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1.
  • Wang, Tao, et al. (författare)
  • A widespread mechanism in ectomycorrhizal fungi to access nitrogen from mineral-associated proteins
  • 2021
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 23:10, s. 5837-5849
  • Tidskriftsartikel (refereegranskat)abstract
    • A large fraction of nitrogen (N) in forest soils is present in mineral-associated proteinaceous compounds. The strong association between proteins and minerals limits microbial accessibility to this source, which is a relatively stable reservoir of soil N. We have shown that the ectomycorrhizal (ECM) fungus Paxillus involutus can acquire N from iron oxide-associated proteins. Using tightly controlled isotopic, spectroscopic and chromatographic experiments, we demonstrated that the capacity to access N from iron oxide-associated bovine serum albumin (BSA) is shared with the ECM fungi Hebeloma cylindrosporum and Piloderma olivaceum. Despite differences in evolutionary history, growth rates, exploration types and the decomposition mechanisms of organic matter, their N acquisition mechanisms were similar to those described for P. involutus. The fungi released N from mineral-associated BSA by direct action of extracellular aspartic proteases on the mineral-associated BSA, without initial desorption of the protein. Hydrolysis was suppressed by the adsorption of proteases to minerals, but this adverse effect was counteracted by the secretion of compounds that conditioned the mineral surface. These data suggest that the enzymatic exudate-driven mechanism to access N from mineral-associated proteins is found in ECM fungi of multiple lineages and exploration types.
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2.
  • Rengefors, Karin, et al. (författare)
  • Evidence of concurrentlocal adaptation and high phenotypic plasticityin a polar microeukaryote.
  • 2015
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2920 .- 1462-2912. ; 17:5, s. 1510-1519
  • Tidskriftsartikel (refereegranskat)abstract
    • Here we investigated whether there is evidence of local adaptation in strains of an ancestrallymarine dinoflagellate to the lacustrine environment they now inhabit(optimal genotypes) and/orif they have evolved phenotypic plasticity (a range of phenotypes). Eleven strains of Polarella glacialis were isolated and cultured from three different environments: the polar seas, ahyposaline,and a hypersaline Antarctic lake. Local adaptation was tested by comparing growth rates of lacustrine and marine strains at their own and reciprocal site conditions. To determine phenotypic plasticity, we measured thereaction norm for salinity.We found evidence of both, limitedlocal adaptation andhigherphenotypic plasticity in lacustrine strains when compared tomarine ancestors. At extreme high salinities,local lake strains outperformed otherstrains, and at extreme low salinities, strains from the hyposaline lake outperformed all other strains. The data suggest that lake populations may have evolved higher phenotypic plasticity in the lake habitats compared to the sea, presumably due to the high temporal variability in salinity in the lacustrine systems. Moreover, the interval of salinity tolerance differed between strains from the hyposalineand hypersaline lakes, indicatinglocal adaptation promoted by different salinity.
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3.
  • Klawonn, Isabell, et al. (författare)
  • Cell-specific nitrogen- and carbon-fixation of cyanobacteria in a temperate marine system (Baltic Sea)
  • 2016
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920 .- 1758-2229. ; 18:12, s. 4596-4609
  • Tidskriftsartikel (refereegranskat)abstract
    • We analysed N2- and carbon (C) fixation in individual cells of Baltic Sea cyanobacteria by combining stable isotope incubations with secondary ion mass spectrometry (SIMS). Specific growth rates based on N2- and C-fixation were higher for cells of Dolichospermum spp. than for Aphanizomenon sp. and Nodularia spumigena. The cyanobacterial biomass, however, was dominated by Aphanizomenon sp., which contributed most to total N2-fixation in surface waters of the Northern Baltic Proper. N2-fixation by Pseudanabaena sp. and colonial picocyanobacteria was not detectable. N2-fixation by Aphanizomenon sp., Dolichospermum spp. and N. spumigena populations summed up to total N2-fixation, thus these genera appeared as sole diazotrophs within the Baltic Sea's euphotic zone, while their mean contribution to total C-fixation was 21%. Intriguingly, cell-specific N2-fixation was 8-fold higher at a coastal station compared to an offshore station, revealing coastal zones as habitats with substantial N2-fixation. At the coastal station, the cell-specific C- to N2-fixation ratio was below the cellular C:N ratio, i.e., N2 was assimilated in excess to C-fixation, whereas the C- to N2-fixation ratio exceeded the C:N ratio in offshore sampled diazotrophs. Our findings highlight SIMS as a powerful tool not only for qualitative but also for quantitative N2-fixation assays in aquatic environments.
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4.
  • Abreu, Fernanda, et al. (författare)
  • Culture-independent characterization of a novel magnetotactic member affiliated to the Beta class of the Proteobacteria phylum from an acidic lagoon
  • 2018
  • Ingår i: Environmental Microbiology. - : Wiley/Blackwell. - 1462-2912 .- 1462-2920. ; 20:7, s. 2615-2624
  • Tidskriftsartikel (refereegranskat)abstract
    • Summary Magnetotactic bacteria (MTB) comprise a group of motile microorganisms common in most mesothermal aquatic habitats with pH values around neutrality. However, during the last two decades, a number of MTB from extreme environments have been characterized including: cultured alkaliphilic strains belonging to the Deltaproteobacteria class of the Proteobacteria phylum; uncultured moderately thermophilic strains belonging to the Nitrospirae phylum; cultured and uncultured moderately halophilic or strongly halotolerant bacteria affiliated with the Deltaproteobacteria and Gammaproteobacteria classes and an uncultured psychrophilic species belonging to the Alphaproteobacteria class. Here, we used culture-independent techniques to characterize MTB from an acidic freshwater lagoon in Brazil (pH ? 4.4). MTB morphotypes found in this acidic lagoon included cocci, rods, spirilla and vibrioid cells. Magnetite (Fe3O4) was the only mineral identified in magnetosomes of these MTB while magnetite magnetosome crystal morphologies within the different MTB cells included cuboctahedral (present in spirilla), elongated prismatic (present in cocci and vibrios) and bullet-shaped (present in rod-shaped cells). Intracellular pH measurements using fluorescent dyes showed that the cytoplasmic pH was close to neutral in most MTB cells and acidic in some intracellular granules. Based on 16S rRNA gene phylogenetic analyses, some of the retrieved gene sequences belonged to the genus Herbaspirillum within the Betaproteobacteria class of the Proteobacteria phylum. Fluorescent in situ hybridization using a Herbaspirillum-specific probe hybridized with vibrioid MTB in magnetically-enriched samples. Transmission electron microscopy of the Herbaspirillum-like MTB revealed the presence of many intracellular granules and a single chain of elongated prismatic magnetite magnetosomes. Diverse populations of MTB have not seemed to have been described in detail in an acid environment. In addition, this is the first report of an MTB phylogenetically affiliated with Betaproteobacteria class.
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5.
  • Andersson, Tilde, et al. (författare)
  • Biogeographical variation in antimicrobial resistance in rivers is influenced by agriculture and is spread through bacteriophages
  • 2022
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 24:10, s. 4869-4884
  • Tidskriftsartikel (refereegranskat)abstract
    • 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. Bacterial viruses, that is bacteriophages, have recently been shown to be important mediators of bacterial resistance genes in environmental milieus and are transferrable to human pathogens. Herein, we investigated the biogeographical impact on resistance spread through river-borne bacteriophages using amplicon deep sequencing of the microbiota, absolute quantification of resistance genes using ddPCR, and phage induction capacity within wastewater. Microbial biodiversity of the rivers is significantly affected by river site, surrounding milieu and time of sampling. Furthermore, areas of land associated with agriculture had a significantly higher ability to induce bacteriophages carrying antibiotic resistance genes, indicating their impact on resistance spread. It is imperative that we continue to analyse global antibiotic resistance problem from a One Health perspective to gain novel insights into mechanisms of resistance spread.
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6.
  • Ji, Boyang, 1983, et al. (författare)
  • The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria
  • 2017
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2920 .- 1462-2912. ; 19:3, s. 1103-1119
  • Tidskriftsartikel (refereegranskat)abstract
    • Magnetotactic bacteria (MTB) are a group of phylogenetically and physiologically diverse Gram-negative bacteria that synthesize intracellular magnetic crystals named magnetosomes. MTB are affiliated with three classes of Proteobacteria phylum, Nitrospirae phylum, Omnitrophica phylum and probably with the candidate phylum Latescibacteria. The evolutionary origin and physiological diversity of MTB compared with other bacterial taxonomic groups remain to be illustrated. Here, we analysed the genome of the marine magneto-ovoid strain MO-1 and found that it is closely related to Magnetococcus marinus MC-1. Detailed analyses of the ribosomal proteins and whole proteomes of 390 genomes reveal that, among the Proteobacteria analysed, only MO-1 and MC-1 have coding sequences (CDSs) with a similarly high proportion of origins from Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria and Gammaproteobacteria. Interestingly, a comparative metabolic network analysis with anoxic network enzymes from sequenced MTB and non-MTB successfully allows the eventual prediction of an organism with a metabolic profile compatible for magnetosome production. Altogether, our genomic analysis reveals multiple origins of MO-1 and M. marinus MC-1 genomes and suggests a metabolism-restriction model for explaining whether a bacterium could become an MTB upon acquisition of magnetosome encoding genes.
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7.
  • Liotenberg, Sylviane, et al. (författare)
  • Oxygen-dependent copper toxicity: targets in the chlorophyll biosynthesis pathway identified in the copper efflux ATPase CopA deficient mutant
  • 2015
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2920 .- 1462-2912. ; 17, s. 1963-1976
  • Tidskriftsartikel (refereegranskat)abstract
    • Characterization of a copA(-) mutant in the purple photosynthetic bacterium Rubrivivax gelatinosus under low oxygen or anaerobic conditions, as well as in the human pathogen Neisseria gonorrhoeae identified HemN as a copper toxicity target enzyme in the porphyrin synthesis pathway. Heme synthesis is, however, unaffected by copper under high oxygen tension because of the aerobic coproporphyrinogen III oxidase HemF. Nevertheless, in the copA(-) mutant under aerobiosis, we show that the chlorophyll biosynthesis pathway is affected by excess copper resulting in a substantial decrease of the photosystem. Analyses of pigments and enzyme activity showed that under low copper concentrations, the mutant accumulated protochlorophyllide, suggesting that the protochlorophyllide reductase activity is affected by excess copper. Increase of copper concentration led to a complete lack of chlorophyll synthesis as a result of the loss of Mg-chelatase activity. Both enzymes are widely distributed from bacteria to plants; both are [4Fe-4S] proteins and oxygen sensitive; our data demonstrate their in vivo susceptibility to copper in the presence of oxygen. Additionally, our study provides the understanding of molecular mechanisms that may contribute to chlorosis in plants when exposed to metals. The role of copper efflux systems and the impact of copper on heme and chlorophyll biosynthesis in phototrophs are addressed
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8.
  • Logares, Ramiro, et al. (författare)
  • Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes
  • 2018
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 20:6, s. 2231-2240
  • Tidskriftsartikel (refereegranskat)abstract
    • Whether or not communities of microbial eukaryotes are structured in the same way as bacteria is a general and poorly explored question in ecology. Here, we investigated this question in a set of planktonic lake microbiotas in Eastern Antarctica that represent a natural community ecology experiment. Most of the analysed lakes emerged from the sea during the last 6000 years, giving rise to waterbodies that originally contained marine microbiotas and that subsequently evolved into habitats ranging from freshwater to hypersaline. We show that habitat diversification has promoted selection driven by the salinity gradient in bacterial communities (explaining approximate to 72% of taxa turnover), while microeukaryotic counterparts were predominantly structured by ecological drift (approximate to 72% of the turnover). Nevertheless, we also detected a number of microeukaryotes with specific responses to salinity, indicating that albeit minor, selection has had a role in the structuring of specific members of their communities. In sum, we conclude that microeukaryotes and bacteria inhabiting the same communities can be structured predominantly by different processes. This should be considered in future studies aiming to understand the mechanisms that shape microbial assemblages.
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9.
  • Münzner, Karla, et al. (författare)
  • In situ plankton community respiration measurements show low respiratory quotients in a eutrophic lake
  • 2019
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 21:4, s. 1425-1435
  • Tidskriftsartikel (refereegranskat)abstract
    • Planktonic community respiration is an important carbon cycling process, typically quantified by converting measured values of dissolved O2 consumption rates into CO2 production rates assuming a respiratory quotient of 1 (RQ = CO2 per O2 by moles). However, the true variability in planktonic RQs between different aquatic ecosystems is poorly understood. We conducted in situ RQ measurements in a eutrophic lake dominated by algal‐derived substances and found that RQs were significantly below 1. In fact, many RQ values were extremely low (0.2–0.6), below theoretical RQs for oxidation of algal organic matter substrates (0.7–0.8), suggesting that other factors than substrate control need to be considered to understand the RQ. This view was further supported by lack of correlations between RQ and microbial variables known to be strongly substrate dependent, including bacterial growth efficiency and the functional capacity of the bacterioplankton community to degrade different compounds. Based on the measured dynamics in methane and nutrient pools, we discuss that methane oxidation and nitrification likely occurred in the lake, contributing to the unusually low RQs. Our findings demonstrate that planktonic RQs in productive lakes can systematically be below 1, suggesting that CO2 emissions from these lakes may currently be overestimated.
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10.
  • Nedialkova, Lubov Petkova, et al. (författare)
  • Temperate phages promote colicin-dependent fitness of Salmonella enterica serovar Typhimurium.
  • 2015
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2920 .- 1462-2912. ; 18, s. 1591-1603
  • Tidskriftsartikel (refereegranskat)abstract
    • Bacteria employ bacteriocins for interference competition in microbial ecosystems. Colicin Ib (ColIb), a pore-forming bacteriocin, confers a significant fitness benefit to Salmonella enterica serovar Typhimurium (S. Tm) in competition against commensal E. coli in the gut. ColIb is released from S. Tm into the environment, where it kills susceptible competitors. However, colicin-specific release proteins, as they are known for other colicins, have not been identified in case of ColIb. Thus, its release mechanism has remained unclear. In the current study, we have established a new link between ColIb release and lysis activity of temperate, lambdoid phages. By the use of phage-cured S. Tm mutant strains, we show that the presence of temperate phages and their lysis genes is necessary and sufficient for release of active ColIb into the culture supernatant. Furthermore, phage-mediated lysis significantly enhanced S. Tm fitness in competition against a ColIb-susceptible competitor. Finally, transduction with the lambdoid phage 933W rescued the defect of E. coli strain MG1655 with respect to ColIb release. In conclusion, ColIb is released from bacteria in the course of phage lysis. Our data reveal a new mechanism for colicin release and point out a novel function of temperate phages in enhancing colicin-dependent bacterial fitness.
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11.
  • Sassenhagen, Ingrid, et al. (författare)
  • Freshwater protists do not go with the flow: Population structure in Gonyostomum semen independent of connectivity among lakes
  • 2015
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 17:12, s. 5063-5072
  • Tidskriftsartikel (refereegranskat)abstract
    • Many recent studies have found genetically differentiated populations in microorganisms despite potentially high dispersal. We designed a study to specifically examine the importance of physical dispersal barriers, i.e. geographic distance and lack of hydrological connectivity, in restricting gene flow and enhancing divergence in limnic microorganisms. We focused on the nuisance microalga Gonyostomum semen, which has recently expanded in Northern Europe and differentiated into genetically distinct populations. G.semen was sampled from six lakes distributed in two adjacent watersheds, which thereby comprised, both connected and non-connected lakes. The individual isolates were genotyped by amplified fragment length polymorphism. Several lake populations were differentiated from each other, but connectivity within watersheds could not explain the observed population genetic pattern. However, isolation by distance was moderate and might limit the gene flow among distant populations. In addition, we found low, but significant linkage disequilibrium, which indicates regular sexual recombination in this species, despite its high degree of asexual reproduction. Therefore, we conclude that the genetic properties of microalgae with occasional sexual reproduction essentially mirror regularly recombining species. Furthermore, the data indicated bottlenecks supporting the hypothesized recent range expansion of this species.
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12.
  • Sefbom, Josefin, et al. (författare)
  • A planktonic diatom displays genetic structure over small spatial scales
  • 2018
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 20:8, s. 2783-2795
  • Tidskriftsartikel (refereegranskat)abstract
    • Marine planktonic microalgae have potentially global dispersal, yet reduced gene flow has been confirmed repeatedly for several species. Over larger distances (>200 km) geographic isolation and restricted oceanographic connectivity have been recognized as instrumental in driving population divergence. Here we investigated whether similar patterns, that is, structured populations governed by geographic isolation and/or oceanographic connectivity, can be observed at smaller (6-152 km) geographic scales. To test this we established 425 clonal cultures of the planktonic diatom Skeletonema marinoi collected from 11 locations in the Archipelago Sea (northern Baltic Sea). The region is characterized by a complex topography, entailing several mixing regions of which four were included in the sampling area. Using eight microsatellite markers and conventional F-statistics, significant genetic differentiation was observed between several sites. Moreover, Bayesian cluster analysis revealed the co-occurrence of two genetic groups spread throughout the area. However, geographic isolation and oceanographic connectivity could not explain the genetic patterns observed. Our data reveal hierarchical genetic structuring whereby despite high dispersal potential, significantly diverged populations have developed over small spatial scales. Our results suggest that biological characteristics and historical events may be more important in generating barriers to gene flow than physical barriers at small spatial scales.
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13.
  • Suarez, Carolina, et al. (författare)
  • Metagenomic evidence of a novel family of anammox bacteria in a subsea environment
  • 2022
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 24:5, s. 2348-2360
  • Tidskriftsartikel (refereegranskat)abstract
    • Bacteria in the order 'Candidatus Brocadiales' within the phylum Planctomycetes (Planctomycetota) have the remarkable ability to perform anaerobic ammonium oxidation (anammox). Two families of anammox bacteria with different biogeographical distributions have been reported, marine Ca. Scalinduaceae and freshwater Ca. Brocadiaceae. Here we report evidence of three new species within a novel genus and family of anammox bacteria, which were discovered in biofilms of a subsea road tunnel under a fjord in Norway. In this particular ecosystem, the nitrogen cycle is likely fuelled by ammonia from organic matter degradation in the fjord sediments and the rock mass above the tunnel, resulting in the growth of biofilms where anammox bacteria can thrive under oxygen limitation. We resolved several metagenome-assembled genomes (MAGs) of anammox bacteria, including three Ca. Brocadiales MAGs that could not be classified at the family level. MAGs of this novel family had all the diagnostic genes for a full anaerobic ammonium oxidation pathway in which nitrite was probably reduced by a NirK-like reductase. A survey of published molecular data indicated that this new family of anammox bacteria occurs in many marine sediments, where its members presumably would contribute to nitrogen loss.
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14.
  • Abdelfattah, Ahmed, et al. (författare)
  • Global analysis of the apple fruit microbiome : are all apples the same?
  • 2021
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 23:10, s. 6038-6055
  • Tidskriftsartikel (refereegranskat)abstract
    • We present the first worldwide study on the apple (Malus x domestica) fruit microbiome that examines questions regarding the composition and the assembly of microbial communities on and in apple fruit. Results revealed that the composition and structure of the fungal and bacterial communities associated with apple fruit vary and are highly dependent on geographical location. The study also confirmed that the spatial variation in the fungal and bacterial composition of different fruit tissues exists at a global level. Fungal diversity varied significantly in fruit harvested in different geographical locations and suggests a potential link between location and the type and rate of postharvest diseases that develop in each country. The global core microbiome of apple fruit was represented by several beneficial microbial taxa and accounted for a large fraction of the fruit microbial community. The study provides foundational information about the apple fruit microbiome that can be utilized for the development of novel approaches for the management of fruit quality and safety, as well as for reducing losses due to the establishment and proliferation of postharvest pathogens. It also lays the groundwork for studying the complex microbial interactions that occur on apple fruit surfaces.
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15.
  • Aliashkevich, Alena, et al. (författare)
  • D-canavanine affects peptidoglycan structure, morphogenesis and fitness in Rhizobiales
  • 2021
  • Ingår i: Environmental Microbiology. - : John Wiley & Sons. - 1462-2912 .- 1462-2920. ; 23:10, s. 5823-5836
  • Tidskriftsartikel (refereegranskat)abstract
    • The bacterial cell wall is made of peptidoglycan (PG), a polymer that is essential for maintenance of cell shape and survival. Many bacteria alter their PG chemistry as a strategy to adapt their cell wall to external challenges. Therefore, identifying these environmental cues is important to better understand the interplay between microbes and their habitat. Here we used the soil bacterium Pseudomonas putida to uncover cell wall modulators from plant extracts and found canavanine (CAN), a non-proteinogenic amino acid. We demonstrated that cell wall chemical editing by CAN is licensed by P. putida BSAR, a broad-spectrum racemase which catalyzes production of DL-CAN from L-CAN, which is produced by many legumes. Importantly, D-CAN diffuses to the extracellular milieu thereby having a potential impact on other organisms inhabiting the same niche. Our results show that D-CAN alters dramatically the PG structure of Rhizobiales (e.g. Agrobacterium tumefaciens, Sinorhizobium meliloti), impairing PG crosslinkage and cell division. Using A. tumefaciens we demonstrated that the detrimental effect of D-CAN is suppressed by a single amino acid substitution in the cell division PG transpeptidase penicillin binding protein 3a. Collectively, this work highlights the role of amino acid racemization in cell wall chemical editing and fitness.
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16.
  • Armengaud, J., et al. (författare)
  • The Importance Of Naturally Attenuated Sars-Cov-2 In The Fight Against Covid-19
  • 2020
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 22:6, s. 1997-2000
  • Tidskriftsartikel (refereegranskat)abstract
    • The current SARS-CoV-2 pandemic is wreaking havoc throughout the world and has rapidly become a global health emergency. A central question concerning COVID-19 is why some individuals become sick and others not. Many have pointed already at variation in risk factors between individuals. However, the variable outcome of SARS-CoV-2 infections may, at least in part, be due also to differences between the viral subspecies with which individuals are infected. A more pertinent question is how we are to overcome the current pandemic. A vaccine against SARS-CoV-2 would offer significant relief, although vaccine developers have warned that design, testing, and production of vaccines may take a year if not longer. Vaccines are based on a handful of different designs (1), but the earliest vaccines were based on live, attenuated virus. As has been the case for other viruses during earlier pandemics, SARS-CoV-2 will mutate and may naturally attenuate over time (2). What makes the current pandemic unique is that, thanks to state-of-the-art nucleic acid sequencing technologies, we can follow in detail how SARS-CoV-2 evolves while it spreads. We argue that knowledge of naturally emerging attenuated SARS-CoV-2 variants across the globe should be of key interest in our fight against the pandemic. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
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17.
  • Bahram, Mohammad, et al. (författare)
  • Metagenomic assessment of the global diversity and distribution of bacteria and fungi
  • 2021
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 23, s. 316-326
  • Tidskriftsartikel (refereegranskat)abstract
    • Bacteria and fungi are of uttermost importance in determining environmental and host functioning. Despite close interactions between animals, plants, their associated microbiomes, and the environment they inhabit, the distribution and role of bacteria and especially fungi across host and environments as well as the cross‐habitat determinants of their community compositions remain little investigated. Using a uniquely broad global dataset of 13 483 metagenomes, we analysed the microbiome structure and function of 25 host‐associated and environmental habitats, focusing on potential interactions between bacteria and fungi. We found that the metagenomic relative abundance ratio of bacteria‐to‐fungi is a distinctive microbial feature of habitats. Compared with fungi, the cross‐habitat distribution pattern of bacteria was more strongly driven by habitat type. Fungal diversity was depleted in host‐associated communities compared with those in the environment, particularly terrestrial habitats, whereas this diversity pattern was less pronounced for bacteria. The relative gene functional potential of bacteria or fungi reflected their diversity patterns and appeared to depend on a balance between substrate availability and biotic interactions. Alongside helping to identify hotspots and sources of microbial diversity, our study provides support for differences in assembly patterns and processes between bacterial and fungal communities across different habitats.
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18.
  • Brindefalk, Björn, et al. (författare)
  • Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters
  • 2016
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 18:12, s. 4442-4455
  • Tidskriftsartikel (refereegranskat)abstract
    • Rhodopsins are light-driven ion-pumping membrane proteins found in many organisms and are proposed to be of global importance for oceanic microbial energy generation. Several studies have focused on marine environments, with less exploration of rhodopsins in brackish waters. We investigated microbial rhodopsins in the Baltic Sea using size-fractionated metagenomic and metatranscriptomic datasets collected along a salinity gradient spanning from similar to 0 to 35 PSU. The normalised genomic abundance of rhodopsins in Bacteria, as well as rhodopsin gene expression, was highest in the smallest size fraction (0.1-0.8 mu m), relative to the medium (0.8-3.0 mu m) and large (> 3.0 mu m) size fractions. The abundance of rhodopsins in the two smaller size fractions displayed a positive correlation with salinity. Proteobacteria and Bacteroidetes rhodopsins were the most abundant while Actinobacteria rhodopsins, or actinorhodopsins, were common at lower salinities. Phylogenetic analysis indicated that rhodopsins have adapted independently to the marine-brackish transition on multiple occasions, giving rise to green light-adapted variants from ancestral blue light-adapted ones. A notable diversity of viral-like rhodopsins was also detected in the dataset and potentially linked with eukaryotic phytoplankton blooms. Finally, a new clade of likely proton-pumping rhodopsin with non-canonical amino acids in the spectral tuning and proton accepting site was identified.
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19.
  • Capo, Eric, et al. (författare)
  • Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential
  • 2022
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 24, s. 2201-2209
  • Forskningsöversikt (refereegranskat)abstract
    • In-depth knowledge about spatial and temporal variation in microbial diversity and function is needed for a better understanding of ecological and evolutionary responses to global change. In particular, the study of microbial ancient DNA preserved in sediment archives from lakes and oceans can help us to evaluate the responses of aquatic microbes in the past and make predictions about future biodiversity change in those ecosystems. Recent advances in molecular genetic methods applied to the analysis of historically deposited DNA in sediments have not only allowed the taxonomic identification of past aquatic microbial communities but also enabled tracing their evolution and adaptation to episodic disturbances and gradual environmental change. Nevertheless, some challenges remain for scientists to take full advantage of the rapidly developing field of paleo-genetics, including the limited ability to detect rare taxa and reconstruct complete genomes for evolutionary studies. Here, we provide a brief review of some of the recent advances in the field of environmental paleomicrobiology and discuss remaining challenges related to the application of molecular genetic methods to study microbial diversity, ecology, and evolution in sediment archives. We anticipate that, in the near future, environmental paleomicrobiology will shed new light on the processes of microbial genome evolution and microbial ecosystem responses to quaternary environmental changes at an unprecedented level of detail. This information can, for example, aid geological reconstructions of biogeochemical cycles and predict ecosystem responses to environmental perturbations, including in the context of human-induced global changes.
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20.
  • Eiler, Alexander, et al. (författare)
  • Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics
  • 2014
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 16:9, s. 2682-2698
  • Tidskriftsartikel (refereegranskat)abstract
    • Little is known about the diversity and structuring of freshwater microbial communities beyond the patterns revealed by tracing their distribution in the landscape with common taxonomic markers such as the ribosomal RNA. To address this gap in knowledge, metagenomes from temperate lakes were compared to selected marine metagenomes. Taxonomic analyses of rRNA genes in these freshwater metagenomes confirm the previously reported dominance of a limited subset of uncultured lineages of freshwater bacteria, whereas Archaea were rare. Diversification into marine and freshwater microbial lineages was also reflected in phylogenies of functional genes and there were also significant differences in functional beta-diversity. The pathways and functions that accounted for these differences are involved in osmoregulation, active transport, carbohydrate and amino acid metabolism. Moreover, predicted genes orthologous to active transporters and recalcitrant organic matter degradation were more common in microbial genomes from oligotrophic versus eutrophic lakes. This comparative metagenomic analysis allowed us to formulate a general hypothesis that oceanic- compared to freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial communities.
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21.
  • Farnelid, Hanna, 1983-, et al. (författare)
  • Cell sorting reveals few novel prokaryote and photosynthetic picoeukaryote associations in the oligotrophic ocean
  • 2021
  • Ingår i: Environmental Microbiology. - : John Wiley & Sons. - 1462-2912 .- 1462-2920. ; 23:3, s. 1469-1480
  • Tidskriftsartikel (refereegranskat)abstract
    • Close associations between single-celled marine organisms can have a central role in biogeochemical processes and are of great interest for understanding the evolution of organisms. The global significance of such associations raises the question of whether unidentified associations are yet to be discovered. In this study, fluorescence-activated cell sorted photosynthetic picoeukayote (PPE) populations and single cells were analysed by sequencing of 16S rRNA genes in the oligotrophic North Pacific Subtropical Gyre. Samples were collected during two cruises, spanning depths near the deep chlorophyll maximum, where the abundance of PPEs was highest. The association between the widespread and significant nitrogen (N-2)-fixing cyanobacterium, UCYN-A and its prymnesiophyte host was prevalent in both population and single-cell sorts. Several bacterial sequences, affiliating with previously described symbiotic taxa were detected but their detection was rare and not well replicated, precluding identification of novel tightly linked species-specific associations. Similarly, no enrichment of dominant seawater taxa such as Prochlorococcus, SAR11 or Synechococcus was observed suggesting that these were not systematically ingested by the PPE in this study. The results indicate that apart from the UCYN-A symbiosis, similar tight species-specific associations with PPEs are unusual in the oligotrophic ocean.
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22.
  • Figueroa, Daniela, 1980-, et al. (författare)
  • Terrestrial dissolved organic matter inflow drives temporal dynamics of the bacterial community of a subarctic estuary (northern Baltic Sea)
  • 2021
  • Ingår i: Environmental Microbiology. - : John Wiley & Sons. - 1462-2912 .- 1462-2920. ; 23:8, s. 4200-4213
  • Tidskriftsartikel (refereegranskat)abstract
    • Climate change is projected to cause increased inflow of terrestrial dissolved organic matter to coastal areas in northerly regions. Estuarine bacterial community will thereby receive larger loads of organic matter and inorganic nutrients available for microbial metabolism. The composition of the bacterial community and its ecological functions may thus be affected. We studied the responses of bacterial community to inflow of terrestrial dissolved organic matter in a subarctic estuary in the northern Baltic Sea, using a 16S rRNA gene metabarcoding approach. Betaproteobacteria dominated during the spring river flush, constituting similar to 60% of the bacterial community. Bacterial diversity increased as the runoff decreased during summer, when Verrucomicrobia, Betaproteobacteria, Bacteroidetes, Gammaproteobacteria and Planctomycetes dominated the community. Network analysis revealed that a larger number of associations between bacterial populations occurred during the summer than in spring. Betaproteobacteria and Bacteroidetes populations appeared to display similar correlations to environmental factors. In spring, freshly discharged organic matter favoured specialists, while in summer a mix of autochthonous and terrestrial organic matter promoted the development of generalists. Our study indicates that increased inflows of terrestrial organic matter-loaded freshwater to coastal areas would promote specialist bacteria, which in turn might enhance the transformation of terrestrial organic matter in estuarine environments.
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23.
  • Forsgren, Eva (författare)
  • Development and evaluation of a core genome multilocus sequence typing scheme for Paenibacillus larvae, the deadly American foulbrood pathogen of honeybees
  • 2021
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920.
  • Tidskriftsartikel (refereegranskat)abstract
    • Paenibacillus larvae is the causative agent of the fatal American foulbrood disease in honeybees (Apis mellifera). Strain identification is vital for preventing the spread of the disease. To date, the most accessible and robust scheme to identify strains is the multilocus sequence typing (MLST) method. However, this approach has limited resolution, especially for epidemiological studies. As the cost of whole-genome sequencing has decreased and as it becomes increasingly available to most laboratories, an extended MLST based on the core genome (cgMLST) presents a valuable tool for high-resolution investigations. In this study, we present a standardized, robust cgMLST scheme for P. larvae typing using whole-genome sequencing. A total of 333 genomes were used to identify, validate and evaluate 2419 core genes. The cgMLST allowed fine-scale differentiation between samples that had the same profile using traditional MLST and allowed for the characterization of strains impossible by MLST. The scheme was successfully used to trace a localized Swedish outbreak, where a cluster of 38 isolates was linked to a country-wide beekeeping operation. cgMLST greatly enhances the power of a traditional typing scheme, while preserving the same stability and standardization for sharing results and methods across different laboratories.
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24.
  • Gonzales-Siles, Lucia, et al. (författare)
  • The different ecological niches of enterotoxigenic Escherichia coli (ETEC).
  • 2016
  • Ingår i: Environmental microbiology. - : Wiley. - 1462-2920 .- 1462-2912. ; 18:3, s. 741-751
  • Tidskriftsartikel (refereegranskat)abstract
    • Enterotoxigenic Escherichia coli (ETEC) is a water and food borne pathogen that infects the small intestine of the human gut and causes diarrhea. ETEC adheres to the epithelium by means of colonization factors and secretes two enterotoxins, the heat labile toxin (LT) and/or the heat stable toxin (ST) that both de-regulate ion channels and cause secretory diarrhea. ETEC, as all E. coli, is a versatile organism able to survive and grow in different environments. During transmission and infection ETEC is exposed to various environmental cues that have an impact on survivability and virulence. The ability to cope with exposure to different stressful habitats is probably shaping the pool of virulent ETEC strains that cause both endemic and epidemic infections. This review will focus on the ecology of ETEC in its different habitats and interactions with other organisms as well as abiotic factors.
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25.
  • Hedén, Su-Lin (författare)
  • Glycerol enhances fungal germination at the water-activity limit for life
  • 2017
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 19, s. 947-967
  • Tidskriftsartikel (refereegranskat)abstract
    • For the most-extreme fungal xerophiles, metabolic activity and cell division typically halts between 0.700 and 0.640 water activity (approximately 70.0-64.0% relative humidity). Here, we investigate whether glycerol can enhance xerophile germination under acute water-activity regimes, using an experimental system which represents the biophysical limit of Earth's biosphere. Spores from a variety of species, including Aspergillus penicillioides, Eurotium halophilicum, Xerochrysium xerophilum (formerly Chrysosporium xerophilum) and Xeromyces bisporus, were produced by cultures growing on media supplemented with glycerol (and contained up to 189 mg glycerol g dry spores(-1)). The ability of these spores to germinate, and the kinetics of germination, were then determined on a range of media designed to recreate stresses experienced in microbial habitats or anthropogenic systems (with water-activities from 0.765 to 0.575). For A. penicillioides, Eurotium amstelodami, E. halophilicum, X. xerophilum and X. bisporus, germination occurred at lower water-activities than previously recorded (0.640, 0.685, 0.651, 0.664 and 0.637 respectively). In addition, the kinetics of germination at low water-activities were substantially faster than those reported previously. Extrapolations indicated theoretical water-activity minima below these values; as low as 0.570 for A. penicillioides and X. bisporus. Glycerol is present at high concentrations (up to molar levels) in many types of microbial habitat. We discuss the likely role of glycerol in expanding the water-activity limit for microbial cell function in relation to temporal constraints and location of the microbial cell or habitat. The findings reported here have also critical implications for understanding the extremes of Earth's biosphere; for understanding the potency of disease-causing microorganisms; and in biotechnologies that operate at the limits of microbial function.
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26.
  • Hernández, Sara B, et al. (författare)
  • Environmental roles of microbial amino acid racemases
  • 2016
  • Ingår i: Environmental Microbiology. - Hoboken : Wiley-Blackwell. - 1462-2912 .- 1462-2920. ; 18:6, s. 1673-1685
  • Forskningsöversikt (refereegranskat)abstract
    • Enzymes catalysing the stereo-chemical inter-conversion of amino acids are known as amino acid racemases. In bacteria, these enzymes are fundamental to synthesize the D-Ala and D-Glu that are critical components of the peptidoglycan. In addition to this structural function in cell wall assembly, D-amino acids produced by microbial amino acid racemases have been described as relevant constituents in other prokaryotic structures (e.g. capsule, non-ribosomal peptides) and have been associated to growth fitness and to processes such as biofilm development, spore germination, and signalling. The recent discovery of broad spectrum racemases able to produce and release several D-amino acids to the environment suggests that these enzymes might have a great impact in microbial ecology. Consequently, new data on the biochemistry and regulation of racemases is key to understand the biological significance of D-enantiomers in nature, in particular their effect on microbial social networks. This review summarizes current knowledge on the environmental roles of bacterial racemases with an emphasis on the potential roles of the new broad spectrum enzymes in natural environments.
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27.
  • Hötzinger, Matthias, et al. (författare)
  • Dynamics of Baltic Sea phages driven by environmental changes
  • 2022
  • Ingår i: Environmental Microbiology. - : John Wiley & Sons. - 1462-2912 .- 1462-2920. ; 23:8, s. 4576-4594
  • Tidskriftsartikel (refereegranskat)abstract
    • Phage predation constitutes a major mortality factor for bacteria in aquatic ecosystems, and thus, directly impacts nutrient cycling and microbial community dynamics. Yet, the population dynamics of specific phages across time scales from days to months remain largely unexplored, which limits our understanding of their influence on microbial succession. To investigate temporal changes in diversity and abundance of phages infecting particular host strains, we isolated 121 phage strains that infected three bacterial hosts during a Baltic Sea mesocosm experiment. Genome analysis revealed a novel Flavobacterium phage genus harboring gene sets putatively coding for synthesis of modified nucleotides and glycosylation of bacterial cell surface components. Another novel phage genus revealed a microdiversity of phage species that was largely maintained during the experiment and across mesocosms amended with different nutrients. In contrast to the newly described Flavobacterium phages, phages isolated from a Rheinheimera strain were highly similar to previously isolated genotypes, pointing to genomic consistency in this population. In the mesocosm experiment, the investigated phages were mainly detected after a phytoplankton bloom peak. This concurred with recurrent detection of the phages in the Baltic Proper during summer months, suggesting an influence on the succession of heterotrophic bacteria associated with phytoplankton blooms.
  •  
28.
  • Juottonen, Heli, et al. (författare)
  • Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly
  • 2020
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 22:8, s. 3158-3171
  • Tidskriftsartikel (refereegranskat)abstract
    • Despite their key role in biogeochemical processes, particularly the methane cycle, archaea are widely underrepresented in molecular surveys because of their lower abundance compared with bacteria and eukaryotes. Here, we use parallel high-resolution small subunit rRNA gene sequencing to explore archaeal diversity in 109 Swedish lakes and correlate archaeal community assembly mechanisms to large-scale latitudinal, climatic (nemoral to arctic) and nutrient (oligotrophic to eutrophic) gradients. Sequencing with universal primers showed the contribution of archaea was on average 0.8% but increased up to 1.5% of the three domains in forest lakes. Archaea-specific sequencing revealed that freshwater archaeal diversity could be partly explained by lake variables associated with nutrient status. Combined with deterministic co-occurrence patterns this finding suggests that ecological drift is overridden by environmental sorting, as well as other deterministic processes such as biogeographic and evolutionary history, leading to lake-specific archaeal biodiversity. Acetoclastic, hydrogenotrophic and methylotrophic methanogens as well as ammonia-oxidizing archaea were frequently detected across the lakes. Archaea-specific sequencing also revealed representatives of Woesearchaeota and other phyla of the DPANN superphylum. This study adds to our understanding of the ecological range of key archaea in freshwaters and links these taxa to hypotheses about processes governing biogeochemical cycles in lakes.
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29.
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30.
  • Leong, Su-lin L., et al. (författare)
  • Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date
  • 2015
  • Ingår i: Environmental Microbiology. - Hoboken, USA : Wiley-Blackwell. - 1462-2912 .- 1462-2920. ; 17:2, s. 496-513
  • Tidskriftsartikel (refereegranskat)abstract
    • Xeromyces bisporus can grow on sugary substrates down to 0.61, an extremely low water activity. Its genome size is approximately 22Mb. Gene clusters encoding for secondary metabolites were conspicuously absent; secondary metabolites were not detected experimentally. Thus, in its dry' but nutrient-rich environment, X.bisporus appears to have relinquished abilities for combative interactions. Elements to sense/signal osmotic stress, e.g. HogA pathway, were present in X.bisporus. However, transcriptomes at optimal (approximate to 0.89) versus low a(w) (0.68) revealed differential expression of only a few stress-related genes; among these, certain (not all) steps for glycerol synthesis were upregulated. Xeromyces bisporus increased glycerol production during hypo- and hyper-osmotic stress, and much of its wet weight comprised water and rinsable solutes; leaked solutes may form a protective slime. Xeromyces bisporus and other food-borne moulds increased membrane fatty acid saturation as water activity decreased. Such modifications did not appear to be transcriptionally regulated in X.bisporus; however, genes modulating sterols, phospholipids and the cell wall were differentially expressed. Xeromyces bisporus was previously proposed to be a chaophile', preferring solutes that disorder biomolecular structures. Both X.bisporus and the closely related xerophile, Xerochrysium xerophilum, with low membrane unsaturation indices, could represent a phylogenetic cluster of chaophiles'.
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31.
  • Li, Yunlong, et al. (författare)
  • RcsB positively regulates the Yersinia Ysc-Yop type III secretion system by activating expression of the master transcriptional regulator LcrF
  • 2015
  • Ingår i: Environmental Microbiology. - : John Wiley & Sons. - 1462-2912 .- 1462-2920. ; 17:4, s. 1219-1233
  • Tidskriftsartikel (refereegranskat)abstract
    • The Rcs phosphorelay is a complex signaling pathway used by the family Enterobacteriaceae to sense, respond and adapt to environmental changes during free-living or host-associated lifestyles. In this study, we show that the Rcs phosphorelay pathway positively regulates the virulence plasmid encoded Ysc-Yop type III secretion system (T3SS) in the enteropathogen Yesinia pseudotuberculosis. Both the overexpression of the wild-type Rcs regulator RcsB or the constitutive active RscB(D56E) variant triggered more abundant Ysc-Yop synthesis and secretion, whereas the non-phosphorylatable mutant RcsB(D56Q) negated this. Congruently, enhanced Yops expression and secretion occurred in an in cis rscB(D56E) mutant but not in an isogenic rscB(D56Q) mutant. Screening for regulatory targets of RcsB identified the virG-lcrF operon that encodes for LcrF, the Ysc-Yop T3SS master regulator. Protein-DNA binding assays confirmed that RcsB directly bound to this operon promoter, which subsequently caused stimulated lcrF transcription. Moreover, active RcsB enhanced the ability of bacteria to deliver Yop effectors into immune cells during cell contact, and this promoted an increase in bacterial viability. Taken together, our study demonstrates the role of the Rcs system in regulating the Ysc-Yop T3SS in Yersinia and reports on RcsB being the first transcriptional activator known to directly control lcrF transcription.
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32.
  • Nilsson, Emelie, et al. (författare)
  • Nutrient driven transcriptional changes during phage infection in an aquatic Gammaproteobacterium
  • 2022
  • Ingår i: Environmental Microbiology. - : John Wiley & Sons. - 1462-2912 .- 1462-2920. ; 24:5, s. 2270-2281
  • Tidskriftsartikel (refereegranskat)abstract
    • Phages modulate bacterial metabolism during infection by regulating gene expression, which influences aquatic nutrient cycling. However, the effects of shifting nutrient regimes are less understood. Here, we analyzed transcriptomes of an ecologically relevant Gammaproteobacterium and its lytic phage in high (HNM) and low (LNM) nutrient medium. Despite different infection characteristics, including reduced burst size and longer latent period in LNM, the phage had a fixed expression profile. Bacterial transcription was instead different depending on nutrient regime, with HNM bacteria focusing on growth while LNM bacteria focused on motility and membrane transport. Additionally, phage infection had a larger effect on bacterial gene expression in LNM compared to HNM, e.g. suppressing increased iron uptake and altering expression of phosphorus uptake genes. Overall, phage infection influenced host metabolism more in LNM, which was more similar to natural conditions, emphasizing the importance of considering natural conditions to understand phage and host ecology.
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33.
  • Saghai, Aurélien, et al. (författare)
  • Diversity of archaea and niche preferences among putative ammonia-oxidizing Nitrososphaeria dominating across European arable soils
  • 2021
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 24, s. 341-356
  • Tidskriftsartikel (refereegranskat)abstract
    • Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of environmental filters on AOA and the delineation of niche preferences of nitrososphaerial lineages remain poorly understood. We used phylogenetic information at fine scale and machine learning approaches to identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea along a 3000 km European gradient. Only limited insights into the ecology of the low-abundant archaeal classes could be inferred, but our analyses underlined the multifactorial nature of niche differentiation within Nitrososphaeria. Mean annual temperature, C:N ratio and pH were the best predictors of their diversity, evenness and distribution. Thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Furthermore, multiple, independent and recent specializations to soil pH were detected in the Nitrososphaeria phylogeny. The coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria highlights that their ecology is best studied at fine phylogenetic scale.
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34.
  • Savio, Domenico, et al. (författare)
  • Bacterial diversity along a 2600 km river continuum
  • 2015
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 17:12, s. 4994-5007
  • Tidskriftsartikel (refereegranskat)abstract
    • The bacterioplankton diversity in large rivers has thus far been under-sampled despite the importance of streams and rivers as components of continental landscapes. Here, we present a comprehensive dataset detailing the bacterioplankton diversity along the midstream of the Danube River and its tributaries. Using 16S rRNA-gene amplicon sequencing, our analysis revealed that bacterial richness and evenness gradually declined downriver in both the free-living and particle-associated bacterial communities. These shifts were also supported by beta diversity analysis, where the effects of tributaries were negligible in regards to the overall variation. In addition, the river was largely dominated by bacteria that are commonly observed in freshwaters. Dominated by the acI lineage, the freshwater SAR11 (LD12) and the Polynucleobacter group, typical freshwater taxa increased in proportion downriver and were accompanied by a decrease in soil and groundwater-affiliated bacteria. Based on views of the meta-community and River Continuum Concept, we interpret the observed taxonomic patterns and accompanying changes in alpha and beta diversity with the intention of laying the foundation for a unified concept for river bacterioplankton diversity.
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35.
  • Seibt, Henrik, et al. (författare)
  • Elevated levels of VCA0117 in response to external signals activates type VI secretion in Vibrio cholerae A1552
  • 2020
  • Ingår i: Environmental Microbiology. - : John Wiley & Sons. - 1462-2912 .- 1462-2920. ; 22:10, s. 4409-4423
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • The type VI nanomachine is critical for Vibrio cholerae to establish infections and to thrive in niches co‐occupied by competing bacteria. The genes for the type VI structural proteins are encoded in one large and two small auxiliary gene clusters. VCA0117 (VasH) – a σ54‐transcriptional activator – is strictly required for functionality of the type VI secretion system since it controls production of the structural protein Hcp. While some strains constitutively produce a functional system, others do not and require specific growth conditions of low temperature and high osmolarity for expression of the type VI machinery. Here, we trace integration of these regulatory signals to the promoter activity of the large gene cluster in which many components of the machinery and VCA0117 itself are encoded. Using in vivo and in vitro assays and variants of VCA0117, we show that activation of the σ54‐promoters of the auxiliary gene clusters by elevated VCA0117 levels are all that is required to overcome the need for specialized growth conditions. We propose a model in which signal integration via the large operon promoter directs otherwise restrictive levels of VCA0117 that ultimately dictates a sufficient supply of Hcp for completion of a functional type VI secretion system.
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36.
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37.
  • Bengtson, Per, et al. (författare)
  • Possible roles of reactive chlorine II: assessing biotic chlorination as a way for organisms to handle oxygen stress
  • 2013
  • Ingår i: Environmental Microbiology. - : Wiley-Blackwell. - 1462-2912 .- 1462-2920. ; 15:4, s. 991-1000
  • Forskningsöversikt (refereegranskat)abstract
    • Natural formation of organically bound chlorine is extensive in many environments. The enzymes associated with the formation of chlorinated organic matter are produced by a large variety of organisms. Little is known about the ecological role of the process, the key question being: why do microorganisms promote chlorination of organic matter? In a recent paper we discuss whether organic matter chlorination may be a result of antagonistic interactions among microorganisms. In the present paper we evaluate whether extracellular microbial formation of reactive chlorine may be used as a defence against oxygen stress, and we discuss whether this process is likely to contribute to the formation of chlorinated organic matter. Our analysis suggests that periodic exposure to elevated concentrations of reactive oxygen species is a common denominator among the multitude of organisms that are able to enzymatically catalyse formation of reactive chlorine. There is also some evidence suggesting that the production of such enzymes in algae and bacteria is induced by oxygen stress. The relative contribution from this process to the extensive formation of chlorinated organic matter in natural environments remains to be empirically assessed.
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38.
  • Lebret, Karen, et al. (författare)
  • Genetic diversity within and genetic differentiation between blooms of a microalgal species
  • 2012
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 14:9, s. 2395-2404
  • Tidskriftsartikel (refereegranskat)abstract
    • The field of genetic diversity in protists, particularly phytoplankton, is under expansion. However, little is known regarding variation in genetic diversity within populations over time. The aim of our study was to investigate intrapopulation genetic diversity and genetic differentiation in the freshwater bloom-forming microalga Gonyostomum semen (Raphidophyceae). The study covered a 2-year period including all phases of the bloom. Amplified fragment length polymorphism (AFLP) was used to determine the genetic structure and diversity of the population. Our results showed a significant differentiation between samples collected during the two blooms from consecutive years. Also, an increase of gene diversity and a loss of differentiation among sampling dates were observed over time within a single bloom. The latter observations may reflect the continuous germination of cysts from the sediment. The life cycle characteristics of G. semen, particularly reproduction and recruitment, most likely explain a high proportion of the observed variation. This study highlights the importance of the life cycle for the intraspecific genetic diversity of microbial species, which alternates between sexual and asexual reproduction.
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39.
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40.
  • Abdelfattah, Ahmed, et al. (författare)
  • Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root
  • 2021
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 23:4, s. 2199-2214
  • Tidskriftsartikel (refereegranskat)abstract
    • While the environment is considered the primary origin of the plant microbiome, the potential role of seeds as a source of transmitting microorganisms has not received much attention. Here we tested the hypothesis that the plant microbiome is partially inherited through vertical transmission. An experimental culturing device was constructed to grow oak seedlings in a microbe-free environment while keeping belowground and aboveground tissues separated. The microbial communities associated with the acorn's embryo and pericarp and the developing seeding's phyllosphere and root systems were analysed using amplicon sequencing of fungal ITS and bacterial 16S rDNA. Results showed that the seed microbiome is diverse and non-randomly distributed within an acorn. The microbial composition of the phyllosphere was diverse and strongly resembled the composition found in the embryo, whereas the roots and pericarp each had a less diverse and distinct microbial community. Our findings demonstrate a high level of microbial diversity and spatial partitioning of the fungal and bacterial community within both seed and seedling, indicating inheritance, niche differentiation and divergent transmission routes for the establishment of root and phyllosphere communities. 
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41.
  • Celepli, Narin, et al. (författare)
  • Meta-omic analyses of Baltic Sea cyanobacteria : diversity, community structure and salt acclimation
  • 2017
  • Ingår i: Environmental Microbiology. - : Wiley-Blackwell. - 1462-2912 .- 1462-2920. ; 19:2, s. 673-686
  • Tidskriftsartikel (refereegranskat)abstract
    • Cyanobacteria are important phytoplankton in the Baltic Sea, an estuarine-like environment with pronounced north to south gradients in salinity and nutrient concentrations. Here, we present a metagenomic and -transcriptomic survey, with subsequent analyses targeting the genetic identity, phylogenetic diversity, and spatial distribution of Baltic Sea cyanobacteria. The cyanobacterial community constituted close to 12% of the microbial population sampled during a pre-bloom period (June-July 2009). The community was dominated by unicellular picocyanobacteria, specifically a few highly abundant taxa (Synechococcus and Cyanobium) with a long tail of low abundance representatives, and local peaks of bloom-forming heterocystous taxa. Cyanobacteria in the Baltic Sea differed genetically from those in adjacent limnic and marine waters as well as from cultivated and sequenced picocyanobacterial strains. Diversity peaked at brackish salinities 3.5-16psu, with low N:P ratios. A shift in community composition from brackish to marine strains was accompanied by a change in the repertoire and expression of genes involved in salt acclimation. Overall, the pre-bloom cyanobacterial population was more genetically diverse, widespread and abundant than previously documented, with unicellular picocyanobacteria being the most abundant clade along the entire Baltic Sea salinity gradient.
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42.
  • Chahlafi, Zahra, et al. (författare)
  • The role of conserved proteins DrpA and DrpB in nitrate respiration of Thermus thermophilus
  • 2018
  • Ingår i: Environmental Microbiology. - : John Wiley & Sons. - 1462-2912 .- 1462-2920. ; 20:10, s. 3851-3861
  • Tidskriftsartikel (refereegranskat)abstract
    • In many Thermus thermophilus strains, nitrate respiration is encoded in mobile genetic regions, along with regulatory circuits that modulate its expression based on anoxia and nitrate presence. The oxygen‐responsive system has been identified as the product of the dnrST (dnr) operon located immediately upstream of the nar operon (narCGHJIKT), which encodes the nitrate reductase (NR) and nitrate/nitrite transporters. In contrast, the nature of the nitrate sensory system is not known. Here, we analyse the putative nitrate‐sensing role of the bicistronic drp operon (drpAB) present downstream of the nar operon in most denitrifying Thermus spp. Expression of drp was found to depend on the master regulator DnrT, whereas the absence of DrpA or DrpB increased the expression of both DnrS and DnrT and, concomitantly, of the NR. Absence of both proteins made expression from the dnr and nar operons independent of nitrate. Polyclonal antisera allowed us to identify DrpA as a periplasmic protein and DrpB as a membrane protein, with capacity to bind to the cytoplasmic membrane. Here, we propose a role for DrpA/DrpB as nitrate sensors during denitrification.
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43.
  • Comte, Jerome, et al. (författare)
  • Contribution of different bacterial dispersal sources to lakes : Population and community effects in different seasons
  • 2017
  • Ingår i: Environmental Microbiology. - : Wiley-Blackwell. - 1462-2912 .- 1462-2920. ; 19:6, s. 2391-2404
  • Tidskriftsartikel (refereegranskat)abstract
    • The diversity and composition of lake bacterial communities are driven by the interplay between local contemporary environmental conditions and dispersal of cells from the surroundings, i.e. the metacommunity. Still, a conceptual understanding of the relative importance of the two types of factors is lacking. For instance, it is unknown which sources of dispersal are most important and under which circumstances. Here, we investigated the seasonal variation in the importance of dispersal from different sources (mixing, precipitation, surface runoff and sediment resuspension) for lake bacterioplankton community and population dynamics. For that purpose, two small forest lakes and their dispersal sources were sampled over a period of 10 months. The influence of dispersal on communities and populations was determined by 454 sequencing of the 16S rRNA gene and SourceTracker analysis. On the community level direct effects of dispersal were questionable from all sources. Instead we found that the community of the preceding sampling occasion, representing growth of resident bacteria, was of great importance. On the population level, however, dispersal of individual taxa from the inlet could be occasionally important even under low water flow. The effect of sediment resuspension and precipitation appeared small.
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44.
  • Jørgensen, Bo Barker, et al. (författare)
  • Sub-seafloor biogeochemical processes and microbial life in the Baltic Sea
  • 2020
  • Ingår i: Environmental Microbiology. - : Society for Applied Microbiology. - 1462-2912 .- 1462-2920. ; 22:5, s. 1688-1706
  • Forskningsöversikt (refereegranskat)abstract
    • The post-glacial Baltic Sea has experienced extreme changes that are archived today in the deep sediments. IODP Expedition 347 retrieved cores down to 100 m depth and studied the climate history and the deep biosphere. We here review the biogeochemical and microbiological highlights and integrate these with other studies from the Baltic seabed. Cell numbers, endospore abundance and organic matter mineralization rates are extremely high. A 100-fold drop in cell numbers with depth results from a small difference between growth and mortality in the ageing sediment. Evidence for growth derives from a D:L amino acid racemization model, while evidence for mortality derives from the abundance and potential activity of lytic viruses. The deep communities assemble at the bottom of the bioturbated zone from the founding surface community by selection of organisms suited for life under deep sediment conditions. The mean catabolic per-cell rate of microorganisms drops steeply with depth to a life in slow-motion, typical for the deep biosphere. The subsurface life under extreme energy limitation is facilitated by exploitation of recalcitrant substrates, by biochemical protection of nucleic acids and proteins, and by repair mechanisms for random mismatches in DNA or damaged amino acids in proteins. This article is protected by copyright. All rights reserved.
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45.
  • Lindh, Markus V., et al. (författare)
  • Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers
  • 2017
  • Ingår i: Environmental Microbiology. - : Wiley-Blackwell. - 1462-2912 .- 1462-2920. ; 19:3, s. 1222-1236
  • Tidskriftsartikel (refereegranskat)abstract
    • Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations. Notably, the occupancy-frequency distributions were significantly bimodal with a satellite mode of rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Temporal changes in population distributions supported several theoretical frameworks. Still, bimodality was found among bacterioplankton communities across the entire Baltic Sea, and was also frequent in globally distributed datasets. Datasets spanning waters with widely different physicochemical characteristics or environmental gradients typically lacked significant bimodal patterns. When such datasets were divided into subsets with coherent environmental conditions, bimodal patterns emerged, highlighting the importance of positive feedbacks between local abundance and occupancy within specific biomes. Thus, metapopulation theory applied to microbial biogeography can provide novel insights into the mechanisms governing shifts in biodiversity resulting from natural or anthropogenically induced changes in the environment.
  •  
46.
  • Martijn, Joran, et al. (författare)
  • Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon
  • 2019
  • Ingår i: Environmental Microbiology. - : John Wiley & Sons. - 1462-2912 .- 1462-2920. ; 21:7, s. 2485-2498
  • Tidskriftsartikel (refereegranskat)abstract
    • Amplicon sequencing of the 16S rRNA gene is the predominant method to quantify microbial compositions and to discover novel lineages. However, traditional short amplicons often do not contain enough information to confidently resolve their phylogeny. Here we present a cost-effective protocol that amplifies a large part of the rRNA operon and sequences the amplicons with PacBio technology. We tested our method on a mock community and developed a read-curation pipeline that reduces the overall read error rate to 0.18%. Applying our method on four environmental samples, we captured near full-length rRNA operon amplicons from a large diversity of prokaryotes. The method operated at moderately high-throughput (22286-37,850 raw ccs reads) and generated a large amount of putative novel archaeal 23S rRNA gene sequences compared to the archaeal SILVA database. These long amplicons allowed for higher resolution during taxonomic classification by means of long (similar to 1000 bp) 16S rRNA gene fragments and for substantially more confident phylogenies by means of combined near full-length 16S and 23S rRNA gene sequences, compared to shorter traditional amplicons (250 bp of the 16S rRNA gene). We recommend our method to those who wish to cost-effectively and confidently estimate the phylogenetic diversity of prokaryotes in environmental samples at high throughput.
  •  
47.
  • Muthusamy, Sarala Devi, et al. (författare)
  • Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria
  • 2017
  • Ingår i: Environmental Microbiology. - : Wiley-Blackwell. - 1462-2912 .- 1462-2920. ; 19:6, s. 2301-2319
  • Forskningsöversikt (refereegranskat)abstract
    • Much of the phenotype of a microorganism consists of its repertoire of metabolisms and how and when its proteins are deployed under different growth conditions. Hence, analyses of protein expression could provide important understanding of how bacteria adapt to different environmental settings. To characterize the flexibility of proteomes of marine bacteria, we investigated protein profiles of three important marine bacterial lineages - Oceanospirillaceae (Neptuniibacter caesariensis strain MED92), Roseobacter (Phaeobacter sp. MED193) and Flavobacteria (Dokdonia sp. MED134) - during transition from exponential to stationary phase. As much as 59-80% of each species' total proteome was expressed. Moreover, all three bacteria profoundly altered their expressed proteomes during growth phase transition, from a dominance of proteins involved in translation to more diverse proteomes, with a striking appearance of enzymes involved in different nutrient-scavenging metabolisms. Whereas the three bacteria shared several overarching metabolic strategies, they differed in important details, including distinct expression patterns of membrane transporters and proteins in carbon and phosphorous metabolism and storage compounds. These differences can be seen as signature metabolisms - metabolisms specific for lineages. These findings suggest that quantitative proteomics can inform about the divergent ecological strategies of marine bacteria in adapting to changes in environmental conditions.
  •  
48.
  • Nieves-Morión, Mercedes, et al. (författare)
  • Predicting substrate exchange in marine diatom-heterocystous cyanobacteria symbioses
  • 2020
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 22:6, s. 2027-2052
  • Forskningsöversikt (refereegranskat)abstract
    • In the open ocean, some phytoplankton establish symbiosis with cyanobacteria. Some partnerships involve diatoms as hosts and heterocystous cyanobacteria as symbionts. Heterocysts are specialized cells for nitrogen fixation, and a function of the symbiotic cyanobacteria is to provide the host with nitrogen. However, both partners are photosynthetic and capable of carbon fixation, and the possible metabolites exchanged and mechanisms of transfer are poorly understood. The symbiont cellular location varies from internal to partial to fully external, and this is reflected in the symbiont genome size and content. In order to identify the membrane transporters potentially involved in metabolite exchange, we compare the draft genomes of three differently located symbionts with known transporters mainly from model free-living heterocystous cyanobacteria. The types and numbers of transporters are directly related to the symbiont cellular location: restricted in the endosymbionts and wider in the external symbiont. Three proposed models of metabolite exchange are suggested which take into account the type of transporters in the symbionts and the influence of their cellular location on the available nutrient pools. These models provide a basis for several hypotheses that given the importance of these symbioses in global N and C budgets, warrant future testing.
  •  
49.
  • Olofsson, Malin, et al. (författare)
  • High single cell diversity in carbon and nitrogen assimilation by a chain‐forming diatom across a century
  • 2019
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 21:1, s. 142-151
  • Tidskriftsartikel (refereegranskat)abstract
    • Almost a century ago Redfield discovered a relatively constant ratio between carbon, nitrogen, and phosphorus in particulate organic matter, and nitrogen and phosphorus of dissolved nutrients in seawater. Since then, the riverine export of nitrogen to the ocean has increased 20‐fold. High abundance of resting stages in sediment layers dated more than a century back, indicate that the common planktonic diatom Skeletonema marinoi has endured this eutrophication. We germinated unique genotypes from resting stages originating from isotope‐dated sediment layers (15 and 80 y old) in a eutrophied fjord. Using secondary ion mass spectrometry (SIMS) combined with stable isotopic tracers, we show that the cell‐specific carbon and nitrogen assimilation rates vary by an order of magnitude on a single cell level, but are significantly correlated during the exponential growth phase; resulting in constant assimilation quota in cells with identical genotypes. The assimilation quota varies largely between different clones independent of age. We hypothesize that the success of S. marinoi in coastal waters may be explained by its high diversity of nutrient demand not only at a clone specific level, but also at the single cell level, whereby the population can sustain and adapt to dynamic nutrient conditions in the environment.
  •  
50.
  • Ricão Canelhas, Monica, et al. (författare)
  • Influence of pulsed and continuous substrate inputs on freshwater bacterial community composition and functioning in bioreactors
  • 2017
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 19:12, s. 5078-5087
  • Tidskriftsartikel (refereegranskat)abstract
    • Aquatic environments are typically not homogenous, but characterized by changing substrate concentration gradients and nutrient patches. This heterogeneity in substrate availability creates a multitude of niches allowing bacteria with different substrate utilization strategies to hypothetically coexist even when competing for the same substrate. To study the impact of heterogeneous distribution of organic substrates on bacterioplankton, bioreactors with freshwater bacterial communities were fed artificial freshwater medium with acetate supplied either continuously or in pulses. After a month-long incubation, bacterial biomass and community-level substrate uptake rates were twice as high in the pulsed treatment compared to the continuously fed reactors even if the same total amount of acetate was supplied to both treatments. The composition of the bacterial communities emerging in the two treatments differed significantly with specific taxa overrepresented in the respective treatments. The higher estimated growth yield in cultures that received pulsed substrate inputs, imply that such conditions enable bacteria to use resources more efficiently for biomass production. This finding agrees with established concepts of basal maintenance energy requirements and high energetic costs to assimilate substrates at low concentration. Our results further imply that degradation of organic matter is influenced by temporal and spatial heterogeneity in substrate availability. 
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