| 1. |
- Lemos, Leandro Nascimento, et al.
(författare)
-
Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils
- 2020
-
Ingår i: Environmental microbiology reports. - : Wiley. - 1758-2229. ; 12:6, s. 651-655
-
Tidskriftsartikel (refereegranskat)abstract
- Soil microbiome is one of the most heterogeneous biological systems. State-of-the-art molecular approaches such as those based on single-amplified genomes (SAGs) and metagenome assembled-genomes (MAGs) are now improving our capacity for disentailing soil microbial-mediated processes. Here we analyzed publicly available datasets of soil microbial genomes and MAG's reconstructed from the Amazon's tropical soil (primary forest and pasture) and active layer of permafrost, aiming to evaluate their genome size. Our results suggest that the Candidate Phyla Radiation (CPR)/Patescibacteria phyla have genomes with an average size 4-fold smaller than the mean identified in the RefSoil database, which lacks any representative of this phylum. Also, by analyzing the potential metabolism of 888 soil microbial genomes, we show that CPR/Patescibacteria representatives share similar functional profiles, but different from other microbial phyla and are frequently neglected in the soil microbial surveys. Finally, we argue that the use of MAGs may be a better choice over SAGs to expand the soil microbial databases, like RefSoil. This article is protected by copyright. All rights reserved.
|
|
| 2. |
- Churakova, Yelena, et al.
(författare)
-
Biogenic silica accumulation in picoeukaryotes : Novel players in the marine silica cycle
- 2023
-
Ingår i: Environmental Microbiology Reports. - : John Wiley & Sons. - 1758-2229. ; 15:4, s. 282-290
-
Tidskriftsartikel (refereegranskat)abstract
- It is well known that the biological control of oceanic silica cycling is dominated by diatoms, with sponges and radiolarians playing additional roles. Recent studies have revealed that some smaller marine organisms (e.g. the picocyanobacterium Synechococcus) also take up silicic acid (dissolved silica, dSi) and accumulate silica, despite not exhibiting silicon dependent cellular structures. Here, we show biogenic silica (bSi) accumulation in five strains of picoeukaryotes (<2-3 mu m), including three novel isolates from the Baltic Sea, and two marine species (Ostreococcus tauri and Micromonas commoda), in cultures grown with added dSi (100 mu M). Average bSi accumulation in these novel biosilicifiers was between 30 and 92 amol Si cell(-1). Growth rate and cell size of the picoeukaryotes were not affected by dSi addition. Still, the purpose of bSi accumulation in these smaller eukaryotic organisms lacking silicon dependent structures remains unclear. In line with the increasing recognition of picoeukaryotes in biogeochemical cycling, our findings suggest that they can also play a significant role in silica cycling.
|
|
| 3. |
- Sjöstedt, Johanna, et al.
(författare)
-
Repeated disturbances affect functional but not compositional resistance and resilience in an aquatic bacterioplankton community
- 2018
-
Ingår i: Environmental microbiology reports. - : Wiley. - 1758-2229. ; 10:4, s. 493-500
-
Tidskriftsartikel (refereegranskat)abstract
- Disturbances are believed to be one of the main factors influencing variations in community diversity and functioning. Here we investigated if exposure to a pH press disturbance affected the composition and functional performance of a bacterial community and its resistance, recovery and resilience to a second press disturbance (salt addition). Lake bacterial assemblages were initially exposed to reduced pH in six mesocosms whereas another six mesocosms were kept as reference. Seven days after the pH disturbance, three tanks from each treatment were exposed to a salt disturbance. Both bacterial production and enzyme activity were negatively affected by the salt treatment, regardless if the communities had been subject to a previous disturbance or not. However, cell-specific enzyme activity had a higher resistance in communities pre-exposed to the pH disturbance compared to the reference treatment. In contrast, for cell-specific bacterial production resistance was not affected, but recovery was faster in the communities that had previously been exposed to the pH disturbance. Over time, bacterial community composition diverged among treatments, in response to both pH and salinity. The difference in functional recovery, resilience and resistance may depend on differences in community composition caused by the pH disturbance, niche breadth or acquired stress resistance.
|
|
| 4. |
- Gohar, Daniyal, et al.
(författare)
-
Global diversity and distribution of mushroom-inhabiting bacteria
- 2022
-
Ingår i: Environmental Microbiology Reports. - : John Wiley & Sons. - 1758-2229. ; 14:2, s. 254-264
-
Tidskriftsartikel (refereegranskat)abstract
- Mushroom-forming fungi are important sources of food and medicine in many regions of the world, and their development and health are known to depend on various microbes. Recent studies have examined the structure of mushroom-inhabiting bacterial (MIB) communities and their association with local environmental variables, but global-scale diversity and determinants of these communities remain poorly understood. Here we examined the MIB global diversity and community composition in relation to climate, soil and host factors. We found a core global mushroom microbiome, accounting for 30% of sequence reads, while comprising a few bacterial genera such as Halomonas, Serratia, Bacillus, Cutibacterium, Bradyrhizobium and Burkholderia. Our analysis further revealed an important role of host phylogeny in shaping the communities of MIB, whereas the effects of climate and soil factors remained negligible. The results suggest that the communities of MIB and free-living bacteria are structured by contrasting community assembly processes and that fungal-bacterial interactions are an important determinant of MIB community structure.
|
|
| 5. |
- McKee, Lauren S., 1985-, et al.
(författare)
-
Polysaccharide degradation by the Bacteroidetes: mechanisms and nomenclature
- 2021
-
Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229. ; 13:5, s. 559-581
-
Forskningsöversikt (refereegranskat)abstract
- The Bacteroidetes phylum is renowned for its ability to degrade a wide range of complex carbohydrates, a trait that has enabled its dominance in many diverse environments. The best studied species inhabit the human gut microbiome and use polysaccharide utilization loci (PULs), discrete genetic structures that encode proteins involved in the sensing, binding, deconstruction, and import of target glycans. In many environmental species, polysaccharide degradation is tightly coupled to the phylum-exclusive type IX secretion system (T9SS), which is used for the secretion of certain enzymes and is linked to gliding motility. In addition, within specific species these two adaptive systems (PULs and T9SS) are intertwined, with PUL-encoded enzymes being secreted by the T9SS. Here, we discuss the most noteworthy PUL and non-PUL mechanisms that confer specific and rapid polysaccharide degradation capabilities to the Bacteroidetes in a range of environments. We also acknowledge that the literature showcasing examples of PULs is rapidly expanding and developing a set of assumptions that can be hard to track back to original findings. Therefore, we present a simple universal description of conserved PUL functions and how they are determined, while proposing a common nomenclature describing PULs and their components, to simplify discussion and understanding of PUL systems.
|
|
| 6. |
- Bahram, Mohammad, et al.
(författare)
-
Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment
- 2019
-
Ingår i: Environmental Microbiology Reports. - : WILEY. - 1758-2229. ; 11:4, s. 487-494
-
Tidskriftsartikel (refereegranskat)abstract
- High-throughput studies of microbial communities suggest that Archaea are a widespread component of microbial diversity in various ecosystems. However, proper quantification of archaeal diversity and community ecology remains limited, as sequence coverage of Archaea is usually low owing to the inability of available prokaryotic primers to efficiently amplify archaeal compared to bacterial rRNA genes. To improve identification and quantification of Archaea, we designed and validated the utility of several primer pairs to efficiently amplify archaeal 16S rRNA genes based on up-to-date reference genes. We demonstrate that several of these primer pairs amplify phylogenetically diverse Archaea with high sequencing coverage, outperforming commonly used primers. Based on comparing the resulting long 16S rRNA gene fragments with public databases from all habitats, we found several novel family- to phylum-level archaeal taxa from topsoil and surface water. Our results suggest that archaeal diversity has been largely overlooked due to the limitations of available primers, and that improved primer pairs enable to estimate archaeal diversity more accurately.
|
|
| 7. |
- Cody, Alison J., et al.
(författare)
-
Wild bird-associated Campylobacter jejuni isolates are a consistent source of human disease, in Oxfordshire, United Kingdom
- 2015
-
Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229. ; 7:5, s. 782-788
-
Tidskriftsartikel (refereegranskat)abstract
- The contribution of wild birds as a source of human campylobacteriosis was investigated in Oxfordshire, United Kingdom (UK) over a 10 year period. The probable origin of human Campylobacter jejuni genotypes, as described by multilocus sequence typing, was estimated by comparison with reference populations of isolates from farm animals and five wild bird families, using the STRUCTURE algorithm. Wild bird-attributed isolates accounted for between 476 (2.1%) and 543 (3.5%) cases annually. This proportion did not vary significantly by study year (P=0.934) but varied seasonally, with wild bird-attributed genotypes comprising a greater proportion of isolates during warmer compared with cooler months (P=0.003). The highest proportion of wild bird-attributed illness occurred in August (P<0.001), with a significantly lower proportion in November (P=0.018). Among genotypes attributed to specific groups of wild birds, seasonality was most apparent for Turdidae-attributed isolates, which were absent during cooler, winter months. This study is consistent with some wild bird species representing a persistent source of campylobacteriosis, and contributing a distinctive seasonal pattern to disease burden. If Oxfordshire is representative of the UK as a whole in this respect, these data suggest that the national burden of wild bird-attributed isolates could be in the order of 10000 annually.
|
|
| 8. |
- Sandegren, Linus, et al.
(författare)
-
Long-term carriage and rapid transmission of extended spectrum beta-lactamase-producing E-coli within a flock of Mallards in the absence of antibiotic selection
- 2018
-
Ingår i: Environmental Microbiology Reports. - : Wiley-Blackwell. - 1758-2229. ; 10:5, s. 576-582
-
Tidskriftsartikel (refereegranskat)abstract
- Wild birds have been suggested as transmitters and reservoirs for antibiotic resistant bacteria. We performed an experimental study investigating carriage time and interindividual transmission of extended spectrum beta-lactamase- (ESBL-)producing Escherichia coli in Mallards (Anas platyrhynchos) to assess if the birds carry the bacteria long enough to transfer them geographically during migration. Mallards were inoculated intraoesophageally with four different strains of ESBL-producing E. coli and kept together in a flock. The ESBL-strains belonged to sequence types previously shown to spread between birds and humans. Culturing from faecal samples showed presence of ESBL-producing E. coli the entire 29 day experimental period. An extensive and rapid transmission of the different ESBL-strains between individuals (including non-inoculated controls) was observed. In necropsy samples, we detected ESBL-strains in the cecum even in faeces-negative birds, indicating that this part of the intestine could function as a reservoir of resistant bacteria. We demonstrate that birds can carry ESBL-producing E. coli for long enough times to travel far during migration and the extensive interindividual transmission suggests spread between individuals in a dense bird population as a mechanism that allow persistence of resistant bacteria.
|
|
| 9. |
- Spang, Anja, et al.
(författare)
-
Towards a systematic understanding of differences between archaeal and bacterial diversity
- 2019
-
Ingår i: Environmental Microbiology Reports. - : WILEY. - 1758-2229. ; 11:1, s. 9-12
-
Tidskriftsartikel (refereegranskat)abstract
- In this crystal ball, we discuss emerging methodologies that can help reaching a synthesis on the biodiversity of Archaea and Bacteria and thereby inform a central enigma in microbiology, i.e. the fundamental split between these primary domains of life and the apparent lower diversity of the Archaea.
|
|
| 10. |
- Sörenson, Eva, 1979-, et al.
(författare)
-
Consistency in microbiomes in cultures of Alexandrium species isolated from brackish and marine waters
- 2019
-
Ingår i: Environmental Microbiology Reports. - : Wiley-Blackwell. - 1758-2229. ; 11:3, s. 425-433
-
Tidskriftsartikel (refereegranskat)abstract
- Phytoplankton and bacteria interactions have a significant role in aquatic ecosystem functioning. Associations can range from mutualistic to parasitic, shaping biogeochemical cycles and having a direct influence on phytoplankton growth. How variations in phenotype and sampling location, affect the phytoplankton microbiome is largely unknown. A high‐resolution characterization of the bacterial community in cultures of the dinoflagellate Alexandrium was performed on strains isolated from different geographical locations and at varying anthropogenic impact levels. Microbiomes of Baltic Sea Alexandrium ostenfeldii isolates were dominated by Betaproteobacteria and were consistent over phenotypic and genotypic Alexandrium strain variation, resulting in identification of an A. ostenfeldii core microbiome. Comparisons with in situ bacterial communities showed that taxa found in this A. ostenfeldii core were specifically associated to dinoflagellate dynamics in the Baltic Sea. Microbiomes of Alexandrium tamarense and minutum, isolated from the Mediterranean Sea, differed from those of A. ostenfeldii in bacterial diversity and composition but displayed high consistency, and a core set of bacterial taxa was identified. This indicates that Alexandrium isolates with diverse phenotypes host predictable, species‐specific, core microbiomes reflecting the abiotic conditions from which they were isolated. These findings enable in‐depth studies of potential interactions occurring between Alexandrium and specific bacterial taxa.
|
|
| 11. |
- Wittorf, Lea, et al.
(författare)
-
Growth yield and selection of nosZ clade II types in a continuous enrichment culture of N2O respiring bacteria
- 2018
-
Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229. ; 10, s. 239-244
-
Tidskriftsartikel (refereegranskat)abstract
- Nitrous oxide (N2O) reducing microorganisms may be key in the mitigation of N2O emissions from managed ecosystems. However, there is still no clear understanding of the physiological and bioenergetic implications of microorganisms possessing either of the two N2O reductase genes (nosZ), clade I and the more recently described clade II type nosZ. It has been suggested that organisms with nosZ clade II have higher growth yields and a lower affinity constant (K-s) for N2O. We compared N2O reducing communities with different nosZI/nosZII ratios selected in chemostat enrichment cultures, inoculated with activated sludge, fed with N2O as a sole electron acceptor and growth limiting factor and acetate as electron donor. From the sequencing of the 16S rRNA gene, FISH and quantitative PCR of nosZ and nir genes, we concluded that betaproteobacterial denitrifying organisms dominated the enrichments with members within the family Rhodocyclaceae being highly abundant. When comparing cultures with different nosZI/nosZII ratios, we did not find support for (i) a more energy conserving N2O respiration pathway in nosZ clade II systems, as reflected in the growth yield per mole of substrate, or (ii) a higher affinity for N2O, defined by (max)/K-s, in organisms with nosZ clade II.
|
|
| 12. |
- Ahlstrom, Christina A., et al.
(författare)
-
Early emergence of mcr-1-positive Enterobacteriaceae in gulls from Spain and Portugal
- 2019
-
Ingår i: Environmental Microbiology Reports. - : WILEY. - 1758-2229. ; 11:5, s. 669-671
-
Tidskriftsartikel (refereegranskat)abstract
- We tested extended-spectrum beta-lactamase producing bacteria from wild gulls (Larus spp.) sampled in 2009 for the presence of mcr-1. We report the detection of mcr-1 and describe genome characteristics of four Escherichia coli and one Klebsiella pneumoniae isolate from Spain and Portugal that also exhibited colistin resistance. Results represent the earliest evidence for colistin-resistant bacteria in European wildlife.
|
|
| 13. |
- Brandsma, J, et al.
(författare)
-
A multi-proxy study of anaerobic ammonium oxidation in marine sediments of the Gullmar Fjord, Sweden
- 2011
-
Ingår i: ENVIRONMENTAL MICROBIOLOGY REPORTS. - : Wiley. - 1758-2229. ; 3:3, s. 360-366
-
Tidskriftsartikel (refereegranskat)abstract
- Anaerobic ammonium oxidation (anammox) is an important process for nitrogen removal in marine pelagic and benthic environments and represents a major sink in the global nitrogen cycle. We applied a suite of complementary methods for the detection and enumeration of anammox activity and anammox bacteria in marine sediments of the Gullmar Fjord, and compared the results obtained with each technique. 15N labelling experiments showed that nitrogen removal through N2 production was essentially limited to the upper 2 cm of the sediment, where anammox contributed 23–47% of the total production. The presence of marine anammox bacteria belonging to the genus ‘Candidatus Scalindua’ was shown by 16S rRNA gene sequence comparison. FISH counts of anammox bacteria correlated well with anammox activity, while quantitative PCR may have underestimated the number of anammox bacterial 16S rRNA gene copies at this site. Potential nitrogen conversion by anammox ranged from 0.6 to 4.8 fmol N cell−1 day−1, in agreement with previous measurements in the marine environment and in bioreactors. Finally, intact ladderane glycerophospholipid concentrations better reflected anammox activity and abundance than ladderane core lipid concentrations, most likely because the core lipid fraction contained a substantial fossil component, especially deeper in the sediment.
|
|
| 14. |
|
|
| 15. |
- Westerholm, Maria, et al.
(författare)
-
Quantification of syntrophic acetate-oxidizing microbial communities in biogas processes
- 2011
-
Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229. ; 3, s. 500-505
-
Tidskriftsartikel (refereegranskat)abstract
- Changes in communities of syntrophic acetate-oxidizing bacteria (SAOB) and methanogens caused by elevated ammonia levels were quantified in laboratory-scale methanogenic biogas reactors operating at moderate temperature (37 degrees C) using quantitative polymerase chain reaction (qPCR). The experimental reactor was subjected to gradually increasing ammonia levels (0.8-6.9 g NH4+-N l(-1)), whereas the level of ammonia in the control reactor was kept low (0.65-0.90 g NH4+-N l(-1)) during the entire period of operation (660 days). Acetate oxidation in the experimental reactor, indicated by increased production of (CO2)-C-14 from acetate labelled in the methyl carbon, occurred when ammonia levels reached 5.5 and 6.9 g NH4+-N l(-1). Syntrophic acetate oxidizers targeted by newly designed qPCR primers were Thermacetogenium phaeum, Clostridium ultunense, Syntrophaceticus schinkii and Tepidanaerobacter acetatoxydans. The results showed a significant increase in abundance of all these bacteria except T. phaeum in the ammonia-stressed reactor, coincident with the shift to syntrophic acetate oxidation. As the abundance of the bacteria increased, a simultaneous decrease was observed in the abundance of aceticlastic methanogens from the families Methanosaetaceae and Methanosarcinaceae. qPCR analyses of sludge from two additional high ammonia processes, in which methane production from acetate proceeded through syntrophic acetate oxidation (reactor SB) or through aceticlastic degradation (reactor DVX), demonstrated that SAOB were significantly more abundant in the SB reactor than in the DVX reactor.
|
|
| 16. |
- Bahram, Mohammad, et al.
(författare)
-
The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics
- 2018
-
Ingår i: Environmental Microbiology Reports. - : WILEY. - 1758-2229. ; 10:2, s. 155-166
-
Tidskriftsartikel (refereegranskat)abstract
- Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr.) Kuyper, to classify fungal and bacterial genomic sequences, and obtained a nearly complete fungal genome containing 93% of core eukaryotic genes. Comparative genomics reveals that I. terrigena is more similar to ectomycorrhizal and brown rot fungi than to white rot fungi. The reduction in lignin degradation capacity has been independent from and significantly faster than in closely related ectomycorrhizal clades supporting that ectomycorrhizal symbiosis evolved independently in Inocybe. The microbiome of I. terrigena fruiting-bodies includes bacteria with known symbiotic functions in other fungal and non-fungal host environments, suggesting potential symbiotic functions of these bacteria in fungal tissues regardless of habitat conditions. Our study demonstrates the usefulness of direct metagenomics analysis of fruiting-body tissues for characterizing fungal genomes and microbiome.
|
|
| 17. |
- Bahram, Mohammad
(författare)
-
The influence of tree genus, phylogeny, and richness on the specificity, rarity, and diversity of ectomycorrhizal fungi
- 2024
-
Ingår i: Environmental Microbiology Reports. - 1758-2229. ; 16
-
Tidskriftsartikel (refereegranskat)abstract
- Partner specificity is a well-documented phenomenon in biotic interactions, yet the factors that determine specificity in plant-fungal associations remain largely unknown. By utilizing composite soil samples, we identified the predictors that drive partner specificity in both plants and fungi, with a particular focus on ectomycorrhizal associations. Fungal guilds exhibited significant differences in overall partner preference and avoidance, richness, and specificity to specific tree genera. The highest level of specificity was observed in root endophytic and ectomycorrhizal associations, while the lowest was found in arbuscular mycorrhizal associations. The majority of ectomycorrhizal fungal species showed a preference for one of their partner trees, primarily at the plant genus level. Specialist ectomycorrhizal fungi were dominant in belowground communities in terms of species richness and relative abundance. Moreover, all tree genera (and occasionally species) demonstrated a preference for certain fungal groups. Partner specificity was not related to the rarity of fungi or plants or environmental conditions, except for soil pH. Depending on the partner tree genus, specific fungi became more prevalent and relatively more abundant with increasing stand age, tree dominance, and soil pH conditions optimal for the partner tree genus. The richness of partner tree species and increased evenness of ectomycorrhizal fungi in multi-host communities enhanced the species richness of ectomycorrhizal fungi. However, it was primarily the partner-generalist fungi that contributed to the high diversity of ectomycorrhizal fungi in mixed forests.More than half of ectomycorrhizal fungi display partner specificity that is determined by tree genus and among-plant phylogenetic relationships. Specific fungi are more common in monospecific stands and at extreme soil pH. Rarity is unrelated to specificity, but it is driven by overall fungal and plant partner richness, certain tree species (Pinus and Salix) and moderately acidic soils. Mainly partner-generalist fungi contribute to the high diversity of ectomycorrhizal fungi in mixed forests. image
|
|
| 18. |
- David Cabrer-Panes, Juan, et al.
(författare)
-
ppGppmediates the growth phase-dependent regulation ofagn43, a phase variable gene, by stimulating its promoter activity
- 2020
-
Ingår i: Environmental Microbiology Reports. - : John Wiley & Sons. - 1758-2229. ; 12:4, s. 444-453
-
Tidskriftsartikel (refereegranskat)abstract
- Antigen 43 (Ag43) is a self-recognizing outer membrane protein ofEscherichia coliexpressed during intracellular growth and biofilm formation, suggesting a role in infection. The expression ofagn43is under phase variation control, meaning that there are regulatory mechanisms adjusting the percentage ofagn43-expressing cells in the population, in addition to mechanisms modulating the transcriptional expression level in each expressing cell. Phenotypic and transcriptional studies indicate that Ag43 expression is induced upon entry into the stationary phase in a ppGpp-dependent and RpoS-independent manner. The use of single-cell approaches and phase variation deficient strains let to conclude that ppGpp stimulatesagn43promoter activity, rather than affecting the percentage ofagn43-expressing cells. The data highlight the relevance that promoter activity regulation may have, without any involvement of the phase variation state, in the final Ag43 expression output. Theagn43promoter of the MG1655 strain carries an AT-rich discriminator between positions -10 and +1, which is highly conserved among theagn43genes present in the different pathotypes ofE. coli. Remarkably, the AT-rich discriminator is required for the positive transcriptional control mediated by ppGpp.
|
|
| 19. |
- Fahad, Zaenab A., et al.
(författare)
-
Fractionation and assimilation of Mg isotopes by fungi is species dependent
- 2016
-
Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229. ; 8:6, s. 956-965
-
Tidskriftsartikel (refereegranskat)abstract
- Symbiotic ectomycorrhizal fungi mobilize nutrients from both organic and inorganic substrates and supply them to their host plants. Their role in mobilizing base cations and phosphorus from mineral substrates through weathering has received increasing attention in recent years but the processes involved remain to be elucidated. We grew selected ectomycorrhizal and nonmycorrhizal fungi in axenic systems containing mineral and organic substrates and examined their capacity to fractionate and assimilate stable isotopes of magnesium. The mycorrhizal fungi were significantly depleted in heavy isotopes with the lowest Mg-26 values (the difference between Mg-26 in fungal tissue and Mg-26 in the substrate) compared with nonmycorrhizal fungi, when grown on mineral substrates containing granite particles. The ectomycorrhizal fungi accumulated significantly higher concentrations of Mg, K and P than the nonmycorrhizal fungi. There was a highly significant statistical relationship between Mg-26 tissue signature and mycelial concentration of Mg, with a clear separation between most ectomycorrhizal fungi and the nonmycorrhizal fungi. These results are consistent with the idea that ectomycorrhizal fungi have evolved efficient mechanisms to mobilize, transport and store Mg within their mycelia.
|
|
| 20. |
- Fahlgren, Camilla, et al.
(författare)
-
Seawater mesocosm experiments in the Arctic uncover differential transfer of marine bacteria to aerosols
- 2015
-
Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229. ; 7:3, s. 460-470
-
Tidskriftsartikel (refereegranskat)abstract
- Biogenic aerosols critically control atmospheric processes. However, although bacteria constitute major portions of living matter in seawater, bacterial aerosolization from oceanic surface layers remains poorly understood. We analysed bacterial diversity in seawater and experimentally generated aerosols from three Kongsfjorden sites, Svalbard. Construction of 16S rRNA gene clone libraries from paired seawater and aerosol samples resulted in 1294 sequences clustering into 149 bacterial and 34 phytoplankton operational taxonomic units (OTUs). Bacterial communities in aerosols differed greatly from correspondingseawater communities in three out of four experiments. Dominant populations of both seawater and aerosols were Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria. Across the entire dataset, most OTUs from seawater could also be found in aerosols; in each experiment, however, several OTUs were either selectively enriched in aerosols or little aerosolized. Notably, a SAR11 clade OTU was consistently abundant in the seawater, but was recorded insignificantly lower proportions in aerosols. A strikingly high proportion of colony-forming bacteria were pigmented in aerosols compared with seawater, suggesting that selection during aerosolization contributes to explaining elevated proportions of pigmented bacteria frequently observed in atmospheric samples. Our findings imply that atmospheric processes could be considerably influenced by spatiotemporal variations in the aerosolization efficiency of different marine bacteria.
|
|
| 21. |
|
|
| 22. |
- Garcia, Sarahi L, et al.
(författare)
-
Successful enrichment of the ubiquitous freshwater acI Actinobacteria
- 2014
-
Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229. ; 6:1, s. 21-27
-
Tidskriftsartikel (refereegranskat)abstract
- Actinobacteriaof the acI lineage are often thenumerically dominant bacterial phylum in surfacefreshwaters, where they can account for>50% oftotal bacteria. Despite their abundance, there are nodescribed isolates. In an effort to obtain enrichmentof these ubiquitous freshwaterActinobacteria, dilutedfreshwater samples from Lake Grosse Fuchskuhle,Germany, were incubated in 96-well culture plates.With this method, a successful enrichment containinghigh abundances of a member of the lineage acI wasestablished. Phylogenetic classification showed thatthe acIActinobacteriaof the enrichment belonged tothe acI-B2 tribe, which seems to prefer acidic lakes.This enrichment grows to low cell densities and thusthe oligotrophic nature of acI-B2 was confirmed.
|
|
| 23. |
- Gómez-Campo, Cristina L., et al.
(författare)
-
Differential requirement for RecFOR pathway components in Thermus thermophilus
- 2024
-
Ingår i: Environmental Microbiology Reports. - : John Wiley & Sons. - 1758-2229. ; 16:3
-
Tidskriftsartikel (refereegranskat)abstract
- Recombinational repair is an important mechanism that allows DNA replication to overcome damaged templates, so the DNA is duplicated timely and correctly. The RecFOR pathway is one of the common ways to load RecA, while the RuvABC complex operates in the resolution of DNA intermediates. We have generated deletions of recO, recR and ruvB genes in Thermus thermophilus, while a recF null mutant could not be obtained. The recO deletion was in all cases accompanied by spontaneous loss of function mutations in addA or addB genes, which encode a helicase-exonuclease also key for recombination. The mutants were moderately affected in viability and chromosome segregation. When we generated these mutations in a Δppol/addAB strain, we observed that the transformation efficiency was maintained at the typical level of Δppol/addAB, which is 100-fold higher than that of the wild type. Most mutants showed increased filamentation phenotypes, especially ruvB, which also had DNA repair defects. These results suggest that in T. thermophilus (i) the components of the RecFOR pathway have differential roles, (ii) there is an epistatic relationship of the AddAB complex over the RecFOR pathway and (iii) that neither of the two pathways or their combination is strictly required for viability although they are necessary for normal DNA repair and chromosome segregation.
|
|
| 24. |
- Hamisi, Mariam, et al.
(författare)
-
Epiphytic cyanobacteria of the seagrass Cymodocea rotundata : diversity, diel nifH expression and nitrogenase activity
- 2013
-
Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229. ; 5:3, s. 367-376
-
Tidskriftsartikel (refereegranskat)abstract
- Seagrasses are photoautotrophic, ecologically important components of many globally widespread coastal ecosystems, in which combined nitrogen may limit their production. We examined the biodiversity and diazotrophic capacity of microbial epiphytes associated with the phyllosphere of the seagrass Cymodocea rotundata of the Western Indian Ocean. Light microscopy, 16S rRNA and nifH gene analysis revealed the dominance of cyanobacteria in the epiphytic microbial community. Most phylotypes were related to free-living uncultured benthic cyanobacteria, while some to cyanobacterial endosymbionts of marine diatoms. Novel and potentially diazotrophic species, some of known pantropical distribution, were also discovered. Significant diel nitrogenase activities (acetylene reduction assay) were recorded (up to 358 +/- 232nmolC2H4g1 of seagrass FWh1). The nifH gene expression patterns showed that heterocystous phylotypes may be the dominant diazotrophs during the day and non-heterocystous at night. These data show that C.rotundata is colonized by diverse diazotrophic cyanobacteria species and suggest that these may be beneficial partners of seagrasses in nitrogen-depleted waters.
|
|
| 25. |
- Huang, Zhaobin, et al.
(författare)
-
A novel alphaproteobacterium with a small genome identified from the digestive gland of multiple species of abalone
- 2020
-
Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229. ; 12:4, s. 387-395
-
Tidskriftsartikel (refereegranskat)abstract
- We identified an alphaproteobacterium in the digestive gland of the abalone species Haliotis discus hannai. This phylotype dominated our 16S rRNA clone libraries from the digestive gland of H. discus hannai. Diversity surveys revealed that this phylotype was associated with H. discus hannai and also in another host species, H. gigantea. Whole genome phylogenies placed this bacterium as a new member affiliated with the family Rhodospirillaceae in Alphaproteobacteria. Gene annotation revealed a nearly complete glycolysis pathway but no TCA cycle, but the presence of anaerobic ribonucleoside-triphosphate reductase and oxygen-insensitive NAD(P)H-dependent nitroreductase, which show the genomic potential for anaerobic metabolism. A large cluster of genes encoding ankyrin repeat proteins (ANK) of eukaryotic-like repeat domains and a large gene set for the flagellar system were also detected. Alginate-binding periplasmic proteins and key genes responsible for alginate assimilation were found in the genome, which could potentially contribute to the breakdown of the host's alginate-rich macroalgal diet. These results raise the possibility that this novel alphaproteobacterium is a widespread member of the abalone microbiome that may use polysaccharides derived from its host's macroalgal diet.
|
|
