scholarly journals Genomics and informatics, conjoined tools vital for understanding and protecting plant health

2021 ◽  
Author(s):  
Seogchan Kang ◽  
Ki-Tae Kim ◽  
Jaeyoung Choi ◽  
Hyun Kim ◽  
Kyeongchae Cheong ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Crop Production ◽  
Cultural Practices ◽  
Community Empowerment ◽  
Individual Species ◽  
Data Preservation ◽  
Sequencing Technologies ◽  
Informatics Infrastructure ◽  
Health Related ◽  
Crop Health

Genomics’ impact on crop production continuously expands. The number of sequenced plant and microbial species and strains representing diverse populations of individual species rapidly increases thanks to the advent of next generation sequencing technologies. Their genomic blueprints revealed candidate genes involved in various functions and processes crucial for crop health and helped understand how the sequenced organisms have evolved at the genome level. Functional genomics quickly translates these blueprints into a detailed mechanistic understanding of how such functions and processes work and are regulated; this understanding guides and empowers efforts to protect crops from diverse biotic and abiotic threats. Metagenome analyses help identify candidate microbes crucial for crop health and uncover how microbial communities associated with crop production respond to environmental conditions and cultural practices, presenting opportunities to enhance crop health by judiciously configuring microbial communities. Efficient conversion of disparate types of massive genomics data into actionable knowledge requires a robust informatics infrastructure supporting data preservation, analysis, and sharing. This review starts with an overview of how genomics came about and has quickly transformed life science. We illuminate how genomics and informatics can be applied to investigate various crop health-related problems using selected studies. We end the review by noting why community empowerment via crowdsourcing is crucial to harnessing genomics to protect global food and nutrition security without continuously expanding the environmental footprint of crop production.

Phylum-Specific Primer Design and Implication in Quantification of the Microbial Community Structure in GuJingGong Pit Mud

2014 ◽  
Vol 1051 ◽  
pp. 311-316 ◽  
Author(s):  
Xi Mei Luo ◽  
Zhi Lei Gao ◽  
Hui Min Zhang ◽  
An Jun Li ◽  
Hong Kui He ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Real Time Quantitative Pcr ◽  
Sequencing Technologies ◽  
Specific Pcr ◽  
Pit Mud ◽  
Almost All ◽  
Polymerase Chain Reaction Primers

In recent years, despite the significant improvement of sequencing technologies such as the pyrosequencing, rapid evaluation of microbial community structures remains very difficult because of the abundance and complexity of organisms in almost all natural microbial communities. In this paper, a group of phylum-specific primers were elaborately designed based on a single nucleotide discrimination technology to quantify the main microbial community structure from GuJingGong pit mud samples using the real-time quantitative PCR (qPCR). Specific PCR (polymerase chain reaction) primers targeting a particular group would provide promising sensitivity and more in-depth assessment of microbial communities.

scholarly journals A phylogenetic transform enhances analysis of compositional microbiota data

2016 ◽  
Author(s):  
Justin D Silverman ◽  
Alex Washburne ◽  
Sayan Mukherjee ◽  
Lawrence A David
Keyword(s):  
Microbial Communities ◽  
Relative Abundance ◽  
Dominant Role ◽  
Phylogenetic Information ◽  
Abundance Data ◽  
Sequencing Technologies ◽  
Environmental Selection ◽  
Health And Disease ◽  
High Throughput Dna Sequencing ◽  
Spurious Results

ABSTRACTHigh-throughput DNA sequencing technologies have revolutionized the study of microbial communities (microbiota) and have revealed their importance in both human health and disease. However, due to technical limitations, data from microbiota surveys reflect the relative abundance of bacterial taxa and not their absolute levels. It is well known that applying common statistical methods, such as correlation or hypothesis testing, to relative abundance data can lead to spurious results. Here, we introduce the PhILR transform, a data transform that utilizes microbial phylogenetic information. This transform enables off-the-shelf statistical tools to be applied to microbiota surveys free from artifacts usually associated with analysis of relative abundance data. Using environmental and human-associated microbial community datasets as benchmarks, we find that the PhILR transform significantly improves the performance of distance-based and machine learning-based statistics, boosting the accuracy of widely used algorithms on reference benchmarks by 90%. Because the PhILR transform relies on bacterial phylogenies, statistics applied in the PhILR coordinate system are also framed within an evolutionary perspective. Regression on PhILR transformed human microbiota data identified evolutionarily neighboring bacterial clades that may have differentiated to adapt to distinct body sites. Variance statistics showed that the degree of covariation of bacterial clades across human body sites tended to increase with phylogenetic relatedness between clades. These findings support the hypothesis that environmental selection, not competition between bacteria, plays a dominant role in structuring human-associated microbial communities.

scholarly journals A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities

2018 ◽  
Author(s):  
Manuel Kleiner ◽  
Xiaoli Dong ◽  
Tjorven Hinzke ◽  
Juliane Wippler ◽  
Erin Thorson ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Carbon Isotope ◽  
Isotope Ratio ◽  
Single Cells ◽  
Stable Carbon Isotope ◽  
Carbon Sources ◽  
Food Sources ◽  
Individual Species ◽  
Stable Carbon

AbstractMeasurements of the carbon stable isotope ratio (δ13C) are widely used in biology to address major questions regarding food sources and metabolic pathways used by organisms. Measurement of these so called stable carbon isotope fingerprints (SIFs) for microbes involved in biogeochemical cycling and microbiota of plants and animals have led to major discoveries in environmental microbiology. Currently, obtaining SIFs for microbial communities is challenging as the available methods either only provide limited taxonomic resolution, such as with the use of lipid biomarkers, or are limited in throughput, such as NanoSIMS imaging of single cells.Here we present “direct Protein-SIF” and the Calis-p software package (https://sourceforge.net/projects/calis-p/), which enable high-throughput measurements of accurate δ13C values for individual species within a microbial community. We benchmark the method using 20 pure culture microorganisms and show that the method reproducibly provides SIF values consistent with gold standard bulk measurements performed with an isotope ratio mass spectrometer. Using mock community samples, we show that SIF values can also be obtained for individual species within a microbial community. Finally, a case study of an obligate bacteria-animal symbiosis showed that direct Protein-SIF confirms previous physiological hypotheses and can provide unexpected new insights into the symbionts’ metabolism. This confirms the usefulness of this new approach to accurately determine δ13C values for different species in microbial community samples.SignificanceTo understand the roles that microorganisms play in diverse environments such as the open ocean and the human intestinal tract, we need an understanding of their metabolism and physiology. A variety of methods such as metagenomics and metaproteomics exist to assess the metabolism of environmental microorganisms based on gene content and gene expression. These methods often only provide indirect evidence for which substrates are used by a microorganism in a community. The direct Protein-SIF method that we developed allows linking microbial species in communities to the environmental carbon sources they consume by determining their stable carbon isotope signature. Direct Protein-SIF also allows assessing which carbon fixation pathway is used by autotrophic microorganisms that directly assimilate CO2.

scholarly journals CAMISIM: Simulating metagenomes and microbial communities

2018 ◽  
Author(s):  
Adrian Fritz ◽  
Peter Hofmann ◽  
Stephan Majda ◽  
Eik Dahms ◽  
Johannes Dröge ◽  
...  
Keyword(s):  
Microbial Communities ◽  
De Novo ◽  
Real Data ◽  
Small Data ◽  
Data Sets ◽  
Sequencing Data ◽  
Taxonomic Profiling ◽  
Benchmark Data ◽  
Sequencing Technologies ◽  
Wide Range

Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, to effectively assess the performance of metagenomic analysis software, a wide range of benchmark data sets are required. Here, we describe the CAMISIM microbial community and metagenome simulator. The software can model different microbial abundance profiles, multi-sample time series and differential abundance studies, includes real and simulated strain-level diversity, and generates second and third generation sequencing data from taxonomic profiles or de novo. Gold standards are created for sequence assembly, genome binning, taxonomic binning, and taxonomic profiling. CAMSIM generated the benchmark data sets of the first CAMI challenge. For two simulated multi-sample data sets of the human and mouse gut microbiomes we observed high functional congruence to the real data. As further applications, we investigated the effect of varying evolutionary genome divergence, sequencing depth, and read error profiles on two popular metagenome assemblers, MEGAHIT and metaSPAdes, on several thousand small data sets generated with CAMISIM. CAMISIM can simulate a wide variety of microbial communities and metagenome data sets together with truth standards for method evaluation. All data sets and the software are freely available at: https://github.com/CAMI-challenge/CAMISIM

scholarly journals Designing Metabolic Division of Labor in Microbial Communities

mSystems ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Meghan Thommes ◽  
Taiyao Wang ◽  
Qi Zhao ◽  
Ioannis C. Paschalidis ◽  
Daniel Segrè
Keyword(s):  
Microbial Communities ◽  
Division Of Labor ◽  
Environmental Sustainability ◽  
Computational Models ◽  
Thought Experiment ◽  
Mixed Integer ◽  
Individual Species ◽  
Large Space ◽  
Individual Organism ◽  
Trade Off

ABSTRACTMicrobes face a trade-off between being metabolically independent and relying on neighboring organisms for the supply of some essential metabolites. This balance of conflicting strategies affects microbial community structure and dynamics, with important implications for microbiome research and synthetic ecology. A “gedanken” (thought) experiment to investigate this trade-off would involve monitoring the rise of mutual dependence as the number of metabolic reactions allowed in an organism is increasingly constrained. The expectation is that below a certain number of reactions, no individual organism would be able to grow in isolation and cross-feeding partnerships and division of labor would emerge. We implemented this idealized experiment usingin silicogenome-scale models. In particular, we used mixed-integer linear programming to identify trade-off solutions in communities ofEscherichia colistrains. The strategies that we found revealed a large space of opportunities in nuanced and nonintuitive metabolic division of labor, including, for example, splitting the tricarboxylic acid (TCA) cycle into two separate halves. The systematic computation of possible solutions in division of labor for 1-, 2-, and 3-strain consortia resulted in a rich and complex landscape. This landscape displayed a nonlinear boundary, indicating that the loss of an intracellular reaction was not necessarily compensated for by a single imported metabolite. Different regions in this landscape were associated with specific solutions and patterns of exchanged metabolites. Our approach also predicts the existence of regions in this landscape where independent bacteria are viable but are outcompeted by cross-feeding pairs, providing a possible incentive for the rise of division of labor.IMPORTANCEUnderstanding how microbes assemble into communities is a fundamental open issue in biology, relevant to human health, metabolic engineering, and environmental sustainability. A possible mechanism for interactions of microbes is through cross-feeding, i.e., the exchange of small molecules. These metabolic exchanges may allow different microbes to specialize in distinct tasks and evolve division of labor. To systematically explore the space of possible strategies for division of labor, we applied advanced optimization algorithms to computational models of cellular metabolism. Specifically, we searched for communities able to survive under constraints (such as a limited number of reactions) that would not be sustainable by individual species. We found that predicted consortia partition metabolic pathways in ways that would be difficult to identify manually, possibly providing a competitive advantage over individual organisms. In addition to helping understand diversity in natural microbial communities, our approach could assist in the design of synthetic consortia.

scholarly journals Mixed-Cropping Between Field Pea Varieties Alters Root Bacterial and Fungal Communities

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Anthony Horner ◽  
Samuel S. Browett ◽  
Rachael E. Antwis
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Crop Production ◽  
Agricultural Soils ◽  
Critical Role ◽  
Agricultural Practices ◽  
Microbial Interactions ◽  
Field Pea ◽  
Fungal Communities ◽  
Mixed Cropping

AbstractModern agricultural practices have vastly increased crop production but negatively affected soil health. As such, there is a call to develop sustainable, ecologically-viable approaches to food production. Mixed-cropping of plant varieties can increase yields, although impacts on plant-associated microbial communities are unclear, despite their critical role in plant health and broader ecosystem function. We investigated how mixed-cropping between two field pea (Pisum sativum L.) varieties (Winfreda and Ambassador) influenced root-associated microbial communities and yield. The two varieties supported significantly different fungal and bacterial communities when grown as mono-crops. Mixed-cropping caused changes in microbial communities but with differences between varieties. Root bacterial communities of Winfreda remained stable in response to mixed-cropping, whereas those of Ambassador became more similar to Winfreda. Conversely, root fungal communities of Ambassador remained stable under mixed-cropping, and those of Winfreda shifted towards the composition of Ambassador. Microbial co-occurrence networks of both varieties were stronger and larger under mixed-cropping, which may improve stability and resilience in agricultural soils. Both varieties produced slightly higher yields under mixed-cropping, although overall Ambassador plants produced higher yields than Winfreda plants. Our results suggest that variety diversification may increase yield and promote microbial interactions.

scholarly journals The impact of Maize (Zea mays L.) and it uses for human development: A review

2017 ◽  
Vol 5 (1) ◽  
pp. 93
Author(s):  
Monday Sunday Adiaha
Keyword(s):  
Crop Production ◽  
Zea Mays L ◽  
Standard Of Living ◽  
Wet Milling ◽  
Food Crop ◽  
Industrial Utilization ◽  
Health Related ◽  
Food Crop Production ◽  
Animal Diet ◽  
The Impact

Corn possesses significances nutrients, minerals and vitamins, which provides nutrition in animal diet as well as man. Its health benefits have been countless since the prehistoric era. Maize has been revealed to have the potential to sustained human health-related cases, raise standard of living of farmers, served as a soil fertility indicator crop, generate income and increase food-crop production for the increasing human population. Industrial utilization of maize has been shown to include: wet milling, production of bio-fuel, ethanol and other sub-byproducts.

scholarly journals Considering the Lives of Microbes in Microbial Communities

mSystems ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Elizabeth A. Shank
Keyword(s):  
Complex Systems ◽  
Microbial Communities ◽  
Single Cell ◽  
Functional Capacity ◽  
Cellular Differentiation ◽  
Microbial Interactions ◽  
Metabolite Production ◽  
Sequencing Technologies ◽  
Microbiome Research ◽  
Visualization Systems

ABSTRACT Over the last decades, sequencing technologies have transformed our ability to investigate the composition and functional capacity of microbial communities. Even so, critical questions remain about these complex systems that cannot be addressed by the bulk, community-averaged data typically provided by sequencing methods. In this Perspective, I propose that future advances in microbiome research will emerge from considering “the lives of microbes”: we need to create methods to explicitly interrogate how microbes exist and interact in native-setting-like microenvironments. This approach includes developing approaches that expose the phenotypic heterogeneity of microbes; exploring the effects of coculture cues on cellular differentiation and metabolite production; and designing visualization systems that capture features of native microbial environments while permitting the nondestructive observation of microbial interactions over space and time with single-cell resolution.

scholarly journals EFFECTS OF NUTRIENT SOLUTION SALINITY ON THE PHYSIOLOGICAL PERFORMANCE OF MELON CULTIVATED IN COCONUT FIBER

2018 ◽  
Vol 31 (3) ◽  
pp. 713-718 ◽  
Author(s):  
PATRÍCIA LÍGIA DANTAS DE MORAIS ◽  
NILDO DA SILVA DIAS ◽  
ANDRÉ MOREIRA DE OLIVEIRA ◽  
OSVALDO NOGUEIRA DE SOUSA NETO ◽  
JOSÉ DARCIO ABRANTES SARMENTO ◽  
...  
Keyword(s):  
Nutrient Solution ◽  
Salt Concentration ◽  
Crop Production ◽  
Cultural Practices ◽  
Intercellular Co2 Concentration ◽  
Co2 Concentration ◽  
Semiarid Region ◽  
Coconut Fiber ◽  
Lack Of Information ◽  
Use Efficiency

ABSTRACT Brackish waters represent great potential for profitable agricultural production; however, productive usage depends on the adoption of proper cultural practices as well as a culture tolerant of salinity, which can require some restrictions related to soil and crop production. Given the lack of information pertaining to hydroponic melon culture, the objective of this study was to investigate physiological changes promoted by the use of brackish water in the preparation of the nutrient solution for melon (Cucumis melo L., cv. AF 015) growth in coconut fiber substrate under greenhouse conditions in Mossoró-RN, a semiarid region of Brazil. The experimental design was completely randomized, with 12 treatments arranged in a 4 x 3 factorial scheme, with 4 salt concentration levels (1.1 - control, 2.5, 4.0 and 5.5 dS m-1) and 3 exposition times (vegetative growth: 10-30 days after transplanting, DAT; flowering: 31 to 50 DAT; and fruiting and ripening: 51-70 DAT, which are the assessment phases of physiological maturation). Increasing salt concentrations in the nutrient solution reduced photosynthetic efficiency, stomatal conductance and transpiration, but increased the intercellular CO2 concentration in melon plants. A salt concentration in the low to intermediate range (2.5 dS m-1) resulted in the best water use efficiency by melon crops.

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