scholarly journals Integration of microbial communities into large-scale ecosystem models

2009 ◽  
Author(s):  
Steven Allison
Keyword(s):  
Microbial Communities ◽  
Large Scale ◽  
Ecosystem Models

scholarly journals Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Pengshuo Yang ◽  
Chongyang Tan ◽  
Maozhen Han ◽  
Lin Cheng ◽  
Xuefeng Cui ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Large Scale ◽  
Network Connectivity ◽  
Small Range ◽  
Environmental Disturbance ◽  
Target Species ◽  
Important Species ◽  
Metagenome Analysis ◽  
Occurrence Patterns ◽  
Edge Networks

Abstract Mainstream studies of microbial community focused on critical organisms and their physiology. Recent advances in large-scale metagenome analysis projects initiated new researches in the complex correlations between large microbial communities. Specifically, previous studies focused on the nodes (i.e. species) of the Species-Centric Networks (SCNs). However, little was understood about the change of correlation between network members (i.e. edges of the SCNs) when the network was disturbed. Here, we introduced a Correlation-Centric Network (CCN) to the microbial research based on the concept of edge networks. In CCN, each node represented a species–species correlation, and edge represented the species shared by two correlations. In this research, we investigated the CCNs and their corresponding SCNs on two large cohorts of microbiome. The results showed that CCNs not only retained the characteristics of SCNs, but also contained information that cannot be detected by SCNs. In addition, when the members of microbial communities were decreased (i.e. environmental disturbance), the CCNs fluctuated within a small range in terms of network connectivity. Therefore, by highlighting the important species correlations, CCNs could unveil new insights when studying not only the functions of target species, but also the stabilities of their residing microbial communities.

Characterization of microbial communities in exhaust air treatment systems of large-scale pig housing facilities

2010 ◽  
Vol 62 (7) ◽  
pp. 1551-1559 ◽  
Author(s):  
J. Haneke ◽  
N. M. Lee ◽  
T. W. Gaul ◽  
H. F. A. Van den Weghe
Keyword(s):  
Microbial Communities ◽  
Large Scale ◽  
Dust Particles ◽  
Nitrifying Bacteria ◽  
Ammonium Concentration ◽  
Nitrogen Compounds ◽  
Air Treatment ◽  
Fattening Period ◽  
Washing Water ◽  
Housing Facilities

Exhaust air treatment has gained importance as an essential factor in intensive livestock areas due to the rising emissions in the environment. Wet filter walls of multi-stage exhaust air treatment systems precipitate gaseous ammonia and dust particles from exhaust air in washing water. Microbial communities in the biomass developed in the washing water of five large-scale exhaust air treatment units of pig housing facilities, were investigated by fluorescence in situ hybridization (FISH) and 16S rDNA sequence analyses. No “standard” nitrifying bacteria were found in the washing water. Instead mainly α-Proteobacteria, aggregating β- and χ-Proteobacteria, a large number of Actinobacteria, as well as individual Planctomycetales and Crenarchaeota were detected after more than twelve months' operation. The main Proteobacteria species present were affiliated to the families Alcaligenaceae, Comamonadaceae and Xanthomonadaceae. Furthermore, we investigated the consumption of inorganic nitrogen compounds in the washing water of one exhaust air treatment unit during a fattening period with and without pH control. Maintaining the pH at 6.0 resulted in a ca. fivefold higher ammonium concentration and a ca. fourfold lower concentration of oxidized nitrogen compounds after the fattening period was finished.

scholarly journals Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

2020 ◽  
Author(s):  
Youwen Qin ◽  
Aki S Havulinna ◽  
Yang Liu ◽  
Pekka Jousilahti ◽  
Scott C Ritchie ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Dietary Habits ◽  
Population Based ◽  
Genome Wide ◽  
Scale Population ◽  
Important Health ◽  
Disease Analysis

Co-evolution between humans and the microbial communities colonizing them has resulted in an intimate assembly of thousands of microbial species mutualistically living on and in their body and impacting multiple aspects of host physiology and health. Several studies examining whether human genetic variation can affect gut microbiota suggest a complex combination of environmental and host factors. Here, we leverage a single large-scale population-based cohort of 5,959 genotyped individuals with matched gut microbial shotgun metagenomes, dietary information and health records up to 16 years post-sampling, to characterize human genetic variations associated with microbial abundances, and predict possible causal links with various diseases using Mendelian randomization (MR). Genome-wide association study (GWAS) identified 583 independent SNP-taxon associations at genome-wide significance (p<5.0×10-8), which included notable strong associations with LCT (p=5.02×10-35), ABO (p=1.1×10-12), and MED13L (p=1.84×10-12). A combination of genetics and dietary habits was shown to strongly shape the abundances of certain key bacterial members of the gut microbiota, and explain their genetic association. Genetic effects from the LCT locus on Bifidobacterium and three other associated taxa significantly differed according to dairy intake. Variation in mucin-degrading Faecalicatena lactaris abundances were associated with ABO, highlighting a preferential utilization of secreted A/B/AB-antigens as energy source in the gut, irrespectively of fibre intake. Enterococcus faecalis levels showed a robust association with a variant in MED13L, with putative links to colorectal cancer. Finally, we identified putative causal relationships between gut microbes and complex diseases using MR, with a predicted effect of Morganella on major depressive disorder that was consistent with observational incident disease analysis. Overall, we present striking examples of the intricate relationship between humans and their gut microbial communities, and highlight important health implications.

scholarly journals Deterioration-Associated Microbiome of Stone Monuments: Structure, Variation, and Assembly

2018 ◽  
Vol 84 (7) ◽  
Author(s):  
Qiang Li ◽  
Bingjian Zhang ◽  
Xiaoru Yang ◽  
Qinya Ge
Keyword(s):  
Microbial Communities ◽  
Large Scale ◽  
Imaging Techniques ◽  
Bacterial Species ◽  
Species Abundance ◽  
Population Variation ◽  
Structure Variation ◽  
Content Type ◽  
Stone Monuments ◽  
Stone Deterioration

ABSTRACTResearch on the microbial communities that colonize stone monuments may provide a new understanding of stone biodeterioration and microbe-induced carbonate precipitation. This work investigated the seasonal variation of microbial communities in 2016 and 2017, as well as its effects on stone monuments. We determined the bacterial and fungal compositions of 12 samples from four well-separated geographic locations by using 16S rRNA and internal transcribed spacer gene amplicon sequencing.Cyanobacteriaand Ascomycota were the predominant bacterial and fungal phyla, respectively, and differences in species abundance among our 12 samples and 2 years showed no consistent temporal or spatial trends. Alpha diversity, estimated by Shannon and Simpson indices, revealed that an increase or decrease in bacterial diversity corresponded to a decrease or increase in the fungal community from 2016 to 2017. Large-scale association analysis identified potential bacteria and fungi correlated with stone deterioration. Functional prediction revealed specific pathways and microbiota associated with stone deterioration. Moreover, a culture-dependent technique was used to identify microbial isolates involved in biodeterioration and carbonatogenesis; 64% of 85 bacterial isolates caused precipitation of carbonates in biomineralization assays. Imaging techniques including scanning electron microscopy with energy-dispersive spectroscopy, X-ray diffraction, and fluorescence imaging identified CaCO3crystals as calcite and vaterite. Although CaCO3precipitation induced by bacteria often has esthetically deleterious impacts on stone monuments, this process may potentially serve as a novel, environmentally friendly bacterial self-inoculation approach to the conservation of stone.IMPORTANCEComprehensive analyses of the microbiomes associated with the deterioration of stone monuments may contribute to the understanding of mechanisms of deterioration, as well as to the identification of potentially beneficial or undesirable microbial communities and their genomic pathways. In our study, we demonstrated thatCyanobacteriawas the predominant bacterial phylum and exhibited an increase from 2016 to 2017, whileProteobacteriashowed a decreasing trend. Apart from esthetic deterioration caused by cyanobacteria and fungi, white plaque, which is composed mainly of CaCO3and is probably induced byCrossiellaandCyanobacteria, was also considered to be another threat to stone monuments. We showed that there was no significant correlation between microbial population variation and geographic location. Specific functional genes and pathways were also enriched in particular bacterial species. The CaCO3precipitation induced by an indigenous community of carbonatogenic bacteria also provides a self-inoculation approach for the conservation of stone.

Do microbial communities adapt to the temperature of their climate?

2020 ◽  
Author(s):  
Daniel Tajmel ◽  
Carla Cruz Paredes ◽  
Johannes Rousk
Keyword(s):  
Environmental Factors ◽  
Microbial Communities ◽  
Large Scale ◽  
Microbial Growth ◽  
Environmental Temperature ◽  
Microbial Processes ◽  
Temperature Relationship ◽  
Maximum Temperature ◽  
Mean Annual Temperature ◽  
The Impact

&lt;p&gt;Terrestrial biogeochemical cycles are regulated by soil microorganisms. The microbial carbon release due to respiration and carbon sequestration through microbial growth determine whether soils become sources or sinks for carbon. Temperature i&amp;#8203;s one of the most important environmental factors controlling both microbial growth and respiration. Therefore, to understand the influence of temperature on microbial processes is crucial. One strategy to predict how ecosystems will respond to warming is to use geographical ecosystem differences, in space-for-time (SFT) substitution approaches. We hypothesized (1) that microbes should be adapted to their environmental temperature leading to microbial communities with warm-shifted temperature relationships in warmer environments, and vice versa. Furthermore, we hypothesized&amp;#160; (2) that other factors should not influence microbial temperature relationships, and (3) that the temperature sensitivity of microbial processes (Q10) should be linked to the microbial temperature relationships.&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;&lt;p&gt;In this project, we investigated the effects of environmental temperature on microbial temperature relationships for microbial growth and respiration along a natural climate gradient along a transect across Europe to predict the impact of a warming climate. The transect was characterized by mean annual temperature (MAT) ranging from - 4 degrees Celsius (Greenland) to 18 degrees Celsius (Southern Spain), while other environmental factor ranges were broad and unrelated to climate, including pH from 4.0 to 8.8, C/N ratio from 7 to 50, SOM from 4% to 94% and plant communities ranging from arctic tundra to Mediterranean grasslands. More than 56 soil samples were analyzed and microbial temperature relationships were determined using controlled short-term laboratory incubations from 0 degrees Celsius to 45 degrees Celsius. The link between microbial temperature relationship and the climate was assessed by using the relationship between the environmental temperature and indices for microbial temperature relationships including the minimum (T&lt;sub&gt;min&lt;/sub&gt;), optimum (T&lt;sub&gt;opt&lt;/sub&gt;) and maximum temperature (T&lt;sub&gt;max&lt;/sub&gt;) for microbial growth as well as for respiration. To estimate the T&lt;sub&gt;min&lt;/sub&gt;, T&lt;sub&gt;opt&amp;#160;&lt;/sub&gt;and T&lt;sub&gt;max&amp;#160;&lt;/sub&gt;the square root equation, the Ratkowsky model was used.&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;&lt;p&gt;We found that microbial communities were adapted to their environmental temperature. The microbial temperature relationship was stronger for microbial growth than for respiration. For 1 degrees Celsius rise in MAT, T&lt;sub&gt;min &lt;/sub&gt;increased 0.22 degrees Celsius for bacterial and 0.28 degrees Celsius for fungal growth, while T&lt;sub&gt;min &lt;/sub&gt;for respiration increased by 0.16 per 1 degrees Celsius rise. T&lt;sub&gt;min&amp;#160;&lt;/sub&gt;was also found to be universally linked to Q10, such that higher T&lt;sub&gt;min &lt;/sub&gt;resulted in higher Q10. Other environmental factors (pH, C/N ratio, SOM, vegetation cover) did not influence the temperature relationships. By incorporating the determined relationships between environmental temperature and microbial growth and respiration into large scale ecosystem models, we can get a better understanding of the influence of microbial adaptation to warmer climate on the C-exchange between soils and atmosphere.&lt;/p&gt;

A statistical thinning model for initialising large-scale ecosystem models

2012 ◽  
Vol 27 (6) ◽  
pp. 567-577 ◽  
Author(s):  
Chris S. Eastaugh ◽  
Hubert Hasenauer
Keyword(s):  
Large Scale ◽  
Ecosystem Models

scholarly journals Resolving the structure of phage-bacteria interactions in the context of natural diversity

2021 ◽  
Author(s):  
Kathryn M Kauffman ◽  
William K Chang ◽  
Julia M Brown ◽  
Fatima Aysha Hussain ◽  
Joy Y Yang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Host Range ◽  
Large Scale ◽  
Genomic Diversity ◽  
Interaction Networks ◽  
Bacterial Strains ◽  
Quantitative Estimates ◽  
Phage Evolution ◽  
Marine Vibrio ◽  
In The Wild

Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in "the wild" remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain quantitative estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that killing in environmental interaction networks is sparse - with phage predator loads low for most bacterial strains and phages host-strain-specific in their killing. Paradoxically, we also find that although overlap in killing is generally rare between phages, recombination is common. Together, these results indicate that the number of hosts that phages infect is often larger than the number that they kill and suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it will be important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on killing host range.

scholarly journals Genomics Tools and Microbiota: Applications to Response in Coastal Ecosystems

2021 ◽  
Vol 2021 (1) ◽  
Author(s):  
Joel E. Kostka ◽  
Konstantinos T. Konstantinidis ◽  
Markus Huettel
Keyword(s):  
Microbial Communities ◽  
Oil Spill ◽  
Large Scale ◽  
Oil And Gas ◽  
Volume Ratio ◽  
Coastal Ecosystems ◽  
Hydrocarbon Degradation ◽  
Oil Contamination ◽  
Genomics Tools ◽  
Microbial Groups

Abstract Microorganisms are central and cross-cutting to oil spill response strategies. Biodegradation mediated by indigenous microbial communities is the ultimate fate of the majority of petroleum (oil and gas) that enters the marine environment. Key ecosystem services provided by microbes, such as organic matter and nutrient cycling, may be adversely affected by oil contamination. The Deepwater Horizon (DWH) oil spill was the first large scale environmental disaster to which the methods of genomics were applied to determine microbial response to a major perturbation. Here we present a case study on coastal ecosystems to highlight the knowledge gained by application of genomics tools to interrogate mechanisms of petroleum hydrocarbon degradation and to elucidate impacts of oil exposure on ecosystem health and functioning. At Pensacola Beach, results showed that oiling led to a large increase in the growth of indigenous microbes in the form of a series of bacterial blooms. Oil contamination strongly selected for microbial groups capable of hydrocarbon degradation. Oil was degraded and benthic microbial communities returned to near baseline levels approximately one year after oil came ashore. These results indicate that when small particles (&lt; 1 cm) of weathered light oil are buried in the coastal zone, biodegradation by indigenous microbial communities is sufficient for the rapid mitigation of oil contamination after a major spill, whereas larger sand-oil-aggregates take longer to completely degrade because of their unfavorable surface to volume ratio. “Operation Deep Clean” removed these aggregates and enhanced biodegradation insofar as many larger oil aggregates were broken down into smaller ones thereby increasing the surface area available for microbial attack. For environmental managers, these results suggest that biodegradation in beach sands is relatively rapid because oxygen can easily penetrate to the buried oil, and resources may be better placed elsewhere in environments where degradation is limited by oxygen availability or microbial access to hydrocarbons. While specialist microbial groups such as nitrifiers show promise as bioindicators of oil contamination in coastal ecosystems, more work is needed to further validate these biomarkers. Despite substantial progress, a predictive understanding of the fate and impacts of oil spills remains hampered by challenges in interpreting the in situ activity and ecosystem response of benthic microbial populations. To advance this understanding, a dedicated funding mechanism is needed to support fundamental research. A polyphasic approach is encouraged that employs metagenomics in the field along with cultivation and microcosm or mesocosm experiments in the laboratory. Further, research during future disasters would be greatly facilitated by improved coordination between the emergency responders directing mitigation efforts and scientists investigating the success of those efforts.

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