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 Variability of the structure of winter microbial communities in Chelyabinsk lakes

2021 ◽  
Vol 29 (4) ◽  
pp. 311-318
Author(s):  
S. V. Andreeva ◽  
Y. Y. Filippova ◽  
E. V. Devyatova ◽  
D. Y. Nokhrin
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Water Bodies ◽  
Coliform Bacteria ◽  
Form Complex ◽  
Freshwater Bodies ◽  
Dynamic Communities ◽  
Chelyabinsk Region ◽  
High Level ◽  
First Time

Microorganisms form complex and dynamic communities that play a key role in the biogeochemical cycles of lakes. A high level of urbanization is currently a serious threat to bacterial communities and the ecosystem of freshwater bodies. To assess the contribution of anthropogenic load to variations in the structure of winter microbial communities in lakes, microorganisms of four water bodies of Chelyabinsk region were studied for the first time. We used cultural, chromatography-mass spectrometric, and modern methods of statistical data processing (particularly, multivariate exploratory analysis and canonical analysis of correspondences). The research showed that the composition of winter microbial communities in lakes Chebarkul’, Smolino, Pervoye, and Shershenevskoye Reservoir did not differ significantly between the main phyla of microorganisms. The dominant microorganisms were found to be of the Firmicutes phylum and Actinobacteria phylum. The structure of bacterial communities had special features depending on the characteristics of the water body and the sampling depths. Thus, in the lakes Smolino, Pervoye, and Shershenevskoye Reservoir, an important role was played by associations between microorganisms – indicators of fecal contamination: coliform bacteria and Enterococcus. On the contrary, in Chebarkul’ Lake, members of the genus Bacillus, which are natural bioremediators, formed stable winter associations. However, the differences between water bodies and sampling depths reflected 28.1% and 9.8% of the variability of the winter microbial communities, respectively. The largest contribution (about 60%) to the variability of the structure was made by intra-water processes, which determined the high heterogeneity of samples from different water areas. We assume that an important role in this variability was played by the high anthropogenic impact in a large industrial metropolis. In our opinion, this line of research is very promising for addressing key environmental issues.

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 Metagenomic Profiling and Identification of Antimicrobial Resistance Genes from Airborne Microbial Communities

2015 ◽  
Vol 7 (1) ◽  
Author(s):  
Tamar Dickerson ◽  
Jonathan L. Jacobs ◽  
Nicole Waybright ◽  
Danielle Swales ◽  
Peggy Lowary ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Antimicrobial Resistance ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Temporal Dynamics ◽  
Animal Health ◽  
Functional Metagenomics ◽  
Antimicrobial Resistance Genes ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Antimicrobial resistance (AMR) is recognized as a severe threat to human and animal health worldwide, yet relatively little is known regarding the bioavailability of AMR genes in airborne microbial communities. Hence, the objective of our study is to use next generation sequencing (NGS) to assess the temporal dynamics of airborne bacterial communities as well as functional metagenomics to investigate the dispersion of AMR genes present within them.

scholarly journals Bacterial diversity in snow from mid-latitude mountain areas: Alps, Eastern Anatolia, Karakoram and Himalaya

2018 ◽  
Vol 59 (77) ◽  
pp. 10-20 ◽  
Author(s):  
Roberto Sergio Azzoni ◽  
Ilario Tagliaferri ◽  
Andrea Franzetti ◽  
Christoph Mayer ◽  
Astrid Lambrecht ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
The Arctic ◽  
Eastern Anatolia ◽  
Mountain Areas ◽  
Air Mass ◽  
Back Trajectories ◽  
Air Masses ◽  
Operational Taxonomic Units ◽  
High Throughput Dna Sequencing

ABSTRACTSnow can be considered an independent ecosystem that hosts active microbial communities. Snow microbial communities have been extensively investigated in the Arctic and in the Antarctica, but rarely in mid-latitude mountain areas. In this study, we investigated the bacterial communities of snow collected in four glacierized areas (Alps, Eastern Anatolia, Karakoram and Himalaya) by high-throughput DNA sequencing. We also investigated the origin of the air masses that produced the sampled snowfalls by reconstructing back-trajectories. A standardized approach was applied to all the analyses in order to ease comparison among different communities and geographical areas. The bacterial communities hosted from 25 to 211 Operational Taxonomic Units (OTUs), and their structure differed significantly between geographical areas. This suggests that snow bacterial communities may largely derive from ‘local’ air bacteria, maybe by deposition of airborne particulate of local origin that occurs during snowfall. However, some evidences suggest that a contribution of bacteria collected during air mass uplift to snow communities cannot be excluded, particularly when the air mass that originated the snow event is particularly rich in dust.

scholarly journals A Deeper Look into the Biodiversity of the Extremely Acidic Copahue volcano-Río Agrio System in Neuquén, Argentina

2019 ◽  
Vol 8 (1) ◽  
pp. 58 ◽  
Author(s):  
Germán Lopez Bedogni ◽  
Francisco L. Massello ◽  
Alejandra Giaveno ◽  
Edgardo Rubén Donati ◽  
María Sofía Urbieta
Keyword(s):  
Extreme Environment ◽  
Low Ph ◽  
Rrna Gene ◽  
Prokaryotic Community ◽  
Operational Taxonomic Units ◽  
Acidic River ◽  
First Time ◽  
The 16S Rrna Gene ◽  
Generation Sequencing ◽  
Autochthonous Species

The Copahue volcano-Río Agrio system, on Patagonia Argentina, comprises the naturally acidic river Río Agrio, that runs from a few meters down the Copahue volcano crater to more than 40 km maintaining low pH waters, and the acidic lagoon that sporadically forms on the crater of the volcano, which is studied for the first time in this work. We used next-generation sequencing of the 16S rRNA gene of the entire prokaryotic community to study the biodiversity of this poorly explored extreme environment. The correlation of the operational taxonomic units (OTUs)s presence with physicochemical variables showed that the system contains three distinct environments: the crater lagoon, the Upper Río Agrio, and the Salto del Agrio waterfall, a point located approximately 12 km down the origin of the river, after it emerges from the Caviahue lake. The prokaryotic community of the Copahue Volcano-Río Agrio system is mainly formed by acidic bacteria and archaea, such as Acidithiobacillus, Ferroplasma, and Leptospirillum, which have been isolated from similar environments around the world. These results support the idea of a ubiquitous acidic biodiversity; however, this highly interesting extreme environment also has apparently autochthonous species such as Sulfuriferula, Acidianus copahuensis, and strains of Acidibacillus and Alicyclobacillus.

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 Dietary Bovine Milk Exosomes Elicit Changes in Microbial Communities in C57BL/6 Mice

2018 ◽  
Author(s):  
Fang Zhou ◽  
Henry A. Paz ◽  
Jiang Shu ◽  
Mahrou Sadri ◽  
Juan Cui ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Gut Microbiome ◽  
Bovine Milk ◽  
Cell Communication ◽  
Intestinal Microbiome ◽  
Operational Taxonomic Units ◽  
Health And Disease ◽  
Cecum Content ◽  
First Time ◽  
Bovine Species

ABSTRACTExosomes and exosome-like vesicles participate in cell-to-cell communication in animals, plant and bacteria. Dietary exosomes in bovine milk are bioavailable in non-bovine species, but a fraction of milk exosomes reaches the large intestine. We hypothesized that milk exosomes alter the composition of the gut microbiome in mice. C57BL/6 mice were fed AIN-93G diets, defined by their content of bovine milk exosomes and RNA cargos: exosome/RNA depleted (ERD) versus exosome/RNA-sufficient (ERS) diets. Feeding was initiated at age three weeks and cecum content was collected at ages 7, 15 and 47 weeks. Microbial communities were identified by 16S rRNA gene sequencing. The dietary intake of exosomes and age had significant effects on the microbial communities in the cecum. At the phylum level, the abundance of Verrucomicrobia was greater in mice fed ERD compared to ERS, and the abundance of both Firmicutes and Tenericutes was smaller in mice fed ERD compared to ERS at age 47 weeks. At the family level, the abundance of Anaeroplasmataceae was greater in mice fed ERD compared to ERS, and the abundance of Bifidobacteriaceae, Lachnospiraceae, and Dehalobacteriaceae was significantly greater in mice fed ERS than mice fed ERD at age 15 weeks. Exosome feeding significantly altered the abundance of 52 operational taxonomic units; diet effects were particularly strong in the Lachnospiraceae, Ruminococcaceae and the Verrucomicrobiaceae families. We conclude that exosomes in bovine milk alter microbial communities in non-bovine species, suggesting that exosomes and their cargos participate in the crosstalk between bacterial and animal kingdoms.IMPORTANCEVirtually all living cells, including bacteria communicate through exosomes, which can be found in all body fluids. Exosomes and the RNA cargos have been implicated in all aspects of health and disease, e.g., metastasis of cancer, neuronal signaling and embryonic development. Previously, we reported that exosomes and their microRNA cargos are not solely derived from endogenous synthesis, but may also be obtained from dietary sources such as bovine milk in non-bovine mammals. Here, we report for the first time that bovine milk exosomes communicate with the intestinal microbiome and alters microbial communities in mice. This is the first report suggesting that the gut microbiome facilitates the signaling by dietary exosomes across kingdoms: animal (cow) → bacteria → animal (mouse).

scholarly journals Dietary bovine milk exosomes elicit changes in bacterial communities in C57BL/6 mice

2019 ◽  
Vol 317 (5) ◽  
pp. G618-G624 ◽  
Author(s):  
Fang Zhou ◽  
Henry A. Paz ◽  
Mahrou Sadri ◽  
Juan Cui ◽  
Stephen D. Kachman ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Gut Microbiome ◽  
Bacterial Communities ◽  
Bovine Milk ◽  
Cell Communication ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
The Family ◽  
Rrna Gene Sequencing

Exosomes and exosome-like vesicles participate in cell-to-cell communication in animals, plant, and bacteria. Dietary exosomes in bovine milk are bioavailable in nonbovine species, but a fraction of milk exosomes reaches the large intestine. We hypothesized that milk exosomes alter the composition of the gut microbiome in mice. C57BL/6 mice were fed AIN-93G diets, defined by their content of bovine milk exosomes and RNA cargos: exosome/RNA-depleted (ERD) versus exosome/RNA-sufficient (ERS) diets. Feeding was initiated at age 3 wk, and cecum content was collected at ages 7, 15, and 47 wk. Microbial communities were identified by 16S rRNA gene sequencing. Milk exosomes altered bacterial communities in the murine cecum. The abundance of three phyla, seven families, and 52 operational taxonomic units (OTUs) was different in the ceca from mice fed ERD and ERS ( P < 0.05). For example, at the phylum level, Tenericutes had more than threefold abundance in ERS mice at ages 15 and 47 wk compared with ERD mice ( P < 0.05). At the family level, Verrucomicrobiaceae were much less abundant in ERS mice compared with ERD mice age 47 wk ( P < 0.05). At the OTU level, four OTUs from the family of Lachnospiraceae were more than two times more abundant in ERS mice compared with ERD at age 7 and 47 wk ( P < 0.05). We conclude that exosomes in bovine milk alter microbial communities in nonbovine species, suggesting that exosomes and their cargos participate in the crosstalk between bacterial and animal kingdoms. NEW & NOTEWORTHY This is the first report that exosomes from bovine milk alter microbial communities in mice. This report suggests that the gut microbiome facilitates cell-to-cell communication by milk exosomes across species boundaries, and milk exosomes facilitate communication across animal and bacteria kingdoms.

scholarly journals Bacterial diversity and community in Qula from the Qinghai–Tibetan Plateau in China

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6044 ◽  
Author(s):  
Yan Zhu ◽  
Yingying Cao ◽  
Min Yang ◽  
Pengchen Wen ◽  
Lei Cao ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Microbial Interactions ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
Different Origins ◽  
Different Levels ◽  
Different Origin

Qula is a cheese-like product usually prepared with unpasteurized yak milk under open conditions, with both endogenous and exogenous microorganisms involved in the fermentation process. In the present study, 15 Qula samples were collected from five different regions in China to investigate the diversity of microbial communities using high-throughput sequencing targeting the V3–V4 region of 16S rRNA gene. The bacterial diversity significantly differed among samples of different origins, indicating a possible effect of geography. The result also showed that microbial communities significantly differed in samples of different origin and these differences were greater at the genus than the phylum level. A total of six phyla were identified in the samples, and Firmicutes and Proteobacteria had a relative abundance >20%. A total of 73 bacterial genera were identified in the samples. Two dominant genera (Lactobacillus and Acetobacter) were common to all samples, and a total of 47 operational taxonomic units at different levels significantly differed between samples of different origin. The predicted functional genes of the bacteria present in samples also indicated differences in bacterial communities between the samples of different origin. The network analysis showed that microbial interactions between bacterial communities in Qula were very complex. This study lays a foundation for further investigations into its food ecology.

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