scholarly journals Variation in genomic traits of microbial communities among ecosystems

FEMS Microbes ◽  
2021 ◽  
Author(s):  
Peter F Chuckran ◽  
Bruce A Hungate ◽  
Egbert Schwartz ◽  
Paul Dijkstra
Keyword(s):  
Stress Response ◽  
Microbial Communities ◽  
Genome Size ◽  
Gc Content ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Low Carbon ◽  
Genomic Features ◽  
Trade Offs ◽  
Σ Factor

Abstract Free-living bacteria in nutrient limited environments often exhibit traits which may reduce the cost of reproduction, such as smaller genome size, low GC content, and fewer sigma (σ) factor and 16S rRNA gene copies. Despite the potential utility of these traits to detect relationships between microbial communities and ecosystem-scale properties, few studies have assessed these traits on a community-scale. Here, we analyzed these traits from publicly available metagenomes derived from marine, soil, host-associated, and thermophilic communities. In marine and thermophilic communities, genome size and GC content declined in parallel, consistent with genomic streamlining, with GC content in thermophilic communities generally higher than in marine systems. In contrast, soil communities averaging smaller genomes featured higher GC content and were often from low-carbon environments, suggesting unique selection pressures in soil bacteria. The abundance of specific σ-factors varied with average genome size and ecosystem type. In oceans, abundance of fliA, a σ-factor controlling flagella biosynthesis, was positively correlated with community average genome size – reflecting known trade-offs between nutrient conservation and chemotaxis. In soils, a high abundance of the stress response σ-factor gene rpoS was associated with smaller average genome size and often located in harsh and/or carbon-limited environments – a result which tracks features observed in culture and indicates an increased capacity for stress response in nutrient-poor soils. This work shows how ecosystem-specific constraints are associated with trade-offs which are embedded in the genomic features of bacteria in microbial communities, and which can be detected at the community level, highlighting the importance of genomic features in microbial community analysis.

scholarly journals Soil, ocean, hot spring, and host-associated environments reveal unique selection pressures on genomic features of bacteria in microbial communities

2021 ◽  
Author(s):  
Peter Francis Chuckran ◽  
Bruce A Hungate ◽  
Egbert Schwartz ◽  
Paul Dijkstra
Keyword(s):  
Stress Response ◽  
Microbial Communities ◽  
Genome Size ◽  
Hot Spring ◽  
Gc Content ◽  
Regulatory Genes ◽  
Microbial Community Analysis ◽  
Genomic Features ◽  
Trade Offs ◽  
Σ Factor

Free-living bacteria in nutrient limited environments often exhibit small genomes which curb the cost of reproduction - a phenomenon known as genomic streamlining. Streamlining has been associated with a suite of traits such as reduced GC content, fewer 16S rRNA copies, and a lower abundance of regulatory genes, such as sigma (σ)-factors. Here, we analyzed these traits from 116 publicly available metagenomes derived from marine, soil, host associated, and thermophilic communities. In marine and thermophilic communities, genome size and GC content declined in parallel, but GC content was higher in thermophilic communities. In soils, the relationship between genome size and GC content was negative, suggesting a different selection pressure on genome size and GC content in soil bacteria. The abundance of σ-factors varied with average genome size, ecosystem type, and the specific functions regulated by the sigma factor. In marine environments, housekeeping and heat-shock σ-factor genes (rpoD and rpoH respectively) increased as genome size declined, and σ-factor responsible for flagella biosynthesis (fliA) decreased, suggesting a trade-off between nutrient conservation and chemotaxis. In soils, a high abundance of fliA and the stress response σ-factor gene (rpoS) was associated with smaller average genome size and often located in harsh and/or carbon-limited environments such as deserts or agricultural fields - suggesting an increased capacity for stress response and mobility in nutrient-poor soils. This work showcases how ecosystem-specific environmental constraints force trade-offs which are then embedded in the genomic features of bacteria in microbial communities, specifically genome size, GC content, and regulatory genes, and further highlights the importance of considering these features in microbial community analysis.

scholarly journals Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Property Change ◽  
And Control ◽  
Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

scholarly journals Characterization of Airborne Microbial Communities at a High-Elevation Site and Their Potential To Act as Atmospheric Ice Nuclei

2009 ◽  
Vol 75 (15) ◽  
pp. 5121-5130 ◽  
Author(s):  
Robert M. Bowers ◽  
Christian L. Lauber ◽  
Christine Wiedinmyer ◽  
Micah Hamady ◽  
Anna G. Hallar ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Elevation ◽  
Small Subunit ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Atmospheric Conditions ◽  
Small Subunit Rrna ◽  
Ice Nuclei ◽  
High Elevation Site ◽  
Bacteria And Fungi

ABSTRACT Bacteria and fungi are ubiquitous in the atmosphere. The diversity and abundance of airborne microbes may be strongly influenced by atmospheric conditions or even influence atmospheric conditions themselves by acting as ice nucleators. However, few comprehensive studies have described the diversity and dynamics of airborne bacteria and fungi based on culture-independent techniques. We document atmospheric microbial abundance, community composition, and ice nucleation at a high-elevation site in northwestern Colorado. We used a standard small-subunit rRNA gene Sanger sequencing approach for total microbial community analysis and a bacteria-specific 16S rRNA bar-coded pyrosequencing approach (4,864 sequences total). During the 2-week collection period, total microbial abundances were relatively constant, ranging from 9.6 × 105 to 6.6 × 106 cells m−3 of air, and the diversity and composition of the airborne microbial communities were also relatively static. Bacteria and fungi were nearly equivalent, and members of the proteobacterial groups Burkholderiales and Moraxellaceae (particularly the genus Psychrobacter) were dominant. These taxa were not always the most abundant in freshly fallen snow samples collected at this site. Although there was minimal variability in microbial abundances and composition within the atmosphere, the number of biological ice nuclei increased significantly during periods of high relative humidity. However, these changes in ice nuclei numbers were not associated with changes in the relative abundances of the most commonly studied ice-nucleating bacteria.

scholarly journals Quantitative Metagenomic Analyses Based on Average Genome Size Normalization

2011 ◽  
Vol 77 (7) ◽  
pp. 2513-2521 ◽  
Author(s):  
Jeremy A. Frank ◽  
Søren J. Sørensen
Keyword(s):  
Microbial Communities ◽  
Genome Size ◽  
Metagenomic Data ◽  
Gene Copy ◽  
Rrna Gene ◽  
Sequence Information ◽  
Ssu Rrna ◽  
Community Members ◽  
Ssu Rrna Gene ◽  
Photosynthetic Carbon

ABSTRACTOver the past quarter-century, microbiologists have used DNA sequence information to aid in the characterization of microbial communities. During the last decade, this has expanded from single genes to microbial community genomics, or metagenomics, in which the gene content of an environment can provide not just a census of the community members but direct information on metabolic capabilities and potential interactions among community members. Here we introduce a method for the quantitative characterization and comparison of microbial communities based on the normalization of metagenomic data by estimating average genome sizes. This normalization can relieve comparative biases introduced by differences in community structure, number of sequencing reads, and sequencing read lengths between different metagenomes. We demonstrate the utility of this approach by comparing metagenomes from two different marine sources using both conventional small-subunit (SSU) rRNA gene analyses and our quantitative method to calculate the proportion of genomes in each sample that are capable of a particular metabolic trait. With both environments, to determine what proportion of each community they make up and how differences in environment affect their abundances, we characterize three different types of autotrophic organisms: aerobic, photosynthetic carbon fixers (theCyanobacteria); anaerobic, photosynthetic carbon fixers (theChlorobi); and anaerobic, nonphotosynthetic carbon fixers (theDesulfobacteraceae). These analyses demonstrate how genome proportionality compares to SSU rRNA gene relative abundance and how factors such as average genome size and SSU rRNA gene copy number affect sampling probability and therefore both types of community analysis.

scholarly journals Microbial community analysis of biofilters reveals a dominance of either comammox Nitrospira or archaea as ammonia oxidizers in freshwater aquaria

2021 ◽  
Author(s):  
Michelle M McKnight ◽  
Josh D Neufeld
Keyword(s):  
Microbial Communities ◽  
Ammonia Oxidation ◽  
16S Rrna Gene Sequencing ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Ammonia Oxidizer ◽  
Future Research ◽  
Rrna Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers

Nitrification by aquarium biofilters transforms toxic ammonia waste (NH3/NH4+) to less toxic nitrate (NO3-) via nitrite (NO2-). Ammonia oxidation is mediated by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the recently discovered complete ammonia oxidizing (comammox) Nitrospira. Prior to the discovery of comammox Nitrospira, previous research revealed that AOA dominate among ammonia oxidizers in freshwater biofilters. Here, we characterized the composition of aquarium filter microbial communities and quantified the abundance of all three known groups of ammonia oxidizers. Aquarium biofilter and water samples were collected from representative freshwater and saltwater systems in Southwestern Ontario, Canada. Using extracted DNA, we performed 16S rRNA gene sequencing and quantitative PCR (qPCR) to assess community composition and quantify the abundance of amoA genes, respectively. Our results show that aquarium biofilter microbial communities were consistently represented by putative heterotrophs of the Proteobacteria and Bacteroides phyla, with distinct profiles associated with fresh versus saltwater biofilters. Among nitrifiers, comammox Nitrospira amoA genes were detected in all 38 freshwater aquarium biofilter samples and were the most abundant ammonia oxidizer in 30 of these samples, with the remaining biofilters dominated by AOA, based on amoA gene abundances. In saltwater biofilters, AOA or AOB were differentially abundant, with no comammox Nitrospira detected. These results demonstrate that comammox Nitrospira play an important role in biofilter nitrification that has been previously overlooked and such microcosms are useful for exploring the ecology of nitrification for future research.

scholarly journals Microbial community analysis with a specific statistical approach after a record breaking snowfall in Southern Italy

2020 ◽  
Vol 70 (1) ◽  
Author(s):  
Pamela Monaco ◽  
Fabio Divino ◽  
Gino Naclerio ◽  
Antonio Bucci
Keyword(s):  
Microbial Communities ◽  
Statistical Approach ◽  
Biological Diversity ◽  
Southern Italy ◽  
Bacterial Species ◽  
Species Level ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Additional Tool ◽  
Snow Samples

Abstract Purpose Snow and ice ecosystems present unexpectedly high microbial abundance and diversity. Although arctic and alpine snow environments have been intensively investigated from a microbiological point of view, few studies have been conducted in the Apennines. Accordingly, the main purpose of this research was to analyze the microbial communities of the snow collected in two different locations of Capracotta municipality (Southern Italy) after a snowfall record occurred on March 2015 (256 cm of snow in less than 24 h). Methods Bacterial communities were analyzed by the Next-Generation Sequencing techniques. Furthermore, a specific statistical approach for taxonomic hierarchy data was introduced, both for the assessment of diversity within microbial communities and the comparison between different microbiotas. In general, diversity and similarity indices are more informative when computed at the lowest level of the taxonomic hierarchy, the species level. This is not the case with microbial data, for which the species level is not necessarily the most informative. Indeed, the possibility to detect a large number of unclassified records at every level of the hierarchy (even at the top) is very realistic due to both the partial knowledge about the cultivable fraction of microbial communities and limitations to taxonomic assignment connected to the quality and completeness of the 16S rRNA gene reference databases. Thus, a global approach considering information from the whole taxonomic hierarchy was adopted in order to obtain a more consistent assessment of the biodiversity. Result The main phyla retrieved in the investigated snow samples were Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Interestingly, DNA from bacteria adapted to thrive at low temperatures, but also from microorganisms normally associated with other habitats, whose presence in the snow could be justified by wind-transport, was found. Biomolecular investigations and statistical data analysis showed relevant differences in terms of biodiversity, composition, and distribution of bacterial species between the studied snow samples. Conclusion The relevance of this research lies in the expansion of knowledge about microorganisms associated with cold environments in contexts poorly investigated such as the Italian Apennines, and in the development of a global statistical approach for the assessment of biological diversity and similarity of microbial communities as an additional tool to be usefully combined with the barcoding methods.

scholarly journals Spatial Distribution of Toxic Metal(loid)s and Microbial Community Analysis in Soil Vertical Profile at an Abandoned Nonferrous Metal Smelting Site

2020 ◽  
Vol 17 (19) ◽  
pp. 7101
Author(s):  
Jiejie Yang ◽  
Siqi Wang ◽  
Ziwen Guo ◽  
Yan Deng ◽  
Menglong Xu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Soil Layer ◽  
Soil Microbial Communities ◽  
Toxic Metal ◽  
Soil Samples ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
High Background ◽  
Top Soil

In this study soils at different depths were collected in a Zn smelting site located in Zhuzhou City, China, in order to understand toxic metal(loid)s distribution and microbial community in vertical soil profile at a smelting site. Except Soil properties and metal(loid)s content, the richness and diversity of microbial communities in soil samples were analyzed via high-throughput Illumina sequencing of 16s rRNA gene amplicons. The results showed that the content of As, Pb, Cu, Cd, Zn, and Mn was relatively high in top soil in comparison to subsoil, while the concentration of Cr in subsoil was comparable with that in top soil due to its relative high background value in this soil layer. The bioavailability of Cd, Mn, Zn, and Pb was relative higher than that of As, Cr, and Cu. The diversity of soil microbial communities decreased with increasing depth, which might be ascribed to the decrease in evenness with increase in depth duo to the influence by environmental conditions, such as pH, TK (total potassium), CEC (cation exchange capacity), ORP (oxidation reduction potential), and Bio-Cu (bioavailable copper). The results also found Acidobacteria, Proteobacteria, Firmicutes, and Chloroflexi were dominant phyla in soil samples. At the genus level, Acinetobacter, Pseudomonas, and Gp7 were dominant soil microorganism. Besides, Environmental factors, such as SOM (soil organic matter), pH, Bio-Cu, Bio-Cd (bioavailable cadmium), and Bio-Pb (bioavailable lead), greatly impacted microbial community in surface soil (1–3 m), while ORP, TK, and AN concentration influenced microbial community in the subsoil (4–10 m).

scholarly journals Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms

Microbiome ◽  
2019 ◽  
Vol 7 (1) ◽  
Author(s):  
Philipp Rausch ◽  
Malte Rühlemann ◽  
Britt M. Hermes ◽  
Shauni Doms ◽  
Tal Dagan ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Microbial Composition ◽  
Evolutionary Patterns ◽  
Trade Offs ◽  
Wide Range ◽  
Taxonomic Groups

Abstract Background The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, and development of both players. These interdependencies inspired a new view of multicellular organisms as “metaorganisms.” The goal of the Collaborative Research Center “Origin and Function of Metaorganisms” is to understand why and how microbial communities form long-term associations with hosts from diverse taxonomic groups, ranging from sponges to humans in addition to plants. Methods In order to optimize the choice of analysis procedures, which may differ according to the host organism and question at hand, we systematically compared the two main technical approaches for profiling microbial communities, 16S rRNA gene amplicon and metagenomic shotgun sequencing across our panel of ten host taxa. This includes two commonly used 16S rRNA gene regions and two amplification procedures, thus totaling five different microbial profiles per host sample. Conclusion While 16S rRNA gene-based analyses are subject to much skepticism, we demonstrate that many aspects of bacterial community characterization are consistent across methods. The resulting insight facilitates the selection of appropriate methods across a wide range of host taxa. Overall, we recommend single- over multi-step amplification procedures, and although exceptions and trade-offs exist, the V3 V4 over the V1 V2 region of the 16S rRNA gene. Finally, by contrasting taxonomic and functional profiles and performing phylogenetic analysis, we provide important and novel insight into broad evolutionary patterns among metaorganisms, whereby the transition of animals from an aquatic to a terrestrial habitat marks a major event in the evolution of host-associated microbial composition.

scholarly journals High peatland methane emissions following permafrost thaw: enhanced acetoclastic methanogenesis during early successional stages

2022 ◽  
Author(s):  
Liam Heffernan ◽  
Maria A. Cavaco ◽  
Maya P. Bhatia ◽  
Cristian Estop-Aragonés ◽  
Klaus-Holger Knorr ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Community Analysis ◽  
Isotopic Signature ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Ecological Conditions ◽  
Ch4 Emissions ◽  
Permafrost Thaw ◽  
Acetoclastic Methanogenesis

Abstract. Permafrost thaw in northern peatlands often leads to increased methane (CH4) emissions, but gaps remain in our understanding of the underlying controls responsible for increased emissions and the duration for which they persist. We assessed how shifting ecological conditions affect microbial communities, and the magnitude and stable isotopic signature (δ13C) of CH4 emissions along a thermokarst bog transect in boreal western Canada. Thermokarst bogs develop following permafrost thaw when dry, elevated peat plateaus collapse and become saturated and dominated by Sphagnum mosses. We differentiated between a young and a mature thermokarst bog stage (~30 and years ~200 since thaw, respectively). The young bog located along the thermokarst edge, was wetter, warmer and dominated by hydrophilic vegetation compared to the mature bog. Using 16S rRNA gene high throughput sequencing, we show that microbial communities were distinct near the surface and converged with depth, but lesser differences remained down to the lowest depth (160 cm). Microbial community analysis and δ13C data from CH4 surface emissions and dissolved gas depth profiles show that hydrogenotrophic methanogenesis was the dominant pathway at both sites. However, the young bog was found to have isotopically heavier δ13C-CH4 in both dissolved gases profiles and surface CH4 emissions, suggesting that acetoclastic methanogenesis was relatively more enhanced throughout the young bog peat profile. Furthermore, young bog CH4 emissions were three times greater than the mature bog. Our study suggests that interactions between ecological conditions and methanogenic communities enhance CH4 emissions in young thermokarst bogs, but these favorable conditions only persist for the initial decades after permafrost thaw.

Understanding Indicator Choice for the Assessment of RD&D Financing of Low-Carbon Energy Technologies

2017 ◽  
Author(s):  
Jonas Sonnenschein
Keyword(s):  
Nordic Countries ◽  
Additional Research ◽  
Policy Implications ◽  
Research Development ◽  
Low Carbon ◽  
Energy Technologies ◽  
Trade Offs ◽  
Standard Set ◽  
Low Carbon Energy

Rapid decarbonization requires additional research, development, and demonstration of low-carbon energy technologies. Various financing instruments are in place to support this development. They are frequently assessed through indicator-based evaluations. There is no standard set of indicators for this purpose. This study looks at the Nordic countries, which are leading countries with respect to eco-innovation. Different indicators to assess financing instruments are analysed with respect to their acceptance, the ease of monitoring, and their robustness. None of the indicators emerges as clearly superior from the analysis. Indicator choice is subject to trade-offs and leaves room for steering evaluation results in a desired direction. The study concludes by discussing potential policy implications of biases in indicator-based evaluation.

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