-Dinh, Mauro Tonolla, Nicola Storelli
Meromictic lakes are interesting ecosystems to study anaerobic microorganisms due their permanent stratification allowing the formation of a stable anoxic environment. The crenogenic meromictic Lake Cadagno harbors an important community of anoxygenic phototrophic sulfur bacteria responsible for almost half of its total productivity. Besides their ability to fix CO2 through photosynthesis, these microorganisms
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Microbial intrusion and seasonal dynamics in the groundwater microbiome of a porous basaltic rock aquifer used as municipal water reservoir FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2021-01-28 Stephen Knobloch, Alexandra Maria Klonowski, Sigrún Tómasdóttir, Bjarni Reyr Kristjánsson, Sverrir Guðmundsson, Viggó Þór Marteinsson
Groundwater is a key resource for safe drinking water supply. Yet unconfined aquifers can be vulnerable to microbial contamination during extreme weather events that lead to surface runoff. The current study characterises the groundwater microbiome of a porous basaltic rock aquifer in South-West Iceland used for drinking water extraction and analyses the microbial community dynamics during surface
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Service crops improve a degraded monoculture system by changing common bean rhizospheric soil microbiota and reducing soil-borne fungal diseases FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2020-12-24 Abán C, Verdenelli R, Gil S, et al.
ABSTRACTIntensive agricultural practices have resulted in progressive soil degradation, with consequences on soil ecosystem services. The inclusion of service crops is a promising alternative to support the sustainability of the agricultural system. The aim of this study was to analyze in a six-year field experiment the effect of Brachiaria brizantha (perennial tropical grass) and Zea mays as service
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Stream sediment bacterial communities exhibit temporally-consistent and distinct thresholds to land use change in a mixed-use watershed FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2020-12-18 Martin G, Dang C, Morrissey E, et al.
ABSTRACTFreshwater ecosystems are susceptible to biodiversity losses due to land conversion. This is particularly true for the conversion of land from forests for agriculture and urban development. Freshwater sediments harbor microorganisms that provide vital ecosystem services. In dynamic habitats like freshwater sediments, microbial communities can be shaped by many processes, although the relative
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Salinity increases growth and pathogenicity of water mold to cause mortality and early hatching in Rana sylvatica embryos FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2020-12-18 Coughlan M, Waters T, Touchon J.
ABSTRACTAmphibian embryos often suffer increased mortality and altered hatching when exposed to road deicing salt runoff or pathogens such as water molds. However, the combined effects of such contaminants on embryos remain understudied. To test how pond salinization interacts with water mold (Saprolegniasp.) to influence hatching timing and survival, we first measured pond water conductivity and temperature
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Genetic and functional diversity of PsyI/PsyR quorum-sensing system in the Pseudomonas syringae complex FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2020-12-17 Morohoshi T, Oshima A, Xie X, et al.
ABSTRACTStrains belonging to the Pseudomonas syringae complex often possess quorum-sensing systems that comprise N-acyl-l-homoserine lactone (AHL) synthases (PsyI) and AHL receptors (PsyR). Here, we investigated the diversity of PsyI/PsyR quorum-sensing systems in 630 strains of the P. syringae complex. AHL production was observed in most strains of Pseudomonas amygdali and Pseudomonas meliae, and
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microeco: an R package for data mining in microbial community ecology FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2020-12-17 Liu C, Cui Y, Li X, et al.
ABSTRACTA large amount of sequencing data is produced in microbial community ecology studies using the high-throughput sequencing technique, especially amplicon-sequencing-based community data. After conducting the initial bioinformatic analysis of amplicon sequencing data, performing the subsequent statistics and data mining based on the operational taxonomic unit and taxonomic assignment tables is
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Survival of the fittest: how the rice microbial community forces Sarocladium oryzae into pathogenicity FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2020-12-14 Peeters K, Audenaert K, Höfte M.
ABSTRACTThe fungus Sarocladium oryzae (Sawada) causes rice sheath rot and produces the phytotoxins cerulenin and helvolic acid. Both toxins show antimicrobial activity but only helvolic acid production in the rice sheath correlates with virulence. Sarocladium oryzae isolates that differ in their toxin production were used to study their interaction with the rice culturable bacterial endophyte community
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Vertical stratification patterns of methanotrophs and their genetic controllers in water columns of oxygen-stratified boreal lakes FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2020-12-14 Rissanen A, Saarela T, Jäntti H, et al.
ABSTRACTThe vertical structuring of methanotrophic communities and its genetic controllers remain understudied in the water columns of oxygen-stratified lakes. Therefore, we used 16S rRNA gene sequencing to study the vertical stratification patterns of methanotrophs in two boreal lakes, Lake Kuivajärvi and Lake Lovojärvi. Furthermore, metagenomic analyses were performed to assess the genomic characteristics
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The pico-sized Mamiellophyceae and a novel Bathycoccus clade from the summer plankton of Russian Arctic Seas and adjacent waters FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2020-12-11 Belevich T, Milyutina I, Abyzova G, et al.
ABSTRACTGlobal climate changes and anthropogenic activity greatly impact Arctic marine biodiversity including phytoplankton which contribute greatly to atmospheric oxygen production. Thus the study of microalgae has rising topicality. Class Mamiellophyceae is an important component of phototrophic picoplankton. To gain more knowledge about Mamiellophyceae distribution and diversity special studies
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An emerging view of the diversity, ecology and function of Archaea in alkaline hydrothermal environments FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2020-12-04 Mueller R, Peach J, Skorupa D, et al.
ABSTRACTThe described diversity within the domain Archaea has recently expanded due to advances in sequencing technologies, but many habitats that likely harbor novel lineages of archaea remain understudied. Knowledge of archaea within natural and engineered hydrothermal systems, such as hot springs and engineered subsurface habitats, has been steadily increasing, but the majority of the work has focused
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Synthetic biology approaches to copper remediation: bioleaching, accumulation and recycling FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2020-12-04 Giachino A, Focarelli F, Marles-Wright J, et al.
ABSTRACTOne of the current aims of synthetic biology is the development of novel microorganisms that can mine economically important elements from the environment or remediate toxic waste compounds. Copper, in particular, is a high-priority target for bioremediation owing to its extensive use in the food, metal and electronic industries and its resulting common presence as an environmental pollutant
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Cupriavidus metallidurans CH34, a historical perspective on its discovery, characterization and metal resistance FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2020-12-03 Mergeay M, Van Houdt R.
ABSTRACTCupriavidus metallidurans, and in particular type strain CH34, became a model bacterium to study bacterial resistance to metals. Although nowadays the routine use of a wide variety of omics and molecular techniques allow refining, deepening and expanding our knowledge on adaptation and resistance to metals, these were not available at the onset of C. metallidurans research starting from its
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Interaction among endophytic bacteria, sweet sorghum (Sorghum bicolor) cultivars and chemical nitrogen fertilization FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2020-11-27 Heijo G, Taulé C, Mareque C, et al.
ABSTRACTThe application of new agricultural technologies to attain sustainable production systems is necessary. The use of plant growth-promoting bacteria to improve plant growth and health has been studied for decades. This work aimed to isolate diazotrophic endophytic bacteria associated with sweet sorghum plants and study the interaction of their inoculation in combination with chemical N-fertilization
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Dissolved inorganic carbon determines the abundance of microbial primary producers and primary production in Tibetan Plateau lakes FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2020-11-26 Yue L, Kong W, Li C, et al.
ABSTRACTClimate change globally accelerates the shrinkage of inland lakes, resulting in increases in both water salinity and dissolved inorganic carbon (DIC). The increases of salinity and DIC generate contrasting effects on microbial primary producers and primary production, however, their combined effects remain unclear in aquatic ecosystems. We hypothesized that increased DIC mitigates the constraints
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Temporal and spatial interactions modulate the soybean microbiome FEMS Microbiol. Ecol. (IF 3.675) Pub Date : 2020-12-26 Moroenyane I, Tremblay J, Yergeau É.
ABSTRACTManaged agricultural ecosystems are unique systems where crops and microbes are intrinsically linked. This study focuses on discerning microbiome successional patterns across all plant organs and tests for evidence of niche differentiation along temporal and spatial axes. Soybean plants were grown in an environmental chamber till seed maturation. Samples from various developmental stages (emergence
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