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SecMet-FISH: Labeling, visualization, and enumeration of secondary metabolite producing microorganisms FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-03-14 Yannick Buijs, Aileen Ute Geers, Iuliana Nita, Mikael Lenz Strube, Mikkel Bentzon-Tilia
Our understanding of the role of secondary metabolites in microbial communities is challenged by intrinsic limitations of culturing bacteria under laboratory conditions and hence cultivation independent approaches are needed. Here, we present a protocol termed Secondary Metabolite FISH (SecMet-FISH), combining advantages of gene-targeted fluorescence in situ hybridization (geneFISH) with in-solution
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Marine particle microbiomes during a spring diatom bloom contain active sulfate-reducing bacteria FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-03-14 R Siebers, D Schultz, M S Farza, A Brauer, D Zühlke, P A Mücke, F Wang, J Bernhardt, H Teeling, D Becher, K Riedel, I V Kirstein, K H Wiltshire, K J Hoff, T Schweder, T Urich, M M Bengtsson
Phytoplankton blooms fuel marine food webs with labile dissolved carbon and also lead to the formation of particulate organic matter composed of living and dead algal cells. These particles contribute to carbon sequestration and are sites of intense algal-bacterial interactions, providing diverse niches for microbes to thrive. We analyzed 16S and 18S ribosomal RNA gene amplicon sequences obtained from
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Fungal traits help to understand the decomposition of simple and complex plant litter FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-03-13 Eva F Leifheit, Tessa Camenzind, Anika Lehmann, Diana R Andrade-Linares, Max Fussan, Sophia Westhusen, Till M Wineberger, Matthias C Rillig
Litter decomposition is a key ecosystem process, relevant for the release and storage of nutrients and carbon in soil. Soil fungi are one of the dominant drivers of organic matter decomposition, but fungal taxa differ substantially in their functional ability to decompose plant litter. Knowledge is mostly based on observational data and subsequent molecular analyses and in vitro studies have been limited
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Agroecological transition: towards a better understanding of the impact of ecology-based farming practices on soil microbial ecotoxicology FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-03-12 Marie-Liesse Vermeire, Clémence Thiour-Mauprivez, Caroline De Clerck
Alternative farming systems have developed since the beginning of industrial agriculture. Organic, biodynamic, conservation farming, agroecology and permaculture, all share a grounding in ecological concepts and a belief that farmers should work with nature rather than damage it. As ecology-based agricultures rely greatly on soil organisms to perform the functions necessary for agricultural production
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Culturable Streptomyces spp. from high altitude, oligotrophic North Western Himalaya: a comprehensive study on the diversity, bioactivity and insights into the proteome of potential species FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-03-05 Aasif Majeed Bhat, Aehtesham Hussain, Qazi Parvaiz Hassan, Adil Bhat
The increasing global concern of antimicrobial resistance and shortage of new antimicrobials necessitates exploring untapped terrestrial environments for new bioactive microbiome diversity. The low temperature and oligotrophic North Western Himalaya (NWH) region has a vast diversity of Streptomyces with potential antimicrobial properties that remain largely unexplored. This study evaluates the diversity
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Pseudomonas aeruginosa from river water: antimicrobial resistance, virulence and molecular typing FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-03-04 Beatriz Rojo-Bezares, Cristina Casado, Tania Ceniceros, María López, Gabriela Chichón, Carmen Lozano, Lidia Ruiz-Roldán, Yolanda Sáenz
P. aeruginosa isolates were recovered from surface river water samples in La Rioja region (Spain) to characterise their antibiotic resistance, molecular typing and virulence mechanisms. Fifty-two P. aeruginosa isolates were isolated from 15 different water samples (45.4%) and belonged to 23 different PFGE patterns. All isolates were susceptible to all antibiotics tested, except one carbapenem-resistant
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More than the sum of its parts: uncovering emerging effects of microbial interactions in complex communities FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-03-04 Patricia Geesink, Jolanda ter Horst, Thijs J G Ettema
Microbial communities are not only shaped by the diversity of microorganisms and their individual metabolic potential, but also by the vast amount of intra- and interspecies interactions that can occur pairwise interactions among microorganisms, we suggest that more attention should be drawn towards the effects on the entire microbiome that emerge from individual interactions between community members
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Where do the antibiotic resistance genes come from? A modulated analysis of sources and loads of resistances in Lake Maggiore FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-02-23 Andrea Di Cesare, Stefano Mammola, Raffaella Sabatino, Diego Fontaneto, Ester M Eckert, Michela Rogora, Tiziana Tonsi, Gianluca Corno
Antibiotic resistance genes (ARGs) are abundant in aquatic ecosystems affected by human activities. Understanding the fate of ARGs across different ecosystems is essential due to the significant role aquatic environments play in the cycle of antibiotic resistance. We quantified selected ARGs in Lake Maggiore, its main tributaries, and the effluent of the main wastewater treatment plant discharging
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Habitat-specific patterns of bacterial communities in a glacier-fed lake on the Tibetan Plateau FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-02-19 Xuezi Guo, Qi Yan, Feng Wang, Wenqiang Wang, Zhihao Zhang, Yongqin Liu, Keshao Liu
Different types of inlet water are expected to affect microbial communities of lake ecosystems due to change the environmental conditions and dispersal of species. However, knowledge of effects of changes in environmental conditions and export of microbial assemblages on lake ecosystems is limited, especially for glacier-fed lakes. Here, we collected water samples from the surface water of a glacier-fed
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Influence of host phylogeny and water physicochemistry on microbial assemblages of the fish skin microbiome FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-02-17 Ashley G Bell, Jamie McMurtrie, Luis M Bolaños, Jo Cable, Ben Temperton, Charles R Tyler
The skin of fish contains a diverse microbiota that has symbiotic functions with the host, facilitating pathogen exclusion, immune system priming and nutrient degradation. The composition of fish skin microbiomes varies across species and in response to a variety of stressors, however, there has been no systematic analysis across these studies to evaluate how these factors shape fish skin microbiomes
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Shared governance in the plant holobiont and implications for one health FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-02-16 Gabriele Berg, Cristina Dorador, Dilfuza Egamberdieva, Joel E Kostka, Choong-Min Ryu, Birgit Wassermann
The Holobiont theory is more than eighty years old, while the importance of microbial communities for plant holobionts was already identified by Lorenz Hiltner more than a century ago. Both concepts are strongly supported by results from the new field of microbiome research. Here, we present ecological and genetic features of the plant holobiont that underpin principles of a shared governance between
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Long-term detection of hartmannibacter diazotrophicus on winter wheat and spring barley roots under field conditions revealed positive correlations on yield parameters with the bacterium abundance FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-02-15 Santiago Quiroga, David Rosado-Porto, Stefan Ratering, Azin Rekowski, Franz Schulz, Marina Krutych, Christian Zörb, Sylvia Schnell
Monitoring of bioinoculants once released into the field remains largely unexplored; thus, more information is required about their survival and interactions after root colonization. Therefore, specific primers were used to perform a long-term tracking to elucidate the effect of Hartmannibacter diazotrophicus on wheat and barley production at two experimental organic agriculture field stations. Three
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Impacts of humic substances, elevated temperature and UVB radiation on bacterial communities of the marine sponge Chondrilla sp. FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-02-15 T M Stuij, D F R Cleary, R J M Rocha, A R M Polonia, D A M Silva, A Louvado, N J de Voogd, N C M Gomes
Sponges are abundant components of coral reefs known for their filtration capabilities and intricate interactions with microbes. They play a crucial role in maintaining the ecological balance of coral reefs. Humic substances (HS) affect bacterial communities across terrestrial, freshwater, and marine ecosystems. However, the specific effects of HS on sponge-associated microbial symbionts have largely
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A quantitative survey of the blueberry (Vaccinium spp.) culturable nectar microbiome: variation between cultivars, locations, and farm management approaches FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-02-15 Caitlin C Rering, Arthur B Rudolph, Qin-Bao Li, Quentin D Read, Patricio R Muñoz, John J Ternest, Charles T Hunter
Microbes in floral nectar can impact both their host plants and floral visitors, yet little is known about the nectar microbiome of most pollinator-dependent crops. In this study, we examined the abundance and composition of the fungi and bacteria inhabiting Vaccinium spp. nectar, as well as nectar volume and sugar concentrations. We compared wild V. myrsinites with two field-grown V. corymbosum cultivars
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A metagenomic alpha-diversity index for microbial functional biodiversity FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-02-10 Damien R Finn
Alpha-diversity indices are an essential tool for describing and comparing biodiversity. Microbial ecologists apply indices originally intended for, or adopted by, macroecology to address questions relating to taxonomy (conserved marker) and function (metagenome-based data). In this Perspective piece, I begin by discussing the nature and mathematical quirks important for interpreting routinely employed
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Microbial community and network responses across strong environmental gradients: how do they compare to macroorganisms? FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-02-08 Clara Arboleda-Baena, Mara Freilich, Claudia Belén Pareja, Ramiro Logares, Rodrigo De la Iglesia, Sergio A Navarrete
The way strong environmental gradients shape multispecific assemblages has allowed us to examine a suite of ecological and evolutionary hypotheses about structure, regulation, and community responses to fluctuating environments. But whether the highly diverse co-occurring microorganisms are shaped in similar ways as macroscopic organisms across the same gradients has yet to be addressed in most ecosystems
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Resilience of aerobic methanotrophs in soils; spotlight on the methane sink under agriculture FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-02-08 Jiyeon Lim, Helena Wehmeyer, Tanja Heffner, Meret Aeppli, Wenyu Gu, Pil Joo Kim, Marcus Horn, Adrian Ho
Aerobic methanotrophs are a specialized microbial group, catalyzing the oxidation of methane. Disturbance-induced loss of methanotroph diversity/abundance thus results in the loss of this biological methane sink. Here, we synthesized and conceptualized the resilience of the methanotrophs to sporadic, recurring, and compounded disturbances in soils. The methanotrophs showed remarkable resilience to
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The reproductive microbiome and maternal transmission of microbiota via eggs in Sceloporus virgatus FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-02-03 Marie E Bunker, Stacey L Weiss
Maternal transmission of microbes occurs across the animal kingdom and is vital for offspring development and long-term health. The mechanisms of this transfer are most well studied in humans and other mammals but are less well understood in egg-laying animals, especially those with no parental care. Here we investigate the transfer of maternal microbes in the oviparous phrynosomatid lizard, Sceloporus
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Microbial assemblages in Arctic coastal thermokarst lakes and lagoons FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-02-03 Sizhong Yang, Xi Wen, Dirk Wagner, Jens Strauss, Jens Kallmeyer, Sara E Anthony, Susanne Liebner
Several studies investigated changes in microbial community composition in thawing permafrost landscapes, but microbial assemblages in the transient ecosystems of the Arctic coastline remain poorly understood. Thermokarst lakes, abrupt permafrost thaw features, are widespread along the pan-Arctic coast and transform into thermokarst lagoons upon coastal erosion and sea-level rise. This study looks
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Unveiling the microbiome of hydroponically-cultivated lettuce: impact of phytophthora cryptogea infection on plant-associated microorganisms FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-02-02 Liese Vlasselaer, Sam Crauwels, Bart Lievens, Barbara De Coninck
Understanding the complex interactions between plants and their associated microorganisms is crucial for optimizing plant health and productivity. While microbiomes of soil-bound cultivated crops are extensively studied, microbiomes of hydroponically-cultivated crops have received limited attention. To address this knowledge gap, we investigated the rhizosphere and root endosphere of hydroponically-cultivated
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Nutrient enrichment increases virulence in an opportunistic environmental pathogen, with greater effect at low bacterial doses FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-02-02 Katja Pulkkinen, Jouni Taskinen
Eutrophication of aquatic ecosystems is associated with an increased risk of pathogen infection via increased pathogen growth and host exposure via increased pathogen doses. Here we studied the effect of nutrients on the virulence of an opportunistic bacterial pathogen of fish, Flavobacterium columnare, in challenge experiments with rainbow trout fingerlings. We hypothesized that removing all nutrients
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Bacterial community distribution and functional potentials provide key insights into their role in the ecosystem functioning of a retreating Eastern Himalayan glacier FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-02-02 Srijana Mukhia, Anil Kumar, Rakshak Kumar
Himalayan glaciers are receding at an exceptional rate, perturbing the local biome and ecosystem processes. Understanding the microbial ecology of an exclusively microbe-driven biome provides insights into their contributions to the ecosystem functioning through biogeochemical fluxes. Here, we investigated the bacterial communities and their functional potential in the retreating East Rathong Glacier
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Temporal and Spatial Variability of Constitutive Mixotroph Abundance and Proportion FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-02-01 Marcella Dobbertin da Costa, Rebecca J Gast, Nicole C Millette
Mixotrophic plankton can comprise a substantial portion of the plankton community compared to phytoplankton and zooplankton. However, there is a gap in the understanding of conditions that influence mixotroph prevalence and activity in situ because current methods often over- or under-estimate mixotroph abundance. A labeled prey tracer method was utilized to identify active mixotrophs present at two
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Temporal dynamics of microbial transcription in wetted hyperarid desert soils FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-02-01 Carlos León-Sobrino, Jean-Baptiste Ramond, Clément Coclet, Ritha-Meriam Kapitango, Gillian Maggs-Kölling, Don A Cowan
Rainfall is rare in hyperarid deserts but, when it occurs, it triggers large biological responses essential for the long-term maintenance of the ecosystem. In drylands, microbes play major roles in nutrient cycling, but their responses to short-lived opportunity windows are poorly understood. Due to its ephemeral nature, mRNA is ideally suited to study microbiome dynamics upon abrupt changes in the
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Integrated microbiota-host-metabolome approaches reveal adaptive ruminal changes to prolonged high-grain feeding and phytogenic supplementation in cattle FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-01-28 Sara Ricci, Cátia Pacífico, Susanne Kreuzer-Redmer, Ezequias Castillo-Lopez, Raul Rivera-Chacon, Arife Sener-Aydemir, Giacomo Rossi, Livio Galosi, Lucia Biagini, Heidi E Schwartz-Zimmermann, Franz Berthiller, Nicole Reisinger, Renee M Petri, Qendrim Zebeli
Diets rich in readily fermentable carbohydrates primarily impact microbial composition and activity, but can also impair the ruminal epithelium barrier function. By combining microbiota, metabolome, and gene expression analysis, we evaluated the impact of feeding a 65% concentrate diet (HG) for four weeks, with or without a phytogenic feed additive (PFA), on the rumen ecosystem of cattle. The breaking
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Rhizosphere assembly alters along a chronosequence in the Hallstätter glacier forefield (Dachstein, Austria) FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-01-25 Wisnu Adi Wicaksono, Max Mora, Samuel Bickel, Christian Berg, Ingolf Kühn, Tomislav Cernava, Gabriele Berg
Rhizosphere microbiome assembly is essential for plant health, but the temporal dimension of this process remains unexplored. We used a chronosequence of 150 years of the retreating Hallstätter glacier (Dachstein, Austria) to disentangle this exemplarily for the rhizosphere of three pioneer alpine plants. Time of deglaciation was an important factor shaping the rhizosphere microbiome. Microbiome functions
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Seasonal dynamics of the microbial methane filter in the water column of a eutrophic coastal basin FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-01-24 Jessica Venetz, Olga M Żygadłowska, Nicky Dotsios, Anna J Wallenius, Niels A G M van Helmond, Wytze K Lenstra, Robin Klomp, Caroline P Slomp, Mike S M Jetten, Annelies J Veraart
In coastal waters, methane-oxidizing bacteria (MOB) can form a methane biofilter and mitigate methane emissions. The metabolism of these MOB is versatile, and the resilience to changing oxygen concentrations is potentially high. It is still unclear how seasonal changes in oxygen availability and water column chemistry affect the functioning of the methane biofilter, and MOB community composition. Here
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Long-term conservation tillage with reduced nitrogen fertilization intensity can improve winter wheat health via positive plant-microorganism feedback in the rhizosphere FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-01-16 Jan Helge Behr, Theresa Kuhl-Nagel, Loreen Sommermann, Narges Moradtalab, Soumitra Paul Chowdhury, Michael Schloter, Saskia Windisch, Ingo Schellenberg, Lorrie Maccario, Sören J Sörensen, Michael Rothballer, Joerg Geistlinger, Kornelia Smalla, Uwe Ludewig, Günter Neumann, Rita Grosch, Doreen Babin
Microbiome-based solutions are regarded key for sustainable agroecosystems. However, it is unclear how agricultural practices affect the rhizosphere microbiome, plant-microorganism interactions and crop performance under field conditions. Therefore, we installed root observation windows in a winter wheat field cultivated either under long-term mouldboard plough (MP) or cultivator tillage (CT). Each
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Seafloor Incubation Experiments at Deep-Sea Hydrothermal Vents Reveal Distinct Biogeographic Signatures of Autotrophic Communities FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-01-11 Heather Fullerton, Lindsey Smith, Alejandra Enriquez, David Butterfield, C Geoffrey Wheat, Craig L Moyer
The discharge of hydrothermal vents on the seafloor provides energy sources for dynamic and productive ecosystems, which are supported by chemosynthetic microbial populations. These populations use the energy gained by oxidizing the reduced chemicals contained within the vent fluids to fix carbon and support multiple trophic levels. Hydrothermal discharge is ephemeral and chemical composition of such
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Upstream cascade reservoirs drive Temporal Beta Diversity increases through species loss in a dammed river FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2024-01-09 Carolina Leite Guimarães Durán, Fernando Miranda Lansac-Tôha, Bianca Ramos de Meira, Loiani Oliveira Santana, Felipe Rafael de Oliveira, Matheus Henrique de Oliveira de Matos, Luiz Felipe Machado Velho
Changes in biodiversity of aquatic environments over time and space due to human activities are a topic of theoretical and conservational interest in ecology. Thus, variation in taxonomic beta diversity of planktonic ciliates community was investigated along a temporal and spatial gradient in two subsystems of a Neotropical floodplain, one impacted by dams (Paraná) and the other free of them along
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Microcystis blooms caused the decreasing richness of and interactions between free-living microbial functional genes in Lake Taihu, China FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-12-27 Qiong Wu, Chunyan Yu, Yanru Liu, Peng Xing, Huabing Li, Biao Li, Shiqiang Wan, Qinglong L Wu
Microcystis blooms have a marked effect on microbial taxonomical diversity in eutrophic lakes, but their influence on the composition of microbial functional genes is still unclear. In this study, the free-living microbial functional genes (FMFG) composition was investigated in the period before Microcystis blooms (March) and during Microcystis blooms (July) using a comprehensive functional gene array
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Seasonality in land-ocean connectivity and local processes control sediment bacterial community structure and function in a High Arctic tidal flat FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-12-19 Eleanor Ruth Handler, Sebastian David Junker Andersen, Rolf Gradinger, Maeve McGovern, Anna Vader, Amanda Poste
Climate change is altering patterns of precipitation, cryosphere thaw, and land-ocean influxes, affecting understudied Arctic estuarine tidal flats. These transitional zones between terrestrial and marine systems are hotspots for biogeochemical cycling, often driven by microbial processes. We investigated surface sediment bacterial community composition and function from May to September along a r
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Nearly (?) sterile avian egg in a passerine bird FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-12-18 Martin Těšický, Lucie Schmiedová, Tereza Krajzingrová, Mercedes Gomez Samblas, Petra Bauerová, Jakub Kreisinger, Michal Vinkler
During early ontogeny, microbiome affects development of the gastrointestinal tract, immunity and survival in vertebrates. Bird eggs are thought to be (1) initially sterile (sterile egg hypothesis) and (2) colonised after oviposition through horizontal trans-shell migration, or (3) initially seeded with bacteria by vertical transfer from mother oviduct. To date, however, little empirical data illuminate
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Lakes-scale pattern of eukaryotic phytoplankton diversity and assembly process shaped by electrical conductivity in central Qinghai-Tibet Plateau FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-12-15 Zhu Huan, Xiong Xiong, Benwen Liu, Liu Guo Xiang
Phytoplankton are the main primary producers in aquatic ecosystems and play an important role in food web and geochemical cycles. Its diversity, community structure, and assembly process are influenced by several factors. Alpine lake ecosystems are relatively weak and extremely sensitive to global climate change. However, the impact of climate change on phytoplankton in Qinghai-Tibet Plateau lakes
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The role of diet and host species in shaping the seasonal dynamics of the gut microbiome FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-12-10 Claire E Williams, Ashli E Brown, Candace L Williams
The gut microbiome plays an important role in the health and fitness of hosts. While previous studies have characterized the importance of various ecological and evolutionary factors in shaping the composition of the gut microbiome, most studies have been cross-sectional in nature, ignoring temporal variation. Thus, it remains unknown how these same factors might affect the stability and dynamics of
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Habitat-related variability in the morphological and taxonomic diversity of microbial communities in two Hungarian epigenic karst caves FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-12-09 Nóra Tünde Lange-Enyedi, Andrea K Borsodi, Péter Németh, György Czuppon, Ivett Kovács, Szabolcs Leél-Őssy, Péter Dobosy, Tamás Felföldi, Attila Demény, Judit Makk
The physical and chemical characteristics of the bedrock, along with the geological and hydrological conditions of karst caves may influence the taxonomic and functional diversity of prokaryotes. Most studies so far have focused on microbial communities of caves including only a few samples and have ignored the chemical heterogeneity of different habitat types such as sampling sites, dripping water
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Carbon amendments in soil microcosms induce uneven response on H2 oxidation activity and microbial community composition FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-12-02 Xavier Baril, Philippe Constant
High-affinity H2-oxidizing bacteria (HA-HOB) thriving in soil are responsible for the most important sink of atmospheric H2. Their activity increases with soil organic carbon content, but the incidence of different carbohydrate fractions on the process has received little attention. Here we tested the hypothesis that carbon amendments impact HA-HOB activity and diversity differentially depending on
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Gut microbiome biogeography in reindeer supersedes millennia of ecological and evolutionary separation FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-11-30 Stefaniya Kamenova, Eric J de Muinck, Vebjørn Veiberg, Tove Aagnes Utsi, Sam M J G Steyaert, Steve D Albon, Leif Egil Loe, Pål Trosvik
Ruminants are dependent on their gut microbiomes for nutrient extraction from plant diets. However, knowledge about the composition, diversity, function, and spatial structure of gut microbiomes, especially in wild ruminants, is limited, largely because analysis has been restricted to faeces or the rumen. In two geographically separated reindeer subspecies, 16S rRNA gene amplicon sequencing revealed
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Wild bee and pollen microbiomes across an urban-rural divide FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-11-29 Phuong N Nguyen, Sandra M Rehan
Wild pollinators and their microbiota are sensitive to land use changes from anthropogenic activities that disrupt landscape and environmental features. As urbanization and agriculture affect bee habitats, human led disturbances are driving changes in bee microbiomes, potentially leading to dysbiosis detrimental to bee fitness. This study examines the bacterial, fungal, and plant compositions of the
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Microbial degradation of naphthenic acids using constructed wetland treatment systems: metabolic and genomic insights for improved bioremediation of process-affected water FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-11-28 Paula C J Reis, Sara Correa-Garcia, Julien Tremblay, Aurélie Beaulieu-Laliberté, Douglas G Muench, Jason M E Ahad, Etienne Yergeau, Jérôme Comte, Christine Martineau
Naphthenic acids (NAs) are a complex mixture of organic compounds released during bitumen extraction from mined oil sands that are important contaminants of oil sands process-affected water (OSPW). NAs can be toxic to aquatic organisms and, therefore, are a main target compound for OSPW. The ability of microorganisms to degrade NAs can be exploited for bioremediation of OSPW using constructed wetland
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Structure of plant–associated microeukaryotes in roots and leaves of aquatic and terrestrial plants revealed by blocking peptide-nucleic acid (PNA) amplification FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-11-28 Avid Azadnia, Vladimir Mikryukov, Sten Anslan, Niloufar Hagh-Doust, Saleh Rahimlou, Heidi Tamm, Leho Tedersoo
Studies of plant–microbe interactions, including mutualistic, antagonistic, parasitic, or commensal microbes, have greatly benefited our understanding of ecosystem functioning. New molecular identification tools have increasingly revealed the association patterns between microorganisms and plants. Here, we integrated long-read PacBio single-molecule sequencing technology with a blocking protein-nucleic
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Chicken manure application alters microbial community structure and the distribution of antibiotic-resistance genes in rhizosphere soil of Cinnamomum camphora forests FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-11-23 Deqiang Chen, Jiawei Zou, Dexing Chen, Xin He, Cuili Zhang, Jinwei Li, Siren Lan, Zhongjian Liu, Shuangquan Zou, Xin Qian
The distribution of antibiotic-resistance genes (ARGs) in environmental soil is greatly affected by livestock and poultry manure fertilization, the application of manure will lead to antibiotic residues and ARGs pollution, and increase the risk of environmental pollution and human health. Cinnamomum camphora is an economically significant tree species in Fujian Province, China. Here, through high-throughput
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Adaptive radiations in natural populations of prokaryotes: innovation is key FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-11-22 Michiel Vos, Daniel Padfield, Christopher Quince, Rutger Vos
Prokaryote diversity makes up most of the tree of life and is crucial to the functioning of the biosphere and human health. However, the patterns and mechanisms of prokaryote diversification have received relatively little attention compared to animals and plants. Adaptive radiation, the rapid diversification of an ancestor species into multiple ecologically divergent species, is a fundamental process
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Impact of dilution on stochastically driven methanogenic microbial communities of hypersaline anoxic sediments FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-11-20 Francisca Font-Verdera, Raquel Liébana, Ramon Rossello-Mora, Tomeu Viver
Sediments underlying the solar salterns of S'Avall are anoxic hypersaline ecosystems dominated by anaerobic prokaryotes, and with the especial relevance of putative methanogenic Archaea. Slurries from salt-saturated sediments, diluted in a gradient of salinity and incubated for >4 years revealed that salt concentration was the major selection force that deterministically structured microbial communities
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Lichen-associated microbial members are prevalent in the snow microbiome of a sub-arctic alpine tundra FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-11-18 D Touchette, C Gostinčar, L G Whyte, I Altshuler
Snow is the largest component of the cryosphere, with its cover and distribution rapidly decreasing over the last decade due to climate warming. It is imperative to characterize the snow (nival) microbial communities to better understand the role of microorganisms inhabiting these rapidly changing environments. Here, we investigated the core nival microbiome, the cultivable microbial members, and the
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Phylogenetics and biomineralization of a novel magnetotactic Gammaproteobacterium from a freshwater lake in Beijing, China FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-11-17 Rongrong Zhang, Peiyu Liu, Yuqin Wang, Andrew P Roberts, Jinling Bai, Yan Liu, Kelei Zhu, Zongjun Du, Guanjun Chen, Yongxin Pan, Jinhua Li
Magnetotactic bacteria (MTB) have the remarkable capability of producing intracellularly membrane-enveloped magnetic nanocrystals (i.e., magnetosomes) and swimming along geomagnetic field lines. Despite more than 50 years of research, bacterial diversity and magnetosome biomineralization within MTB are relatively less known in the Gammaproteobacteria class than other groups. This is incompatible with
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Eating patterns contribute to shaping the gut microbiota in the mucosal simulator of the human intestinal microbial ecosystem FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-11-17 Yorick Minnebo, Kim De Paepe, Jeroen Raes, Tom Van de Wiele
Eating patterns, i.e. meal frequency and circadian timing of meals, are often modified in weight loss and metabolic healing strategies. However, in-depth research into the effects on the gut microbiome remains scarce, particularly across various colon regions and niches. We identified eating patterns to contribute in shaping the in vitro gut biomass production, metabolism, and microbial community compositions
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Soil-specific responses in the antibiotic resistome of culturable Acinetobacter spp. and other non-fermentative Gram-negative bacteria following experimental manure application FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-11-14 Puspendu Sarda, Dana Elhottová, Eduardo Pérez-Valera
Acinetobacter spp. and other non-fermenting Gram-negative bacteria (NFGNB) represent an important group of opportunistic pathogens due to their propensity for multiple, intrinsic, or acquired antimicrobial resistance (AMR). Antimicrobial resistant bacteria and their genes can spread to the environment through livestock manure. This study investigated the effects of fresh manure from dairy cows under
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Rhizosphere microbial community structure differs between constant subzero and freeze-thaw temperature regimes in a subarctic soil FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-11-14 S J Doherty, R R Busby, C C M Baker, R A Barbato
In the Arctic and subarctic, climate change is causing reduced snowpack extent and earlier snowmelt. Shallower snowpack decreases the thermal insulation of underlying soil and results in more freeze-thaw conditions reflective of dynamic air temperatures. The aim of this study was to determine the effect of alternative temperature regimes on overall microbial community structure and rhizosphere recruitment
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Erwiniaceae bacteria play defensive and nutritional roles in two widespread ambrosia beetles. FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-11-13 Juan Carlos Cambronero-Heinrichs,Andrea Battisti,Peter H W Biedermann,Giacomo Cavaletto,Víctor Castro-Gutierrez,Lorenzo Favaro,Giacomo Santoiemma,Davide Rassati
Ambrosia beetles are fungal-growing insects excavating galleries deep inside the wood. Their success as invaders increased scientific interest towards them. However, most studies on their microbiota targeted their fungal associates whereas the role of bacterial associates is understudied. To explore the role of abundant microbial associates, we isolated bacteria from active galleries of two widespread
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Vegetation type, not the legacy of warming, modifies the response of microbial functional genes and greenhouse gas fluxes to drought in Oro-Arctic and alpine regions. FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-11-13 Ellen L Fry,Deborah Ashworth,Kimberley A J Allen,Nathalie Isabelle Chardon,Christian Rixen,Mats P Björkman,Robert G Björk,Thomas Stålhandske,Mathias Molau,Brady Locke-King,Isabelle Cantillon,Catriona McDonald,Hongwei Liu,Franciska T De Vries,Nick J Ostle,Brajesh K Singh,Richard D Bardgett
Climate warming and summer droughts alter soil microbial activity, affecting greenhouse gas (GHG) emissions in Arctic and alpine regions. However, the long-term effects of warming, and implications for future microbial resilience, are poorly understood. Using one alpine and three Arctic soils subjected to in situ long-term experimental warming, we simulated drought in laboratory incubations to test
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Impact of wastewater treatment upgrade and nitrogen removal on bacterial communities and their interactions in eutrophic prairie streams. FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-11-13 Nathanael T Bergbusch,Alicia R Wong,Jennifer N Russell,Vanessa J Swarbrick,Claire Freeman,Jordyn Bergsveinson,Christopher K Yost,Simon C Courtenay,Peter R Leavitt
Eutrophication can impact bacteria by altering fluxes and processing of nutrients and organic matter. However, relatively little is known of how bacterial communities, diversity, and interactions with phytoplankton might respond to nutrient management. We used 16S rRNA amplicon sequencing to compare bacterial assemblages in the water column upstream (control) and downstream (impact) of a wastewater
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Phylogenetically related soil actinomycetes distinguish isolation sites by their metabolic activities. FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-11-13 Jan Kopecky,Zdenek Kamenik,Marek Omelka,Jitka Novotna,Tommaso Stefani,Marketa Sagova-Mareckova
Soil environments are inhabited by microorganisms adapted to its diversified microhabitats. The metabolic activity of individual strains/populations reflects resources available at a particular spot, quality of which may not comply with broad soil characteristics. To explore the potential of individual strains to adapt to particular micro-niches of carbon sources, a set of 331 Actinomycetia strains
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Marine nitrogen-fixers in the Canadian Arctic Gateway are dominated by biogeographically distinct non-cyanobacterial communities FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-11-12 Brent M Robicheau, Jennifer Tolman, Sonja Rose, Dhwani Desai, Julie LaRoche
We describe diazotrophs present during a 2015 GEOTRACES expedition through the Canadian Arctic Gateway (CAG) using nifH metabarcoding. In the less studied Labrador Sea, Bradyrhizobium sp. and Vitreoscilla sp. nifH variants were dominant, while in Baffin Bay, a Stutzerimonas stutzeri variant was dominant. In comparison, the Canadian Arctic Archipelago (CAA) was characterized by a broader set of dominant
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Bacterial communities of the threatened Western Pond Turtle maybe impacted by land use FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-11-11 Alison White, Madison Giannetto, Lubna Mulla, Amber Del Rosario, Tammy Lim, Edward Culver, Matthew Timmer, Jessie Bushell, Max R Lambert, Obed Hernández-Gómez
As semi-aquatic species that use both terrestrial and aquatic habitats, freshwater turtles and their microbial communities are especially sensitive to the impacts of habitat disturbance. In this study, we use 16S rRNA amplicon sequencing to characterize the shell and cloacal bacterial communities of turtles in the San Francisco Bay Area. We captured western pond turtles (Actinemys/Emys marmorata) across
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Hierarchical shift of the Aedes albopictus microbiota caused by anti-microbiota vaccine increases fecundity and egg hatching rate in female mosquitoes FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-10-29 Lourdes Mateos-Hernández, Apolline Maitre, Lianet Abuin-Denis, Dasiel Obregon, Edwige Martin, Patricia Luis, Jennifer Maye, Alejandra Wu-Chuang, Claire Valiente Moro, Alejandro Cabezas-Cruz
Recent studies show that mosquito-microbiota interactions affects vector competence and fitness. We investigated if host antibodies modifying microbiota impact mosquito physiology. We focused on three prevalent bacteria (Acinetobacter, Pantoea, and Chryseobacterium), originally isolated from the Asian tiger mosquito Aedes albopictus. Our goal was to assess the impact of host antibodies on mosquito
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Vesicle-enriched secretomes alter bacterial competitive abilities and are drivers of evolution in microbial communities FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-10-25 Omar M Warsi, Lars Gedda, Katarina Edwards, Dan I Andersson
Microbial membrane vesicles can carry compounds that inhibit bacterial growth, but how they impact the fitness of the vesicle-producing bacterial species and influence community dynamics remain unexplored questions. To address these questions, we examined the effect of vesicle-enriched secretomes (VESs) in different single-species and multi-species systems. Effects of VESs on single-species growth
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Novel ecological implications of non-toxic microcystis towards toxic ecotype in population—Promoting toxic ecotype dominance at various N levels and cooperative defense against luteolin-stress FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-10-25 Zhonghui Guo, Jieming Li, Di Luo, Mingxia Zhang
Microcystin (MC)-producing (MC+) and MC-free (MC−) Microcystis always co-exist and interact during Microcystis-dominated cyanobacterial blooms (MCBs), where MC+ Microcystis abundance and extracellular MCs content (EMC) determine the hazard extent of MCBs. The study elucidated intraspecific interaction between MC+ and MC− Microcystis at various nitrogen (N) levels (0.5-50 mg/L) and how such N-mediated
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Aeromonas hydrophila infection in tilapia triggers changes in the microbiota composition of fish internal organs FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-10-23 Tamir Ofek, Ido Izhaki, Malka Halpern
Aeromonas hydrophila is a major pathogenic species that causes mass mortality in various freshwater fish species including hybrid tilapia, the main fish species in Israeli aquaculture. Our hypothesis was that A. hydrophila infection may cause changes in the microbiota composition of fish internal organs, and therefore we aimed to study the effect of A. hydrophila infection by injection or by net handling
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Novel insights in cryptic diversity of snow and glacier ice algae communities combining 18S rRNA gene and ITS2 amplicon sequencing FEMS Microbiol. Ecol. (IF 4.2) Pub Date : 2023-10-23 Daniel Remias, Lenka Procházková, Linda Nedbalová, Liane G Benning, Stefanie Lutz
Melting snow and glacier surfaces host microalgal blooms in polar and mountainous regions. The aim of this study was to determine the dominant taxa at the species level in the European Arctic and the Alps. A standardized protocol for amplicon metabarcoding using 18S rRNA gene and ITS2 markers was developed. This is important because previous biodiversity studies have been hampered by the dominance