scholarly journals Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in Hyper-Arid Environments

2016 ◽  
Vol 7 ◽  
Author(s):  
Alexander Crits-Christoph ◽  
Courtney K. Robinson ◽  
Bing Ma ◽  
Jacques Ravel ◽  
Jacek Wierzchos ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Microbial Communities ◽  
Arid Environments

scholarly journals Comparative Study of the Rhizosphere and Root Endosphere Microbiomes of Cholistan Desert Plants

2021 ◽  
Vol 12 ◽  
Author(s):  
Salma Mukhtar ◽  
Samina Mehnaz ◽  
Kauser Abdulla Malik
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Arid Regions ◽  
Soil Moisture Content ◽  
Abiotic Factors ◽  
Arid Environments ◽  
Desert Plants ◽  
Limited Information ◽  
Cholistan Desert ◽  
Capparis Decidua

Microbial communities associated with the rhizosphere and roots of desert halophytes play an important role in plants’ growth and development. Very limited information has been available on the microbial diversity of arid environments of Pakistan. Hence in the current study, the microbial diversity of rhizosphere and root endosphere of desert halophytes, Zygophyllum simplex, Haloxylon salicoricum, Aerva javanica, and Capparis decidua was evaluated. The rhizosphere and root endosphere samples of desert halophytes collected from the three geographic sites of Cholistan desert, Punjab, Pakistan were analyzed by using 16S rRNA based Illumina sequencing. The results showed that Proteobacteria were more abundant in the rhizospheric soils while Actinobacteria were more dominant in the root endosphere of halophytes. Bacteroidetes, Firmicutes, and Deinococcus-Thermus were identified from all rhizospheric soils and roots across the three sites, with variable percentage. Bacillus, Kocuria, Pseudomonas, Halomonas, and Flavobacterium were commonly identified from the rhizosphere and root endosphere of halophytes across all the three sites. At the genus level, microbial diversity from Haloxylon showed the greatest variations between the rhizosphere and root endosphere from the site 2. This study revealed that microbial diversity analysis can be used to study how changes in abiotic factors such as soil moisture content and salinity affect the microbial communities associated with the rhizospheric soils and root endosphere of halophytes across the three sites. This study will also help in the discovery of potential inoculants for crops growing in arid and semi-arid regions of Pakistan.

scholarly journals An ecophysiological explanation for manganese enrichment in rock varnish

2021 ◽  
Vol 118 (25) ◽  
pp. e2025188118
Author(s):  
Usha F. Lingappa ◽  
Chris M. Yeager ◽  
Ajay Sharma ◽  
Nina L. Lanza ◽  
Demosthenes P. Morales ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Imaging Techniques ◽  
Manganese Content ◽  
Chemical Imaging ◽  
Arid Environments ◽  
Metagenomic Dna ◽  
Paramagnetic Resonance ◽  
Desert Varnish ◽  
Specific Uptake ◽  
Petrographic Thin Section

Desert varnish is a dark rock coating that forms in arid environments worldwide. It is highly and selectively enriched in manganese, the mechanism for which has been a long-standing geological mystery. We collected varnish samples from diverse sites across the western United States, examined them in petrographic thin section using microscale chemical imaging techniques, and investigated the associated microbial communities using 16S amplicon and shotgun metagenomic DNA sequencing. Our analyses described a material governed by sunlight, water, and manganese redox cycling that hosts an unusually aerobic microbial ecosystem characterized by a remarkable abundance of photosynthetic Cyanobacteria in the genus Chroococcidiopsis as the major autotrophic constituent. We then showed that diverse Cyanobacteria, including the relevant Chroococcidiopsis taxon, accumulate extraordinary amounts of intracellular manganese—over two orders of magnitude higher manganese content than other cells. The speciation of this manganese determined by advanced paramagnetic resonance techniques suggested that the Cyanobacteria use it as a catalytic antioxidant—a valuable adaptation for coping with the substantial oxidative stress present in this environment. Taken together, these results indicated that the manganese enrichment in varnish is related to its specific uptake and use by likely founding members of varnish microbial communities.

scholarly journals Temporal and spatial changes in phyllosphere microbiome of acacia trees growing in arid environments

2020 ◽  
Author(s):  
Ashraf Al-Ashhab ◽  
Shiri Meshner ◽  
Rivka Alexander-Shani ◽  
Hana Dimerets ◽  
Michael Brandwein ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Diversity ◽  
16S Rdna ◽  
Air Temperature ◽  
Bacterial Communities ◽  
Abiotic Factors ◽  
Keystone Species ◽  
Arid Environments ◽  
Acacia Tortilis ◽  
Biotic Factor

Abstract Background: The evolutionary relationships between plants and their microbiome are of high importance to the survival of plants in extreme conditions. Changes in microbiome of plants can affect plant development, growth and health. Along the arid Arava, southern Israel, acacia trees ( Acacia raddiana and Acacia tortilis ) are considered keystone species. In this study, we investigated the ecological effects of plant species, microclimate (different areas within the tree canopies) and seasonality on the endophytic and epiphytic microbiome associated with these two tree species. 186 leaf samples were collected along different seasons throughout the year and their microbial communities were studied using the diversity of the 16S rDNA gene sequenced on the 150-PE Illumina sequencing platform. Results: our results showed amplifying V4 region of the 16S rDNA better presented the bacterial communities of both end and epiphytes of Acacia trees than V2, V3 and V5 regions of the 16S r DNA. When comparing the bacterial diversity of endo and epiphytes of the two acacia trees (shannon, choa1, PD and observed number of OTU’s), the epiphytes diversity indices showed about twice higher diversity compared to endophytes. The bacterial community compositions comparing both end and epiphytes were also significantly different. Interestingly, Acacia tortilis (umbral canopy shape) had a higher epiphytes bacterial diversity compared to Acacia raddiana, but were not statistically different. However the endophyte bacterial communities were significantly different compared to the two Acacia species (Firmicutes dominated Acacia raddiana and Proteobacteria dominated the Acacia tortilis ) . Alongside the biotic factor, Abiotic factors such as air temperature and precipitation also showed to significantly effect endo and epiphytes bacterial communities, while air humidity only affected the epiphytes bacterial communities.Conclusions: These results shed light on the unique desert phyllosphere microbiome in mitigating stress conditions highlighting the importance of epiphytic and endophytic microbial communities which are driven by different genotypic and abiotic factors. This paper also shows only a few bacteria species (OTUS’s) to dominate both epi and endophytes highlighting the importance of climate change (precipitation, Air temperature) in affecting arid land ecosystems where acacia trees are considered keystone species in many arid regions.

scholarly journals Temporal and spatial changes in phyllosphere microbiome of acacia trees growing in arid environments

2021 ◽  
Author(s):  
Ashraf Al-Ashhab ◽  
Shiri Meshner ◽  
Rivka Alexander-Shani ◽  
Hana Dimerets ◽  
Michael Brandwein ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Diversity ◽  
Air Temperature ◽  
Bacterial Communities ◽  
Abiotic Factors ◽  
Keystone Species ◽  
Tree Canopy ◽  
Arid Environments ◽  
Acacia Tortilis ◽  
Acacia Species

Abstract Background: The evolutionary relationships and interactions between plants and their microbiomes are of high importance to the survival of plants in extreme conditions. Changes in the plant’s microbiome can affect plant development, growth and health. Along the arid Arava, southern Israel, acacia trees (Acacia raddiana and Acacia tortilis) are considered keystone species. In this study, we investigated the ecological effects of plant species, microclimate (different areas within the tree canopy) and seasonality on the epiphytic and endophytic microbiomes associated with these two tree species. One hundred and thirty nine leaf samples were collected throughout the year and their microbial communities were assessed using 16S rDNA gene amplified with five different primers (targeting different gene regions) and sequenced (150 bp paired-end) on an Illumina MiSeq sequencing platform.Results: Epiphytic bacterial diversity estimates (Shannon-Wiener, Chao1, Simpson and observed number of OTUs), were found to be nearly double compared to endophyte counterparts, in addition epi- and endophyte communities were significantly different from each other. Interestingly, the epiphytic bacterial diversity was similar in the two acacia species but the canopy sides and sample months exhibited different diversity, while the endophytic bacterial communities were different in the two acacia species but similar throughout the year. Abiotic factors, such as air temperature and precipitation, were shown to significantly affect both epi- and endophytes communities. Bacterial community compositions showed that Firmicutes dominate Acacia raddiana and Proteobacteria dominate Acacia tortilis; these bacterial communities only consisted of a small number of bacterial families mainly Bacillaceae and Comamonadaceae in the endophyte for A. raddiana and A. tortilis, respectively, and Geodematophilaceae and Micrococcaceae for epiphyte bacterial communities. Interestingly, about 60% of the obtained bacterial classification were unclassified below family level. Conclusions: These results shed light on the unique desert phyllosphere microbiome highlighting the importance of multiple genotypic and abiotic factors in shaping the epiphytic and endophytic microbial communities. This study also shows that only a few bacterial families dominate both epi- and endophytes, highlighting the importance of climate change (precipitation, air temperature and humidity) in affecting arid land ecosystems where acacia trees are considered keystone species.

scholarly journals Microbial communities from arid environments on a global scale. A systematic review

2020 ◽  
Vol 53 (1) ◽  
Author(s):  
Javiera Vásquez-Dean ◽  
Felipe Maza ◽  
Isidora Morel ◽  
Rodrigo Pulgar ◽  
Mauricio González
Keyword(s):  
Systematic Review ◽  
Microbial Communities ◽  
Global Scale ◽  
Arid Environments

scholarly journals Temporal and spatial changes in phyllosphere microbiome of acacia trees growing in super arid environments

2020 ◽  
Author(s):  
Ashraf Al-Ashhab ◽  
Shiri Meshner ◽  
Rivka Alexander-Shani ◽  
Michael Brandwein ◽  
Yael Bar Lavan ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Keystone Species ◽  
Arid Environments ◽  
Sequencing Platform ◽  
Spatial Changes ◽  
Tree Canopies ◽  
Different Seasons ◽  
Putative Marker ◽  
First Time ◽  
The Relationship

AbstractAlong the arid Arava, southern Israel, acacia trees (Acacia raddiana and Acacia tortilis) are considered keystone species. In this study, we investigated the ecological effects of plant species, microclimate (different areas within the tree canopies) and seasonality on the endophytic and epiphytic microbiome associated with these two tree species. 186 leaf samples were collected along different seasons throughout the year and their microbial communities were studied using the diversity of the 16S rDNA gene sequenced on the 150-PE Illumina sequencing platform. Results show that endophytic, but not epiphytic, microbiome communities were different between the two acacia species. Endophytic, but not epiphytic, microbiome was affected by temporal changes (seasons) in air temperature. Acacia canopy microclimate was also found to have a significant effect on exosphere microbiome, with A. tortilis having a higher microbial diversity than A. raddiana with significantly different community compositions in different seasons.ImportanceThe evolutionary relationships and interactions between plants and their microbiome are of high importance to the survival of plants in extreme conditions. Changes in microbiome of plants can affect plant development, growth and health. In this study, we explored the relationship between keystone desert trees and their microbiome along seasonal variation. These results shed light on the importance and uniqueness of desert phyllosphere microbiome. Although acacia trees are considered keystone species in many arid regions, to the best of our knowledge, this is the first time that microbial descriptors have been applied in these systems. This work constitutes a new approach to the assessment of these important trees and a stepping stone in the application of microbial communities as a putative marker in a changing environment.

scholarly journals A rather dry subject; investigating the study of arid-associated microbial communities

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Peter Osborne ◽  
Lindsay J. Hall ◽  
Noga Kronfeld-Schor ◽  
David Thybert ◽  
Wilfried Haerty
Keyword(s):  
Microbial Communities ◽  
Land Surface ◽  
Animal Species ◽  
Arid Environment ◽  
Harsh Environments ◽  
Arid Environments ◽  
Microbial Life ◽  
Microbial Ecosystems ◽  
Limited Food ◽  
Extremes Of Temperature

AbstractAlmost one third of Earth’s land surface is arid, with deserts alone covering more than 46 million square kilometres. Nearly 2.1 billion people inhabit deserts or drylands and these regions are also home to a great diversity of plant and animal species including many that are unique to them. Aridity is a multifaceted environmental stress combining a lack of water with limited food availability and typically extremes of temperature, impacting animal species across the planet from polar cold valleys, to Andean deserts and the Sahara. These harsh environments are also home to diverse microbial communities, demonstrating the ability of bacteria, fungi and archaea to settle and live in some of the toughest locations known. We now understand that these microbial ecosystems i.e. microbiotas, the sum total of microbial life across and within an environment, interact across both the environment, and the macroscopic organisms residing in these arid environments. Although multiple studies have explored these microbial communities in different arid environments, few studies have examined the microbiota of animals which are themselves arid-adapted. Here we aim to review the interactions between arid environments and the microbial communities which inhabit them, covering hot and cold deserts, the challenges these environments pose and some issues arising from limitations in the field. We also consider the work carried out on arid-adapted animal microbiotas, to investigate if any shared patterns or trends exist, whether between organisms or between the animals and the wider arid environment microbial communities. We determine if there are any patterns across studies potentially demonstrating a general impact of aridity on animal-associated microbiomes or benefits from aridity-adapted microbiomes for animals. In the context of increasing desertification and climate change it is important to understand the connections between the three pillars of microbiome, host genome and environment.

scholarly journals A technical pipeline for screening microbial communities as a function of substrate specificity through single cell fluorescent imaging

2021 ◽  
Author(s):  
Shaun A. Leivers ◽  
Leidy Lagos ◽  
Sabina Leanti La Rosa ◽  
Bjørge Westereng
Keyword(s):  
Substrate Specificity ◽  
Microbial Communities ◽  
Single Cell ◽  
Monosaccharide Composition ◽  
Fluorescent Imaging ◽  
Fluorescent Label ◽  
Human Gut ◽  
Single Strain ◽  
Multifaceted Approach ◽  
The Common

The study of specific glycan uptake and metabolism has been shown to be an effective tool in aiding with the continued unravelling of the complexities in the human gut microbiome. To this aim fluorescent labelling of glycans may provide a powerful route towards target. In this study, we successfully used the fluorescent label 2-aminobenzamide (2-AB), most commonly employed for enhancing the detection of protein anchored glycans, to monitor and study microbial degradation of labelled glycans. Both single strain and co-cultured fermentations of microbes from the common human-gut derived Bacteroides genus, were able to grow when supplemented with 2-AB labelled glycans of different monosaccharide composition, degrees of acetylation and polymerization. Utilizing a multifaceted approach that combines chromatography, mass spectrometry, microscopy and flow cytometry techniques, it was possible to comprehensively track the metabolism of the labelled glycans in both supernatants and at a single cell level. We envisage this combination of complimentary techniques will help further the understanding of substrate specificity and the role it plays within microbial communities.

scholarly journals Rhizosphere Microbiome of Arid Land Medicinal Plants and Extra Cellular Enzymes Contribute to Their Abundance

2020 ◽  
Vol 8 (2) ◽  
pp. 213 ◽  
Author(s):  
Abdul Latif Khan ◽  
Sajjad Asaf ◽  
Raeid M. M. Abed ◽  
Yen Ning Chai ◽  
Ahmed N. Al-Rawahi ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Extracellular Enzymes ◽  
Growth Conditions ◽  
Soil Conditions ◽  
Arid Environments ◽  
Operational Taxonomic Units ◽  
Rhizosphere Microbiome ◽  
First Time ◽  
Generation Sequencing

Revealing the unexplored rhizosphere microbiome of plants in arid environments can help in understanding their interactions between microbial communities and plants during harsh growth conditions. Here, we report the first investigation of rhizospheric fungal and bacterial communities of Adenium obesum, Aloe dhufarensis and Cleome austroarabica using next-generation sequencing approaches. A. obesum and A. dhufarensis grows in dry tropical and C. austroarabica in arid conditions of Arabian Peninsula. The results indicated the presence of 121 fungal and 3662 bacterial operational taxonomic units (OTUs) whilst microbial diversity was significantly high in the rhizosphere of A. obesum and A. dhufarensis and low in C. austroarabica. Among fungal phyla, Ascomycota and Basidiomycota were abundantly associated within rhizospheres of all three plants. However, Mucoromycota was only present in the rhizospheres of A. obesum and A. dhufarensis, suggesting a variation in fungal niche on the basis of host and soil types. In case of bacterial communities, Actinobacteria, Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, and Verrucomicrobia were predominant microbial phyla. These results demonstrated varying abundances of microbial structure across different hosts and locations in arid environments. Rhizosphere’s extracellular enzymes analysis revealed varying quantities, where, glucosidase, cellulase, esterase, and 1-aminocyclopropane-1-carboxylate deaminase were significantly higher in the rhizosphere of A. dhufarensis, while phosphatase and indole-acetic acid were highest in the rhizosphere of A. obesum. In conclusion, current findings usher for the first time the core microbial communities in the rhizospheric regions of three arid plants that vary greatly with location, host and soil conditions, and suggest the presence of extracellular enzymes could help in maintaining plant growth during the harsh environmental conditions.

scholarly journals Phylogenetic and functional substrate specificity for endolithic microbial communities in hyper-arid environments

2015 ◽  
Author(s):  
Alexander Crits-Christoph ◽  
Courtney K Robinson ◽  
Bing Ma ◽  
Jacques Ravel ◽  
Jacek Wierzchos ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Essential Element ◽  
Gene Clusters ◽  
Taxonomic Diversity ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Relative Distribution ◽  
Arid Environments ◽  
Functional Capabilities ◽  
Nutrient Resources

Under extreme water deficit, endolithic (inside rock) microbial ecosystems are considered environmental refuges for life in cold and hot deserts, yet their diversity and functional adaptations remain vastly unexplored. The metagenomic analyses of the communities from two rock substrates, calcite and ignimbrite, revealed that they were dominated by Cyanobacteria, Actinobacteria, and Chloroflexi. The relative distribution of major phyla was significantly different between the two substrates and biodiversity estimates, from 16S rRNA gene sequences and from the metagenome data, all pointed to a higher taxonomic diversity in the calcite community. While both endolithic communities showed adaptations to extreme aridity and to the rock habitat, their functional capabilities revealed significant differences. ABC transporters and pathways for osmoregulation were more diverse in the calcite chasmoendolithic community. In contrast, the ignimbrite cryptoendolithic community was enriched in pathways for secondary metabolites, such as non-ribosomal peptides (NRPS) and polyketides (PKS). Assemblies of the metagenome data produced population genomes for the major phyla found in both communities and revealed a greater diversity of Cyanobacteria population genomes for the calcite substrate. Draft genomes of the dominant Cyanobacteria in each community were constructed with more than 93% estimated completeness. The two annotated proteomes shared 64% amino acid identity and a significantly higher number of genes involved in iron update, and NRPS gene clusters, were found in the draft genomes from the ignimbrite. Both the community-wide and genome-specific differences may be related to higher water availability and the colonization of large fissures and cracks in the calcite in contrast to a harsh competition for colonization space and nutrient resources in the narrow pores of the ignimbrite. Together, these results indicated that the habitable architecture of both lithic substrates- chasmoendolithic versus cryptoendolithic - might be an essential element in determining the colonization and the diversity of the microbial communities in endolithic substrates at the dry limit for life.

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