scholarly journals Where microorganisms meet rocks in the Earth's Critical Zone

2011 ◽  
Vol 8 (2) ◽  
pp. 2523-2562 ◽  
Author(s):  
D. M. Akob ◽  
K. Küsel
Keyword(s):  
Microbial Communities ◽  
Mycorrhizal Fungi ◽  
Critical Zone ◽  
Deep Subsurface ◽  
Role Changes ◽  
And Function ◽  
Future Work ◽  
Earth’S Critical Zone

Abstract. The Earth's Critical Zone (CZ) is the critical, outer shell of the Earth that provides an arena for the interplay of diverse physical, chemical, and biological processes that are fundamental for sustaining life. As microbes are the principle drivers of biogeochemical cycles, it is necessary to understand the biodiversity of the CZ unseen majority and their impact on life-sustaining processes. This review aims to summarize the factors controlling where microbes (prokaryotes and micro-eukaryotes) live within the CZ and what is known to date about their diversity and function. Microbes live in all regions of the CZ down to 5 km depth, but due to changing habitat complexity, e.g., variability in pore spaces, water, oxygen, and nutrients, their functional role changes with depth. The abundance of prokaryotes and micro-eukaryotes decreases from a maximum of 1010 or 107 cells g soil−1 up to eight orders of magnitude with depth. Symbiotic mycorrhizal fungi and free-living decomposers are best understood in soil habitats, where they are up to 103 cells g soil−1. However, little is known about their identity and impact on weathering in the deep subsurface. The relatively low abundance of micro-eukaryotes in the deep subsurface suggests that these organisms are either limited in space or nutrients or unable to cope with oxygen limitations. Since deep regions of the CZ are limited in the recent input of photosynthesis-derived carbon, microbes are dependent on deposited organic material or on chemolithoautotrophic metabolism that allows for the establishment of a complete food chain independent from the surface. However, the energy flux available might only allow cell growth over tens to thousands of years. The recent development of "omics" technologies has provided microbial ecologists with methods to link the composition and function of in situ microbial communities. We should expect new metabolic discoveries as we have a closer look utilizing a polyphasic approach into the microbial communities of the CZ. Thus, future work is still needed to link microbial biodiversity to the exact role of microbes in weathering and geochemical cycling in the CZ, especially in subsurface habitats.

scholarly journals Where microorganisms meet rocks in the Earth's Critical Zone

2011 ◽  
Vol 8 (12) ◽  
pp. 3531-3543 ◽  
Author(s):  
D. M. Akob ◽  
K. Küsel
Keyword(s):  
Mycorrhizal Fungi ◽  
Critical Zone ◽  
Deep Subsurface ◽  
Functional Roles ◽  
Weathering Processes ◽  
Reactive Gases ◽  
And Function ◽  
Fundamental Physical ◽  
Earth’S Critical Zone

Abstract. The Critical Zone (CZ) is the Earth's outer shell where all the fundamental physical, chemical, and biological processes critical for sustaining life occur and interact. As microbes in the CZ drive many of these biogeochemical cycles, understanding their impact on life-sustaining processes starts with an understanding of their biodiversity. In this review, we summarize the factors controlling where terrestrial CZ microbes (prokaryotes and micro-eukaryotes) live and what is known about their diversity and function. Microbes are found throughout the CZ, down to 5 km below the surface, but their functional roles change with depth due to habitat complexity, e.g. variability in pore spaces, water, oxygen, and nutrients. Abundances of prokaryotes and micro-eukaryotes decrease from 1010 or 107 cells g soil−1 or rock−1, or ml water−1 by up to eight orders of magnitude with depth. Although symbiotic mycorrhizal fungi and free-living decomposers have been studied extensively in soil habitats, where they occur up to 103 cells g soil−1, little is known regarding their identity or impact on weathering in the deep subsurface. The relatively low abundance of micro-eukaryotes in the deep subsurface suggests that they are limited in space, nutrients, are unable to cope with oxygen limitations, or some combination thereof. Since deep regions of the CZ have limited access to recent photosynthesis-derived carbon, microbes there depend on deposited organic material or a chemolithoautotrophic metabolism that allows for a complete food chain, independent from the surface, although limited energy flux means cell growth may take tens to thousands of years. Microbes are found in all regions of the CZ and can mediate important biogeochemical processes, but more work is needed to understand how microbial populations influence the links between different regions of the CZ and weathering processes. With the recent development of "omics" technologies, microbial ecologists have new methods that can be used to link the composition and function of in situ microbial communities. In particular, these methods can be used to search for new metabolic pathways that are relevant to biogeochemical nutrient cycling and determine how the activity of microorganisms can affect transport of carbon, particulates, and reactive gases between and within CZ regions.

scholarly journals Plumage iridescence is associated with distinct feather microbiota in a tropical passerine

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Veronika Gvoždíková Javůrková ◽  
Erik D. Enbody ◽  
Jakub Kreisinger ◽  
Kryštof Chmel ◽  
Jakub Mrázek ◽  
...  
Keyword(s):  
Sexual Selection ◽  
Community Structure ◽  
Microbial Communities ◽  
Plumage Coloration ◽  
Microbial Load ◽  
Sexual Dichromatism ◽  
Physiological Processes ◽  
Fitness Consequences ◽  
Future Work

Abstract Birds present a stunning diversity of plumage colors that have long fascinated evolutionary ecologists. Although plumage coloration is often linked to sexual selection, it may impact a number of physiological processes, including microbial resistance. At present, the degree to which differences between pigment-based vs. structural plumage coloration may affect the feather microbiota remains unanswered. Using quantitative PCR and DGGE profiling, we investigated feather microbial load, diversity and community structure among two allopatric subspecies of White-shouldered Fairywren, Malurus alboscapulatus that vary in expression of melanin-based vs. structural plumage coloration. We found that microbial load tended to be lower and feather microbial diversity was significantly higher in the plumage of black iridescent males, compared to black matte females and brown individuals. Moreover, black iridescent males had distinct feather microbial communities compared to black matte females and brown individuals. We suggest that distinctive nanostructure properties of iridescent male feathers or different investment in preening influence feather microbiota community composition and load. This study is the first to point to structural plumage coloration as a factor that may significantly regulate feather microbiota. Future work might explore fitness consequences and the role of microorganisms in the evolution of avian sexual dichromatism, with particular reference to iridescence.

scholarly journals Expression and Function Studies of CYC/TB1-Like Genes in the Asymmetric Flower Canna (Cannaceae, Zingiberales)

2020 ◽  
Vol 11 ◽  
Author(s):  
Qianxia Yu ◽  
Xueyi Tian ◽  
Canjia Lin ◽  
Chelsea D. Specht ◽  
Jingping Liao
Keyword(s):  
Flower Development ◽  
Expression Patterns ◽  
Asymmetric Distribution ◽  
Inflorescence Architecture ◽  
Flower Primordia ◽  
Fertile Stamen ◽  
Spatiotemporal Expression ◽  
And Function

The asymmetric flower, lacking any plane of symmetry, is rare among angiosperms. Canna indica L. has conspicuously asymmetric flowers resulting from the presence of a half-fertile stamen, while the other androecial members develop as petaloid staminodes or abort early during development. The molecular basis of the asymmetric distribution of fertility and petaloidy in the androecial whorls remains unknown. Ontogenetic studies have shown that Canna flowers are borne on monochasial (cincinnus) partial florescences within a racemose inflorescence, with floral asymmetry likely corresponding to the inflorescence architecture. Given the hypothesized role of CYC/TB1 genes in establishing floral symmetry in response to the influence of the underlying inflorescence architecture, the spatiotemporal expression patterns of three Canna CYC/TB1 homologs (CiTBL1a, CiTBL1b-1, and CiTBL1b-2) were analyzed during inflorescence and floral development using RNA in situ hybridization and qRT-PCR. In the young inflorescence, both CiTBL1a and CiTBL1b-1 were found to be expressed in the bracts and at the base of the lateral florescence branches, whereas transcripts of CiTBL1b-2 were mainly detected in flower primordia and inflorescence primordia. During early flower development, expression of CiTBL1a and CiTBL1b-1 were both restricted to the developing sepals and petals. In later flower development, expression of CiTBL1a was reduced to a very low level while CiTBL1b-1 was detected with extremely high expression levels in the petaloid androecial structures including the petaloid staminodes, the labellum, and the petaloid appendage of the fertile stamen. In contrast, expression of CiTBL1b-2 was strongest in the fertile stamen throughout flower development, from early initiation of the stamen primordium to maturity of the ½ anther. Heterologous overexpression of CiTBL genes in Arabidopsis led to dwarf plants with smaller petals and fewer stamens, and altered the symmetry of mature flowers. These data provide evidence for the involvement of CYC/TB1 homologs in the development of the asymmetric Cannaceae flower.

Proteinase-activated receptors in ovine cervical function

2005 ◽  
Vol 17 (7) ◽  
pp. 693 ◽  
Author(s):  
Sharon E. Mitchell ◽  
John J. Robinson ◽  
Margaret E. King ◽  
Lynda M. Williams
Keyword(s):  
Gene Expression ◽  
In Situ Hybridisation ◽  
Prostaglandin F2α ◽  
Cervical Dilation ◽  
Proteinase Activated Receptors ◽  
Pregnant Ewe ◽  
High Level ◽  
And Function

In sheep, inflammation not only functions in cervical dilation at parturition, but also plays an important part in the non-pregnant ewe cervix, as demonstrated by the high level of expression of interleukin (IL)-8 at oestrus. Ewes artificially induced to ovulate have significantly lower levels of IL-8 gene expression at oestrus compared with natural oestrus, indicating an inhibition of inflammation and function, offering an explanation for the low rates of conception in vaginally inseminated synchronised ewes. To identify potential pro-inflammatory agents to combat the anti-inflammatory effects of hormonal synchronisation of oestrus, we have investigated the role of proteinase-activated receptor (PAR)-1 and PAR-2. To localise and measure the level of expression of these receptors, ovine-specific probes were derived for PAR-1 and PAR-2 and used for quantitative in situ hybridisation in the ovine cervix. Both PAR-1 and PAR-2 were expressed in the luminal epithelium of the cervix throughout the oestrous cycle, with expression being highest at oestrus. The gene expression of PAR-2 at oestrus was approximately 30% higher than that of PAR-1. Artificial synchronisation of oestrus by either an intravaginal progesterone sponge or prostaglandin F2α injections did not inhibit PAR-1 or PAR-2 expression at oestrus; rather, in the case of PAR-2, progesterone synchronisation increased it. Both synchronising procedures increased the expression of PAR-1 and PAR-2 during the luteal phase of the cycle. Therefore, agonists of PAR-1 and PAR-2 may be potentially useful pro-inflammatory agents countering the inhibition of inflammation by hormonal synchronisation.

scholarly journals Structure prediction of crystals, surfaces and nanoparticles

2020 ◽  
Vol 378 (2186) ◽  
pp. 20190600
Author(s):  
Scott M. Woodley ◽  
Graeme M. Day ◽  
R. Catlow
Keyword(s):  
Machine Learning ◽  
Energy Function ◽  
Structure Prediction ◽  
Search Algorithm ◽  
Structure And Function ◽  
Current Status ◽  
Organic Systems ◽  
And Function

We review the current techniques used in the prediction of crystal structures and their surfaces and of the structures of nanoparticles. The main classes of search algorithm and energy function are summarized, and we discuss the growing role of methods based on machine learning. We illustrate the current status of the field with examples taken from metallic, inorganic and organic systems. This article is part of a discussion meeting issue ‘Dynamic in situ microscopy relating structure and function’.

Geobiology of In Situ Uranium Leaching

2013 ◽  
Vol 825 ◽  
pp. 372-375 ◽  
Author(s):  
Carla Zammit ◽  
Kan Li ◽  
Barbara Etschmann ◽  
Joël Brugger ◽  
Frank Reith
Keyword(s):  
Microbial Communities ◽  
Underground Mining ◽  
Close Association ◽  
Cost Effective ◽  
Open Pit ◽  
Uranium Recovery ◽  
Production Studies ◽  
Site Rehabilitation ◽  
And Function

Driven by the world’s thirst for energy, the demand for uranium is rapidly increasing. Hence, producers of uranium are struggling to keep up with demands and are exploring more cost-effective methods of extraction. Uranium is currently mined via open pit and underground mining as well as with in situ leaching methods, with in situ leaching currently accounting for approximately 45 % of total uranium production. Studies have shown that the presence of uranium in soils strongly affects the composition and function of resident microbial communities. In view of the close association of biological processes and uranium geochemistry, it is surprising how little information is available on the effect of microbial communities on in situ leaching. Hence, this review focuses on the possibility to exploit the properties of such microorganisms and identify opportunities to use natural microbial processes to improve uranium recovery and mine site rehabilitation.

Progress in ultrastructural and molecular analysis of the nuclear matrix

1992 ◽  
Vol 50 (1) ◽  
pp. 508-509
Author(s):  
Edward G. Fey
Keyword(s):  
Electron Microscopy ◽  
Nuclear Matrix ◽  
Structure And Function ◽  
Matrix Proteins ◽  
Rna Transcription ◽  
Nuclear Matrix Proteins ◽  
The Past ◽  
And Function

In the past few years, considerable advances have been made regarding the structure and function of the nuclear matrix. In the first half of this presentation, the field of nuclear matrix research will be summarized. Emphasis will be placed on those studies where molecular interactions are demonstrated in situ utilizing high resolution light and/or electron microscopy. Studies demonstrating the role of the nuclear matrix in DNA synthesis and replication, RNA transcription and processing, and the binding of matrix attachment regions to specific nuclear matrix proteins will be summarized.

scholarly journals Ooids forming in situ within microbial mats (Kiritimati atoll, central Pacific)

PalZ ◽  
2021 ◽  
Author(s):  
Pablo Suarez-Gonzalez ◽  
Joachim Reitner
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Microbial Mats ◽  
Formation Processes ◽  
Central Pacific ◽  
Environmental Processes ◽  
Definition Of ◽  
First Time

AbstractOoids (subspherical particles with a laminated cortex growing around a nucleus) are ubiquitous in the geological record since the Archean and have been widely studied for more than two centuries. However, various questions about them remain open, particularly about the role of microbial communities and organic matter in their formation and development. Although ooids typically occur rolling around in agitated waters, here, we describe for the first time aragonite ooids forming statically within microbial mats from hypersaline ponds of Kiritimati (Kiribati, central Pacific). Subspherical particles had been previously observed in these mats and classified as spherulites, but these particles grow around autochthonous micritic nuclei, and many of them have laminated cortices, with alternating radial fibrous laminae and micritic laminae. Thus, they are compatible with the definition of the term ‘ooid’ and are in fact very similar to many modern and fossil examples. Kiritimati ooids are more abundant and developed in some ponds and in some particular layers of the microbial mats, which leads to the discussion and interpretation of their formation processes as product of mat evolution, through a combination of organic and environmental factors. Radial fibrous laminae are formed during periods of increased supersaturation, either by metabolic or environmental processes. Micritic laminae are formed in closer association with the mat exopolymer (EPS) matrix, probably during periods of lower supersaturation and/or stronger EPS degradation. Therefore, this study represents a step forward in the understanding of ooid development as influenced by microbial communities, providing a useful analogue for explaining similar fossil ooids.

scholarly journals Strigolactones in the Rhizosphere: Friend or Foe?

2017 ◽  
Vol 30 (9) ◽  
pp. 683-690 ◽  
Author(s):  
Carolien De Cuyper ◽  
Sofie Goormachtig
Keyword(s):  
Mycorrhizal Fungi ◽  
Arbuscular Mycorrhizal ◽  
In Planta ◽  
Negative Effects ◽  
Physiological Processes ◽  
Endogenous Plant Hormones ◽  
Close Proximity ◽  
Host Detection ◽  
And Function

Strigolactones are well-known endogenous plant hormones that play a major role in planta by influencing different physiological processes. Moreover, ex planta, strigolactones are important signaling molecules in root exudates and function as host detection cues to launch mutualistic interactions with arbuscular mycorrhizal fungi in the rhizosphere. However, parasitic plants belonging to the Orobanchaceae family hijacked this communication system to stimulate their seed germination when in close proximity to the roots of a suitable host. As a result, the secretion of strigolactones by the plant can have both favorable and detrimental outcomes. Here, we discuss these dual positive and negative effects of strigolactones and we provide a detailed overview on the role of these molecules in the complex dialogs between plants and different organisms in the rhizosphere.

Diversity and function of soil microbes on montane gradients: the state of knowledge in a changing world

2020 ◽  
Vol 96 (9) ◽  
Author(s):  
Caitlin I Looby ◽  
Patrick H Martin
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Functional Groups ◽  
Soil Microbes ◽  
Diversity Indices ◽  
Saprotrophic Fungi ◽  
Microbial Biogeography ◽  
And Function ◽  
Important Progress

ABSTRACT Mountains have a long history in the study of diversity. Like macroscopic taxa, soil microbes are hypothesized to be strongly structured by montane gradients, and recently there has been important progress in understanding how microbes are shaped by these conditions. Here, we summarize this literature and synthesize patterns of microbial diversity on mountains. Unlike flora and fauna that often display a mid-elevation peak in diversity, we found a decline (34% of the time) or no trend (33%) in total microbial diversity with increasing elevation. Diversity of functional groups also varied with elevation (e.g. saprotrophic fungi declined 83% of the time). Most studies (82%) found that climate and soils (especially pH) were the primary mechanisms driving shifts in composition, and drivers differed across taxa—fungi were mostly determined by climate, while bacteria (48%) and archaea (71%) were structured primarily by soils. We hypothesize that the central role of soils—which can vary independently of other abiotic and geographic gradients—in structuring microbial communities weakens diversity patterns expected on montane gradients. Moving forward, we need improved cross-study comparability of microbial diversity indices (i.e. standardizing sequencing) and more geographic replication using experiments to broaden our knowledge of microbial biogeography on global gradients.

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