scholarly journals Influence of plant host and organ, management strategy, and spore traits on microbiome composition

2020 ◽  
Author(s):  
Kristi Gdanetz ◽  
Zachary Noel ◽  
Frances Trail
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Life Histories ◽  
Management Strategies ◽  
Alpha Diversity ◽  
Fungal Spore ◽  
Organ Specificity ◽  
Growth Stages ◽  
Plant Host ◽  
Network Analyses

ABSTRACTMicrobiomes from maize and soybean were characterized in a long-term three-crop rotation research site, under four different land management strategies, to begin unraveling the effects of common farming practices on microbial communities. The fungal and bacterial communities of leaves, stems, and roots in host species were characterized across the growing season using amplicon sequencing and compared with the results of a similar study on wheat. Communities differed across hosts, and among plant growth stages and organs, and these effects were most pronounced in the bacterial communities of the wheat and maize phyllosphere. Roots consistently showed the highest number of bacterial OTUs compared to above-ground organs, whereas the alpha diversity of fungi was similar between above- and below-ground organs. Network analyses identified putatively influential members of the microbial communities of the three host plant species. The fungal taxa specific to roots, stems, or leaves were examined to determine if the specificity reflected their life histories based on previous studies. The analysis suggests that fungal spore traits are drivers of organ specificity in the fungal community. Identification of influential taxa in the microbial community and understanding how community structure of specific crop organs is formed, will provide a critical resource for manipulations of microbial communities. The ability to predict how organ specific communities are influenced by spore traits will enhance our ability to introduce them sustainably.

scholarly journals Influence of plant host and organ, management strategy, and spore traits on microbiome composition

2021 ◽  
Author(s):  
Kristi Gdanetz ◽  
Zachary Albert Noel ◽  
Frances Trail
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Life Histories ◽  
Management Strategies ◽  
Alpha Diversity ◽  
Fungal Spore ◽  
Organ Specificity ◽  
Growth Stages ◽  
Plant Host ◽  
Network Analyses

Microbiomes from maize and soybean were characterized in a long-term three-crop rotation research site, under four different land management strategies, to begin unraveling the effects of common farming practices on microbial communities. The fungal and bacterial communities of leaves, stems, and roots in host species were characterized across the growing season using amplicon sequencing and compared with the results of a similar study on wheat. Communities differed across hosts, and among plant growth stages and organs, and these effects were most pronounced in the bacterial communities of the wheat and maize phyllosphere. Roots consistently showed the highest number of bacterial OTUs compared to above-ground organs, whereas the alpha diversity of fungi was similar between above- and below-ground organs. Network analyses identified putatively influential members of the microbial communities of the three host plant species. The fungal taxa specific to roots, stems, or leaves were examined to determine if the specificity reflected their life histories based on previous studies. The analysis suggests that fungal spore traits are drivers of organ specificity in the fungal community. Identification of influential taxa in the microbial community and understanding how community structure of specific crop organs is formed, will provide a critical resource for manipulations of microbial communities. The ability to predict how organ specific communities are influenced by spore traits will enhance our ability to introduce them sustainably.

scholarly journals Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia

2019 ◽  
Author(s):  
Ze Ren ◽  
Hongkai Gao
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Central Asia ◽  
Fungal Community ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Hydrological Modeling ◽  
Alpha Diversity ◽  
Environmental Variation ◽  
Fungal Communities

Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of bacterial community and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while fungal community and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.

scholarly journals Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia

2019 ◽  
Author(s):  
Ze Ren ◽  
Hongkai Gao
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Central Asia ◽  
Fungal Community ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Hydrological Modeling ◽  
Alpha Diversity ◽  
Environmental Variation ◽  
Fungal Communities

Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of bacterial community and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while fungal community and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.

scholarly journals Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7715 ◽  
Author(s):  
Ze Ren ◽  
Hongkai Gao
Keyword(s):  
Microbial Communities ◽  
Central Asia ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Vegetation Index ◽  
Hydrological Modeling ◽  
Alpha Diversity ◽  
Environmental Variation ◽  
Fungal Communities ◽  
Taxonomic Groups

Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community (BC) and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community (FC) and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of BC and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while FC and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.

scholarly journals Crop Host Signatures Reflected by Co-association Patterns of Keystone Bacteria in the Rhizosphere Microbiota

2021 ◽  
Author(s):  
Simon Lewin ◽  
Davide Francioli ◽  
Andreas Ulrich ◽  
Steffen Kolb
Keyword(s):  
Oilseed Rape ◽  
Growth Stages ◽  
Plant Host ◽  
Crop Species ◽  
Differential Abundance ◽  
Core Microbiota ◽  
Network Analyses ◽  
Bacterial Microbiota ◽  
Species Effect ◽  
Occurrence Patterns

Abstract Background: The native crop bacterial microbiota of the rhizosphere is envisioned to be engineered for sustainable agriculture. This requires the identification of keystone rhizosphere Bacteria and an understanding on how these govern crop-specific microbiome assembly from soils. We identified the metabolically active bacterial microbiota (SSU RNA) inhabiting two compartments of the rhizosphere of wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rye (Secale cereale), and oilseed rape (Brassica napus L.) at different growth stages. Results: Based on metabarcoding analysis the bacterial microbiota was shaped by the two rhizosphere compartments, i.e. close and distant. Thereby implying a different spatial extend of bacterial microbiota acquirement by the cereals species versus oilseed rape. We derived core microbiota of each crop species. Massilia (barley and wheat) and unclassified Chloroflexi of group ‘KD4-96’ (oilseed rape) were identified as keystone Bacteria by combining LEfSe biomarker and network analyses. Subsequently, differential associations between networks of each crop species’ core microbiota revealed host plant-specific interconnections for specific genera, such as the unclassified Tepidisphaeraceae ‘WD2101 soil group’. Conclusions: Our results provide keystone rhizosphere Bacteria derived from for crop hosts and revealed that cohort subnetworks and differential associations elucidated host species effect that was not evident from differential abundance of single bacterial genera enriched or unique to a specific plant host. Thus, we underline the importance of co-occurrence patterns within the rhizosphere microbiota that emerge in crop-specific microbiomes, which will be essential to modify native crop microbiome for future agriculture and to develop effective bio-fertilizers.

scholarly journals Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4452 ◽  
Author(s):  
Katherine E. Dahlhausen ◽  
Ladan Doroud ◽  
Alana J. Firl ◽  
Adam Polkinghorne ◽  
Jonathan A. Eisen
Keyword(s):  
Microbial Communities ◽  
Antibiotic Treatment ◽  
Intestinal Flora ◽  
Alpha Diversity ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Phascolarctos Cinereus ◽  
Network Analyses ◽  
Eucalyptus Leaves ◽  
Arboreal Marsupials

Koalas (Phascolarctos cinereus) are arboreal marsupials native to Australia that eat a specialized diet of almost exclusively eucalyptus leaves. Microbes in koala intestines are known to break down otherwise toxic compounds, such as tannins, in eucalyptus leaves. Infections by Chlamydia, obligate intracellular bacterial pathogens, are highly prevalent in koala populations. If animals with Chlamydia infections are received by wildlife hospitals, a range of antibiotics can be used to treat them. However, previous studies suggested that koalas can suffer adverse side effects during antibiotic treatment. This study aimed to use 16S rRNA gene sequences derived from koala feces to characterize the intestinal microbiome of koalas throughout antibiotic treatment and identify specific taxa associated with koala health after treatment. Although differences in the alpha diversity were observed in the intestinal flora between treated and untreated koalas and between koalas treated with different antibiotics, these differences were not statistically significant. The alpha diversity of microbial communities from koalas that lived through antibiotic treatment versus those who did not was significantly greater, however. Beta diversity analysis largely confirmed the latter observation, revealing that the overall communities were different between koalas on antibiotics that died versus those that survived or never received antibiotics. Using both machine learning and OTU (operational taxonomic unit) co-occurrence network analyses, we found that OTUs that are very closely related to Lonepinella koalarum, a known tannin degrader found by culture-based methods to be present in koala intestines, was correlated with a koala’s health status. This is the first study to characterize the time course of effects of antibiotics on koala intestinal microbiomes. Our results suggest it may be useful to pursue alternative treatments for Chlamydia infections without the use of antibiotics or the development of Chlamydia-specific antimicrobial compounds that do not broadly affect microbial communities.

scholarly journals Crop host signatures reflected by co-association patterns of keystone Bacteria in the rhizosphere microbiota

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Simon Lewin ◽  
Davide Francioli ◽  
Andreas Ulrich ◽  
Steffen Kolb
Keyword(s):  
Oilseed Rape ◽  
Growth Stages ◽  
Plant Host ◽  
Crop Species ◽  
Differential Abundance ◽  
Core Microbiota ◽  
Network Analyses ◽  
Bacterial Microbiota ◽  
Species Effect ◽  
Occurrence Patterns

Abstract Background The native crop bacterial microbiota of the rhizosphere is envisioned to be engineered for sustainable agriculture. This requires the identification of keystone rhizosphere Bacteria and an understanding on how these govern crop-specific microbiome assembly from soils. We identified the metabolically active bacterial microbiota (SSU RNA) inhabiting two compartments of the rhizosphere of wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rye (Secale cereale), and oilseed rape (Brassica napus L.) at different growth stages. Results Based on metabarcoding analysis the bacterial microbiota was shaped by the two rhizosphere compartments, i.e. close and distant. Thereby implying a different spatial extent of bacterial microbiota acquirement by the cereals species versus oilseed rape. We derived core microbiota of each crop species. Massilia (barley and wheat) and unclassified Chloroflexi of group ‘KD4-96’ (oilseed rape) were identified as keystone Bacteria by combining LEfSe biomarker and network analyses. Subsequently, differential associations between networks of each crop species’ core microbiota revealed host plant-specific interconnections for specific genera, such as the unclassified Tepidisphaeraceae ‘WD2101 soil group’. Conclusions Our results provide keystone rhizosphere Bacteria derived from for crop hosts and revealed that cohort subnetworks and differential associations elucidated host species effect that was not evident from differential abundance of single bacterial genera enriched or unique to a specific plant host. Thus, we underline the importance of co-occurrence patterns within the rhizosphere microbiota that emerge in crop-specific microbiomes, which will be essential to modify native crop microbiomes for future agriculture and to develop effective bio-fertilizers.

scholarly journals Coupling Root Diameter With Rooting Depth to Reveal the Heterogeneous Assembly of Root-Associated Bacterial Communities in Soybean

2021 ◽  
Vol 12 ◽  
Author(s):  
Wen Luo ◽  
Xiaoyu Zai ◽  
Jieyu Sun ◽  
Da Li ◽  
Yuanli Li ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Plant Root ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Root Diameter ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rooting Depth

Root diameter and rooting depth lead to morphological and architectural heterogeneity of plant roots; however, little is known about their effects on root-associated microbial communities. Bacterial community assembly was explored across 156 samples from three rhizocompartments (the rhizosphere, rhizoplane, and endosphere) for different diameters (0.0–0.5 mm, 0.5–1.0 mm, 1.0–2.0 mm, and>2.0 mm) and depths (0–5 cm, 5–10 cm, 10–15 cm, and 15–20 cm) of soybean [Glycine max (L.) Merrill] root systems. The microbial communities of all samples were analyzed using amplicon sequencing of bacterial 16S rRNA genes. The results showed that root diameter significantly affected the rhizosphere and endosphere bacterial communities, while rooting depth significantly influenced the rhizosphere and rhizoplane bacterial communities. The bacterial alpha diversity decreased with increasing root diameter in all three rhizocompartments, and the diversity increased with increasing rooting depth only in the rhizoplane. Clearly, the hierarchical enrichment process of the bacterial community showed a change from the rhizosphere to the rhizoplane to the endosphere, and the bacterial enrichment was higher in thinner or deeper roots (except for the roots at a depth of 15–20 cm). Network analysis indicated that thinner or deeper roots led to higher bacterial network complexity. The core and keystone taxa associated with the specific root diameter class and rooting depth class harbored specific adaptation or selection strategies. Root diameter and rooting depth together affected the root-associated bacterial assembly and network complexity in the root system. Linking root traits to microbiota may enhance our understanding of plant root-microbe interactions and their role in developing environmentally resilient root ecosystems.

scholarly journals Bacterial Community Dynamics across the Gastrointestinal Tracts of Dairy Calves during Preweaning Development

2018 ◽  
Vol 84 (9) ◽  
pp. e02675-17 ◽  
Author(s):  
Juliana Dias ◽  
Marcos Inácio Marcondes ◽  
Shirley Motta de Souza ◽  
Barbara Cardoso da Mata e Silva ◽  
Melline Fontes Noronha ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Early Life ◽  
Community Dynamics ◽  
Temporal Dynamics ◽  
Alpha Diversity ◽  
Dairy Calves ◽  
Dairy Calf ◽  
Content Type ◽  
Bacterial Community Dynamics

ABSTRACTMicrobial communities play critical roles in the gastrointestinal tracts (GIT) of preruminant calves by influencing performance and health. However, little is known about the establishment of microbial communities in the calf GIT or their dynamics during development. In this study, next-generation sequencing was used to assess changes in the bacterial communities of the rumen, jejunum, cecum, and colon in 26 crossbred calves at four developmental stages (7, 28, 49, and 63 days old). Alpha diversity differed among GIT regions with the lowest diversity and evenness in the jejunum, whereas no changes in alpha diversity were observed across developmental stage. Beta diversity analysis showed both region and age effects, with low numbers of operational taxonomic units (OTUs) shared between regions within a given age group or between ages in a given region. Taxonomic analysis revealed that several taxa coexisted in the rumen, jejunum, cecum, and colon but that their abundances differed considerably by GIT region and age. As calves aged, we observed lower abundances of taxa such asBacteroides,Parabacteroides, andParaprevotellawith higher abundances ofBulleidiaandSucciniclasticumin the rumen. The jejunum also displayed taxonomic changes with increases inClostridiaceaeandTuricibactertaxa in older calves. In the lower gut, taxa such asLactobacillus,Blautia, andFaecalibacteriumdecreased and S24-7,Paraprevotella, andPrevotellaincreased as calves aged. These data support a model whereby early and successive colonization by bacteria occurs across the GIT of calves and provides insights into the temporal dynamics of the GIT microbiota of dairy calves during preweaning development.IMPORTANCEThe gastrointestinal tracts (GIT) of ruminants, such as dairy cows, house complex microbial communities that contribute to their overall health and support their ability to produce milk. For example, the rumen microbiota converts feed into usable nutrients, while the jejunal microbiota provides access to protein. Thus, establishing a properly functioning GIT microbiota in dairy calves is critical to their productivity as adult cows. However, little is known about the establishment, maintenance, and dynamics of the calf GIT microbiota in early life. In this study, we evaluated the bacterial communities in the rumen, jejunum, cecum, and colon in dairy calves across preweaning development and show that they are highly variable early on in life before transitioning to a stable community. Understanding the dairy calf GIT microbiota has implications for ensuring proper health during early life and will aid in efforts to develop strategies for improving downstream production.

scholarly journals Growth and Phenology of Vulpia Myuros in Comparison with Apera Spica-Venti, Alopecurus Myosuroides and Lolium Multiflorum in Monoculture and in Winter Wheat

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1495
Author(s):  
Muhammad Javaid Akhter ◽  
Bo Melander ◽  
Solvejg Kopp Mathiassen ◽  
Rodrigo Labouriau ◽  
Svend Vendelbo Nielsen ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Weed Management ◽  
Lolium Multiflorum ◽  
Management Strategies ◽  
Integrated Weed Management ◽  
Growth Stages ◽  
Neighborhood Design ◽  
Alopecurus Myosuroides ◽  
Winter Cereals ◽  
Arable Weed

Vulpia myuros has become an increasing weed problem in winter cereals in Northern Europe. However, the information about V. myuros and its behavior as an arable weed is limited. Field and greenhouse experiments were conducted in 2017/18 and 2018/19, at the Department of Agroecology in Flakkebjerg, Denmark to investigate the emergence, phenological development and growth characteristics of V. myuros in monoculture and in mixture with winter wheat, in comparison to Apera spica-venti, Alopecurus myosuroides and Lolium multiflorum. V. myuros emerged earlier than A. myosuroides and A. spica-venti but later than L. multiflorum. Significant differences in phenological development were recorded among the species. Overall phenology of V. myuros was more similar to that of L. multiflorum than to A. myosuroides and A. spica-venti. V. myuros started seed shedding earlier than A. spica-venti and L. multiflorum but later than A. myosuroides. V. myuros was more sensitive to winter wheat competition in terms of biomass production and fecundity than the other species. Using a target-neighborhood design, responses of V. myuros and A. spica-venti to the increasing density of winter wheat were quantified. At early growth stages “BBCH 26–29”, V. myuros was suppressed less than A. spica-venti by winter wheat, while opposite responses were seen at later growth stages “BBCH 39–47” and “BBCH 81–90”. No significant differences in fecundity characteristics were observed between the two species in response to increasing winter wheat density. The information on the behavior of V. myuros gathered by the current study can support the development of effective integrated weed management strategies for V. myuros.

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