Cataloguing the bacterial diversity in the active ectomycorrhizal zone of Astraeus from a dry deciduous forest of Shorea

The plant microbiome has been considered one of the most researched areas of microbial biodiversity, yet very little information is available on the microbial communities prevailing in the mushroom's ectomycorrhizosphere. Ectomycorrhizal symbioses often result in the formation of a favourable niche which enables the thriving of various microbial symbionts where these symbionts endorse functions, such as quorum sensing, biofilm formation, volatile microbial compound (VOC) production, regulation of microbial gene expression, symbiosis and virulence. The identification of hidden uncultured microbial communities around the active ectomycorrhizal zone of Astraeus from dry deciduous sal forest of Jharkhand, India was carried out using MinION Oxford Nanopore sequencing of 16S rRNA amplicons genes. High richness of Operational Taxonomic Units (1,905 OTUs) was observed. We recorded 25 distinct phyla. Proteobacteria (36%) was the most abundant phylum, followed by Firmicutes (28%), Actinobacteria (10%) and Bacteroidetes (6%), whereas Gammaproteobacteria was the most abundant class of bacterial communities in the active ectomycorrhizal zone. The ectomycorrhizosphere soil has abundant phosphate-solubilising bacteria (PSB). This is the first report of the ectomycorrhizosphere microbiome associated with Astraeus.

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

Annals of Glaciology ◽

10.1017/aog.2018.18 ◽

2018 ◽

Vol 59 (77) ◽

pp. 10-20 ◽

Cited By ~ 4

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.

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

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.00160.2019 ◽

2019 ◽

Vol 317 (5) ◽

pp. G618-G624 ◽

Cited By ~ 15

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.

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

PeerJ ◽

10.7717/peerj.6044 ◽

2018 ◽

Vol 6 ◽

pp. e6044 ◽

Cited By ~ 2

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

Microorganisms ◽

10.3390/microorganisms8020213 ◽

2020 ◽

Vol 8 (2) ◽

pp. 213 ◽

Cited By ~ 2

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.

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New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

Microorganisms ◽

10.3390/microorganisms9030659 ◽

2021 ◽

Vol 9 (3) ◽

pp. 659

Author(s):

Elias Asimakis ◽

Panagiota Stathopoulou ◽

Apostolis Sapounas ◽

Kanjana Khaeso ◽

Costas Batargias ◽

...

Keyword(s):

Relative Abundance ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Mutual Exclusion ◽

Bacterial Composition ◽

Operational Taxonomic Units ◽

Host Diet ◽

Dominant Bacteria ◽

High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

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Extremely Halophilic Biohydrogen Producing Microbial Communities from High-Salinity Soil and Salt Evaporation Pond

Fuels ◽

10.3390/fuels2020014 ◽

2021 ◽

Vol 2 (2) ◽

pp. 241-252

Author(s):

Dyah Asri Handayani Taroepratjeka ◽

Tsuyoshi Imai ◽

Prapaipid Chairattanamanokorn ◽

Alissara Reungsang

Keyword(s):

Microbial Communities ◽

High Throughput ◽

High Throughput Sequencing ◽

High Salinity ◽

Amplicon Sequencing ◽

Spatial Proximity ◽

Lignocellulosic Waste ◽

Evaporation Pond ◽

Operational Taxonomic Units ◽

Determining Factor

Extreme halophiles offer the advantage to save on the costs of sterilization and water for biohydrogen production from lignocellulosic waste after the pretreatment process with their ability to withstand extreme salt concentrations. This study identifies the dominant hydrogen-producing genera and species among the acclimatized, extremely halotolerant microbial communities taken from two salt-damaged soil locations in Khon Kaen and one location from the salt evaporation pond in Samut Sakhon, Thailand. The microbial communities’ V3–V4 regions of 16srRNA were analyzed using high-throughput amplicon sequencing. A total of 345 operational taxonomic units were obtained and the high-throughput sequencing confirmed that Firmicutes was the dominant phyla of the three communities. Halanaerobium fermentans and Halanaerobacter lacunarum were the dominant hydrogen-producing species of the communities. Spatial proximity was not found to be a determining factor for similarities between these extremely halophilic microbial communities. Through the study of the microbial communities, strategies can be developed to increase biohydrogen molar yield.

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Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice

Microorganisms ◽

10.3390/microorganisms8111657 ◽

2020 ◽

Vol 8 (11) ◽

pp. 1657

Author(s):

Abdul-Salam Juhmani ◽

Alessandro Vezzi ◽

Mohammad Wahsha ◽

Alessandro Buosi ◽

Fabio De Pascale ◽

...

Keyword(s):

Microbial Communities ◽

Bacterial Communities ◽

Host Response ◽

Environmental Parameters ◽

16S Rrna Genes ◽

Rrna Genes ◽

Nutrient Concentrations ◽

Lagoon Of Venice ◽

Anthropogenic Stressors ◽

Rich Diversity

Seaweeds are a group of essential photosynthetic organisms that harbor a rich diversity of associated microbial communities with substantial functions related to host health and defense. Environmental and anthropogenic stressors may disrupt the microbial communities and their metabolic activity, leading to host physiological alterations that negatively affect seaweeds’ performance and survival. Here, the bacterial communities associated with one of the most common seaweed, Ulva laetevirens Areshough, were sampled over a year at three sites of the lagoon of Venice affected by different environmental and anthropogenic stressors. Bacterial communities were characterized through Illumina sequencing of the V4 hypervariable region of 16S rRNA genes. The study demonstrated that the seaweed associated bacterial communities at sites impacted by environmental stressors were host-specific and differed significantly from the less affected site. Furthermore, these communities were significantly distinct from those of the surrounding seawater. The bacterial communities’ composition was significantly correlated with environmental parameters (nutrient concentrations, dissolved oxygen saturation, and pH) across sites. This study showed that several more abundant bacteria on U. laetevirens at stressed sites belonged to taxa related to the host response to the stressors. Overall, environmental parameters and anthropogenic stressors were shown to substantially affect seaweed associated bacterial communities, which reflect the host response to environmental variations.

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Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework

Microbiome ◽

10.1186/s40168-021-01023-y ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Alberto Pascual-García

Keyword(s):

Microbial Communities ◽

Microbial Ecology ◽

Environmental Conditions ◽

The Novel ◽

Methodological Framework ◽

Operational Taxonomic Units ◽

Traditional Classification ◽

Taxonomical Classification ◽

Novel Concept

AbstractIn this comment, we analyse the conceptual framework proposed by Aguirre de Cárcer (Microbiome 7:142, 2019), introducing the novel concept of Phylogenetic Core Groups (PCGs). This notion aims to complement the traditional classification in operational taxonomic units (OTUs), widely used in microbial ecology, to provide a more intrinsic taxonomical classification which avoids the use of pre-determined thresholds. However, to introduce this concept, the author frames his proposal in a wider theoretical framework based on a conceptualization of selection that we argue is a tautology. This blurs the subsequent formulation of an assembly principle for microbial communities, favouring that some contradictory examples introduced to support the framework appear aligned in their conclusions. And more importantly, under this framework and its derived methodology, it is not possible to infer PCGs from data in a consistent way. We reanalyse the proposal to identify its logical and methodological flaws and, through the analysis of synthetic scenarios, we propose a number of methodological refinements to contribute towards the determination of PCGs in a consistent way. We hope our analysis will promote the exploration of PCGs as a potentially valuable tool, helping to bridge the gap between environmental conditions and community composition in microbial ecology.

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Detection of Protozoan Hosts for Legionella pneumophila in Engineered Water Systems by Using a Biofilm Batch Test

Applied and Environmental Microbiology ◽

10.1128/aem.00926-10 ◽

2010 ◽

Vol 76 (21) ◽

pp. 7144-7153 ◽

Cited By ~ 36

Author(s):

Rinske M. Valster ◽

Bart A. Wullings ◽

Dick van der Kooij

Keyword(s):

Legionella Pneumophila ◽

Biofilm Formation ◽

18S Rrna Gene ◽

Rrna Gene ◽

Batch Test ◽

Free Living ◽

Water Types ◽

Operational Taxonomic Units ◽

Hartmannella Vermiformis

ABSTRACT Legionella pneumophila proliferates in aquatic habitats within free-living protozoa, 17 species of which have been identified as hosts by using in vitro experiments. The present study aimed at identifying protozoan hosts for L. pneumophila by using a biofilm batch test (BBT). Samples (600 ml) collected from 21 engineered freshwater systems, with added polyethylene cylinders to promote biofilm formation, were inoculated with L. pneumophila and subsequently incubated at 37°C for 20 days. Growth of L. pneumophila was observed in 16 of 18 water types when the host protozoan Hartmannella vermiformis was added. Twelve of the tested water types supported growth of L. pneumophila or indigenous Legionella anisa without added H. vermiformis. In 12 of 19 BBT flasks H. vermiformis was indicated as a host, based on the ratio between maximum concentrations of L. pneumophila and H. vermiformis, determined with quantitative PCR (Q-PCR), and the composition of clone libraries of partial 18S rRNA gene fragments. Analyses of 609 eukaryotic clones from the BBTs revealed that 68 operational taxonomic units (OTUs) showed the highest similarity to free-living protozoa. Forty percent of the sequences clustering with protozoa showed ≥99.5% similarity to H. vermiformis. None of the other protozoa serving as hosts in in vitro studies were detected in the BBTs. In several tests with growth of L. pneumophila, the protozoa Diphylleia rotans, Echinamoeba thermarum, and Neoparamoeba sp. were identified as candidate hosts. In vitro studies are needed to confirm their role as hosts for L. pneumophila. Unidentified protozoa were implicated as hosts for uncultured Legionella spp. grown in BBT flasks at 15°C.

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