Metagenomic Achievements in Microbial Diversity Determination in Croplands

Wolińska, Agnieszka

doi:10.1016/b978-0-12-814849-5.00002-2

Cited by 30 publications

(29 citation statements)

References 163 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The Next-Generation Sequencing (NGS) technology is one of the most important techniques for microbiological research [13,[15][16][17][18]. It has contributed to the emergence of metagenomics, i.e., an analysis of the genome of microorganisms by only DNA extraction without the necessity of cultivating microorganisms on artificial media [16,18,19]. Dijk et al [20] and Wolińska et al [21] suggested that the NGS technique contributed to overcoming the shortages and limitations that are connected with detection of only the most abundant and cultivated genera.…”

Section: Next Generation Sequencing Platforms As An Effective Tool Inmentioning

confidence: 99%

“…Three basic platforms can be distinguished in NGS: Roche 454-pyrosequencing, Ion Torrent, and Illumina sequencing. They differ in the average length of the base pair reading (Roche 454-500 base pairs, Ion Torrent~200-300 base pairs, Illumina~120-150 for SR200, and 250-300 base pairs for v2 250PE and v3 300 PE, respectively) [16,18,25]. The Ion Torrent and the Illumina rely on a slightly different mechanism of detection of nucleotide sequences.…”

Section: Next Generation Sequencing Platforms As An Effective Tool Inmentioning

confidence: 99%

“…NGS facilitates studies of endophytic microbiomes, reveals bacterial biodiversity, and gives the possibility of in-depth analysis of bacterial communities in taxonomic and phylogenetic terms [18,19,32]. It is applied as an effective tool for the identification and characterization of endophytic bacteria, providing an understanding of their interactions with host plants [12,15,17,23].…”

Section: Next Generation Sequencing Platforms As An Effective Tool Inmentioning

confidence: 99%

See 2 more Smart Citations

Agricultural and Other Biotechnological Applications Resulting from Trophic Plant-Endophyte Interactions

2019

View full text Add to dashboard Cite

Endophytic microbiota plays a role not only in supplying plants with the basic nutrients indispensable for their growth, but also helps them in the mechanisms of adaptation to various environmental stresses (i.e., salinity, drought), which is important in the aspect of crop yields. From the agricultural and biotechnological points of view, the knowledge of endophytes and their roles in increasing crop yields, plant resistance to diseases, and helping to survive environmental stress is extremely desirable. This paper reviews some of the beneficial plant–microbe interactions that might be potentially used in both agriculture (plant growth stimulation effect, adaptation of host organisms in salinity and drought conditions, and support of defense mechanisms in plants), and in biotechnology (bioactive metabolites, application of endophytes for bioremediation and biotransformation processes, and production of biofertilizers and biopreparations). Importantly, relatively recent reports on endophytes from the last 10 years are summarized in this paper.

show abstract

Section: Next Generation Sequencing Platforms As An Effective Tool Inmentioning

confidence: 99%

Section: Next Generation Sequencing Platforms As An Effective Tool Inmentioning

confidence: 99%

Section: Next Generation Sequencing Platforms As An Effective Tool Inmentioning

confidence: 99%

See 1 more Smart Citation

Agricultural and Other Biotechnological Applications Resulting from Trophic Plant-Endophyte Interactions

2019

View full text Add to dashboard Cite

show abstract

“…For example, Nitrospira in phylum Nitrospirae was known as aerobic chemolithoautotrophic which was usually associated with ammonia-oxidization which mainly found in soils, groundwater, rhizosphere and surface of the plants 38 . Various enriched Alphaproteobacteria in wild macaques such as Gemmata 39 , Planctomyces 40 , Bradyrhizobium 41 , Rhodospirillaceae 42 , and Limnohabitans 43 were typical bacteria found in soil or freshwater which were mostly autotrophs or symbionts in the rhizosphere or bacterioplanktons. There was no evidence supported that these bacteria can be colonized on the epithelia of oral cavity.…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of oral-gut microbiota between captive and wild long-tailed macaque in Thailand

Sawaswong

Praianantathavorn

Chanchaem

et al. 2021

Sci Rep

View full text Add to dashboard Cite

Long-tailed macaques (Macaca fascicularis), distributed in Southeast Asia, are generally used in biomedical research. At present, the expansion of human communities overlapping of macaques’ natural habitat causes human-macaque conflicts. To mitigate this problem in Thailand, the National Primate Research Center of Thailand, Chulalongkorn University (NPRCT-CU), was granted the permit to catch the surplus wild-born macaques and transfer them to the center. Based on the fact that the diets provided and the captive environments were different, their oral-gut microbiota should be altered. Thus, we investigated and compared the oral and fecal microbiome between wild-born macaques that lived in the natural habitats and those transferred to and reared in the NPRCT-CU for 1 year. The results from 16S rRNA high-throughput sequencing showed that the captive macaques had distinct oral-gut microbiota profiles and lower bacterial richness compared to those in wild macaques. The gut of wild macaques was dominated by Firmicutes which is probably associated with lipid absorption and storage. These results implicated the effects of captivity conditions on the microbiome that might contribute to crucial metabolic functions. Our study should be applied to the animal health care program, with respect to microbial functions, for non-human primates.

show abstract

“…In recent years metagenomics has developed. It is a method of genome analysis consisting of all microorganisms inhabiting the environment [76]. Modern research methods allow us to explore the influence of various environmental factors on soil microorganisms [18].…”

Section: Introductionmentioning

confidence: 99%

Edaphic Factors And Their Influence On The Microbiological Biodiversity Of The Soil Environment

Furtak

Gałązka

2019

Postępy Mikrobiologii - Advancements of Microbiology

View full text Add to dashboard Cite

The edaphic factors are the soil properties that affect the diversity of organisms living in the soil environment. These include soil structure, temperature, pH, and salinity. Some of them are influenced by man, but most are independent of human activity. These factors influence the species composition of soil microbial communities, but also their activity and functionality. The correlations between different abiotic factors and microbial groups described in this manuscript indicate both the complexity of the soil environment and its sensitivity to various stimuli. 1. Introduction. 2. Soil type and structure. 3. Soil pH and salinity. 4. Soil temperature. 5. Soil moisture. 6. Organic carbon and nitrogen content. 7. Heavy metals content. 8. Conclusions CZYNNIKI EDAFICZNE I ICH WPŁYW NA BIORÓŻNORODNOŚĆ MIKROBIOLOGICZNĄ ŚRODOWISKA GLEBOWEGO Streszczenie: Czynniki edaficzne to właściwości gleby, które wpływają na różnorodność wszystkich organizmów żyjących w środowisku glebowym. Należą do nich m.in. struktura gleby, temperatura, pH, zakwaszenie i zasolenie. Na niektóre z nich człowiek ma wpływ, ale większość z nich jest niezależna od działalności człowieka. Czynniki te, wpływają na skład gatunkowy zbiorowisk mikroorganizmów glebowych, ale także na ich aktywność oraz funkcjonalność. Opisane w niniejszym manuskrypcie korelacje pomiędzy różnymi czynnikami abiotycznymi oraz grupami drobnoustrojów wskazują zarówno na złożoność środowiska glebowego, jak i jego wrażliwość na różne bodźce. 1.Wprowadzenie. 2. Typ i struktura gleby. 3. pH i zasolenie gleby. 4. Temperatura gleby. 5. Wilgotność gleby. 6. Zawartość węgla organicznego i azotu. 7. Zawartość metali ciężkich. 8. Podsumowanie.

show abstract

Metagenomic Achievements in Microbial Diversity Determination in Croplands

Cited by 30 publications

References 163 publications

Agricultural and Other Biotechnological Applications Resulting from Trophic Plant-Endophyte Interactions

Agricultural and Other Biotechnological Applications Resulting from Trophic Plant-Endophyte Interactions

Comparative analysis of oral-gut microbiota between captive and wild long-tailed macaque in Thailand

Edaphic Factors And Their Influence On The Microbiological Biodiversity Of The Soil Environment

Contact Info

Product

Resources

About