scholarly journals High functional diversity stimulates diversification in experimental microbial communities

2016 ◽  
Vol 2 (6) ◽  
pp. e1600124 ◽  
Author(s):  
Alexandre Jousset ◽  
Nico Eisenhauer ◽  
Monika Merker ◽  
Nicolas Mouquet ◽  
Stefan Scheu
Keyword(s):  
Ecosystem Services ◽  
Functional Diversity ◽  
Bacterial Communities ◽  
Evolutionary Dynamics ◽  
Resource Competition ◽  
Bacterial Species ◽  
Focal Species ◽  
Evolutionary Diversification ◽  
The Impact ◽  
High Diversity

There is a growing awareness that biodiversity not only drives ecosystem services but also affects evolutionary dynamics. However, different theories predict contrasting outcomes on when do evolutionary processes occur within a context of competition. We tested whether functional diversity can explain diversification patterns. We tracked the survival and diversification of a focal bacterial species (Pseudomonas fluorescens) growing in bacterial communities of variable diversity and composition. We found that high functional diversity reduced the fitness of the focal species and, at the same time, fostered its diversification. This pattern was linked to resource competition: High diversity increased competition on a portion of the resources while leaving most underexploited. The evolved phenotypes of the focal species showed a better use of underexploited resources, albeit at a cost of lower overall growth rates. As a result, diversification alleviated the impact of competition on the fitness of the focal species. We conclude that biodiversity can stimulate evolutionary diversification, provided that sufficient alternative niches are available.

scholarly journals Mutation rate dynamics reflect ecological change in an emerging zoonotic pathogen

PLoS Genetics ◽  
2021 ◽  
Vol 17 (11) ◽  
pp. e1009864
Author(s):  
Gemma G. R. Murray ◽  
Andrew J. Balmer ◽  
Josephine Herbert ◽  
Nazreen F. Hadijirin ◽  
Caroline L. Kemp ◽  
...  
Keyword(s):  
Genome Size ◽  
Mutation Rate ◽  
Evolutionary Dynamics ◽  
Bacterial Species ◽  
Invasive Disease ◽  
Mutation Rates ◽  
Ecological Change ◽  
Zoonotic Pathogen ◽  
Wide Range ◽  
The Impact

Mutation rates vary both within and between bacterial species, and understanding what drives this variation is essential for understanding the evolutionary dynamics of bacterial populations. In this study, we investigate two factors that are predicted to influence the mutation rate: ecology and genome size. We conducted mutation accumulation experiments on eight strains of the emerging zoonotic pathogen Streptococcus suis. Natural variation within this species allows us to compare tonsil carriage and invasive disease isolates, from both more and less pathogenic populations, with a wide range of genome sizes. We find that invasive disease isolates have repeatedly evolved mutation rates that are higher than those of closely related carriage isolates, regardless of variation in genome size. Independent of this variation in overall rate, we also observe a stronger bias towards G/C to A/T mutations in isolates from more pathogenic populations, whose genomes tend to be smaller and more AT-rich. Our results suggest that ecology is a stronger correlate of mutation rate than genome size over these timescales, and that transitions to invasive disease are consistently accompanied by rapid increases in mutation rate. These results shed light on the impact that ecology can have on the adaptive potential of bacterial pathogens.

scholarly journals The Bacterial Microbiome of the Tomato Fruit Is Highly Dependent on the Cultivation Approach and Correlates With Flavor Chemistry

2021 ◽  
Vol 12 ◽  
Author(s):  
Carolina Escobar Rodríguez ◽  
Johannes Novak ◽  
Franziska Buchholz ◽  
Pia Uetz ◽  
Laura Bragagna ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Plant Pathogens ◽  
Tomato Fruit ◽  
Bacterial Species ◽  
Sugar Content ◽  
Aroma Compounds ◽  
Plant Metabolites ◽  
Secondary Plant Metabolites ◽  
Cultivation Method ◽  
The Impact

The modes of interactions between plants and plant-associated microbiota are manifold, and secondary metabolites often play a central role in plant-microbe interactions. Abiotic and biotic (including both plant pathogens and endophytes) stress can affect the composition and concentration of secondary plant metabolites, and thus have an influence on chemical compounds that make up for the taste and aroma of fruit. While the role of microbiota in growth and health of plants is widely acknowledged, relatively little is known about the possible effect of microorganisms on the quality of fruit of plants they are colonizing. In this work, tomato (Solanum lycopersicum L.) plants of five different cultivars were grown in soil and in hydroponics to investigate the impact of the cultivation method on the flavor of fruit, and to assess whether variations in their chemical composition are attributable to shifts in bacterial microbiota. Ripe fruit were harvested and used for bacterial community analysis and for the analysis of tomato volatiles, sugars and acids, all contributing to flavor. Fruit grown in soil showed significantly higher sugar content, whereas tomatoes from plants under hydroponic conditions had significantly higher levels of organic acids. In contrast, aroma profiles of fruit were shaped by the tomato cultivars, rather than the cultivation method. In terms of bacterial communities, the cultivation method significantly defined the community composition in all cultivars, with the bacterial communities in hydroponic tomatoes being more variable that those in tomatoes grown in soil. Bacterial indicator species in soil-grown tomatoes correlated with higher concentrations of volatiles described to be perceived as “green” or “pungent.” A soil-grown specific reproducibly occurring ASV (amplicon sequence variants) classified as Bacillus detected solely in “Solarino” tomatoes, which were the sweetest among all cultivars, correlated with the amount of aroma-relevant volatiles as well as of fructose and glucose in the fruit. In contrast, indicator bacterial species in hydroponic-derived tomatoes correlated with aroma compounds with “sweet” and “floral” notes and showed negative correlations with glucose concentrations in fruit. Overall, our results point toward a microbiota-related accumulation of flavor and aroma compounds in tomato fruit, which is strongly dependent on the cultivation substrate and approach.

scholarly journals Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations

2019 ◽  
Vol 85 (15) ◽  
Author(s):  
D. P. R. Herlemann ◽  
S. Markert ◽  
C. Meeske ◽  
A. F. Andersson ◽  
I. de Bruijn ◽  
...  
Keyword(s):  
Carbon Storage ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Microbial Community Composition ◽  
Environmental Research ◽  
Rrna Gene ◽  
Cell Counts ◽  
Enclosure Experiments ◽  
The Impact

ABSTRACTEnclosure experiments are frequently used to investigate the impact of changing environmental conditions on microbial assemblages. Yet, how the incubation itself challenges complex bacterial communities is thus far unknown. In this study, metaproteomic profiling, 16S rRNA gene analyses, and cell counts were combined to evaluate bacterial communities derived from marine, mesohaline, and oligohaline conditions after long-term batch incubations. Early in the experiment, the three bacterial communities were highly diverse and differed significantly in their compositions. Manipulation of the enclosures with terrigenous dissolved organic carbon resulted in notable differences compared to the control enclosures at this early phase of the experiment. However, after 55 days, bacterial communities in the manipulated and the control enclosures under marine and mesohaline conditions were all dominated by gammaproteobacteriumSpongiibacter. In the oligohaline enclosures, actinobacterial cluster I of the hgc group (hgc-I) remained abundant in the late phase of the incubation. Metaproteome analyses suggested that the ability to use outer membrane-based internal energy stores, in addition to the previously described grazing resistance, may enable the gammaproteobacteriumSpongiibacterto prevail in long-time incubations. Under oligohaline conditions, the utilization of external recalcitrant carbon appeared to be more important (hgc-I). Enclosure experiments with complex natural microbial communities are important tools to investigate the effects of manipulations. However, species-specific properties, such as individual carbon storage strategies, can cause manipulation-independent effects and need to be considered when interpreting results from enclosures.IMPORTANCEIn microbial ecology, enclosure studies are often used to investigate the effect of single environmental factors on complex bacterial communities. However, in addition to the manipulation, unintended effects (“bottle effect”) may occur due to the enclosure itself. In this study, we analyzed the bacterial communities that originated from three different salinities of the Baltic Sea, comparing their compositions and physiological activities both at the early stage and after 55 days of incubation. Our results suggested that internal carbon storage strategies impact the success of certain bacterial species, independent of the experimental manipulation. Thus, while enclosure experiments remain valid tools in environmental research, microbial community composition shifts must be critically followed. This investigation of the metaproteome during long-term batch enclosures expanded our current understanding of the so-called “bottle effect,” which is well known to occur during enclosure experiments.

scholarly journals Abundant and Diverse Clustered Regularly Interspaced Short Palindromic Repeat Spacers in Clostridium difficile Strains and Prophages Target Multiple Phage Types within This Pathogen

mBio ◽  
2014 ◽  
Vol 5 (5) ◽  
Author(s):  
Katherine R. Hargreaves ◽  
Cesar O. Flores ◽  
Trevor D. Lawley ◽  
Martha R. J. Clokie
Keyword(s):  
Clostridium Difficile ◽  
Genome Evolution ◽  
Evolutionary Dynamics ◽  
Bacterial Species ◽  
Phage Infection ◽  
Content Type ◽  
Phage Types ◽  
Human Pathogenic Bacterium ◽  
Protospacer Adjacent Motif ◽  
The Impact

ABSTRACT Clostridium difficile is an important human-pathogenic bacterium causing antibiotic-associated nosocomial infections worldwide. Mobile genetic elements and bacteriophages have helped shape C. difficile genome evolution. In many bacteria, phage infection may be controlled by a form of bacterial immunity called the clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas) system. This uses acquired short nucleotide sequences (spacers) to target homologous sequences (protospacers) in phage genomes. C. difficile carries multiple CRISPR arrays, and in this paper we examine the relationships between the host- and phage-carried elements of the system. We detected multiple matches between spacers and regions in 31 C. difficile phage and prophage genomes. A subset of the spacers was located in prophage-carried CRISPR arrays. The CRISPR spacer profiles generated suggest that related phages would have similar host ranges. Furthermore, we show that C. difficile strains of the same ribotype could either have similar or divergent CRISPR contents. Both synonymous and nonsynonymous mutations in the protospacer sequences were identified, as well as differences in the protospacer adjacent motif (PAM), which could explain how phages escape this system. This paper illustrates how the distribution and diversity of CRISPR spacers in C. difficile, and its prophages, could modulate phage predation for this pathogen and impact upon its evolution and pathogenicity. IMPORTANCE Clostridium difficile is a significant bacterial human pathogen which undergoes continual genome evolution, resulting in the emergence of new virulent strains. Phages are major facilitators of genome evolution in other bacterial species, and we use sequence analysis-based approaches in order to examine whether the CRISPR/Cas system could control these interactions across divergent C. difficile strains. The presence of spacer sequences in prophages that are homologous to phage genomes raises an extra level of complexity in this predator-prey microbial system. Our results demonstrate that the impact of phage infection in this system is widespread and that the CRISPR/Cas system is likely to be an important aspect of the evolutionary dynamics in C. difficile .

scholarly journals The Role of Selected Ecosystem Services in Different Farming Systems in Poland Regarding the Differentiation of Agricultural Land Structure

2021 ◽  
Vol 13 (12) ◽  
pp. 6673
Author(s):  
Lidia Luty ◽  
Kamila Musiał ◽  
Monika Zioło
Keyword(s):  
Ecosystem Services ◽  
Agricultural Land ◽  
Soil Formation ◽  
Farming Systems ◽  
Agricultural System ◽  
Organic System ◽  
Supporting Soil ◽  
Management Method ◽  
The Impact

The functioning of various agroecosystems is nowadays shaped by different farming systems, which may impair their functions, as well as being beneficial to them. The benefits include ecosystem services, defined as economic and noneconomic values gained by humans from ecosystems, through supporting soil formation and nutrient circulation, and the impact of agriculture on climate and biodiversity. Their mutual flow and various disturbances depend on the agroecosystem’s management method, which is associated with the type of management of agricultural land (AL) in individual farms. This paper raises a problem of transformation in the structure of three main farming systems in Poland, in 2004–2018, in relation to the implementation of 16 selected ecosystem services and their scale. Special attention was given to organic farming, as the most environmentally friendly and sustainable. The analysis demonstrates the increase in ALs in that type of production during the analyzed period of time. Disparities of transformation associated with the type of agricultural system were noticeable at the regional level, which were presented in 16 Polish voivodeships. The results of the analysis confirm that the organic system, which is an important carrier of various ecosystem services, gained a stable position. Moreover, areas with integrated farming still do not exceed 0.5% of total agricultural lands in such voivodeships. The analysis of factors influencing the deterioration or disappearance of selected environmental services characterizing agricultural systems indicates the need to depart from an intensive conventional management system.

scholarly journals The Value of Urban Nature in Terms of Providing Ecosystem Services Related to Health and Well-Being: An Empirical Comparative Pilot Study of Cities in Germany and the Czech Republic

Land ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 341
Author(s):  
Ralf-Uwe Syrbe ◽  
Ina Neumann ◽  
Karsten Grunewald ◽  
Patrycia Brzoska ◽  
Jiři Louda ◽  
...  
Keyword(s):  
Public Health ◽  
Ecosystem Services ◽  
Green Space ◽  
Well Being ◽  
Urban Green Space ◽  
Urban Nature ◽  
Urban Green ◽  
Green Areas ◽  
The Impact ◽  
Health And Well Being

The quality of life in our cities critically depends on the intelligent planning and shaping of urban living space, in particular urban nature. By providing a wide range of ecosystem services (ES), urban nature essentially contributes to the well-being of city dwellers and plays a major role in avoiding common diseases through its positive impact on physical and mental health. Health is one of the most important factors underlying human welfare and is, thus, vital to sustainable development. The ES of urban green space provide other social-cultural functions alongside public health, for example by fostering environmental justice and citizenship participation. Thus, they should always be considered when searching for solutions to urban problems. The aim of this research was to determine the impact of green areas in three selected cities on the health and well-being of people by self-reporting of green areas’ visitors. To this end, we posed the research question: which types and characteristics of urban green space are most appreciated by city dwellers? Based on our findings, we have drawn up recommendations for practices to promote better living conditions. We have also pinpointed obstacles to and opportunities for leisure time activities as well as ways of supporting the public health of citizens.

scholarly journals Identifying key processes and sectors in the interaction between climate and socio-economic systems: a review toward integrating Earth–human systems

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Kaoru Tachiiri ◽  
Xuanming Su ◽  
Ken’ichi Matsumoto
Keyword(s):  
Ecosystem Services ◽  
Gross Domestic Product ◽  
Significant Influence ◽  
Ghg Emissions ◽  
Climate Impacts ◽  
Ecological Impacts ◽  
The Other ◽  
Economic Damage ◽  
Economic Systems ◽  
The Impact

AbstractFor the purpose of identifying the key processes and sectors involved in the interaction between Earth and socio-economic systems, we review existing studies on those processes/sectors through which the climate impacts socio-economic systems, which then in turn affect the climate. For each process/sector, we review the direct physical and ecological impacts and, if available, the impact on the economy and greenhouse gas (GHG) emissions. Based on this review, land sector is identified as the process with the most significant impact on GHG emissions, while labor productivity has the largest impact on the gross domestic product (GDP). On the other hand, the energy sector, due to the increase in the demand for cooling, will have increased GHG emissions. Water resources, sea level rise, natural disasters, ecosystem services, and diseases also show the potential to have a significant influence on GHG emissions and GDP, although for most of these, a large effect was reported only by a limited number of studies. As a result, more studies are required to verify their influence in terms of feedbacks to the climate. In addition, although the economic damage arising from migration and conflict is uncertain, they should be treated as potentially damaging processes.

scholarly journals Analysing the Impact of Climate Change on Hydrological Ecosystem Services in Laguna del Sauce (Uruguay) Using the SWAT Model and Remote Sensing Data

2021 ◽  
Vol 13 (10) ◽  
pp. 2014
Author(s):  
Celina Aznarez ◽  
Patricia Jimeno-Sáez ◽  
Adrián López-Ballesteros ◽  
Juan Pablo Pacheco ◽  
Javier Senent-Aparicio
Keyword(s):  
Climate Change ◽  
Remote Sensing ◽  
Ecosystem Services ◽  
Water Resources ◽  
Swat Model ◽  
Remote Sensing Data ◽  
Erosion Control ◽  
Sensing Data ◽  
Extreme Precipitation Events ◽  
The Impact

Assessing how climate change will affect hydrological ecosystem services (HES) provision is necessary for long-term planning and requires local comprehensive climate information. In this study, we used SWAT to evaluate the impacts on four HES, natural hazard protection, erosion control regulation and water supply and flow regulation for the Laguna del Sauce catchment in Uruguay. We used downscaled CMIP-5 global climate models for Representative Concentration Pathways (RCP) 2.6, 4.5 and 8.5 projections. We calibrated and validated our SWAT model for the periods 2005–2009 and 2010–2013 based on remote sensed ET data. Monthly NSE and R2 values for calibration and validation were 0.74, 0.64 and 0.79, 0.84, respectively. Our results suggest that climate change will likely negatively affect the water resources of the Laguna del Sauce catchment, especially in the RCP 8.5 scenario. In all RCP scenarios, the catchment is likely to experience a wetting trend, higher temperatures, seasonality shifts and an increase in extreme precipitation events, particularly in frequency and magnitude. This will likely affect water quality provision through runoff and sediment yield inputs, reducing the erosion control HES and likely aggravating eutrophication. Although the amount of water will increase, changes to the hydrological cycle might jeopardize the stability of freshwater supplies and HES on which many people in the south-eastern region of Uruguay depend. Despite streamflow monitoring capacities need to be enhanced to reduce the uncertainty of model results, our findings provide valuable insights for water resources planning in the study area. Hence, water management and monitoring capacities need to be enhanced to reduce the potential negative climate change impacts on HES. The methodological approach presented here, based on satellite ET data can be replicated and adapted to any other place in the world since we employed open-access software and remote sensing data for all the phases of hydrological modelling and HES provision assessment.

scholarly journals The Influence of Diet and Sex on the Gut Microbiota of Lean and Obese JCR:LA-cp Rats

2021 ◽  
Vol 9 (5) ◽  
pp. 1037
Author(s):  
Craig Resch ◽  
Mihir Parikh ◽  
J. Alejandro Austria ◽  
Spencer D. Proctor ◽  
Thomas Netticadan ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Control Diet ◽  
Bacterial Species ◽  
Alpha Diversity ◽  
Short Chain Fatty Acids ◽  
Female Rats ◽  
Dependent Manner ◽  
Male And Female ◽  
Ground Flaxseed ◽  
The Impact

There is an increased interest in the gut microbiota as it relates to health and obesity. The impact of diet and sex on the gut microbiota in conjunction with obesity also demands extensive systemic investigation. Thus, the influence of sex, diet, and flaxseed supplementation on the gut microbiota was examined in the JCR:LA-cp rat model of genetic obesity. Male and female obese rats were randomized into four groups (n = 8) to receive, for 12 weeks, either (a) control diet (Con), (b) control diet supplemented with 10% ground flaxseed (CFlax), (c) a high-fat, high sucrose (HFHS) diet, or (d) HFHS supplemented with 10% ground flaxseed (HFlax). Male and female JCR:LA-cp lean rats served as genetic controls and received similar dietary interventions. Illumine MiSeq sequencing revealed a richer microbiota in rats fed control diets rather than HFHS diets. Obese female rats had lower alpha-diversity than lean female; however, both sexes of obese and lean JCR rats differed significantly in β-diversity, as their gut microbiota was composed of different abundances of bacterial types. The feeding of an HFHS diet affected the diversity by increasing the phylum Bacteroidetes and reducing bacterial species from phylum Firmicutes. Fecal short-chain fatty acids such as acetate, propionate, and butyrate-producing bacterial species were correspondingly impacted by the HFHS diet. Flax supplementation improved the gut microbiota by decreasing the abundance of Blautia and Eubacterium dolichum. Collectively, our data show that an HFHS diet results in gut microbiota dysbiosis in a sex-dependent manner. Flaxseed supplementation to the diet had a significant impact on gut microbiota diversity under both flax control and HFHS dietary conditions.

scholarly journals Does agricultural intensification cause tipping points in ecosystem services?

2021 ◽  
Author(s):  
Stephen C. L. Watson ◽  
Adrian C. Newton ◽  
Lucy E. Ridding ◽  
Paul M. Evans ◽  
Steven Brand ◽  
...  
Keyword(s):  
Ecosystem Services ◽  
Agricultural Intensification ◽  
Spatial Dynamics ◽  
Policy Option ◽  
List Type ◽  
Tipping Points ◽  
Software Models ◽  
Non Linear ◽  
Study Interval ◽  
The Impact

Abstract Context Agricultural intensification is being widely pursued as a policy option to improve food security and human development. Yet, there is a need to understand the impact of agricultural intensification on the provision of multiple ecosystem services, and to evaluate the possible occurrence of tipping points. Objectives To quantify and assess the long-term spatial dynamics of ecosystem service (ES) provision in a landscape undergoing agricultural intensification at four time points 1930, 1950, 1980 and 2015. Determine if thresholds or tipping points in ES provision may have occurred and if there are any detectable impacts on economic development and employment. Methods We used the InVEST suite of software models together with a time series of historical land cover maps and an Input–Output model to evaluate these dynamics over an 85-year period in the county of Dorset, southern England. Results Results indicated that trends in ES were often non-linear, highlighting the potential for abrupt changes in ES provision to occur in response to slight changes in underlying drivers. Despite the fluctuations in provision of different ES, overall economic activity increased almost linearly during the study interval, in line with the increase in agricultural productivity. Conclusions Such non-linear thresholds in ES will need to be avoided in the future by approaches aiming to deliver sustainable agricultural intensification. A number of positive feedback mechanisms are identified that suggest these thresholds could be considered as tipping points. However, further research into these feedbacks is required to fully determine the occurrence of tipping points in agricultural systems.

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