scholarly journals Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling

Microbiome ◽  
2019 ◽  
Vol 7 (1) ◽  
Author(s):  
Jennifer E. Schmidt ◽  
Angela D. Kent ◽  
Vanessa L. Brisson ◽  
Amélie C. M. Gaudin
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Nitrogen Cycling ◽  
Community Composition ◽  
Network Structure ◽  
Host Selection ◽  
Agricultural Management ◽  
Plant Selection ◽  
Selection Processes ◽  
Rhizosphere Microbial Community

Abstract Background Rhizosphere microbial communities are key regulators of plant performance, yet few studies have assessed the impact of different management approaches on the rhizosphere microbiomes of major crops. Rhizosphere microbial communities are shaped by interactions between agricultural management and host selection processes, but studies often consider these factors individually rather than in combination. We tested the impacts of management (M) and rhizosphere effects (R) on microbial community structure and co-occurrence networks of maize roots collected from long-term conventionally and organically managed maize-tomato agroecosystems. We also explored the interaction between these factors (M × R) and how it impacts rhizosphere microbial diversity and composition, differential abundance, indicator taxa, co-occurrence network structure, and microbial nitrogen-cycling processes. Results Host selection processes moderate the influence of agricultural management on rhizosphere microbial communities, although bacteria and fungi respond differently to plant selection and agricultural management. We found that plants recruit management-system-specific taxa and shift N-cycling pathways in the rhizosphere, distinguishing this soil compartment from bulk soil. Rhizosphere microbiomes from conventional and organic systems were more similar in diversity and network structure than communities from their respective bulk soils, and community composition was affected by both M and R effects. In contrast, fungal community composition was affected only by management, and network structure only by plant selection. Quantification of six nitrogen-cycling genes (nifH, amoA [bacterial and archaeal], nirK, nrfA, and nosZ) revealed that only nosZ abundance was affected by management and was higher in the organic system. Conclusions Plant selection interacts with conventional and organic management practices to shape rhizosphere microbial community composition, co-occurrence patterns, and at least one nitrogen-cycling process. Reframing research priorities to better understand adaptive plant-microbe feedbacks and include roots as a significant moderating influence of management outcomes could help guide plant-oriented strategies to improve productivity and agroecosystem sustainability.

scholarly journals Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Vanessa L. Brisson ◽  
Jennifer E. Schmidt ◽  
Trent R. Northen ◽  
John P. Vogel ◽  
Amélie C. M. Gaudin
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Microbial Community Analysis ◽  
Agricultural System ◽  
Community Members ◽  
Genetic Groups ◽  
Maize Domestication ◽  
Rhizosphere Microbial Community

Abstract Maize domestication and breeding have resulted in drastic and well documented changes in aboveground traits, but belowground effects on root system functioning and rhizosphere microbial communities remain poorly understood, despite their critical importance for nutrient and water acquisition. We investigated the rhizosphere microbial community composition and structure of ten Zea mays accessions along an evolutionary transect (two teosinte, three inbred maize lines, and five modern maize hybrids) grown in nutrient depleted soil from a low input agricultural system. Microbial community analysis revealed significant differences in community composition between soil compartments (proximal vs. distal rhizosphere) and between plant genetic groups (teosinte, inbred, and modern hybrid). Only a small portion of the microbial community was differentially selected across plant genetic groups: 3.7% of prokaryotic community members and 4.9% of fungal community members were significantly associated with a specific plant genetic group. Indicator species analysis showed the greatest differentiation between modern hybrids and the other two plant genetic groups. Co-occurrence network analysis revealed that microbial co-occurrence patterns of the inbred maize lines’ rhizosphere were significantly more similar to those of the teosintes than to the modern hybrids. Our results suggest that advances in hybrid development significantly impacted rhizosphere microbial communities and network assembly.

scholarly journals Diversity and structure of the rhizosphere microbial communities of wild and cultivated ginseng

2021 ◽  
Author(s):  
Xiaoxue Fang ◽  
Huaying Wang ◽  
Ling Zhao ◽  
Manqi Wang ◽  
Mingzhou Sun
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Its Region ◽  
Rrna Gene ◽  
In The Wild ◽  
Underlying Mechanisms ◽  
Wild Ginseng ◽  
Rhizosphere Microbial Community

Abstract Background Different plant species, even different plant varieties, will promote different combinations of microbial communities related to them. Here, the objective was to explore the differences in the rhizosphere microbial communities in the wild ginseng, farmland cultivated ginseng and understory wild ginseng. The rhizosphere soil was obtained from three type of ginsengs, namely wild ginseng (WDG), farmland cultivated ginseng (CDG) and understory wild ginseng (LXG) (all ginsengs grown in the field). The 16S rRNA gene and internal transcribed spacer (ITS) region were analyzed to investigate the diversity and structure of the microbial community. Result We found the fungal communities were more influenced bacterial communities. There were differences in the microbial community composition under three types of ginsengs. Moreover, higher bacterial diversity and lower fungal diversity in CDG compared with WDG. Changes in rhizosphere microbial community composition and diversity of WDG and CDG may be caused by domestication. Furthermore, the relative abundance of potential phytopathogens, Chloroflexi, Fusarium and Alternaria were higher in CDG compared to WDG and LXG. This may be related to the fact that cultivated ginseng has a short life cycle and is susceptible to disease. Conclusion We found differences in the rhizosphere microbial community of the three types of ginsengs, and the abundance of pathogenic microorganisms is significantly different. This result provided insights into the underlying mechanisms of ginseng planting and disease resistance.

scholarly journals Habitat Elevation Shapes Microbial Community Composition and Alter the Metabolic Functions in Wild Sable (Martes zibellina) Guts

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 865
Author(s):  
Lantian Su ◽  
Xinxin Liu ◽  
Guangyao Jin ◽  
Yue Ma ◽  
Haoxin Tan ◽  
...  
Keyword(s):  
Microbial Community ◽  
Environmental Factors ◽  
Microbial Communities ◽  
Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Functional Genes ◽  
Martes Zibellina ◽  
Clear Cutting ◽  
Metabolic Functions

In recent decades, wild sable (Carnivora Mustelidae Martes zibellina) habitats, which are often natural forests, have been squeezed by anthropogenic disturbances such as clear-cutting, tilling and grazing. Sables tend to live in sloped areas with relatively harsh conditions. Here, we determine effects of environmental factors on wild sable gut microbial communities between high and low altitude habitats using Illumina Miseq sequencing of bacterial 16S rRNA genes. Our results showed that despite wild sable gut microbial community diversity being resilient to many environmental factors, community composition was sensitive to altitude. Wild sable gut microbial communities were dominated by Firmicutes (relative abundance 38.23%), followed by Actinobacteria (30.29%), and Proteobacteria (28.15%). Altitude was negatively correlated with the abundance of Firmicutes, suggesting sable likely consume more vegetarian food in lower habitats where plant diversity, temperature and vegetation coverage were greater. In addition, our functional genes prediction and qPCR results demonstrated that energy/fat processing microorganisms and functional genes are enriched with increasing altitude, which likely enhanced metabolic functions and supported wild sables to survive in elevated habitats. Overall, our results improve the knowledge of the ecological impact of habitat change, providing insights into wild animal protection at the mountain area with hash climate conditions.

scholarly journals Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity

2021 ◽  
Vol 12 ◽  
Author(s):  
Scott F. George ◽  
Noah Fierer ◽  
Joseph S. Levy ◽  
Byron Adams
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Environmental Conditions ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Vapor Flow ◽  
Arid Soils ◽  
Opposite Pattern ◽  
Dry Valley

Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (∼5–10 km2) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteria phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars.

scholarly journals Towards a function-first framework to make soil microbial ecology predictive

2021 ◽  
Author(s):  
Johannes Rousk ◽  
Lettice Hicks
Keyword(s):  
Microbial Community ◽  
Environmental Factors ◽  
Microbial Communities ◽  
Functional Response ◽  
Community Composition ◽  
Ecosystem Function ◽  
Bacterial Growth ◽  
Response Curve ◽  
Ecosystem Functions ◽  
Soil Microbial

<p>Soil microbial communities perform vital ecosystem functions, such as the decomposition of organic matter to provide plant nutrition. However, despite the functional importance of soil microorganisms, attribution of ecosystem function to particular constituents of the microbial community has been impeded by a lack of information linking microbial function to community composition and structure. Here, we propose a function-first framework to predict how microbial communities influence ecosystem functions.</p><p>We first view the microbial community associated with a specific function as a whole, and describe the dependence of microbial functions on environmental factors (e.g. the intrinsic temperature dependence of bacterial growth rates). This step defines the aggregate functional response curve of the community. Second, the contribution of the whole community to ecosystem function can be predicted, by combining the functional response curve with current environmental conditions. Functional response curves can then be linked with taxonomic data in order to identify sets of “biomarker” taxa that signal how microbial communities regulate ecosystem functions. Ultimately, such indicator taxa may be used as a diagnostic tool, enabling predictions of ecosystem function from community composition.</p><p>In this presentation, we provide three examples to illustrate the proposed framework, whereby the dependence of bacterial growth on environmental factors, including temperature, pH and salinity, is defined as the functional response curve used to interlink soil bacterial community structure and function. Applying this framework will make it possible to predict ecosystem functions directly from microbial community composition.</p>

Soil microbial communities in microaggregates are less affected by top-down effects of collembolans than those in macroaggregates

2021 ◽  
Author(s):  
Amandine Erktan ◽  
MD Ekramul Haque ◽  
Jérôme Cortet ◽  
Paul Henning Krogh ◽  
Stefan Scheu
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Trophic Interactions ◽  
Phospholipid Fatty Acid ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Trophic Levels ◽  
Soil Matrix ◽  
Fungal Abundance

<p>Trophic regulation of microbial communities is receiving growing interest in soil ecology. Most studies investigated the effect of higher trophic levels on microbial communities at the bulk soil level. However, microbes are not equally accessible to consumers. They may be hidden in small pores and thus protected from consumers, suggesting that trophic regulation may depend on the localization of microbes within the soil matrix. As microaggregates (< 250 µm) usually are more stable than macroaggregates (> 250 µm) and embedded in the latter, we posit that they will be less affected by trophic regulations than larger aggregates. We quantified the effect of four contrasting species of collembolans (Ceratophysella denticulata, Protaphorura fimata, Folsomia candida, Sinella curviseta) on the microbial community composition in macro- (250 µm – 2mm) and microaggregates (50 – 250 µm). To do so, we re-built consumer-prey systems comprising remaining microbial background (post-autoclaving), fungal prey (Chaetomium globosum), and collembolan species (added as single species or combined). After three months, we quantified microbial community composition using phospholipid fatty acid markers (PLFAs). We found that the microbial communities in macroaggregates were more affected by the addition of collembolans than the communities in microaggregates. In particular, the fungal-to-bacterial (F:B) ratio significantly decreased in soil macroaggregates in the presence of collembolans. In the microaggregates, the F:B ratio remained lower and unaffected by collembolan inoculation. Presumably, fungal hyphae were more abundant in macroaggregates because they offered more habitat space for them, and the collembolans reduced fungal abundance because they consumed them. On the contrary, microaggregates presumably contained microbial communities protected from consumers. In addition, collembolans increased the formation of macroaggregates but did not influence their stability, despite their negative effect on fungal abundance, a well-known stabilizing agent. Overall, we show that trophic interactions between microbial communities and collembolans depend on the aggregate size class considered and, in return, soil macroaggregation is affected by these trophic interactions.</p>

scholarly journals Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence

2019 ◽  
Vol 85 (7) ◽  
Author(s):  
Alexander Burkert ◽  
Thomas A. Douglas ◽  
Mark P. Waldrop ◽  
Rachel Mackelprang
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Community Composition ◽  
Environmental Conditions ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Subzero Temperatures ◽  
Dormant Cells

ABSTRACTPermafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the classBacilliwere more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of theClostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.IMPORTANCEPermafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.

scholarly journals Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities

2016 ◽  
Vol 83 (4) ◽  
Author(s):  
Nastassia V. Patin ◽  
Michelle Schorn ◽  
Kristen Aguinaldo ◽  
Tommie Lincecum ◽  
Bradley S. Moore ◽  
...  
Keyword(s):  
Microbial Community ◽  
Secondary Metabolites ◽  
Microbial Communities ◽  
Community Composition ◽  
Marine Sediments ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Next Generation ◽  
Content Type ◽  
Predatory Bacteria

ABSTRACT Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities. IMPORTANCE Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S. arenicola extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments.

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