scholarly journals Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops

2018 ◽  
Author(s):  
Keara L Grady ◽  
Jackson W. Sorensen ◽  
Nejc Stopnisek ◽  
John Guittar ◽  
Ashley Shade
Keyword(s):  
Crop Production ◽  
Panicum Virgatum ◽  
Gene Diversity ◽  
Perennial Grasses ◽  
Biofuel Production ◽  
Rrna Gene ◽  
Growing Seasons ◽  
Miscanthus Giganteus ◽  
Biofuel Crops ◽  
Ecological Filtering

AbstractPerennial grasses are promising feedstocks for biofuel production, and there is potential to leverage their native microbiomes to increase their productivity and resilience to environmental stress. Here, we characterize the 16S rRNA gene diversity and seasonal assembly of bacterial and archaeal microbiomes of two perennial cellulosic feedstocks, switchgrass (Panicum virgatum L.) and miscanthus (Miscanthus × giganteus). We sampled leaves and soil every three weeks from pre-emergence through senescence for two consecutive switchgrass growing seasons and one miscanthus season, and identified core leaf taxa based on abundance and occupancy. Virtually all leaf taxa are also detected in soil; source-sink modeling shows non-random, ecological filtering by the leaf, suggesting that soil is important reservoir of phyllosphere diversity. Core leaf taxa include early, mid, and late season groups that were consistent across years and crops. This consistency in leaf microbiome dynamics and core members is promising for microbiome manipulation or management to support biofuel crop production.

scholarly journals Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Keara L. Grady ◽  
Jackson W. Sorensen ◽  
Nejc Stopnisek ◽  
John Guittar ◽  
Ashley Shade
Keyword(s):  
Crop Production ◽  
Panicum Virgatum ◽  
Gene Diversity ◽  
Perennial Grasses ◽  
Biofuel Production ◽  
Rrna Gene ◽  
Miscanthus X Giganteus ◽  
Growing Seasons ◽  
Biofuel Crops ◽  
Ecological Filtering

Abstract Perennial grasses are promising feedstocks for biofuel production, with potential for leveraging their native microbiomes to increase their productivity and resilience to environmental stress. Here, we characterize the 16S rRNA gene diversity and seasonal assembly of bacterial and archaeal microbiomes of two perennial cellulosic feedstocks, switchgrass (Panicum virgatum L.) and miscanthus (Miscanthus x giganteus). We sample leaves and soil every three weeks from pre-emergence through senescence for two consecutive switchgrass growing seasons and one miscanthus season, and identify core leaf taxa based on occupancy. Virtually all leaf taxa are also detected in soil; source-sink modeling shows non-random, ecological filtering by the leaf, suggesting that soil is an important reservoir of phyllosphere diversity. Core leaf taxa include early, mid, and late season groups that were consistent across years and crops. This consistency in leaf microbiome dynamics and core members is promising for microbiome manipulation or management to support crop production.

scholarly journals Potential uses of biomass from fast-growing crop miscanthus×giganteus

2012 ◽  
Vol 66 (2) ◽  
pp. 223-233 ◽  
Author(s):  
Nada Babovic ◽  
Gordana Drazic ◽  
Ana Djordjevic
Keyword(s):  
Panicum Virgatum ◽  
Large Scale ◽  
Low Cost ◽  
Water Concentration ◽  
High Water ◽  
Perennial Grasses ◽  
Great Promise ◽  
Cellulose Content ◽  
Production Chain ◽  
Miscanthus Giganteus

There is an increasing interest in perennial grasses as a renewable source of bioenergy and feedstock for second-generation cellulosic biofuels. Switchgrass (Panicum virgatum) and miscanthus (Miscanthus?giganteus), belonging to the parennial grasses group, are the major lignocellulosic materials being studied today as sources for direct energy production, biofuels, bioremediation and other. They have the ability to grow at low cost on marginal land where they will not compete with the traditional food crops. Miscanthus?giganteus possesses a number of advantages in comparison with the other potential energy crops such as are: high yields, low moisture content at harvest, high water and nitrogen use efficiencies, low need for annual agronomic inputs such as fertilizers and pesticides, high cellulose content, non-invasive character, low susceptibility to pests and diseases and broad adaptation to temperate growing environments. The main problems are low rate of survival during the first winter after the creation of plantation and the relatively high establishment costs. Miscanthus?giganteus is grown primarily for heat and electricity generation but can also be used to produce transport fuels. Miscanthus biomass has a very good combustion quality due to its low water concentration as well as its low Cl, K, N, S and ash concentrations compared to other lignocellulose plants. It is expected that miscanthus will provide cheaper and more sustainable source of cellulose for production of bioethanol than annual crops such as corn. Miscanthus has great promise as a renewable energy source, but it can only be realised when the grass production has been optimised for large-scale commercial cultivation. However, further research is still needed to optimise agronomy of miscanthus, to develop the production chain and pre-treatment as well as to optimise energy conversation route to produce heat, electricity, and/or fuels from biomass, if miscanthus is to compete with fossil fuel use and be widely produced.

scholarly journals Digesting the indigestible: Biosynthesis of the plant secondary wall

2011 ◽  
Vol 33 (2) ◽  
pp. 24-28
Author(s):  
Raymond Wightman ◽  
Simon Turner
Keyword(s):  
Cell Walls ◽  
Panicum Virgatum ◽  
Second Generation ◽  
Plant Biomass ◽  
Biofuel Production ◽  
Bioenergy Crops ◽  
Second Generation Biofuels ◽  
Biofuel Crops ◽  
Secondary Cell Walls ◽  
Micro Organisms

Biofuels have recently been the subject of intense debate with regard to‘food versus fuel’. Consequently, attention has focused upon so-called ‘second-generation’ biofuels that use alternatives to food-based feedstocks. In the best-developed forms of second-generation biofuels, sugars from starch digestion could be replaced with sugars released from the plant cell walls. This biomass could come from either agricultural residue, such as part of the maize culm, or from purpose grown biofuel crops, such as Miscanthus or Switchgrass (Panicum virgatum), that generate huge yields even when grown on marginal land with minimal agricultural inputs. For these and other potential bioenergy crops such as trees, the majority of the plant biomass is composed of woody secondary cell walls. If all cell wall sugars were readily accessible to fermenting micro-organisms, a 5 kg log could theoretically produce up to 2.5 litres of ethanol. The secondary cell walls are frequently the first line of defence against pests and pathogens, as well as providing structure and support for upward plant growth (Figure 1). Consequently, by their very nature, secondary cell walls are designed for strength and to resist degradation. The compact organization of the wall makes its digestion, a process known as saccharification, very difficult so biomass is currently too costly to be a viable feedstock. Knowledge of how the walls are constructed, however, would allow us to efficiently deconstruct them. This article gives an overview of secondary walls and potential modifications expected to be beneficial to improved biofuel production.

scholarly journals Impact of Harvest on Switchgrass Leaf Microbial Communities

Genes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 22
Author(s):  
Esther Singer ◽  
Elizabeth M. Carpenter ◽  
Jason Bonnette ◽  
Tanja Woyke ◽  
Thomas E. Juenger
Keyword(s):  
Microbial Community ◽  
Panicum Virgatum ◽  
Leaf Surface ◽  
Its Region ◽  
Amplicon Sequencing ◽  
Biofuel Production ◽  
Rrna Gene ◽  
Community Studies ◽  
Community Members ◽  
Increase Productivity

Switchgrass is a promising feedstock for biofuel production, with potential for leveraging its native microbial community to increase productivity and resilience to environmental stress. Here, we characterized the bacterial, archaeal and fungal diversity of the leaf microbial community associated with four switchgrass (Panicum virgatum) genotypes, subjected to two harvest treatments (annual harvest and unharvested control), and two fertilization levels (fertilized and unfertilized control), based on 16S rRNA gene and internal transcribed spacer (ITS) region amplicon sequencing. Leaf surface and leaf endosphere bacterial communities were significantly different with Alphaproteobacteria enriched in the leaf surface and Gammaproteobacteria and Bacilli enriched in the leaf endosphere. Harvest treatment significantly shifted presence/absence and abundances of bacterial and fungal leaf surface community members: Gammaproteobacteria were significantly enriched in harvested and Alphaproteobacteria were significantly enriched in unharvested leaf surface communities. These shifts were most prominent in the upland genotype DAC where the leaf surface showed the highest enrichment of Gammaproteobacteria, including taxa with 100% identity to those previously shown to have phytopathogenic function. Fertilization did not have any significant impact on bacterial or fungal communities. We also identified bacterial and fungal taxa present in both the leaf surface and leaf endosphere across all genotypes and treatments. These core taxa were dominated by Methylobacterium, Enterobacteriaceae, and Curtobacterium, in addition to Aureobasidium, Cladosporium, Alternaria and Dothideales. Local core leaf bacterial and fungal taxa represent promising targets for plant microbe engineering and manipulation across various genotypes and harvest treatments. Our study showcases, for the first time, the significant impact that harvest treatment can have on bacterial and fungal taxa inhabiting switchgrass leaves and the need to include this factor in future plant microbial community studies.

Effects of cereal rye seeding rate on waterhemp (Amaranthus tuberculatus) emergence and soybean growth and yield

2021 ◽  
pp. 1-25
Author(s):  
Mandy Bish ◽  
Brian Dintelmann ◽  
Eric Oseland ◽  
Jacob Vaughn ◽  
Kevin Bradley
Keyword(s):  
Crop Production ◽  
Production Systems ◽  
Soil Seed Bank ◽  
Linear Regression Analysis ◽  
Growth And Yield ◽  
Seeding Rate ◽  
Early Season ◽  
Cereal Rye ◽  
Herbicide Resistant ◽  
Growing Seasons

Abstract The evolution of herbicide-resistant weeds has resulted in the necessity to integrate non-chemical control methods with chemicals for effective management in crop production systems. In soybean, control of the pigweed species, particularly herbicide-resistant waterhemp and Palmer amaranth, have become predominant concerns. Cereal rye planted as a winter cover crop can effectively suppress early-season weed emergence in soybean, including waterhemp, when planted at a rate of 123 kg ha−1. The objectives of this study were to determine the effects of different cereal rye seeding rates (0, 34, 56, 79, 110, and 123 kg ha−1) on early-season waterhemp suppression and soybean growth and yield. Soybean was planted into fall-seeded cereal rye, which was terminated within four days of soybean planting. The experiment was conducted over the 2018, 2019, and 2020 growing seasons in Columbia, Missouri. Effects of cereal rye on early-season waterhemp suppression varied by year and were most consistent at 56 kg ha−1 or higher seeding rates. Linear regression analysis of cereal rye biomass, height, or stand at soybean planting showed inverse relationships with waterhemp emergence. No adverse effects to soybean growth or yield were observed at any of the cereal rye seeding rates relative to plots that lacked cereal rye cover. Result differences among the years suggest that the successfulness of cereal rye on suppression of early-season waterhemp emergence is likely influenced by the amount of waterhemp seed present in the soil seed bank.

scholarly journals 16S rRNA gene and 18S rRNA gene diversity in microbial mat communities in meltwater ponds on the McMurdo Ice Shelf, Antarctica

Polar Biology ◽  
2021 ◽  
Author(s):  
Eleanor E. Jackson ◽  
Ian Hawes ◽  
Anne D. Jungblut
Keyword(s):  
16S Rrna ◽  
18S Rrna ◽  
High Throughput Sequencing ◽  
Microbial Mats ◽  
Gene Diversity ◽  
Salinity Gradient ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Ice Shelf ◽  
The Impact

AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.

scholarly journals Intragenomic and intraspecific heterogeneity in rrs may surpass interspecific variability in a natural population of Veillonella

Microbiology ◽  
2010 ◽  
Vol 156 (7) ◽  
pp. 2080-2091 ◽  
Author(s):  
Anne-Laure Michon ◽  
Fabien Aujoulat ◽  
Laurent Roudière ◽  
Olivier Soulier ◽  
Isabelle Zorgniotti ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Diversity ◽  
Natural Populations ◽  
Variable Region ◽  
Housekeeping Gene ◽  
Single Copy ◽  
Population Based ◽  
Rrna Gene ◽  
Gene Copies

As well as intraspecific heterogeneity, intragenomic heterogeneity between 16S rRNA gene copies has been described for a range of bacteria. Due to the wide use of 16S rRNA gene sequence analysis for taxonomy, identification and metagenomics, evaluating the extent of these heterogeneities in natural populations is an essential prerequisite. We investigated inter- and intragenomic 16S rRNA gene heterogeneity of the variable region V3 in a population of 149 clinical isolates of Veillonella spp. of human origin and in 13 type or reference Veillonella strains using PCR-temporal temperature gel electrophoresis (TTGE). 16S rRNA gene diversity was high in the studied population, as 45 different banding patterns were observed. Intragenomic heterogeneity was demonstrated for 110 (74 %) isolates and 8 (61.5 %) type or reference strains displaying two or three different gene copies. Polymorphic nucleotide positions accounted for 0.5–2.5 % of the sequence and were scattered in helices H16 and H17 of the rRNA molecule. Some of them changed the secondary structure of H17. Phylotaxonomic structure of the population based on the single-copy housekeeping gene rpoB was compared with TTGE patterns. The intragenomic V3 heterogeneity, as well as recombination events between strains or isolates of different rpoB clades, impaired the 16S rRNA-based identification for some Veillonella species. Such approaches should be conducted in other bacterial populations to optimize the interpretation of 16S rRNA gene sequences in taxonomy and/or diversity studies.

scholarly journals Safe-Site Effects on Rhizosphere Bacterial Communities in a High-Altitude Alpine Environment

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Sonia Ciccazzo ◽  
Alfonso Esposito ◽  
Eleonora Rolli ◽  
Stefan Zerbe ◽  
Daniele Daffonchio ◽  
...  
Keyword(s):  
High Altitude ◽  
Developmental Stage ◽  
Bacterial Communities ◽  
Developmental Stages ◽  
Gene Diversity ◽  
Intergenic Spacer ◽  
Intermediate Stage ◽  
Plant Colonization ◽  
Early Developmental Stage ◽  
Rrna Gene

The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites) which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS) site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P<0.05) on 16S rRNA gene diversity revealed significant differences (P<0.05) between BS site and the vegetated sites with a weak similarity to the RW site. The intermediate plant colonization stage FI did not differ significantly from the RW and the M vegetated sites. These results pointed out the effect of different floristic communities rhizospheres on their soil bacterial communities.

scholarly journals Soil Denitrifier Community Size Changes with Land Use Change to Perennial Bioenergy Cropping Systems

2016 ◽  
Author(s):  
Karen A. Thompson ◽  
Bill Deen ◽  
Kari E. Dunfield
Keyword(s):  
Land Use ◽  
16S Rrna ◽  
Land Use Change ◽  
Crop Production ◽  
Large Scale ◽  
Perennial Grasses ◽  
N2o Emissions ◽  
Research Station ◽  
N2o Production ◽  
Nirs Gene

Abstract. Dedicated biomass crops are required for future bioenergy production. However, the effects of large-scale land use change (LUC) from traditional annual crops, such as corn-soybean rotations to the perennial grasses (PGs) switchgrass and miscanthus on soil microbial community functioning is largely unknown. Specifically, ecologically significant denitrifying communities, which regulate N2O production and consumption in soils, may respond differently to LUC due to differences in carbon (C) and nitrogen (N) inputs between crop types and management systems. Our objective was to quantify bacterial denitrifying gene abundances as influenced by corn-soybean crop production compared to PG biomass production. A field trial was established in 2008 at the Elora Research Station in Ontario, Canada (n = 30), with miscanthus and switchgrass grown alongside corn-soybean rotations at different N rates (0 and 160 kg N ha-1) and biomass harvest dates within PG plots. Soil was collected on four dates from 2011–2012 and quantitative PCR was used to enumerate the total bacterial community (16S rRNA), and communities of bacterial denitrifiers by targeting nitrite reductase (nirS) and N2O reductase (nosZ) genes. Miscanthus produced significantly larger yields and supported larger nosZ denitrifying communities than corn-soybean rotations regardless of management, indicating large-scale LUC from corn-soybean to miscanthus may be suitable in variable Ontario conditions while potentially mitigating soil N2O emissions. Harvesting switchgrass in the spring decreased yields in N-fertilized plots, but did not affect gene abundances. Standing miscanthus overwinter resulted in higher 16S rRNA and nirS gene copies than in fall-harvested crops. However, the size of the total (16S rRA) and denitrifying communities changed differently over time and in response to LUC, indicating varying controls on these communities.

Sign in / Sign up

Export Citation Format

Share Document