scholarly journals Microbial Communities in Methane Cycle: Modern Molecular Methods Gain Insights into Their Global Ecology

Environments ◽  
2021 ◽  
Vol 8 (2) ◽  
pp. 16
Author(s):  
Sergey Kharitonov ◽  
Mikhail Semenov ◽  
Alexander Sabrekov ◽  
Oleg Kotsyurbenko ◽  
Alena Zhelezova ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Global Climate ◽  
Methane Flux ◽  
Molecular Methods ◽  
Methane Cycle ◽  
Selective Enrichment ◽  
Global Climate Changes ◽  
Wide Range

The role of methane as a greenhouse gas in the concept of global climate changes is well known. Methanogens and methanotrophs are two microbial groups which contribute to the biogeochemical methane cycle in soil, so that the total emission of CH4 is the balance between its production and oxidation by microbial communities. Traditional identification techniques, such as selective enrichment and pure-culture isolation, have been used for a long time to study diversity of methanogens and methanotrophs. However, these techniques are characterized by significant limitations, since only a relatively small fraction of the microbial community could be cultured. Modern molecular methods for quantitative analysis of the microbial community such as real-time PCR (Polymerase chain reaction), DNA fingerprints and methods based on high-throughput sequencing together with different “omics” techniques overcome the limitations imposed by culture-dependent approaches and provide new insights into the diversity and ecology of microbial communities in the methane cycle. Here, we review available knowledge concerning the abundances, composition, and activity of methanogenic and methanotrophic communities in a wide range of natural and anthropogenic environments. We suggest that incorporation of microbial data could fill the existing microbiological gaps in methane flux modeling, and significantly increase the predictive power of models for different environments.

scholarly journals STRUKTUR KOMUNITAS MIKROBA TANAH DAN IMPLIKASINYA DALAM MEWUJUDKAN SISTEM PERTANIAN BERKELANJUTAN

el–Hayah ◽  
2012 ◽  
Vol 1 (4) ◽  
Author(s):  
Prihastuti Prihastuti
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Soil Microbial Community ◽  
Soil Microbial Communities ◽  
Organic Soil ◽  
Plant Type ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Wide Range

<p>Soils are made up of organic and an organic material. The organic soil component contains all the living creatures in the soil and the dead ones in various stages of decomposition.  Biological activity in soil helps to recycle nutrients, decompose organic matter making nutrient available for plant uptake, stabilize humus, and form soil particles.<br />The extent of the diversity of microbial in soil is seen to be critical to the maintenance of soil health and quality, as a wide range of microbial is involved in important soil functions.  That ecologically managed soils have a greater quantity and diversity of soil microbial. The two main drivers of soil microbial community structure, i.e., plant type and soil type, are thought to exert their function in a complex manner. The fact that in some situations the soil and in others the plant type is the key factor determining soil microbial diversity is related to their complexity of the microbial interactions in soil, including interactions between microbial and soil and microbial and plants. <br />The basic premise of organic soil stewardship is that all plant nutrients are present in the soil by maintaining a biologically active soil environment. The diversity of microbial communities has on ecological function and resilience to disturbances in soil ecosystems. Relationships are often observed between the extent of microbial diversity in soil, soil and plant quality and ecosystem sustainability. Agricultural management can be directed toward maximizing the quality of the soil microbial community in terms of disease suppression, if it is possible to shift soil microbial communities.</p><p>Keywords: structure, microbial, implication, sustainable agriculture<br /><br /></p>

scholarly journals Riddles in the cold: Antarctic endemism and microbial succession impact methane cycling in the Southern Ocean

2020 ◽  
Vol 287 (1931) ◽  
pp. 20201134 ◽  
Author(s):  
Andrew R. Thurber ◽  
Sarah Seabrook ◽  
Rory M. Welsh
Keyword(s):  
Microbial Community ◽  
Greenhouse Gas Emission ◽  
Ross Sea ◽  
Methane Flux ◽  
Rrna Gene ◽  
Methane Seep ◽  
Microbial Succession ◽  
Methane Cycle ◽  
16S Rrna Gene Analysis ◽  
Successional Stage

Antarctica is estimated to contain as much as a quarter of earth's marine methane, however we have not discovered an active Antarctic methane seep limiting our understanding of the methane cycle. In 2011, an expansive (70 m × 1 m) microbial mat formed at 10 m water depth in the Ross Sea, Antarctica which we identify here to be a high latitude hydrogen sulfide and methane seep. Through 16S rRNA gene analysis on samples collected 1 year and 5 years after the methane seep formed, we identify the taxa involved in the Antarctic methane cycle and quantify the response rate of the microbial community to a novel input of methane. One year after the seep formed, ANaerobic MEthane oxidizing archaea (ANME), the dominant sink of methane globally, were absent. Five years later, ANME were found to make up to 4% of the microbial community, however the dominant member of this group observed (ANME-1) were unexpected considering the cold temperature (−1.8°C) and high sulfate concentrations (greater than 24 mM) present at this site. Additionally, the microbial community had not yet formed a sufficient filter to mitigate the release of methane from the sediment; methane flux from the sediment was still significant at 3.1 mmol CH 4 m −2 d −1 . We hypothesize that this 5 year time point represents an early successional stage of the microbiota in response to methane input. This study provides the first report of the evolution of a seep system from a non-seep environment, and reveals that the rate of microbial succession may have an unrealized impact on greenhouse gas emission from marine methane reservoirs.

scholarly journals Fine scale diversification of endolithic microbial communities in the hyper-arid Atacama Desert

2017 ◽  
Author(s):  
Victoria Meslier ◽  
Maria Cristina Casero ◽  
Micah Dailey ◽  
Jacek Wierzchos ◽  
Carmen Ascaso ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Water Retention ◽  
High Throughput Sequencing ◽  
Arid Zone ◽  
Global Climate ◽  
Atacama Desert ◽  
Sampling Strategy ◽  
Physical Structure ◽  
Community Diversity ◽  
Fine Scale

ABSTRACTThe expansion of desertification across our planet is accelerating as the result of human activity and global climate change. In hyper-arid deserts, endolithic microbial communities colonize the rocks’ interior as a survival strategy. Yet, the composition of these communities and the drivers promoting their assembly are still poorly understood. Using a sampling strategy that minimized climate regime and biogeography effects, we analyzed the diversity and community composition of endoliths from four different lithic substrates – calcite, gypsum, ignimbrite and granite – collected in the hyper-arid zone of the Atacama Desert, Chile. By combining microscopy, mineralogy, and high throughput sequencing, we found these communities to be highly specific to their lithic substrate, although they were all dominated by the same four main phyla, Cyanobacteria, Actinobacteria, Chloroflexi and Proteobacteria. This finding indicates a fine scale diversification of the microbial reservoir driven by substrate properties. Our data suggest that the overall rock chemistry is not an essential driver of community structure and we propose that the architecture of the rock, i.e. the space available for colonization and its physical structure, linked to water retention capabilities, is ultimately the driver of community diversity and composition at the dry limit of life.Originality-Significance StatementIn this study, we demonstrated that endolithic microbial communities are highly specific to their substrates, suggesting a fine scale diversification of the available microbial reservoir. By using an array of rock substrates from the same climatic region, we established, for the first time, that the architecture of the rock is linked to water retention and is ultimately the driver of community diversity and composition at the dry limit for life.

scholarly journals Genetic, Phenotypic, and Commercial Characterization of an Almond Collection from Sardinia

Plants ◽  
2018 ◽  
Vol 7 (4) ◽  
pp. 86 ◽  
Author(s):  
Emma Rapposelli ◽  
Maria Rigoldi ◽  
Daniela Satta ◽  
Donatella Delpiano ◽  
Sara Secci ◽  
...  
Keyword(s):  
Global Climate ◽  
Industrial Applications ◽  
Yield Potential ◽  
High Yield ◽  
Phenotypic Traits ◽  
Industrial Processing ◽  
High Oleic ◽  
Global Climate Changes ◽  
Content Ratio ◽  
Wide Range

Background: Recent nutritional and medical studies have associated the regular consumption of almonds with a wide range of health benefits. As a consequence, kernel quality has become an important goal for breeding, considering not only the chemical composition conferring a specific organoleptic quality but also physical traits related to industrial processing. Methods: We characterized an almond collection from Sardinia through analysis of 13 morpho-physiological traits and eight essential oil profiles. The genetic structure of the collection was studied by analyzing the polymorphism of 11 simple sequence repeats (SSR). Results: Both commercial and phenotypic traits showed wide ranges of variation. Most genotypes were early flowering with low yield potential. Several genotypes showed moderate to high yield and very interesting oil compositions of kernels. Based on 11 SSR profiles and Bayesian clustering, the Sardinian cultivars were assigned to groups which were differentiated for several agronomic and commercial traits. Conclusions: Several cultivars showed a high kernel oil content and high oleic to linoleic content ratio. Based on morphological traits, we propose that some of the analyzed cultivars could be interesting for industrial applications. Finally, we highlight the importance of characterizing early blooming cultivars for sites which are experiencing a rise in mean temperatures due to the effects of global climate changes.

scholarly journals Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology

2021 ◽  
Vol 12 ◽  
Author(s):  
Lauren M. Lui ◽  
Erica L.-W. Majumder ◽  
Heidi J. Smith ◽  
Hans K. Carlson ◽  
Frederick von Netzer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
High Throughput Sequencing ◽  
Spatial Scales ◽  
Data Types ◽  
Modeling Framework ◽  
Rapid Acquisition ◽  
Mechanistic Understanding ◽  
And Function

Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.

scholarly journals Wetland plant evolutionary history influences soil and endophyte microbial community composition

2020 ◽  
Author(s):  
Marisa B. Szubryt ◽  
Kelly Skinner ◽  
Edward J. O’Loughlin ◽  
Jason Koval ◽  
Stephanie M. Greenwald ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Plant Species ◽  
Evolutionary History ◽  
Microbial Community Composition ◽  
Methane Flux ◽  
Sample Type ◽  
Wetland Plant ◽  
Wetland Ecosystems

AbstractMethane is a microbially derived greenhouse gas whose emissions are highly variable throughout wetland ecosystems. Differences in plant community composition account for some of this variability, suggesting an influence of plant species on microbial community structure and function in these ecosystems. Given that closely related plant species have similar morphological and biochemical features, we hypothesize that plant evolutionary history is related to differences in microbial community composition. To examine species-specific patterns in microbiomes, we selected five monoculture-forming wetland plant species based on the evolutionary distances among them. We detected significant differences in microbial communities between sample types (unvegetated soil, bulk soil, rhizosphere soil, internal root tissues, and internal leaf tissues) associated with these plant species based on 16S relative abundances. We additionally found that differences in plant evolutionary history were correlated with variation in microbial communities across plant species within each sample type. Using qPCR, we observed substantial differences in overall methanogen and methanotroph population sizes between plant species and sample types. Methanogens tended to be most abundant in rhizosphere soils while methanotrophs were the most abundant in roots. Given that microbes influence methane flux and that plants affect methanogen and methanotroph populations, plant species contribute to variable degrees of methane emissions. Incorporating the influence of plant evolutionary history into future modeling efforts may improve predictions of wetland methane emission since microbial community differences correlate with differences in plant evolutionary history.

scholarly journals Global changes and animal phenotypic responses: melanin-based plumage redness of scops owls increased with temperature and rainfall during the last century

2009 ◽  
Vol 5 (4) ◽  
pp. 532-534 ◽  
Author(s):  
Paolo Galeotti ◽  
Diego Rubolini ◽  
Roberto Sacchi ◽  
Mauro Fasola
Keyword(s):  
Climate Changes ◽  
Global Climate ◽  
Temporal Trends ◽  
Global Changes ◽  
Global Climate Changes ◽  
Specimen Collection ◽  
Evolutionary Response ◽  
Wide Range ◽  
Migration Strategies ◽  
Colour Morphs

The ecological effects of global climate changes include shifts of species' distribution and changes in migration strategies and phenotype. Colour polymorphism, which can be envisaged as a species' evolutionary response to alternating conditions or to a wide range of habitats, may be affected by climate changes as well. The scops owl ( Otus scops ) shows two main colour morphs, dark- and pale-reddish, as well as intermediate morphs. We investigated temporal trends in an index of plumage colour of Italian scops owls from museum collections (1870–2007). We found a significant increase in plumage redness over the last century, which was correlated with an increase in temperature and rainfall of the years before specimen collection. However, the temporal increase in plumage redness persisted after controlling for climatic variables, suggesting that other environmental factors could be involved. Our study indicates that ongoing climate changes might have either shifted the selective balance between colour morphs, or differentially affected migration and movement patterns of colour morphs.

scholarly journals Effects of Distinct Revegetation Methods on Growth and Microbial Properties of Vallisneria natans

Water ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 1294
Author(s):  
Ning Wang ◽  
Qi Li ◽  
Mengqi Jiang ◽  
Weizhen Zhang ◽  
Hao Zhang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
High Throughput ◽  
Water Purification ◽  
High Throughput Sequencing ◽  
Rhizosphere Soil ◽  
Soil Microbial Communities ◽  
Agar Gel ◽  
Vallisneria Natans ◽  
Significant Difference

This study investigated the effects of the mud-sinking (MS) method, agar gel-sinking (AS) method and agar gel-sinking with artificial aquatic mat (ASA) method on the growth, physiological characteristics, water purification capacity, and associated microbial community of the different organs of Vallisneria natans (V. natans). Results showed that the growth of agar-based growth (group AS and ASA) were more effective than the mud-wrapped method (group MS), exhibiting longer length, higher fresh weight and biomass of agar-based V. natans with the artificial aquatic mat (group ASA) being higher than those of other groups. MS caused a stress response in the oxidative system, which then inhibited photosynthesis. Results of water quality measurements showed that the three planting methods positively affected water purification without significant differences (p > 0.05). Besides, there was no significant difference (p > 0.05) between the microbial communities in terms of the roots and those found in rhizosphere soils in the MS group with high throughput sequencing. Meanwhile, the addition of agar in the AS and ASA groups increased the diversity of rhizosphere soil microbial communities and reduced the diversity of root microbial communities. Microbial community compositions in the rhizosphere soil and root differed significantly (p < 0.05). High throughput sequencing and scanning electron microscopy (SEM) also revealed that the biofilm on the surfaces were different, with Proteobacteria and Cyanophyta consistently dominating. This study provides new insights on the more effective revegetation methods of V. natans, researched the environmental impact of the addition of agar, and provides some theoretical support for the revegetation of submerged macrophytes under ecological restoration.

scholarly journals Obtainment of Lignocellulose Degradation Microbial Community: The Effect of Acid-Base Combination After Restrictive Enrichment

2021 ◽  
Author(s):  
Binbin Hua ◽  
Xiaofen Wang ◽  
Zongjun Cui
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Lignocellulose Degradation ◽  
Community Resources ◽  
Formation Processes ◽  
Acid Base ◽  
Theoretical System ◽  
Structure Changes ◽  
Degradation Ability

Abstract Acid-base combination is used in some cases expecially after restricted enrichment, and has created many lignocellulose-degrading communities. While how it worked is not well understood. In this study, compost was used as inoculum source. Induced community structure changes were analyzed with high throughput sequencing to elucidate the formation processes and determine the mechanisms of acid-base combination. We found that after restricted enrichment, retaining primarily bacteria not only included that could decompose and utilize lignocellulose, such as Clostridium and Pseudomonas, but also synergistic microbiota such as Pseudoxanomonas and Alkalobacillaceae. When the proportion of these two types of bacteria was not balanced, the degradation ability of the microbial community was low or pH changes of it did not compound regular changes , which maybe lead to the failure of restricted enrichment. Microbial communities were re-constituted by acid-base combination, whereby the degrading and synergistic strains were adjusted to a more appropriate proportion. Acid-base combination fixed the instability of microbial communities caused by randomness of restrictive screening enrichment. In this study, the mechanism of acid-base combination was analyzed, which enriched the theoretical system of restricted culture, and provided an effective and controllable technical method for obtaining high-quality lignocellulose-degrading microbial community resources.

scholarly journals Spatial microbial community dynamics using a continuous species interaction model

2021 ◽  
Author(s):  
Anshuman Swain ◽  
Levi Fussell ◽  
William F Fagan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Mutation Rate ◽  
Community Dynamics ◽  
Evolutionary Game ◽  
Species Interaction ◽  
Higher Order ◽  
Community Formation ◽  
Continuous Space ◽  
Wide Range

AbstractComprehending the assembly and maintenance of microbial diversity in natural communities, despite the abundance of antagonistic interactions, is a major problem of interest in biology. A common framework to study the problem is through cyclic dominance games over pairwise interactions. Recent papers incorporating higher-order interactions in these models have successfully explained high diversity of microbes, especially in communities where antibiotic producing, sensitive, and resistant strains co-exist. But most of these models are based on a small number of discrete species, assume a notion of pure cyclic dominance, and focus on low mutation rate regimes, none of which best represents the highly interlinked, quickly evolving and continuous nature of microbial phenotypic space. Here, we present a model of species in a continuous space, with mutual higher order interactions, to examine the assembly and stability of microbial communities. Specifically, we focus on toxin production, vulnerability, and inhibition among the simulated species. We observe intricate interaction between certain parameters that generates highly divergent patterns of diversity and spatial community dynamics. We find that spatial properties are better predicted by species interaction constraints rather than mobility, and that community formation time, mobility, and mutation rate best explain the patterns of diversity.Significance StatementUnderstanding the assembly and maintenance of diverse microbial communities in nature is a question of great interest to theoretical biologists. Previous works, utilizing evolutionary game theory and other techniques, have explained the role of higher order interactions for the coexistence of diverse microbes in different kinds of environments. But these models are usually based on a small number of discrete species and low//no mutation rate, which is not how many natural microbial communities function. In this work, we explore a new framework which incorporates a continuous species model along with a wide range of mutation rates to comprehend the process of microbial community formation.

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