Microbial indicators for soil quality Schloter, Michael; Nannipieri, Paolo; Sørensen, Søren J. ...
Biology and fertility of soils,
2018/1, Letnik:
54, Številka:
1
Journal Article
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The living soil is instrumental to key life support functions (LSF) that safeguard life on Earth. The soil microbiome has a main role as a driver of these LSF. Current global developments, like ...anthropogenic threats to soil (e.g., via intensive agriculture) and climate change, pose a burden on soil functioning. Therefore, it is important to dispose of robust indicators that report on the nature of deleterious changes and thus soil quality. There has been a long debate on the best selection of biological indicators (bioindicators) that report on soil quality. Such indicators should ideally describe organisms with key functions in the system, or with key regulatory/connecting roles (so-called
keystone species
). However, in the light of the huge functional redundancy in most soil microbiomes, finding specific keystone markers is not a trivial task. The current rapid development of molecular (DNA-based) methods that facilitate deciphering microbiomes with respect to key functions will enable the development of improved criteria by which molecular information can be tuned to yield molecular markers of soil LSF. This review critically examines the current state-of-the-art in molecular marker development and recommends avenues to come to improved future marker systems.
The increasing use and discharge of nanoparticles (NPs) pose risks to microorganisms that maintain the health of aquatic ecosystems. Although NPs are toxic to microorganisms, they tend to form ...microbial aggregates to protect themselves. Two main mechanisms account for the reduced toxicity: the dense physical structure acts as a barrier to NP exposure in the interior of the aggregate, and aggregation stabilizes a complex microbial ecosystem that enhances the ability of the community to adapt to prolonged NP exposure. We highlight the opportunities and challenges for managing microbial aggregates in wastewater treatment to remove or control NPs. For example, understanding the resistance mechanisms can help to design smart NPs that are less toxic to useful microorganisms or more toxic towards pathogenic microorganisms.
NPs inevitably enter aquatic ecosystems – natural and engineered – owing to their massive use and rapid growth trend in industry and commerce. NPs come into contact with microbial aggregates, which are ubiquitous in aquatic environments.
NPs exert well-known toxicities to microorganisms but, compared to planktonic cells, microorganisms in microbial aggregates are much more able to protect themselves against NPs toxicity.
The dense physical structure of the aggregates acts as a barrier to NP exposure in the interior of the aggregate. Aggregation also stabilizes microbial diversity and interactions, which enhance the ability of the community to adapt to prolonged NP exposure.
Because microbial aggregates are relatively good at resisting NP toxicity, their already common use in the treatment of wastewaters becomes even more beneficial when the wastewater contains NPs.
Conjugative plasmids: vessels of the communal gene pool Norman, Anders; Hansen, Lars H.; Sørensen, Søren J.
Philosophical transactions of the Royal Society of London. Series B. Biological sciences,
08/2009, Letnik:
364, Številka:
1527
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Comparative whole-genome analyses have demonstrated that horizontal gene transfer (HGT) provides a significant contribution to prokaryotic genome innovation. The evolution of specific prokaryotes is ...therefore tightly linked to the environment in which they live and the communal pool of genes available within that environment. Here we use the term supergenome to describe the set of all genes that a prokaryotic 'individual' can draw on within a particular environmental setting. Conjugative plasmids can be considered particularly successful entities within the communal pool, which have enabled HGT over large taxonomic distances. These plasmids are collections of discrete regions of genes that function as 'backbone modules' to undertake different aspects of overall plasmid maintenance and propagation. Conjugative plasmids often carry suites of 'accessory elements' that contribute adaptive traits to the hosts and, potentially, other resident prokaryotes within specific environmental niches. Insight into the evolution of plasmid modules therefore contributes to our knowledge of gene dissemination and evolution within prokaryotic communities. This communal pool provides the prokaryotes with an important mechanistic framework for obtaining adaptability and functional diversity that alleviates the need for large genomes of specialized 'private genes'.
Antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) are constantly shed into the aquatic environment, with hospital wastewater potentially acting as an important source for ...resistance spread into the environment. A systematic review was conducted aiming to investigate the role of hospital wastewater on dissemination of antimicrobial resistance in the aquatic environment. Studies included in the review compared the prevalence of ARB and/or ARGs in hospital versus community wastewater. Data were extracted on ARB and/or ARG prevalence. Data on sampling techniques, microbiological methodology and risk of bias of included studies were recorded.
Thirty-seven studies were included. Higher frequencies of antibiotic resistance determinants were found in hospital wastewater compared to community sources in 30/37 (81%) of included studies. However, trends for specific multi-drug-resistant bacteria differed. Antibiotic-resistant Gram-negative were more prevalent in hospital compared to community wastewaters, with higher concentrations of extended-spectrum-beta-lactamase-producing pathogens and carbapenemase-producing Enterobacteriaceae in hospital sources in 9/9 studies and 6/7 studies, respectively. Hospitals did not contribute consistently to the abundance of vancomycin-resistant Enterococci (VRE); 5/10 studies found higher abundance of VRE in hospital compared to community wastewaters. Reporting on sampling methods, wastewater treatment processes and statistical analysis were at high risk of bias. Extreme heterogeneity in study methods and outcome reporting precluded meta-analysis.
Current evidence concurs that hospital wastewater is an important source for antibiotic resistance in aquatic environments, mainly multidrug-resistant Gram-negative bacteria. Future research is needed to assess the effect of wastewater treatment processes on overall antibiotic resistance in the aquatic environment.
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•Hospital wastewaters were richer in AR than community wastewater in 30/37 (81%) studies.•Higher density of ESBL bacteria in hospital wastewater was found in 9/9 studies.•Higher density of CRE bacteria in hospital wastewater was found in 6/7 studies.•VRE were variably more common in hospital or community wastewaters.•There is a need for developing reporting standards for environmental studies.
Highlights • Synergistic interactions affect biovolume and functionality of multispecies biofilms. • Properties and functions relevant to human health are altered in multispecies biofilms. • ...Multispecies biofilms are hot spots for generation of novel genotypes by means of horizontal gene transfer (HGT). • Recent advances in technologies enable omic studies of interactions in multispecies biofilms.
The composition of the human gut microbiome matures within the first years of life. It has been hypothesized that microbial compositions in this period can cause immune dysregulations and potentially ...cause asthma. Here we show, by associating gut microbial composition from 16S rRNA gene amplicon sequencing during the first year of life with subsequent risk of asthma in 690 participants, that 1-year-old children with an immature microbial composition have an increased risk of asthma at age 5 years. This association is only apparent among children born to asthmatic mothers, suggesting that lacking microbial stimulation during the first year of life can trigger their inherited asthma risk. Conversely, adequate maturation of the gut microbiome in this period may protect these pre-disposed children.
The high prevalence and significance of multispecies biofilms have now been demonstrated in various bacterial habitats with medical, industrial, and ecological relevance. It is highly evident that ...several species of bacteria coexist and interact in biofilms, which highlights the need for evaluating the approaches used to study these complex communities. This review focuses on the establishment of multispecies biofilms in vitro , interspecies interactions in microhabitats, and how to select communities for evaluation. Studies have used different experimental approaches; here we evaluate the benefits and drawbacks of varying the degree of complexity. This review aims to facilitate multispecies biofilm research in order to expand the current limited knowledge on interspecies interactions.
Conjugal plasmids can provide microbes with full complements of new genes and constitute potent vehicles for horizontal gene transfer. Conjugal plasmid transfer is deemed responsible for the rapid ...spread of antibiotic resistance among microbes. While broad host range plasmids are known to transfer to diverse hosts in pure culture, the extent of their ability to transfer in the complex bacterial communities present in most habitats has not been comprehensively studied. Here, we isolated and characterized transconjugants with a degree of sensitivity not previously realized to investigate the transfer range of IncP- and IncPromA-type broad host range plasmids from three proteobacterial donors to a soil bacterial community. We identified transfer to many different recipients belonging to 11 different bacterial phyla. The prevalence of transconjugants belonging to diverse Gram-positive Firmicutes and Actinobacteria suggests that inter-Gram plasmid transfer of IncP-1 and IncPromA-type plasmids is a frequent phenomenon. While the plasmid receiving fractions of the community were both plasmid- and donor- dependent, we identified a core super-permissive fraction that could take up different plasmids from diverse donor strains. This fraction, comprising 80% of the identified transconjugants, thus has the potential to dominate IncP- and IncPromA-type plasmid transfer in soil. Our results demonstrate that these broad host range plasmids have a hitherto unrecognized potential to transfer readily to very diverse bacteria and can, therefore, directly connect large proportions of the soil bacterial gene pool. This finding reinforces the evolutionary and medical significances of these plasmids.
Asthma is believed to arise through early life aberrant immune development in response to environmental exposures that may influence the airway microbiota. Here, we examine the airway microbiota ...during the first three months of life by 16S rRNA gene amplicon sequencing in the population-based Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC
) cohort consisting of 700 children monitored for the development of asthma since birth. Microbial diversity and the relative abundances of Veillonella and Prevotella in the airways at age one month are associated with asthma by age 6 years, both individually and with additional taxa in a multivariable model. Higher relative abundance of these bacteria is furthermore associated with an airway immune profile dominated by reduced TNF-α and IL-1β and increased CCL2 and CCL17, which itself is an independent predictor for asthma. These findings suggest a mechanism of microbiota-immune interactions in early infancy that predisposes to childhood asthma.
Decompensated cirrhosis is characterized by disturbed hemodynamics, immune dysfunction, and high risk of infections. Translocation of viable bacteria and bacterial products from the gut to the blood ...is considered a key driver in this process. Intestinal decontamination with rifaximin may reduce bacterial translocation (BT) and decrease inflammation. A randomized, placebo-controlled trial investigated the effects of rifaximin on inflammation and BT in decompensated cirrhosis.
Fifty-four out-patients with cirrhosis and ascites were randomized, mean age 56 years (± 8.4), and model for end-stage liver disease score 12 (± 3.9). Patients received rifaximin 550-mg BD (n = 36) or placebo BD (n = 18). Blood and fecal (n = 15) sampling were conducted at baseline and after 4 weeks. Bacterial DNA in blood was determined by real-time qPCR 16S rRNA gene quantification. Bacterial composition in feces was analyzed by 16S rRNA gene sequencing.
Circulating markers of inflammation, including tumor necrosis factor alpha, interleukins 6, 10, and 18, stromal cell-derived factor 1-α, transforming growth factor β-1, and high sensitivity C-reactive protein, were unaltered by rifaximin treatment. Rifaximin altered abundance of bacterial taxa in blood marginally, only a decrease in Pseudomonadales was observed. In feces, rifaximin decreased bacterial richness, but effect on particular species was not observed. Subgroup analyses on patients with severely disturbed hemodynamics (n = 34) or activated lipopolysaccharide binding protein (n = 37) revealed no effect of rifaximin.
Four weeks of treatment with rifaximin had no impact on the inflammatory state and only minor effects on BT and intestinal bacterial composition in stable, decompensated cirrhosis (NCT01769040).
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