scholarly journals Study of Oak Ridge soils using BONCAT-FACS-Seq reveals that a large fraction of the soil microbiome is active

2018 ◽  
Author(s):  
Estelle Couradeau ◽  
Joelle Sasse ◽  
Danielle Goudeau ◽  
Nandita Nath ◽  
Terry C. Hazen ◽  
...  
Keyword(s):  
Soil Microbes ◽  
Sequence Similarity ◽  
Large Fraction ◽  
Amplicon Sequencing ◽  
Bulk Soil ◽  
Soil Microbiome ◽  
Active Fraction ◽  
Soil Microbial Diversity ◽  
Oak Ridge

AbstractThe ability to link soil microbial diversity to soil processes requires technologies that differentiate active subpopulations of microbes from so-called relic DNA and dormant cells. Measures of microbial activity based on various techniques including DNA labelling have suggested that most cells in soils are inactive, a fact that has been difficult to reconcile with observed high levels of bulk soil activities. We hypothesized that measures of in situ DNA synthesis may be missing the soil microbes that are metabolically active but not replicating, and we therefore applied BONCAT (Bioorthogonal Non Canonical Amino Acid Tagging) i.e. a proxy for activity that does not rely on cell division, to measure translationally active cells in soils. We compared the active population of two soil depths from Oak Ridge (TN) incubated under the same conditions for up to seven days. Depending on the soil, a maximum of 25 – 70% of the cells were active, accounting for 3-4 million cells per gram of soil type, which is an order of magnitude higher than previous estimates. The BONCAT positive cell fraction was recovered by fluorescence activated cell sorting (FACS) and identified by 16S rDNA amplicon sequencing. The diversity of the active fraction was a selected subset of the bulk soil community. Excitingly, some of the same members of the community were recruited at both depths independently from their abundance rank. On average, 86% of sequence reads recovered from the active community shared >97% sequence similarity with cultured isolates from the field site. Our observations are in line with a recent report that, of the few taxa that are both abundant and ubiquitous in soil, 45% are also cultured – and indeed some of these ubiquitous microorganisms were found to be translationally active. The use of BONCAT on soil microbiomes provides evidence that a large portion of the soil microbes can be active simultaneously. We conclude that BONCAT coupled to FACS and sequencing is effective for interrogating the active fraction of soil microbiomes in situ and provides new perspectives to link metabolic capacity to overall soil ecological traits and processes.

scholarly journals DNA- and RNA-SIP Reveal Nitrospira spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters

mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
Arda Gülay ◽  
S. Jane Fowler ◽  
Karolina Tatari ◽  
Bo Thamdrup ◽  
Hans-Jørgen Albrechtsen ◽  
...  
Keyword(s):  
16S Rrna ◽  
Ammonia Oxidation ◽  
Sequence Similarity ◽  
Sodium Chlorate ◽  
Amplicon Sequencing ◽  
Stable Isotope Probing ◽  
Ammonia Oxidizer ◽  
16S Rrna Sequence ◽  
Dna And Rna

ABSTRACT Nitrification, the oxidative process converting ammonia to nitrite and nitrate, is driven by microbes and plays a central role in the global nitrogen cycle. Our earlier investigations based on 16S rRNA and amoA amplicon analysis, amoA quantitative PCR and metagenomics of groundwater-fed biofilters indicated a consistently high abundance of comammox Nitrospira. Here, we hypothesized that these nonclassical nitrifiers drive ammonia-N oxidation. Hence, we used DNA and RNA stable isotope probing (SIP) coupled with 16S rRNA amplicon sequencing to identify the active members in the biofilter community when subjected to a continuous supply of NH4+ or NO2− in the presence of 13C-HCO3− (labeled) or 12C-HCO3− (unlabeled). Allylthiourea (ATU) and sodium chlorate were added to inhibit autotrophic ammonia- and nitrite-oxidizing bacteria, respectively. Our results confirmed that lineage II Nitrospira dominated ammonia oxidation in the biofilter community. A total of 78 (8 by RNA-SIP and 70 by DNA-SIP) and 96 (25 by RNA-SIP and 71 by DNA-SIP) Nitrospira phylotypes (at 99% 16S rRNA sequence similarity) were identified as complete ammonia- and nitrite-oxidizing, respectively. We also detected significant HCO3− uptake by Acidobacteria subgroup10, Pedomicrobium, Rhizobacter, and Acidovorax under conditions that favored ammonia oxidation. Canonical Nitrospira alone drove nitrite oxidation in the biofilter community, and activity of archaeal ammonia-oxidizing taxa was not detected in the SIP fractions. This study provides the first in situ evidence of ammonia oxidation by comammox Nitrospira in an ecologically relevant complex microbiome. IMPORTANCE With this study we provide the first in situ evidence of ecologically relevant ammonia oxidation by comammox Nitrospira in a complex microbiome and document an unexpectedly high H13CO3− uptake and growth of proteobacterial and acidobacterial taxa under ammonia selectivity. This finding raises the question of whether comammox Nitrospira is an equally important ammonia oxidizer in other environments.

scholarly journals Comparative study of microbial structure and functional profile of sunflower rhizosphere grown in two fields

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Blessing Chidinma Nwachukwu ◽  
Ayansina Segun Ayangbenro ◽  
Olubukola Oluranti Babalola
Keyword(s):  
Microbial Communities ◽  
Malic Acid ◽  
Clay Content ◽  
Amplicon Sequencing ◽  
Bulk Soil ◽  
Soil Microbiome ◽  
Microbial Composition ◽  
Soil Microbial ◽  
Carbon Substrates ◽  
Microbial Groups

Abstract Background Microbial communities inhabiting the rhizosphere play pivotal roles in determining plant health and yield. Manipulation of the rhizosphere microbial community is a promising means to enhance the productivity of economically viable and important agricultural crops such as sunflower (Helianthus annuus). This study was designed to gain insights into the taxonomic and functional structures of sunflower rhizosphere and bulk soil microbiome at two different locations (Sheila and Itsoseng) in South Africa. Results Microbial DNA extracted from the sunflower rhizosphere and bulk soils was subjected to next-generation sequencing using 16S amplicon sequencing technique. Firmicutes, Actnobacteria and Proteobacteria predominated sunflower rhizosphere soils. Firmicutes, Cyanobacteria, Deinococcus-Thermus and Fibrobacteres were positively influenced by Na+ and clay content, while Actinobacteria, Thaumarchaeota, Bacteroidetes, Planctomycetes, Aquificae and Chloroflexi were positively influenced by soil resistivity (Res) and Mg2+. The community-level physiological profiling (CLPP) analysis showed that the microbial communities in SHR and ITR used the amino acids tryptophan and malic acid efficiently. The metabolisms of these carbon substrates may be due to the dominant nature of some of the organisms, such as Actinobacteria in the soils. Conclusion The CLPP measurements of soil from sunflower rhizosphere were different from those of the bulk soil and the degree of the variations were based on the type of carbon substrates and the soil microbial composition. This study has shown the presence of certain taxa of rhizobacteria in sunflower rhizosphere which were positively influenced by Na+ and Mg2+, and taxa obtained from SHR and ITR were able to effectively utilized tryptophan and malic acid. Many unclassified microbial groups were also discovered and it is therefore recommended that efforts should further be made to isolate, characterize and identify these unclassified microbial species, as it might be plausible to discover new microbial candidates that can further be harnessed for biotechnological purpose.

IN SITU AND PILOT ORGAN PERFUSION TECHNIQUES FOR THE STUDY OF METABOLIC DYNAMICS

1972 ◽  
Vol 68 (2_Supplb) ◽  
pp. S9-S25 ◽  
Author(s):  
John Urquhart ◽  
Nancy Keller
Keyword(s):  
Cardiac Output ◽  
Large Fraction ◽  
Experimental Studies ◽  
Test Substance ◽  
Organ Perfusion ◽  
Systemic Blood ◽  
Experimental Control ◽  
Arterial Blood ◽  
Vascular Connections

ABSTRACT Two techniques for organ perfusion with blood are described which provide a basis for exploring metabolic or endocrine dynamics. The technique of in situ perfusion with autogenous arterial blood is suitable for glands or small organs which receive a small fraction of the animal's cardiac output; thus, test stimulatory or inhibitory substances can be added to the perfusing blood and undergo sufficient dilution in systemic blood after passage through the perfused organ so that recirculation does not compromise experimental control over test substance concentration in the perfusate. Experimental studies with the in situ perfused adrenal are described. The second technique, termed the pilot organ method, is suitable for organs which receive a large fraction of the cardiac output, such as the liver. Vascular connections are made between the circulation of an intact, anaesthetized large (> 30 kg) dog and the liver of a small (< 3 kg) dog. The small dog's liver (pilot liver) is excised and floated in a bath of canine ascites, and its venous effluent is continuously returned to the large dog. Test substances are infused into either the hepatic artery or portal vein of the pilot liver, but the small size of the pilot liver and its blood flow in relation to the large dog minimize recirculation effects. A number of functional parameters of the pilot liver are described.

scholarly journals Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures

Biology ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 569
Author(s):  
Chakriya Sansupa ◽  
Sara Fareed Mohamed Wahdan ◽  
Terd Disayathanoowat ◽  
Witoon Purahong
Keyword(s):  
Bacterial Community ◽  
Forest Soil ◽  
Culture Media ◽  
Enrichment Culture ◽  
Sequence Similarity ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Soil Samples ◽  
Enrichment Cultures ◽  
Total Community

This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.

scholarly journals Improvement of Soil Microbial Diversity through Sustainable Agricultural Practices and Its Evaluation by -Omics Approaches: A Perspective for the Environment, Food Quality and Human Safety

2021 ◽  
Vol 9 (7) ◽  
pp. 1400
Author(s):  
Marta Bertola ◽  
Andrea Ferrarini ◽  
Giovanna Visioli
Keyword(s):  
Microbial Diversity ◽  
Food Quality ◽  
Plant Biomass ◽  
Soil Microbial Communities ◽  
Well Being ◽  
Plant Health ◽  
Soil Microbiome ◽  
Soil Microbial Diversity ◽  
Soil Biodiversity ◽  
Soil Microbial

Soil is one of the key elements for supporting life on Earth. It delivers multiple ecosystem services, which are provided by soil processes and functions performed by soil biodiversity. In particular, soil microbiome is one of the fundamental components in the sustainment of plant biomass production and plant health. Both targeted and untargeted management of soil microbial communities appear to be promising in the sustainable improvement of food crop yield, its nutritional quality and safety. –Omics approaches, which allow the assessment of microbial phylogenetic diversity and functional information, have increasingly been used in recent years to study changes in soil microbial diversity caused by agronomic practices and environmental factors. The application of these high-throughput technologies to the study of soil microbial diversity, plant health and the quality of derived raw materials will help strengthen the link between soil well-being, food quality, food safety and human health.

A gene with sequence similarity to Drosophila engrailed is expressed during the development of the neural tube and vertebrae in the mouse

Development ◽  
1988 ◽  
Vol 104 (2) ◽  
pp. 305-316 ◽  
Author(s):  
D. Davidson ◽  
E. Graham ◽  
C. Sime ◽  
R. Hill
Keyword(s):  
In Situ Hybridization ◽  
Neural Tube ◽  
Mouse Embryo ◽  
Sequence Similarity ◽  
Anterior Part ◽  
Limb Bud ◽  
Tissue Type ◽  
Restricted Domains ◽  
Restricted Region

The mouse genes En-1 and En-2 display sequence similarity, in and around the homeobox region, to the engrailed family in Drosophila. This paper describes their pattern of expression in the 12.5-day mouse embryo as determined by in situ hybridization. En-2 is expressed in a subset of cells expressing En-1. Both genes are expressed in the developing midbrain and its junction with the hindbrain. In addition, En-1 is expressed in the floor of the hindbrain, a restricted ventrolateral segment of the neural tube throughout the trunk and anterior part of the tail, the dermatome of tail somites, the centrum and costal processes in developing vertebrae, a restricted region of facial mesenchyme and the limb-bud ectoderm. Supplementary studies of 9.5-day and 10.5-day embryos showed that the same pattern of expression pertained in the neural tube, but that expression in the somites is at first confined to the dermatome and later found at a low level in restricted sclerotomal regions. Both genes are expressed in restricted domains which do not cross tissue-type boundaries. In several instances, however, boundaries of expression lie within morphologically undifferentiated tissue. These results suggest that En-1 and En-2 may be involved in the establishment or maintenance of the spatial integrity of specific domains within developing tissues.

scholarly journals The hormone neuroparsin seems essential in Lepidoptera but not in domesticated silkworms

2019 ◽  
Author(s):  
Jan A. Veenstra
Keyword(s):  
Bombyx Mori ◽  
Genome Assembly ◽  
Galleria Mellonella ◽  
Sequence Similarity ◽  
Neuroendocrine Cells ◽  
Primary Sequence ◽  
Genome Assemblies ◽  
Limited Sequence ◽  
Wax Moth

AbstractThe primary sequence of the Arthropod neurohormone neuroparsin is so variable that so far no orthologs from moths and butterflies have been characterized, even though classical neurosecretory stains identify cells that are homologous to those producing this hormone in other insect species. Here Lepidopteran cDNAs showing limited sequence similarity to other insect neuroparsins are described. That these cDNAs do indeed code for authentic neuroparsins was confirmed by in situ hybridization in the wax moth, Galleria mellonella, which labeled the neuroparsin neuroendocrine cells. Although in virtually all genome assemblies from Lepidoptera a neuroparsin gene could be identified, the genome assembly from the silkworm, Bombyx mori, has a neuroparsin gene containing a 16 nucleotide deletion that renders this gene nonfunctional. Although only a small number of all silkworm strains carry this deletion, it suggests that the domestication of the silkworm has rendered the function of this neurohormone dispensable.

scholarly journals Analysis of the Bacterial and Fungal Community Profiles in Bulk Soil and Rhizospheres of Three Mungbean [Vigna radiata (L.) R. Wilczek] Genotypes through PCR-DGGE

2020 ◽  
Vol 77 ◽  
pp. 1-26
Author(s):  
Anna Mae M. de los Reyes ◽  
Eureka Teresa M. Ocampo ◽  
Ma. Carmina C. Manuel ◽  
Bernadette C. Mendoza
Keyword(s):  
Plant Growth ◽  
Crop Production ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Diversity Index ◽  
Agricultural Practices ◽  
Fungal Communities ◽  
Bulk Soil ◽  
Initial Assessment ◽  
Rhizosphere Effect ◽  
Soil Microbial Diversity

Each plant species is regarded to substantially influence and thus, select for specific rhizosphere microbial populations. This is considered in the exploitation of soil microbial diversity associated with important crops, which has been of interest in modern agricultural practices for sustainable productivity. This study used PCR-DGGE (polymerase chain reaction - denaturing gradient gel electrophoresis) in order to obtain an initial assessment of the bacterial and fungal communities associated in bulk soil and rhizospheres of different mungbean genotypes under natural field conditions. Integrated use of multivariate analysis and diversity index showed plant growth stage as the primary driver of community shifts in both microbial groups while rhizosphere effect was found to be less discrete in fungal communities. On the other hand, genotype effect was not discerned but not inferred to be absent due to possible lack of manifestations of differences among genotypes based on tolerance to drought under non-stressed environment, and due to detection limits of DGGE. Sequence analysis of prominent members further revealed that Bacillus and Arthrobacter species were dominant in bacterial communities whereas members of Ascomycota and Basidiomycota were common in fungal communities of mungbean. Overall, fungal communities had higher estimated diversity and composition heterogeneity, and were more dynamic under plant growth influence, rhizosphere effect and natural environmental conditions during mungbean growth in upland field. These primary evaluations are prerequisite to understanding the interactions between plant and rhizosphere microorganisms with the intention of employing their potential use for sustainable crop production.

scholarly journals In situ Impact of the Antagonistic Fungal Strain, Trichoderma gamsii T30 on the Plant Pathogenic Fungus, Rhizoctonia solani in Soil

2019 ◽  
Vol 68 (2) ◽  
pp. 211-216
Author(s):  
MUHAMMAD ANEES ◽  
MUHAMMAD ABID ◽  
SOBIA CHOHAN ◽  
MUHAMMAD JAMIL ◽  
NADEEM AHMED ◽  
...  
Keyword(s):  
Population Density ◽  
Rhizoctonia Solani ◽  
Pathogenic Fungus ◽  
Suppressive Effect ◽  
Fungal Strain ◽  
Soil Microbiome ◽  
Target Dna ◽  
Wide Range ◽  
First Time

Rhizoctonia solani is a soil-borne fungus causing a wide range of plants diseases. Trichoderma gamsii strain T30 has previously been reported as antagonistic against R. solani. Although there are a few studies about the influence of Trichoderma strains on the R. solani densityin a pathosystem in the presence of plant hosts, this report for the first time comprehensively describes in situ effects of a T. gamsii strain on the population density of R. solani in the soil microcosmic conditions. The population dynamics of R. solani were followed in the autoclaved and non-autoclaved soils in artificially prepared microcosms up to day 25 after co-inoculation with T. gamsii in the variable ratios (R1/T1; R1/T0.1; R1/T0.01 of R. solani/T. gamsii). The population density of R. solani was evaluated by qPCR. In the autoclaved soil, target DNA copies of R. solani increased in the control samples from 1 × 105 to 6.5 × 106. At R1/T0.01, the number of target DNA copies were not significantly changed until day 11; however, it decreased by around five times at day 25. At R1/T0.1 and R1/T1, the number of DNA copies was reduced to 2.1 × 106 and 7.6 × 105 at day 11, respectively and the reduction was as much as 17 times at day 25. In the non-autoclaved soil, the number of the fungal cells decreased at day 25 whether inoculated or not with Trichoderma indicating a general suppression by the soil microbiome. In brief, T. gamsii significantly inhibited the growth of R. solani in the soil in situ and there was a general suppressive effect of the natural microbiome.

scholarly journals Soil microbial diversity in organic and non-organic pasture systems

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11184
Author(s):  
Mohan Acharya ◽  
Amanda J. Ashworth ◽  
Yichao Yang ◽  
Joan M. Burke ◽  
Jung Ae Lee ◽  
...  
Keyword(s):  
Species Richness ◽  
Microbial Diversity ◽  
Bacterial Species ◽  
Soil Microbiome ◽  
Organic Soils ◽  
Pasture Management ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Organic Systems ◽  
Microbiome Diversity

Understanding the effects of organic pasture management on the soil microbiome is important for sustainable forage production since soil microbiome diversity contributes to improved nutrient cycling, soil structure, plant growth, and environmental resiliency; however, the soil microbiome response to pasture management is largely unknown. This study assessed the soil microbial diversity, richness, and community structure following 10 years of pasture management (organic or non-organic) of the V4 region of the 16S rRNA using the Illumina MiSeq platform. Soil samples were collected from 0–15 cm in July and August from 2017–2018 and soil nutrient properties (nutrients, carbon, nitrogen, and pH) quantified and correlated with soil microbial diversity. Overall, greater soil bacterial species richness (P ≤ 0.05) occurred in organic relative to non-organic (conventional) systems. Management affected bacterial species richness (Chao1), with greater richness occurring in organic pasture soils and less richness occurring in non-organic systems (P ≤ 0.05). Similarly, management affected bacterial evenness (Simpson’s index), with a more diverse community occurring in organically managed soils relative to non-organic pastures (P ≤ 0.05). Linear discriminant analysis effect size analysis showed statistically significant and biologically consistent differences in bacterial taxa in organic compared with non-organic soils. Therefore, there was a shift in bacterial community structure in organic relative to non-organic soils (P ≤ 0.05). Additionally, soil nutrients (Fe, Mg, Ni, S, Al, K, Cd, and Cu), pH, C, and N were correlated with one or more dominant bacterial phyla (Gemmatimonadetes, Planctomycetes, Firmicutes, Chloroflexi, Actinobacteria, and Acidobacteria). Overall, pasture management affected soil microbial diversity, with greater diversity occurring in organic than non-organic systems, likely owing to applications of organic poultry litter in organic systems compared to non-organic management (use of inorganic-fertilizers and herbicides). Results indicate that when pastures are converted to organic production systems, soil microbial richness and diversity may increase, thereby resulting in enhanced soil microbiome diversity and overall ecosystem services.

Sign in / Sign up

Export Citation Format

Share Document