A high‐throughput ultrasonic spraying inoculation method promotes colony cultivation of rare microbial species

The availability of natural agarwood tends to decrease and encourage some parties to cultivate agarwood producing plants by using biological inoculation method that is microbe. In relation to this, many manufacturers produce inoculant products used to inoculate agarwood trees. This research is aimed to get some agarwood inoculant products in South Kalimantan. The inoculant products used in this study were obtained based on information from agarwood farmers in South Kalimantan. Based on observation result, inokulan products have varied form ie liquid, capsule, and stick. In addition, these products do not fullfil the packaging standards such as the absence of date of manufacture, trade license, and expiry date. The result of identification of dominant microbes inokulan product design showed some products formed from microbial species that function in agarwood formation that have not been studied even at risk of endangering human health. The results of this study are expected to be an input for farmers to be more careful in choosing the right inoculantproducts and become a driver for producers to improve the quality of inoculants produced.slsKeyword: inoculants; fungi; agarwood; quality; south kalimantanKetersediaan gubal gaharu alam semakin menurun, mendorong beberapa pihak untuk membudidayakan tanaman penghasil gaharu dengan menggunakan metode inokulasi biologis yaitu mikroba. Sehubungan dengan hal tersebut, banyak produsen membuat produk inokulan yang digunakan untuk menginokulasi pohon gaharu. Penelitian ini bertujuan untuk mendapatkan beberapa produk inokulan gaharu yang ada di Kalimantan Selatan. Produk-produk inokulan yang digunakan pada studi ini diperoleh berdasarkan informasi petani gaharu di Kalimantan Selatan. Berdasarkan hasil pengamatan diketahui produk-produk inokulan memiliki bentuk bervariasi yakni cair, kapsul, dan stik. Selain itu, produk-produk tersebut belum memenuhi standar kemasan antara lain tidak adanya informasi tanggal pembuatan, ijn dagang, dan tanggal kadaluarsa. Hasil identifikasi mikroba dominan penyusun produk inokulan menunjukkan beberapa produk terbentuk dari jenis-jenis mikroba yang fungsinya dalam pembentukan gaharu belum banyak dipelajari bahkan beresiko membahayakan kesehatan manusia. Hasil penelitian ini diharapkan dapat menjadi masukan bagi petani untuk lebih teliti dalam memilih produk inokulan yang tepat serta menjadi pendorong bagi produsen untuk meningkatkan mutu inokulan yang diproduksi.Kata kunci : inokulan; cendawan; gaharu; kualitas; Kalimantan Selatan

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mSphere of Influence: Turning to Soil for Medicines

mSphere ◽

10.1128/msphere.01258-20 ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Ching-Hsuan Lin

Keyword(s):

High Throughput ◽

Antimicrobial Compounds ◽

Appl Environ ◽

Microbial Species ◽

Link Type

ABSTRACT Ching-Hsuan Lin works in the field of Candida biology. In this mSphere of Influence article, he reflects on how the papers “Use of ichip for high-throughput in situ cultivation of uncultivable microbial species” by D. Nichols, N. Cahoon, E. M. Trakhtenberg, L. Pham, et al. (Appl Environ Microbiol 76:2445–2450, 2010, https://doi.org/10.1128/AEM.01754-09) and “A new antibiotic kills pathogens without detectable resistance” by L. L. Ling, T. Schneider, A. J. Peoples, A. L. Spoering, et al. (Nature 517:455–459, 2015, https://doi.org/10.1038/nature14098) made an impact on him by inspiring him to explore new bioactive antimicrobial compounds with his collaborators.

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HIGH-THROUGHPUT SEQUENCING ANALYSIS OF MICROBIAL POPULATIONS IN ARCTIC ROCK SAMPLE

SWS Journal of EARTH AND PLANETARY SCIENCES ◽

10.35603/eps2019/issue2.03 ◽

2019 ◽

Vol 1 (2) ◽

pp. 29-38

Author(s):

Piyush Kumar Gupta ◽

Rama Shanker Verma ◽

Maria Frolova ◽

Arkady Ayzenshtadt

Keyword(s):

Microbial Diversity ◽

Human Health ◽

High Throughput ◽

Raw Material ◽

Severe Toxicity ◽

Sequencing Analysis ◽

Dependent Manner ◽

Taxonomic Level ◽

Microbial Species ◽

Metagenomic Study

Recent developments in the existing molecular genetic tools have augmented our current understanding towards the deleterious effects of nanoparticles on human health. During building construction, the rapid generation of nanoparticles has greatly affected to human with severe toxicity by generating free radicals inside their body as potential health hazards. However, there is still need of analyzing nanoparticle toxicity based on the type of microbial diversity present on surface and its potential impacts on human health. In this study, we used rocks as raw material collected from Arkhangelsk (arctic) region of Russia and fabricated into particles of nanometer range in size by planetary ball milling. The paper presents data of the elemental composition on the basis of which the value of the specific mass energy of atomization of the raw material of the rock was calculated. The energy parameters of the micro- and nanosystems of the sample were calculated: free surface energy and surface activity. These nanoparticles were showing minimal cytotoxicity to human embryonic kidney cells in a dose-dependent manner. The high-throughput next-generation sequencing (NGS) was used to perform 16S rRNA metagenomic study for determining the type of microbial diversity present on nanoparticle’s surface. The first highest abundance was found for actinobacteria at phylum taxonomic level indicating a population of gram + ve bacteria having economic importance to human. The second highest abundance was seen for proteobacteria at similar taxonomic level exhibiting population of gram - ve bacteria causing pathogenicity in human. The highest abundance of top 25 microbial species was also discussed in this study. In future, this metagenomic study will also identify other microbial species based on 18S rRNA sequencing.

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Use of Ichip for High-Throughput In Situ Cultivation of “Uncultivable” Microbial Species

Applied and Environmental Microbiology ◽

10.1128/aem.01754-09 ◽

2010 ◽

Vol 76 (8) ◽

pp. 2445-2450 ◽

Cited By ~ 350

Author(s):

D. Nichols ◽

N. Cahoon ◽

E. M. Trakhtenberg ◽

L. Pham ◽

A. Mehta ◽

...

Keyword(s):

Growth Factors ◽

High Throughput ◽

Applied Research ◽

New Method ◽

Diffusion Chambers ◽

Microbial Species ◽

Naturally Occurring ◽

Environmental Cell ◽

Parallel Cultivation

ABSTRACT One of the oldest unresolved microbiological phenomena is why only a small fraction of the diverse microbiological population grows on artificial media. The “uncultivable” microbial majority arguably represents our planet's largest unexplored pool of biological and chemical novelty. Previously we showed that species from this pool could be grown inside diffusion chambers incubated in situ, likely because diffusion provides microorganisms with their naturally occurring growth factors. Here we utilize this approach and develop a novel high-throughput platform for parallel cultivation and isolation of previously uncultivated microbial species from a variety of environments. We have designed and tested an isolation chip (ichip) composed of several hundred miniature diffusion chambers, each inoculated with a single environmental cell. We show that microbial recovery in the ichip exceeds manyfold that afforded by standard cultivation, and the grown species are of significant phylogenetic novelty. The new method allows access to a large and diverse array of previously inaccessible microorganisms and is well suited for both fundamental and applied research.

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A model ecosystem of twelve cryopreservable microbial species allowing for a non-invasive approach

10.1101/2020.10.23.351742 ◽

2020 ◽

Author(s):

Kazufumi Hosoda ◽

Shigeto Seno ◽

Naomi Murakami ◽

Hideo Matsuda ◽

Yutaka Osada ◽

...

Keyword(s):

Machine Learning ◽

Experimental Model ◽

High Throughput ◽

Learning Model ◽

Invasive Approach ◽

Model Ecosystem ◽

Non Invasive ◽

Microbial Species ◽

Machine Learning Model ◽

Diverse Interactions

AbstractWe developed a synthetic ecosystem of 12 cryopreservable microbial species with diverse interactions as an experimental “model ecosystem.” We created a machine learning model that noninvasively distinguished the 12 species on micrographs enabling high-throughput measurements. Our synthetic ecosystems maintained a certain diversity for at least six months.

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