Gypsum-hosted endolithic communities of the Lake St. Martin impact structure, Manitoba, Canada: spectroscopic detectability and implications for Mars

2014 ◽  
Vol 13 (4) ◽  
pp. 366-377 ◽  
Author(s):  
T. Rhind ◽  
J. Ronholm ◽  
B. Berg ◽  
P. Mann ◽  
D. Applin ◽  
...  
Keyword(s):  
Microbial Community ◽  
Impact Crater ◽  
Organic Molecules ◽  
Soil Surface ◽  
Spectroscopic Technique ◽  
Community Members ◽  
Exterior Surface ◽  
Terrestrial Environments ◽  
High Degree ◽  
Endolithic Communities

AbstractThere is increasing evidence that Mars may have once been a habitable environment. Gypsum is targeted in the search for Martian biosignatures because it can host extensive cryptoendolithic communities in extreme terrestrial environments and is widespread on Mars. In this study the viability of using different spectroscopy-based techniques to identify the presence of gypsum endolithic communities was investigated by analysing various cryptoendoliths collected from the Lake St. Martin impact crater (LSM), a Mars analogue site found in Manitoba, Canada. Concurrently, the cryptoendolithic microbial community structure present was also analysed to aid in assigning spectroscopic features to microbial community members. Two main morphologies of endolithic communities were collected from gypsum deposits at LSM: true cryptoendolithic communities and annular deposits on partially buried boulders and cobbles <1 cm below the soil surface. Endolithic communities were found to be visibly present only in gypsum with a high degree of translucency and could occur as deep as 3 cm below the exterior surface. The bacterial community was dominated by a phylum (Chloroflexi) that has not been previously observed in gypsum endoliths. The exterior surfaces of gypsum boulders and cobbles are devoid of spectroscopic features attributable to organic molecules and detectable by reflectance, Raman, or ultraviolet-induced fluorescence spectroscopies. However, exposed interior surfaces show unique endolithic signatures detectable by each spectroscopic technique. This indicates that cryptoendolithic communities can be detected via spectroscopy-based techniques, provided they are either partially or fully exposed and enough photon–target interactions occur to enable detection.

scholarly journals The Coevolution of Plants and Microbes Underpins Sustainable Agriculture

2021 ◽  
Vol 9 (5) ◽  
pp. 1036
Author(s):  
Dongmei Lyu ◽  
Levini A. Msimbira ◽  
Mahtab Nazari ◽  
Mohammed Antar ◽  
Antoine Pagé ◽  
...  
Keyword(s):  
Microbial Community ◽  
Plant Growth ◽  
Stress Resistance ◽  
Mycorrhizal Fungi ◽  
Plant Tissues ◽  
Terrestrial Plants ◽  
Plant Host ◽  
Symbiotic Relationships ◽  
Wide Range ◽  
Terrestrial Environments

Terrestrial plants evolution occurred in the presence of microbes, the phytomicrobiome. The rhizosphere microbial community is the most abundant and diverse subset of the phytomicrobiome and can include both beneficial and parasitic/pathogenic microbes. Prokaryotes of the phytomicrobiome have evolved relationships with plants that range from non-dependent interactions to dependent endosymbionts. The most extreme endosymbiotic examples are the chloroplasts and mitochondria, which have become organelles and integral parts of the plant, leading to some similarity in DNA sequence between plant tissues and cyanobacteria, the prokaryotic symbiont of ancestral plants. Microbes were associated with the precursors of land plants, green algae, and helped algae transition from aquatic to terrestrial environments. In the terrestrial setting the phytomicrobiome contributes to plant growth and development by (1) establishing symbiotic relationships between plant growth-promoting microbes, including rhizobacteria and mycorrhizal fungi, (2) conferring biotic stress resistance by producing antibiotic compounds, and (3) secreting microbe-to-plant signal compounds, such as phytohormones or their analogues, that regulate aspects of plant physiology, including stress resistance. As plants have evolved, they recruited microbes to assist in the adaptation to available growing environments. Microbes serve themselves by promoting plant growth, which in turn provides microbes with nutrition (root exudates, a source of reduced carbon) and a desirable habitat (the rhizosphere or within plant tissues). The outcome of this coevolution is the diverse and metabolically rich microbial community that now exists in the rhizosphere of terrestrial plants. The holobiont, the unit made up of the phytomicrobiome and the plant host, results from this wide range of coevolved relationships. We are just beginning to appreciate the many ways in which this complex and subtle coevolution acts in agricultural systems.

scholarly journals DISCo-microbe: design of an identifiable synthetic community of microbes

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8534 ◽  
Author(s):  
Dana L. Carper ◽  
Travis J. Lawrence ◽  
Alyssa A. Carrell ◽  
Dale A. Pelletier ◽  
David J. Weston
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Dna Sequence ◽  
Sequence Alignment ◽  
Amplicon Sequencing ◽  
Ribosomal Database Project ◽  
Community Members ◽  
Dna Sequence Alignment ◽  
Diverse Community

Background Microbiomes are extremely important for their host organisms, providing many vital functions and extending their hosts’ phenotypes. Natural studies of host-associated microbiomes can be difficult to interpret due to the high complexity of microbial communities, which hinders our ability to track and identify individual members along with the many factors that structure or perturb those communities. For this reason, researchers have turned to synthetic or constructed communities in which the identities of all members are known. However, due to the lack of tracking methods and the difficulty of creating a more diverse and identifiable community that can be distinguished through next-generation sequencing, most such in vivo studies have used only a few strains. Results To address this issue, we developed DISCo-microbe, a program for the design of an identifiable synthetic community of microbes for use in in vivo experimentation. The program is composed of two modules; (1) create, which allows the user to generate a highly diverse community list from an input DNA sequence alignment using a custom nucleotide distance algorithm, and (2) subsample, which subsamples the community list to either represent a number of grouping variables, including taxonomic proportions, or to reach a user-specified maximum number of community members. As an example, we demonstrate the generation of a synthetic microbial community that can be distinguished through amplicon sequencing. The synthetic microbial community in this example consisted of 2,122 members from a starting DNA sequence alignment of 10,000 16S rRNA sequences from the Ribosomal Database Project. We generated simulated Illumina sequencing data from the constructed community and demonstrate that DISCo-microbe is capable of designing diverse communities with members distinguishable by amplicon sequencing. Using the simulated data we were able to recover sequences from between 97–100% of community members using two different post-processing workflows. Furthermore, 97–99% of sequences were assigned to a community member with zero sequences being misidentified. We then subsampled the community list using taxonomic proportions to mimic a natural plant host–associated microbiome, ultimately yielding a diverse community of 784 members. Conclusions DISCo-microbe can create a highly diverse community list of microbes that can be distinguished through 16S rRNA gene sequencing, and has the ability to subsample (i.e., design) the community for the desired number of members and taxonomic proportions. Although developed for bacteria, the program allows for any alignment input from any taxonomic group, making it broadly applicable. The software and data are freely available from GitHub (https://github.com/dlcarper/DISCo-microbe) and Python Package Index (PYPI).

Selective Bacterial Community Enrichment Between the Pitcher Plants Sarracenia Minor and Sarracenia Flava

2020 ◽  
Author(s):  
Nikolas M. Stasulli ◽  
Scott M. Yourstone ◽  
Ilon Weinstein ◽  
Elizabeth Ademski ◽  
Elizabeth A. Shank
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Prey Availability ◽  
Microbial Community Composition ◽  
Geographic Location ◽  
Rrna Gene ◽  
Natural Ecosystems ◽  
Community Members ◽  
Pitcher Plants ◽  
Naturally Occurring

Abstract BackgroundThe interconnected and overlapping habitats present in natural ecosystems remain a challenge in determining the forces driving microbial community composition. The cup-like leaf structures of some carnivorous plants, including the family Sarraceniaceae, are self-contained ecological habitats that represent systems for exploring such microbial ecology questions. We investigated whether Sarracenia minor and Sarracenia flava, when sampled at the same geographic location and time, cultivate unique microbiota; an indication of biotic selection of microbes due to eliminating many of the environmental variable present in other studies comparing samples harvested over several time points. ResultsDNA was extracted from the decomposing detritus trapped in the base of each Sarracenia leaf pitcher. We profiled a portion of the 16S rRNA gene across the bacterial community members present in this detritus using Illumina MiSeq technology. We identified a surprising amount of diversity within each pitcher, but also discovered that the two Sarracenia species each contained distinct, enriched microbial community members. This suggests a non-random establishment of microbial communities within these two Sarracenia species.ConclusionsOverall, our results indicate that microbial selection is occurring within the pitchers of these two closely related plant species, which is not due to factors such as geographic location, weather, or prey availability. This suggests that specific features of S. minor and S. flava may play a role in fostering specific insect-decomposing microbiomes. These naturally occurring microbial ecosystems can be developed to answer important questions about microbial community succession, disruption, and member contributions to the community. This study will help further establish carnivorous pitcher plants as a model system for studying confined, naturally occurring bacterial communities.

scholarly journals Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Vanessa L. Brisson ◽  
Jennifer E. Schmidt ◽  
Trent R. Northen ◽  
John P. Vogel ◽  
Amélie C. M. Gaudin
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Microbial Community Analysis ◽  
Agricultural System ◽  
Community Members ◽  
Genetic Groups ◽  
Maize Domestication ◽  
Rhizosphere Microbial Community

Abstract Maize domestication and breeding have resulted in drastic and well documented changes in aboveground traits, but belowground effects on root system functioning and rhizosphere microbial communities remain poorly understood, despite their critical importance for nutrient and water acquisition. We investigated the rhizosphere microbial community composition and structure of ten Zea mays accessions along an evolutionary transect (two teosinte, three inbred maize lines, and five modern maize hybrids) grown in nutrient depleted soil from a low input agricultural system. Microbial community analysis revealed significant differences in community composition between soil compartments (proximal vs. distal rhizosphere) and between plant genetic groups (teosinte, inbred, and modern hybrid). Only a small portion of the microbial community was differentially selected across plant genetic groups: 3.7% of prokaryotic community members and 4.9% of fungal community members were significantly associated with a specific plant genetic group. Indicator species analysis showed the greatest differentiation between modern hybrids and the other two plant genetic groups. Co-occurrence network analysis revealed that microbial co-occurrence patterns of the inbred maize lines’ rhizosphere were significantly more similar to those of the teosintes than to the modern hybrids. Our results suggest that advances in hybrid development significantly impacted rhizosphere microbial communities and network assembly.

scholarly journals A Key Motif in the Cholesterol-Dependent Cytolysins Reveals a Large Family of Related Proteins

mBio ◽  
2020 ◽  
Vol 11 (5) ◽  
Author(s):  
Jordan C. Evans ◽  
Bronte A. Johnstone ◽  
Sara L. Lawrence ◽  
Craig J. Morton ◽  
Michelle P. Christie ◽  
...  
Keyword(s):  
Large Family ◽  
Structural Similarity ◽  
Particle Analysis ◽  
Critical Component ◽  
Content Type ◽  
Conserved Motif ◽  
Forming Mechanism ◽  
Terrestrial Environments ◽  
Pore Complexes ◽  
High Degree

ABSTRACT The cholesterol-dependent cytolysins (CDCs) are bacterial, β-barrel, pore-forming toxins. A central enigma of the pore-forming mechanism is how completion of the prepore is sensed to initiate its conversion to the pore. We identified a motif that is conserved between the CDCs and a diverse family of nearly 300 uncharacterized proteins present in over 220 species that span at least 10 bacterial and 2 eukaryotic phyla. Except for this motif, these proteins exhibit little similarity to the CDCs at the primary structure level. Studies herein show this motif is a critical component of the sensor that initiates the prepore-to-pore transition in the CDCs. We further show by crystallography, single particle analysis, and biochemical studies of one of these CDC-like (CDCL) proteins from Elizabethkingia anophelis, a commensal of the malarial mosquito midgut, that a high degree of structural similarity exists between the CDC and CDCL monomer structures and both form large oligomeric pore complexes. Furthermore, the conserved motif in the E. anophelis CDCL crystal structure occupies a nearly identical position and makes similar contacts to those observed in the structure of the archetype CDC, perfringolysin O (PFO). This suggests a common function in the CDCs and CDCLs and may explain why only this motif is conserved in the CDCLs. Hence, these studies identify a critical component of the sensor involved in initiating the prepore-to-pore transition in the CDCs, which is conserved in a large and diverse group of distant relatives of the CDCs. IMPORTANCE The cholesterol-dependent cytolysins’ pore-forming mechanism relies on the ability to sense the completion of the oligomeric prepore structure and initiate the insertion of the β-barrel pore from the assembled prepore structure. These studies show that a conserved motif is an important component of the sensor that triggers the prepore-to-pore transition and that it is conserved in a large family of previously unidentified CDC-like proteins, the genes for which are present in a vast array of microbial species that span most terrestrial environments, as well as most animal and human microbiomes. These studies establish the foundation for future investigations that will probe the contribution of this large family of CDC-like proteins to microbial survival and human disease.

scholarly journals Medicinal Plants Used in the Ejisu-Juaben Municipality, Southern Ghana: An Ethnobotanical Study

Medicines ◽  
2018 ◽  
Vol 6 (1) ◽  
pp. 1 ◽  
Author(s):  
Kwame Appiah ◽  
Clement Oppong ◽  
Hossein Mardani ◽  
Richard Omari ◽  
Sylvia Kpabitey ◽  
...  
Keyword(s):  
Medicinal Plants ◽  
Skin Diseases ◽  
Current Knowledge ◽  
Ethnobotanical Study ◽  
Community Members ◽  
Medicinal Uses ◽  
Oral Transmission ◽  
Informant Consensus ◽  
Indigenous Uses ◽  
High Degree

Background: The in-depth traditional knowledge of medicinal plants is at risk of extinction due to the dependency on oral transmission, and as such, there is an urgent need to document such knowledge. This study aimed to document indigenous uses of medicinal plants among community members in the Ejisu-Juaben Municipality. Methods: Data was collected in 2016 from community members and local herbalists in the Ejisu-Juaben Municipality through a semi-structured questionnaire. Statistical tools and ethnobotanical indices, i.e., informant consensus factor (ICF), fidelity level (FL), and use value (UV) were used to analyse the data. Results: One hundred and six medicinal plants belonging to 45 families were reported to cure 68 different human diseases. The most frequently used plant part in this study was the leaves (52%). Decoction (57.5%) and oral administration (58.3%) were the most utilised herbal preparation and administration route respectively. Cleistopholis patens had the highest UV (0.54) with pain & fevers and skin diseases having the highest ICF values (0.88 and 0.85 respectively). Furthermore, new medicinal uses of Hilleria latifolia and ten other species were recorded for the treatment of the traditional local disease, aseram. Conclusions: The current knowledge and uses of medicinal plants are still high in the study area based on the high degree of consensus among informants. This study could allow for the preservation of knowledge and biodiversity of medicinal plants, both of which are threatened with extinction.

Hotspots created by earthworms, and their contribution to soil nitrogen cycling

2020 ◽  
Author(s):  
Joann Whalen ◽  
Hicham Benslim
Keyword(s):  
Microbial Community ◽  
Nitrogen Cycling ◽  
Nitrogen Mineralization ◽  
Soil Nitrogen ◽  
Intestinal Tract ◽  
Soil Surface ◽  
Nitrogen Supply ◽  
Built Environments ◽  
Soil Nitrogen Cycling ◽  
Soil Nitrogen Supply

&lt;p&gt;Earthworms create hotspots that support microbial diversity and activity in soil. These hotspots may be internal to the earthworm, such as in their intestinal tract, or external to the earthworm in the biopores, casts and middens they create on the soil surface and within the soil profile. This presentation summarizes some of the key hotspots associated with earthworms, and how the biostimulated microbial community in these areas contributes to soil nitrogen cycling. We will present observations about the diversity and activity of nitrogen-cycling microorganisms that live within the earthworm and in its built environments, as well as the population- and community-level contributions of earthworms to denitrification, nitrogen mineralization, and the soil nitrogen supply in temperate agroecosystems.&lt;/p&gt;

Practicing Anthropology: Forging New Roles and Relationships with Communities

2005 ◽  
Vol 27 (3) ◽  
pp. 2-3
Author(s):  
Bill Roberts ◽  
Adrienne Hillery
Keyword(s):  
Daily Basis ◽  
Community Members ◽  
Cultural Brokers ◽  
Immigrant Populations ◽  
Physical Wellbeing ◽  
Emic Perspective ◽  
Meaningful Relationships ◽  
High Degree ◽  
Multidimensional Concept ◽  
Gain Access

The articles in this issue of Practicing Anthropology are all positive examples of people working to make a difference by using anthropology to construct meaningful relationships and roles through their work with a community of "other" people. What does community mean in the 21st century? This is a question anthropology is uniquely positioned to help answer, but the answer isn't necessarily short or sweet. The articles in this issue apply the concept of community in a variety of ways to different human groups, suggesting that community is a multidimensional concept. In keeping with anthropological tradition, all the authors in this issue attempt to represent the real concerns of the community members with whom they work by privileging an emic viewpoint. Anthropologists gain access to an emic perspective by employing ethnographic methods that generate insight and empathy into the lives of community members with whom they work. This empathy is part of the passion and conviction that characterizes the high degree of concern many anthropologists feel in formulating recommendations they think will improve some part of the context in which communities struggle on a daily basis. All of the articles in this issue also take on issues of mental and physical wellbeing in American communities, and deal with minority, disadvantaged, and immigrant populations. These anthropologists use their unique position of empathy and understanding to function many times as cultural brokers or advocates, helping create improvements in these communities by forging new bonds with their members.

scholarly journals Normalization of environmental metagenomic DNA enhances the discovery of under-represented microbial community members

2015 ◽  
Vol 60 (4) ◽  
pp. 359-366 ◽  
Author(s):  
J.-B. Ramond ◽  
T.P. Makhalanyane ◽  
M.I. Tuffin ◽  
D.A. Cowan
Keyword(s):  
Microbial Community ◽  
Community Members ◽  
Metagenomic Dna
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