From Microscopy to Genomic Approach in Soil Biodiversity Assessment

Popescu, L; Cao, Zhijun

doi:10.21775/cimb.027.195

Cited by 5 publications

(5 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…However, it needs more consumption of work and times, while probably some strains (for example, those non-pathogens to the great wax moth) could be not obtained [17,50]. Then, the metagenome has been developing for diversity research of soil microbes in the recent decade [51], it can detect the soil EFs species, but it cannot isolate the EFs strain and discover new EFs species. In addition, selective media with the advantages of more simple and economical technology have been using to separate the soil EFs [52].…”

Section: Discussionmentioning

confidence: 99%

Biodiversity of Entomopathogenic Fungi in the Soils of South China

et al. 2019

View full text Add to dashboard Cite

The southern part of China, located in tropical and south subtropical areas has unique natural environments, but the distributions of entomopathogenic fungi (EFs) in the soil are not clear. In this research, 198 soil samples were collected from the four Provinces (Autonomous Region) of South China. The results indicated that a total of 292 fungal isolates were obtained from 176 soil samples. Then, based on the morphological and rDNA-ITS sequences analysis, 213 EFs isolates of 19 species in 12 genera were identified. Furthermore, Purpureocillium lilacinum with 75 isolates was recognized as the absolutely dominant EF species, while Isaria javanica, Metarhizium anisopliae, and Beauveria bassiana (respectively with 29, 26, and 26 isolates) were the richer species. The data also indicated that Guangxi Province has the best EFs diversity with the Shannon–Wiener index (SWI) of 2.29, the soils covered with grass had the best EFs diversity with the 2.14 SWI, while the orchard and fallow land had the lowest SWI of 1.52, which suggested that the diversity of plants and insects on ground, as well as the massive application of broad-spectrum fungicides, affect the EFs diversity in the soil. Finally, the rare species, Nectria mauritiicola and Scopulariopsis brumptii were first reported about their entomopathogenic activities against Bemisia tabaci. Our experiment will give new insights to the understanding of EFs distribution characteristics and their biodiversity conservation.

show abstract

Section: Discussionmentioning

confidence: 99%

Biodiversity of Entomopathogenic Fungi in the Soils of South China

et al. 2019

View full text Add to dashboard Cite

show abstract

“…In spite of all these false hopes, limitations, and biases (Lombard et al, 2011; Prosser, 2015), it is fair to say that, at the moment, bulk “meta”-something-“omics” approaches (metagenomics, metatranscriptomics, metaproteomics, metabolomics) capture virtually all the funding dedicated to soil microbial diversity, and their use seems to be crucial to insure microbiologists’ career advancement. Year after year, articles praising the merits of metagenomics to uncover the secrets of soils (e.g., van Elsas et al, 2008; Vogel et al, 2009; Delmont et al, 2011; Fierer, 2017; Popescu and Cao, 2018) still make headlines 6 and attract record numbers of citations.…”

Section: The Microbiological Scenementioning

confidence: 99%

Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

et al. 2018

View full text Add to dashboard Cite

Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.

show abstract

“…In particular, the multiciliated surface cells (MSC) on the surface of some aquatic embryos may have a role in managing extraembryonic microbes. These widespread epithelial cells create a synchronized metachronal beat which generates current around developing catshark (Scyliorhinus canicula [144]), frog [145][146][147][148]; caecilian [149,150]; salamander [151][152][153][154], Australian lungfish (Neoceratodus fosteri; [3], and multiple invertebrates [155] including amphioxus [156]. A more restrictive MSC population associated with the lateral line system has also been reported for bichir (Polypterus senegalensis, P. palmas; [157,158]), gar (Lepisosteus platyrhincus [159,160]) and sturgeon (Acipenser transmontanus [157]), and they have been found in the olfactory pit of the paddlefish (Polyodon spatula [161]).…”

Section: Vertebrate Embryos With Multiciliated Surface Cellsmentioning

confidence: 99%

“…The revelation that we are "animals in a bacterial world" [1,2] has largely been driven by new culture-free microbial identification techniques. These include rDNA metabarcoding [3] as well as the sequencing of entire microbial communities, or metagenomics [4]. However, parallel lines of research have identified organisms that do not require a (primarily gut) microbiome [5].…”

Section: Introductionmentioning

confidence: 99%

Developing Inside a Layer of Germs—A Potential Role for Multiciliated Surface Cells in Vertebrate Embryos

Kerney

2021

Diversity

View full text Add to dashboard Cite

This paper reviews current research on the microbial life that surrounds vertebrate embryos. Several clades are believed to develop inside sterile—or near-sterile—embryonic microhabitats, while others thrive within a veritable zoo of microbial life. The occurrence of embryo-associated microbes in some groups, but not others, is an under-appreciated transition (possibly transitions) in vertebrate evolution. A lack of comparable studies makes it currently impossible to correlate embryo-associated microbiomes with other aspects of vertebrate evolution. However, there are embryonic features that should instruct a more targeted survey. This paper concludes with a hypothesis for the role of multiciliated surface cells in amphibian and some fish embryos, which may contribute to managing embryo-associated microbial consortia. These cells are known to exist in some species that harbor in ovo microbes or have relatively porous egg capsules, although most have not been assayed for embryo-associated microbiota. Whether the currents generated within these extraembryonic microhabitats contribute to culturing consistent microbial communities remains to be seen.

show abstract

From Microscopy to Genomic Approach in Soil Biodiversity Assessment

Cited by 5 publications

References 0 publications

Biodiversity of Entomopathogenic Fungi in the Soils of South China

Biodiversity of Entomopathogenic Fungi in the Soils of South China

Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

Developing Inside a Layer of Germs—A Potential Role for Multiciliated Surface Cells in Vertebrate Embryos

Contact Info

Product

Resources

About