The Experts below are selected from a list of 27555 Experts worldwide ranked by ideXlab platform
Noah Fierer - One of the best experts on this subject based on the ideXlab platform.
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plant domestication and the assembly of bacterial and Fungal Communities associated with strains of the common sunflower helianthus annuus
New Phytologist, 2017Co-Authors: Jonathan W Leff, Ryan C Lynch, Nolan C Kane, Noah FiererAbstract:Summary Root and rhizosphere microbial Communities can affect plant health, but it remains undetermined how plant domestication may influence these bacterial and Fungal Communities. We grew 33 sunflower (Helianthus annuus) strains (n = 5) that varied in their extent of domestication and assessed rhizosphere and root endosphere bacterial and Fungal Communities. We also assessed Fungal Communities in the sunflower seeds to investigate the degree to which root and rhizosphere Communities were influenced by vertical transmission of the microbiome through seeds. Neither root nor rhizosphere bacterial Communities were affected by the extent of sunflower domestication, but domestication did affect the composition of rhizosphere Fungal Communities. In particular, more modern sunflower strains had lower relative abundances of putative Fungal pathogens. Seed-associated Fungal Communities strongly differed across strains, but several lines of evidence suggest that there is minimal vertical transmission of fungi from seeds to the adult plants. Our results indicate that plant-associated Fungal Communities are more strongly influenced by host genetic factors and plant breeding than bacterial Communities, a finding that could influence strategies for optimizing microbial Communities to improve crop yields.
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Changes in Bacterial and Fungal Communities across Compost Recipes, Preparation Methods, and Composting Times
2016Co-Authors: Deborah A. Neher, Jonathan W Leff, Thomas R. Weicht, Scott T. Bates, Noah FiererAbstract:Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial Communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and Fungal Communities in compost produced at a commercial-scale. Bacterial and Fungal Communities responded to both compost recipe and composting method. Specifically, bacterial Communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal Communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and Fungal Communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed b
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changes in bacterial and Fungal Communities across compost recipes preparation methods and composting times
PLOS ONE, 2013Co-Authors: Deborah A. Neher, Jonathan W Leff, Noah Fierer, Thomas R. Weicht, Scott T. BatesAbstract:Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial Communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and Fungal Communities in compost produced at a commercial-scale. Bacterial and Fungal Communities responded to both compost recipe and composting method. Specifically, bacterial Communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal Communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and Fungal Communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed to generate compost with the desired properties.
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the influence of soil properties on the structure of bacterial and Fungal Communities across land use types
Soil Biology & Biochemistry, 2008Co-Authors: Christian L Lauber, Michael S Strickland, Mark A Bradford, Noah FiererAbstract:Abstract Land-use change can have significant impacts on soil conditions and microbial Communities are likely to respond to these changes. However, such responses are poorly characterized as few studies have examined how specific changes in edaphic characteristics do, or do not, influence the composition of soil bacterial and Fungal Communities across land-use types. Soil samples were collected from four replicated ( n = 3) land-use types (hardwood and pine forests, cultivated and livestock pasture lands) in the southeastern US to assess the effects of land-use change on microbial community structure and distribution. We used quantitative PCR to estimate bacterial–Fungal ratios and clone libraries targeting small-subunit rRNA genes to independently characterize the bacterial and Fungal Communities. Although some soil properties (soil texture and nutrient status) did significantly differ across land-use types, other edaphic factors (e.g., pH) did not vary consistently with land-use. Bacterial–Fungal ratios were not significantly different across the land-uses and distinct land-use types did not necessarily harbor distinct soil Fungal or bacterial Communities. Rather, the composition of bacterial and Fungal Communities was most strongly correlated with specific soil properties. Soil pH was the best predictor of bacterial community composition across this landscape while Fungal community composition was most closely associated with changes in soil nutrient status. Together these results suggest that specific changes in edaphic properties, not necessarily land-use type itself, may best predict shifts in microbial community composition across a given landscape. In addition, our results demonstrate the utility of using sequence-based approaches to concurrently analyze bacterial and Fungal Communities as such analyses provide detailed phylogenetic information on individual Communities and permit the robust assessment of the biogeographical patterns exhibited by soil microbial Communities.
Otso Ovaskainen - One of the best experts on this subject based on the ideXlab platform.
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interactions between soil and dead wood inhabiting Fungal Communities during the decay of norway spruce logs
The ISME Journal, 2017Co-Authors: Raisa Makipaa, Tiina Rajala, Dmitry Schigel, Katja T Rinne, Taina Pennanen, Nerea Abrego, Otso OvaskainenAbstract:We investigated the interaction between Fungal Communities of soil and dead wood substrates. For this, we applied molecular species identification and stable isotope tracking to both soil and decaying wood in an unmanaged boreal Norway spruce-dominated stand. Altogether, we recorded 1990 operational taxonomic units, out of which more than 600 were shared by both substrates and 589 were found to exclusively inhabit wood. On average the soil was more species-rich than the decaying wood, but the species richness in dead wood increased monotonically along the decay gradient, reaching the same species richness and community composition as soil in the late stages. Decaying logs at all decay stages locally influenced the Fungal Communities from soil, some Fungal species occurring in soil only under decaying wood. Stable isotope analyses suggest that mycorrhizal species colonising dead wood in the late decay stages actively transfer nitrogen and carbon between soil and host plants. Most importantly, Piloderma sphaerosporum and Tylospora sp. mycorrhizal species were highly abundant in decayed wood. Soil- and wood-inhabiting Fungal Communities interact at all decay phases of wood that has important implications in Fungal community dynamics and thus nutrient transportation.
Binbin Liu - One of the best experts on this subject based on the ideXlab platform.
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Tillage Changes Vertical Distribution of Soil Bacterial and Fungal Communities.
Frontiers in microbiology, 2018Co-Authors: Ruibo Sun, Wenxu Dong, Yinping Tian, Binbin LiuAbstract:Tillage can strongly affect the long-term productivity of an agricultural system by altering the composition and spatial distribution of nutrients and microbial Communities. The impact of tillage methods on the vertical distribution of soil microbial Communities is not well understood, and the correlation between microbial Communities and soil nutrients vertical distributions is also not clear. In the present study, we investigated the effects of conventional plowing tillage (CT: moldboard plowing), reduced tillage (RT: rotary tillage), and no tillage (NT) on the composition of bacterial and Fungal Communities within the soil profile (0-5, 5-10, 10-20, and 20-30 cm) using high-throughput sequencing of the microbial 16S/ITS gene. Microbial Communities differed by soil properties and sampling depth. Tillage treatment strongly affected the microbial community structure and distribution by soil depth, and changed the vertical distribution of soil bacterial and Fungal Communities differently. Depth decay of bacterial Communities was significantly smaller in CT than in RT and NT, and that of Fungal Communities were significantly greater in RT than CT and NT. The presence/absence of species was the main contributing factor for the vertical variation of bacterial Communities, whereas for Fungal Communities the main factor was the difference in relative abundance of the species, suggesting niche-based process was more important for bacterial than Fungal community in structuring the vertical distribution. Soil total carbon was correlated more with soil bacterial (especially the anaerobic and facultatively anaerobic groups) than with Fungal community. These results suggested different roles of bacteria and fungi in carbon sequestration of crop residue and in shaping soil carbon distribution, which might impact on soil fertility.
Jonathan W Leff - One of the best experts on this subject based on the ideXlab platform.
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plant domestication and the assembly of bacterial and Fungal Communities associated with strains of the common sunflower helianthus annuus
New Phytologist, 2017Co-Authors: Jonathan W Leff, Ryan C Lynch, Nolan C Kane, Noah FiererAbstract:Summary Root and rhizosphere microbial Communities can affect plant health, but it remains undetermined how plant domestication may influence these bacterial and Fungal Communities. We grew 33 sunflower (Helianthus annuus) strains (n = 5) that varied in their extent of domestication and assessed rhizosphere and root endosphere bacterial and Fungal Communities. We also assessed Fungal Communities in the sunflower seeds to investigate the degree to which root and rhizosphere Communities were influenced by vertical transmission of the microbiome through seeds. Neither root nor rhizosphere bacterial Communities were affected by the extent of sunflower domestication, but domestication did affect the composition of rhizosphere Fungal Communities. In particular, more modern sunflower strains had lower relative abundances of putative Fungal pathogens. Seed-associated Fungal Communities strongly differed across strains, but several lines of evidence suggest that there is minimal vertical transmission of fungi from seeds to the adult plants. Our results indicate that plant-associated Fungal Communities are more strongly influenced by host genetic factors and plant breeding than bacterial Communities, a finding that could influence strategies for optimizing microbial Communities to improve crop yields.
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Changes in Bacterial and Fungal Communities across Compost Recipes, Preparation Methods, and Composting Times
2016Co-Authors: Deborah A. Neher, Jonathan W Leff, Thomas R. Weicht, Scott T. Bates, Noah FiererAbstract:Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial Communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and Fungal Communities in compost produced at a commercial-scale. Bacterial and Fungal Communities responded to both compost recipe and composting method. Specifically, bacterial Communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal Communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and Fungal Communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed b
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changes in bacterial and Fungal Communities across compost recipes preparation methods and composting times
PLOS ONE, 2013Co-Authors: Deborah A. Neher, Jonathan W Leff, Noah Fierer, Thomas R. Weicht, Scott T. BatesAbstract:Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial Communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and Fungal Communities in compost produced at a commercial-scale. Bacterial and Fungal Communities responded to both compost recipe and composting method. Specifically, bacterial Communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal Communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and Fungal Communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed to generate compost with the desired properties.
Ruibo Sun - One of the best experts on this subject based on the ideXlab platform.
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Tillage Changes Vertical Distribution of Soil Bacterial and Fungal Communities.
Frontiers in microbiology, 2018Co-Authors: Ruibo Sun, Wenxu Dong, Yinping Tian, Binbin LiuAbstract:Tillage can strongly affect the long-term productivity of an agricultural system by altering the composition and spatial distribution of nutrients and microbial Communities. The impact of tillage methods on the vertical distribution of soil microbial Communities is not well understood, and the correlation between microbial Communities and soil nutrients vertical distributions is also not clear. In the present study, we investigated the effects of conventional plowing tillage (CT: moldboard plowing), reduced tillage (RT: rotary tillage), and no tillage (NT) on the composition of bacterial and Fungal Communities within the soil profile (0-5, 5-10, 10-20, and 20-30 cm) using high-throughput sequencing of the microbial 16S/ITS gene. Microbial Communities differed by soil properties and sampling depth. Tillage treatment strongly affected the microbial community structure and distribution by soil depth, and changed the vertical distribution of soil bacterial and Fungal Communities differently. Depth decay of bacterial Communities was significantly smaller in CT than in RT and NT, and that of Fungal Communities were significantly greater in RT than CT and NT. The presence/absence of species was the main contributing factor for the vertical variation of bacterial Communities, whereas for Fungal Communities the main factor was the difference in relative abundance of the species, suggesting niche-based process was more important for bacterial than Fungal community in structuring the vertical distribution. Soil total carbon was correlated more with soil bacterial (especially the anaerobic and facultatively anaerobic groups) than with Fungal community. These results suggested different roles of bacteria and fungi in carbon sequestration of crop residue and in shaping soil carbon distribution, which might impact on soil fertility.
