| 1. |
- Lemos, Leandro Nascimento, et al.
(författare)
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Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils
- 2020
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Ingår i: Environmental microbiology reports. - : Wiley. - 1758-2229. ; 12:6, s. 651-655
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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.
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| 2. |
- Churakova, Yelena, et al.
(författare)
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Biogenic silica accumulation in picoeukaryotes : Novel players in the marine silica cycle
- 2023
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Ingår i: Environmental Microbiology Reports. - : John Wiley & Sons. - 1758-2229. ; 15:4, s. 282-290
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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.
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| 3. |
- Sjöstedt, Johanna, et al.
(författare)
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Repeated disturbances affect functional but not compositional resistance and resilience in an aquatic bacterioplankton community
- 2018
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Ingår i: Environmental microbiology reports. - : Wiley. - 1758-2229. ; 10:4, s. 493-500
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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.
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| 4. |
- Gohar, Daniyal, et al.
(författare)
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Global diversity and distribution of mushroom-inhabiting bacteria
- 2022
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Ingår i: Environmental Microbiology Reports. - : John Wiley & Sons. - 1758-2229. ; 14:2, s. 254-264
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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.
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| 5. |
- McKee, Lauren S., 1985-, et al.
(författare)
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Polysaccharide degradation by the Bacteroidetes: mechanisms and nomenclature
- 2021
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Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229. ; 13:5, s. 559-581
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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.
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| 6. |
- Bahram, Mohammad, et al.
(författare)
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Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment
- 2019
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Ingår i: Environmental Microbiology Reports. - : WILEY. - 1758-2229. ; 11:4, s. 487-494
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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.
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| 7. |
- Cody, Alison J., et al.
(författare)
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Wild bird-associated Campylobacter jejuni isolates are a consistent source of human disease, in Oxfordshire, United Kingdom
- 2015
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Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229. ; 7:5, s. 782-788
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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.
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| 8. |
- Sandegren, Linus, et al.
(författare)
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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
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Ingår i: Environmental Microbiology Reports. - : Wiley-Blackwell. - 1758-2229. ; 10:5, s. 576-582
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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.
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| 9. |
- Spang, Anja, et al.
(författare)
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Towards a systematic understanding of differences between archaeal and bacterial diversity
- 2019
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Ingår i: Environmental Microbiology Reports. - : WILEY. - 1758-2229. ; 11:1, s. 9-12
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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.
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| 10. |
- Sörenson, Eva, 1979-, et al.
(författare)
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Consistency in microbiomes in cultures of Alexandrium species isolated from brackish and marine waters
- 2019
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Ingår i: Environmental Microbiology Reports. - : Wiley-Blackwell. - 1758-2229. ; 11:3, s. 425-433
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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.
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