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- Murray, Alison E., et al.
(författare)
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Roadmap for naming uncultivated Archaea and Bacteria
- 2020
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Ingår i: Nature Microbiology. - : NATURE PUBLISHING GROUP. - 2058-5276. ; 5:8, s. 987-994
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Tidskriftsartikel (refereegranskat)abstract
- The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity. In this Consensus Statement, the authors discuss the issue of naming uncultivated prokaryotic microorganisms, which currently do not have a formal nomenclature system due to a lack of type material or cultured representatives, and propose two recommendations including the recognition of DNA sequences as type material.
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| 2. |
- Wang, Fang, et al.
(författare)
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Emerging contaminants: A One Health perspective
- 2024
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Ingår i: Innovation. - 2666-6758. ; 5
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Forskningsöversikt (refereegranskat)abstract
- Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health. Despite global efforts to mitigate legacy pollutants, the continuous introduction of new substances remains a major threat to both people and the planet. In response, global initiatives are focusing on risk assessment and regulation of emerging contaminants, as demonstrated by the ongoing efforts to establish the UN's Intergovernmental Science-Policy Panel on Chemicals, Waste, and Pollution Prevention. This review identifies the sources and impacts of emerging contaminants on planetary health, emphasizing the importance of adopting a One Health approach. Strategies for monitoring and addressing these pollutants are discussed, underscoring the need for robust and socially equitable environmental policies at both regional and international levels. Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.
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| 3. |
- Brussaard, Lijbert, et al.
(författare)
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Biodiversity and ecosystem functioning in soil
- 1997
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Ingår i: Ambio: a Journal of Human Environment. - 0044-7447. ; 26:8, s. 563-570
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Tidskriftsartikel (refereegranskat)abstract
- We review the current knowledge on biodiversity in soils, its role in ecosystem processes, its importance for human purposes, and its resilience against stress and disturbance. The number of existing species is vastly higher than the number described, even in the macroscopically visible taxa, and biogeographical syntheses are largely lacking. A major effort in taxonomy and the training of a new generation of systematists is imperative. This effort has to be focussed on the groups of soil organisms that, to the best of our knowledge, play key roles in ecosystem functioning. To identify such groups, spheres of influence (SOI) of soil biota - such as the root biota, the shredders of organic matter and the soil bioturbators - are recognized that presumably control ecosystem processes, for example, through interactions with plants. Within those SOI, functional groups of soil organisms are recognized. Research questions of the highest urgency are the assignment of species to functional groups and determining the redundancy of species within functional groups. These priorities follow from the need to address the extent of any loss of functioning in soils, associated with intensive agriculture, forest disturbance, pollution of the environment, and global environmental change. The soil biota considered at present to be most at risk are species-poor functional groups among macrofaunal shredders of organic matter, bioturbators of soil, specialized bacteria like nitrifiers and nitrogen fixers, and fungiforming mycorrhizas. An experimental approach in addressing these research priorities is needed, using longterm and large-scale field experiments and modern methods of geostatistics and geographic information systems.
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| 4. |
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| 5. |
- Karlsson, Anna, 1969-
(författare)
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Anaerobic degradation of phenol and related aromatics
- 2000
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Phenol and other simple aromatic compounds have been found in water leached from landfills, showing that these types of compounds could be either present in disposed waste, or released from it via transformation and degradation processes. Hence, the fate anddegradation potential of such compounds under landfilling conditions is of great concern. Therefore, using micro-organisms from landfills, I have investigated the anaerobic biodegradation of phenol, dimethyl phthalate, 3-chlorobenzoate, 2,4,6-trichlorophenol, tetrabromophthalic acid and aniline. The compounds were chosen to represent substrates of potentially important reactions in the transformation and degradation of aromatic compounds. 24 waste samples from landfills and a time series of samples taken over five years from fourlandfill simulation reactors (in all 20 waste samples) were used as sources of microorganisms. The capacity of these waste samples to degrade the halogenated aromatics was poor or completely absent, indicating that halogenated compounds could be more persistent inlandfills than in other previously investigated anaerobic environments. Phenol and dimethyl phthalate were more readily transformed by most landfill samples, but the degradation capacity was poorer in the landfill simulation experiments. Here the unique sampling series showed an increase in degradation capacity with time, indicating that one to two years is needed to allow a micro-flora capable of degrading aromatic compounds to develop. However, the landfill samples showed higher degradation potentials than the simulation reactor samples, even from the later stages.A more extensive study designed to elucidate the phenol degradation pathway under anaerobic, fermenting conditions is also presented. Here, phenol was for the first time shown to be degraded to non-aromatic products in a non-methanogenic fermenting culture. The endproductsformed were benzoate, acetate and butyrate. The conversion of phenol to benzoate was proved to be an electron sink reaction, used during processes such as degradation of glucose and is a new example of the diversity of compounds that can used as electronsinks/ acceptors in anaerobic environments. The degradation pathway in the studied cultureproceeds via fom1ation of 4-hydroxybenzoate, 4-hydroxybenzoyl-CoA and benzoyl-CoA, and the activity of a CoA-transferase which activates 4-hydroxybenzoate was measured.
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| 6. |
- Šket, Robert, et al.
(författare)
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Hypoxia and Inactivity Related Physiological Changes (Constipation, Inflammation) Are Not Reflected at the Level of Gut Metabolites and Butyrate Producing Microbial Community : The PlanHab Study
- 2017
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Ingår i: Frontiers in Physiology. - : Frontiers Research Foundation. - 1664-042X. ; 8:4
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Tidskriftsartikel (refereegranskat)abstract
- We explored the assembly of intestinal microbiota in healthy male participants during the run-in (5 day) and experimental phases [21-day normoxic bed rest (NBR), hypoxic bedrest (HBR)], and hypoxic ambulation (HAmb) in a strictly controlled laboratory environment, balanced fluid, and dietary intakes, controlled circadian rhythm, microbial ambiental burden, and 24/7 medical surveillance. The fraction of inspired O2 (FiO2) and partial pressure of inspired O2 (PiO2) were 0.209 and 133.1 ± 0.3 mmHg for NBR and 0.141 ± 0.004 and 90.0 ± 0.4 mmHg for both hypoxic variants (HBR and HAmb; ~4,000 m simulated altitude), respectively. A number of parameters linked to intestinal transit spanning Bristol Stool Scale, defecation rates, zonulin, α1-antitrypsin, eosinophil derived neurotoxin, bile acids, reducing sugars, short chain fatty acids, total soluble organic carbon, water content, diet composition, and food intake were measured (167 variables). The abundance, structure, and diversity of butyrate producing microbial community were assessed using the two primary bacterial butyrate synthesis pathways, butyryl-CoA: acetate CoA-transferase (but) and butyrate kinase (buk) genes. Inactivity negatively affected fecal consistency and in combination with hypoxia aggravated the state of gut inflammation (p < 0.05). In contrast, gut permeability, various metabolic markers, the structure, diversity, and abundance of butyrate producing microbial community were not significantly affected. Rearrangements in the butyrate producing microbial community structure were explained by experimental setup (13.4%), experimentally structured metabolites (12.8%), and gut metabolite-immunological markers (11.9%), with 61.9% remaining unexplained. Many of the measured parameters were found to be correlated and were hence omitted from further analyses. The observed progressive increase in two immunological intestinal markers suggested that the transition from healthy physiological state toward the developed symptoms of low magnitude obesity-related syndromes was primarily driven by the onset of inactivity (lack of exercise in NBR) that were exacerbated by systemic hypoxia (HBR) and significantly alleviated by exercise, despite hypoxia (HAmb). Butyrate producing community in colon exhibited apparent resilience toward short-term modifications in host exercise or hypoxia. Progressive constipation (decreased intestinal motility) and increased local inflammation marker suggest that changes in microbial colonization and metabolism were taking place at the location of small intestine.
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| 7. |
- Šket, Robert, et al.
(författare)
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Hypoxia and inactivity related physiological changes precede or take place in absence of significant rearrangements in bacterial community structure : The PlanHab randomized trial pilot study
- 2017
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 12:12
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Tidskriftsartikel (refereegranskat)abstract
- We explored the assembly of intestinal microbiota in healthy male participants during the randomized crossover design of run-in (5 day) and experimental phases (21-day normoxic bed rest (NBR), hypoxic bed rest (HBR) and hypoxic ambulation (HAmb) in a strictly controlled laboratory environment, with balanced fluid and dietary intakes, controlled circadian rhythm, microbial ambiental burden and 24/7 medical surveillance. The fraction of inspired O2 (FiO2) and partial pressure of inspired O2 (PiO2) were 0.209 and 133.1 ± 0.3 mmHg for NBR and 0.141 ± 0.004 and 90.0 ± 0.4 mmHg for both hypoxic variants (HBR and HAmb; ~4000 m simulated altitude), respectively. A number of parameters linked to intestinal environment such as defecation frequency, intestinal electrical conductivity (IEC), sterol and polyphenol content and diversity, indole, aromaticity and spectral characteristics of dissolved organic matter (DOM) were measured (64 variables). The structure and diversity of bacterial microbial community was assessed using 16S rRNA amplicon sequencing. Inactivity negatively affected frequency of defecation and in combination with hypoxia increased IEC (p < 0.05). In contrast, sterol and polyphenol diversity and content, various characteristics of DOM and aromatic compounds, the structure and diversity of bacterial microbial community were not significantly affected over time. A new in-house PlanHab database was established to integrate all measured variables on host physiology, diet, experiment, immune and metabolic markers (n = 231). The observed progressive decrease in defecation frequency and concomitant increase in IEC suggested that the transition from healthy physiological state towards the developed symptoms of low magnitude obesity-related syndromes was dose dependent on the extent of time spent in inactivity and preceded or took place in absence of significant rearrangements in bacterial microbial community. Species B. thetaiotamicron, B. fragilis, B. dorei and other Bacteroides with reported relevance for dysbiotic medical conditions were significantly enriched in HBR, characterized with most severe inflammation symptoms, indicating a shift towards host mucin degradation and proinflammatory immune crosstalk.
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