scholarly journals Energy, ecology and the distribution of microbial life

2013 ◽  
Vol 368 (1622) ◽  
pp. 20120383 ◽  
Author(s):  
Jennifer L. Macalady ◽  
Trinity L. Hamilton ◽  
Christen L. Grettenberger ◽  
Daniel S. Jones ◽  
Leah E. Tsao ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Energy Resource ◽  
Biological Species ◽  
Main Stream ◽  
Species Definition ◽  
Microbial Life ◽  
Elemental Cycling ◽  
Culture Independent ◽  
Population Sizes ◽  
Micro Organisms

Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time.

scholarly journals Multicellular and unicellular responses of microbial biofilms to stress

2020 ◽  
Vol 401 (12) ◽  
pp. 1365-1374
Author(s):  
Daniel K.H. Rode ◽  
Praveen K. Singh ◽  
Knut Drescher
Keyword(s):  
Microbial Communities ◽  
Stress Responses ◽  
Spatial Scales ◽  
Organizational Level ◽  
Internal Stresses ◽  
Microbial Life ◽  
Microbial Biofilms ◽  
Applied Stresses

AbstractBiofilms are a ubiquitous mode of microbial life and display an increased tolerance to different stresses. Inside biofilms, cells may experience both externally applied stresses and internal stresses that emerge as a result of growth in spatially structured communities. In this review, we discuss the spatial scales of different stresses in the context of biofilms, and if cells in biofilms respond to these stresses as a collection of individual cells, or if there are multicellular properties associated with the response. Understanding the organizational level of stress responses in microbial communities can help to clarify multicellular functions of biofilms.

scholarly journals A culture-independent method for studying transfer of IncI1 plasmids from wild-type Escherichia coli in complex microbial communities

2018 ◽  
Vol 152 ◽  
pp. 18-26 ◽  
Author(s):  
Mehreen Anjum ◽  
Jonas Stenløkke Madsen ◽  
Carmen Espinosa-Gongora ◽  
Bimal Jana ◽  
Maria Wiese ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Microbial Communities ◽  
Independent Method ◽  
Wild Type ◽  
Culture Independent

Research Tools and Methods for the Analysis of Microbiota in Dairy Products

2018 ◽  
pp. 23-53 ◽  
Author(s):  
Sylvia Klaubauf ◽  
Frank J. J. Segers
Keyword(s):  
Dna Sequencing ◽  
Production Process ◽  
Microbial Communities ◽  
Dairy Products ◽  
Starter Cultures ◽  
Direct Pcr ◽  
Culture Independent ◽  
Profiling Techniques ◽  
Tools And Methods ◽  
Culture Dependent

Microorganisms play important roles in dairy products. They can be a source of spoilage, or they promote health or cause diseases. In dairy fermentations, microorganisms are of great importance due to their function as starter cultures and during the production process of dairy products. In order to better understand and improve the process, it is essential to identify the species that are involved and to monitor the development of microbial communities. There are several different approaches for the detection and analysis of the microbiota. The methods can be culture dependent and, for example, make use of morphological and physiological characters or DNA sequencing. Culture-independent methods include direct PCR and qPCR, but also electrophoresis-based profiling techniques as well as metagenomics. Descriptions of relevant methods are provided and their applications are discussed in this chapter.

FT-Raman spectroscopic analysis of endolithic microbial communities from Beacon sandstone in Victoria Land, Antarctica

1998 ◽  
Vol 10 (1) ◽  
pp. 63-74 ◽  
Author(s):  
N.C. Russell ◽  
H.G.M. Edwards ◽  
D.D. Wynn-Williams
Keyword(s):  
Microbial Communities ◽  
Accurate Analysis ◽  
Raman Spectroscopic ◽  
Victoria Land ◽  
Fourier Transform Raman Spectroscopy ◽  
Diverse Field ◽  
Small Footprint ◽  
Micro Organisms

Laser-based Fourier-Transform Raman spectroscopy (FTRS) has been used to identify in situ compounds of ecophysiological significance in diverse field-fresh Antarctic cryptoendolithic microbial communities. FTRS does not disrupt the community and permits characterization of visible and invisible compounds in their natural configuration within cells and their current or former microhabitat. The small “footprint” of the microscopic laser beam permits accurate analysis of discrete zones of compounds produced by extant or degraded micro-organisms with minimum destruction of the biota. This spatial chemical analysis is applicable to any translucent or exposed habitat or biotic assemblage. Two hydrated forms of biodegradative calcium oxalate were differentiated in black-pigmented and hyaline lichen zones of endolithic communities. The oxalate was restricted to zones containing fungi. Communities dominated by cyanobacteria at Battleship Promontory (77°S) and a newly discovered site at Timber Peak (74°S) contrasted chemically with those dominated by eukaryotic algae at East Beacon (78°S). FTRS also showed the zonation of pigments including chlorophyll and UV-protective carotenoids in situ. At extreme sites on the polar plateau, it revealed the presence of “fossil” endolithics where detrimental climatic changes had made the microbes non-viable or amorphous, being represented solely by their residual bio-molecules. The technique has potential for past or present life-detection anywhere in the world without destruction of the microniche.

scholarly journals Mini-Review: Probing the limits of extremophilic life in extraterrestrial environment-simulated experiments

2012 ◽  
Vol 11 (4) ◽  
pp. 251-256 ◽  
Author(s):  
Claudia A.S. Lage ◽  
Gabriel Z.L. Dalmaso ◽  
Lia C.R.S. Teixeira ◽  
Amanda G. Bendia ◽  
Ivan G. Paulino-Lima ◽  
...  
Keyword(s):  
Chemical Elements ◽  
Microbial Life ◽  
Radiation Sources ◽  
Interesting Possibility ◽  
Terrestrial Environments ◽  
Radiation Resistant ◽  
Extraterrestrial Environment ◽  
Life On Earth ◽  
Micro Organisms ◽  
The Universe

AbstractAstrobiology is a relatively recent scientific field that seeks to understand the origin and dynamics of life in the Universe. Several hypotheses have been proposed to explain life in the cosmic context throughout human history, but only now, technology has allowed many of them to be tested. Laboratory experiments have been able to show how chemical elements essential to life, such as carbon, nitrogen, oxygen and hydrogen combine in biologically important compounds. Interestingly, these compounds are ubiquitous. How these compounds were combined to the point of originating cells and complex organisms is still to be unveiled by science. However, our 4.5 billion years old Solar system appeared in a 10 billion years old Universe. Thus, simple cells such as micro-organisms may have had time to form in planets older than ours or in other suitable places in the Universe. One hypothesis related to the appearance of life on Earth is called panspermia, which predicts that microbial life could have been formed in the Universe billions of years ago, travelling between planets, and inseminating units of life that could have become more complex in habitable planets such as Earth. A project designed to test the viability of extremophile micro-organisms exposed to simulated extraterrestrial environments is in progress at the Carlos Chagas Filho Institute of Biophysics (UFRJ, Brazil) to test whether microbial life could withstand inhospitable environments. Radiation-resistant (known or novel ones) micro-organisms collected from extreme terrestrial environments have been exposed (at synchrotron accelerators) to intense radiation sources simulating Solar radiation, capable of emitting radiation in a few hours equivalent to many years of accumulated doses. The results obtained in these experiments reveal an interesting possibility of the existence of microbial life beyond Earth.

scholarly journals Methylotrophy in a Lake: from Metagenomics to Single-Organism Physiology

2011 ◽  
Vol 77 (14) ◽  
pp. 4705-4711 ◽  
Author(s):  
Ludmila Chistoserdova
Keyword(s):  
Microbial Communities ◽  
Metabolic Flexibility ◽  
Functional Metagenomics ◽  
Content Type ◽  
Comparative Analyses ◽  
Single Organism ◽  
Genomic Divergence ◽  
Lake Washington ◽  
Culture Independent ◽  
Environmental Importance

ABSTRACTThis review provides a brief summary of ongoing studies in Lake Washington (Seattle, WA) directed at an understanding of the content and activities of microbial communities involved in methylotrophy. One of the findings from culture-independent approaches, including functional metagenomics, is the prominent presence ofMethyloteneraspecies in the site and their inferred activity in C1metabolism, highlighting the local environmental importance of this group. Comparative analyses of individual genomes ofMethylophilaceaefrom Lake Washington provide insights into their genomic divergence and suggest significant metabolic flexibility.

scholarly journals Connecting structure and function from organisms to molecules in small animal symbioses through chemo-histo-tomography

2020 ◽  
Author(s):  
Benedikt Geier ◽  
Janina Oetjen ◽  
Bernhard Ruthensteiner ◽  
Maxim Polikarpov ◽  
Harald Gruber-Vodicka ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Mass Spectrometry Imaging ◽  
Natural Habitat ◽  
Anatomic Structure ◽  
X Ray ◽  
Culture Independent ◽  
Metabolic Interactions ◽  
Micro Organisms

AbstractOur understanding of metabolic interactions between small symbiotic animals and bacteria or parasitic eukaryotes that reside within their body is extremely limited. This gap in knowledge originates from a methodological challenge, namely to connect histological changes in host tissues induced by beneficial and parasitic (micro)organisms to the underlying metabolites. To close this gap, we developed chemo-histo-tomography (CHEMHIST), a culture-independent approach to connect anatomic structure and metabolic function in millimeter-sized symbiotic animals. CHEMHIST combines spatial metabolomics based on mass spectrometry imaging (MSI) and microanatomy-based micro-computed X-ray tomography (microCT) on the same animal. Both high-resolution MSI and microCT allowed us to correlate the distribution of metabolites to the same animal’s three-dimensional (3D) histology down to sub-micrometer resolutions. Our protocol is compatible with tissue specific DNA sequencing and fluorescence in situ hybridization (FISH) for the taxonomic identification and localization of the associated micro(organisms). Building CHEMHIST upon in situ imaging, we sampled an earthworm from its natural habitat and created an interactive 3D model of its physical and chemical interactions with bacteria and parasitic nematodes in its tissues. Combining MSI and microCT, we introduce a workflow to connect metabolic and anatomic phenotypes of small symbiotic animals that often represent keystone species for ecosystem-functioning.SignificanceMetabolites mediate the establishment and persistence of most inter-kingdom symbioses. Still, to pinpoint the metabolites each partner displays upon interaction remains the biggest challenge in studying multi-organismal assemblages. Addressing this challenge, we developed a correlative imaging workflow to connect the in situ production of metabolites with the organ-scale and cellular 3D distributions of mutualistic and pathogenic (micro)organisms in the same host animal. Combining mass spectrometry imaging and micro-computed X-ray tomography provided a culture-independent approach, which is essential to include the full spectrum of naturally occurring interactions. To introduce the potential of combining high-resolution tomography with metabolite imaging, we resolve the metabolic interactions between an invertebrate host, its symbiotic bacteria and tissue parasites at unprecedented detail for model and non-model symbioses.

scholarly journals Two different microbial communities did not cause differences in occlusion of particulate organic matter in a sandy agricultural soil

2016 ◽  
Author(s):  
Frederick Büks ◽  
Philip Rebensburg ◽  
Peter Lentzsch ◽  
Martin Kaupenjohann
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Particulate Organic Matter ◽  
Agricultural Soil ◽  
Agricultural Soils ◽  
Soil Aggregates ◽  
Soil Extract ◽  
Microbial Life ◽  
Physico Chemical ◽  
Airborne Microbes

Abstract. Apart from physico-chemical interactions between soil components, microbial life is assumed to be an important factor of soil structure forming processes. Bacterial exudates, the entanglement by fungal hypae and bacterial pseudomycelia as well as fungal glomalin are supposed to provide the occlusion of particulate organic matter (POM) through aggregation of soil particles. This work investigates the resilience of POM occlusion in face of different microbial communities under controlled environmental conditions. We hypothesized that the formation of different communities would cause different grades of POM occlusion. For this purpose samples of a sterile sandy agricultural soil were incubated for 76 days in bioreactors. Particles of pyrochar from pine wood were added as POM analogue. One variant was inoculated with a native soil extract, whereas the control was infected by airborne microbes. A second control soil remained non-incubated. During the incubation, soil samples were taken for taxon-specific qPCR to determine the abundance of Eubacteria, Fungi, Archaea, Acidobacteria, Actinobacteria, α-Proteobacteria and β-Proteobacteria. After the incubation soil aggregates (100–2000 μm) were collected by sieving and disaggregated using ultrasound to subject the released POM to an analysis of organic carbon (OC). Our results show, that the eubacterial DNA of both incubated variants reached a similar concentration after 51 days. However, the structural composition of the two communities was completely different. The soil-born variant was dominated by Acidobacteria, Actinobacteria and an additional fungal population, whereas the air-born variant mainly contained β-Proteobacteria. Both variants showed a strong occlusion of POM into aggregates during the incubation. Yet, despite the different population structure, there were only marginal differences in the release of POM along with the successive destruction of soil aggregates by ultrasonication. This leads to the tentative assumption that POM occlusion in agricultural soils could be resilient in face of changing microbial communities.

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