scholarly journals Functional Redundancy in Local Spatial Scale Microbial Communities Suggest Stochastic Processes at an Urban Wilderness Preserve in Austin, TX, USA

2020 ◽  
Author(s):  
Justin Stewart ◽  
Amy Ontai ◽  
Kizil Yusoof ◽  
Teresa Bilinski
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Structure Function ◽  
Microbial Communities ◽  
Spatial Scale ◽  
Spatial Scales ◽  
Substrate Utilization ◽  
Carbon Substrate ◽  
Utilization Patterns ◽  
Edaphic Properties

AbstractEmpirical evidence supports selection of soil microbial communities by edaphic properties across large spatial scales, however; less is known as smaller spatial scales (e.g 10s-100s of meters). The goal of this research was to evaluate the relationship between ecosystem characteristics and bacterial community structure/function in soils across small spatial scales in an urban preserve. We employed 16s rRNA gene sequencing, community level physiological profiling (CLPP), and soil chemical analysis to address this goal. We found no significant relationship between gradients in soil characteristics and community structure/function. In contrast, Acidobacteria, Bacteroidetes, and Nitrospirae responded to variation in edaphic properties. Taxa exhibited a wide range in dispersal, supporting our finding of community wide differences in taxonomy. Furthermore, there was high metabolic diversity within the bacterial communities despite preferential metabolism of water-soluble polymers (Tween 40/80). Carbon substrate utilization patterns also suggest dominance of functional generalists. Pairwise comparison of carbon substrate utilization patterns indicates that there are high levels of microbial functional redundancy within soils across the sampling area. Lastly, we found that edaphic properties did not shape the overall community structure and/or function, and our analyses suggest that stochasticity may play a role in bacterial community assembly in soils with the local spatial scale of this research study.Graphical AbstractOne Sentence Summary: Microorganisms at small spatial scales were functionally similar despite subtle differences in community composition.

scholarly journals Functional redundancy in local spatial scale microbial communities suggests stochastic processes at an urban wilderness preserve in Austin, TX, USA

2021 ◽  
Vol 368 (3) ◽  
Author(s):  
Justin D. Stewart ◽  
Amy Ontai ◽  
Kizil Yusoof ◽  
Kelly S. Ramirez ◽  
Teresa Bilinski
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Structure Function ◽  
Microbial Communities ◽  
Carbon Metabolism ◽  
Spatial Scales ◽  
Soil Microbial Communities ◽  
Functional Redundancy ◽  
Rrna Gene ◽  
Edaphic Properties

ABSTRACT Empirical evidence supports selection of soil microbial communities by edaphic properties across large spatial scales; however, less is known at smaller spatial scales. The goal of this research was to evaluate relationships between ecosystem characteristics and bacterial community structure/function at broad taxonomic resolutions in soils across small spatial scales. We employed 16S rRNA gene sequencing, community-level physiological profiling and soil chemical analysis to address this goal. We found weak relationships between gradients in soil characteristics and community structure/function. Specific operational taxonomic units did not respond to edaphic variation, but Acidobacteria, Bacteroidetes and Nitrospirae shifted their relative abundances. High metabolic diversity within the bacterial communities was observed despite general preference of Tween 40/80. Carbon metabolism patterns suggest dominance of functional specialists at our times of measurement. Pairwise comparison of carbon metabolism patterns indicates high levels of functional redundancy. Lastly, at broad taxonomic scales, community structure and function weakly covary with edaphic properties. This evidence suggests that stochasticity or unmeasured environmental gradients may be influential in bacterial community assembly in soils at small spatial scales.

scholarly journals Soil Microsite Outweighs Cultivar Genotype Contribution to Brassica Rhizobacterial Community Structure

2021 ◽  
Vol 12 ◽  
Author(s):  
Scott A. Klasek ◽  
Marcus T. Brock ◽  
Hilary G. Morrison ◽  
Cynthia Weinig ◽  
Loïs Maignien
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Spatial Scales ◽  
Abiotic Factors ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Host Genotype ◽  
Rhizosphere Community ◽  
Scale Variation

Microorganisms residing on root surfaces play a central role in plant development and performance and may promote growth in agricultural settings. Studies have started to uncover the environmental parameters and host interactions governing their assembly. However, soil microbial communities are extremely diverse and heterogeneous, showing strong variations over short spatial scales. Here, we quantify the relative effect of meter-scale variation in soil bacterial community composition among adjacent field microsites, to better understand how microbial communities vary by host plant genotype as well as soil microsite heterogeneity. We used bacterial 16S rDNA amplicon sequencing to compare rhizosphere communities from four Brassica rapa cultivars grown in three contiguous field plots (blocks) and evaluated the relative contribution of resident soil communities and host genotypes in determining rhizosphere community structure. We characterize concomitant meter-scale variation in bacterial community structure among soils and rhizospheres and show that this block-scale variability surpasses the influence of host genotype in shaping rhizosphere communities. We identified biomarker amplicon sequence variants (ASVs) associated with bulk soil and rhizosphere habitats, each block, and three of four cultivars. Numbers and percent abundances of block-specific biomarkers in rhizosphere communities far surpassed those from bulk soils. These results highlight the importance of fine-scale variation in the pool of colonizing microorganisms during rhizosphere assembly and demonstrate that microsite variation may constitute a confounding effect while testing biotic and abiotic factors governing rhizosphere community structure.

scholarly journals Intercropping with Potato-Onion Enhanced the Soil Microbial Diversity of Tomato

2020 ◽  
Vol 8 (6) ◽  
pp. 834
Author(s):  
Naihui Li ◽  
Danmei Gao ◽  
Xingang Zhou ◽  
Shaocan Chen ◽  
Chunxia Li ◽  
...  
Keyword(s):  
Community Structure ◽  
Organic Carbon ◽  
Bacterial Community ◽  
Soil Organic Carbon ◽  
Microbial Communities ◽  
Fungal Community ◽  
Soil Microbial Communities ◽  
Tomato Seedling ◽  
Soil Microbial ◽  
Potato Onion

Intercropping can achieve sustainable agricultural development by increasing plant diversity. In this study, we investigated the effects of tomato monoculture and tomato/potato-onion intercropping systems on tomato seedling growth and changes of soil microbial communities in greenhouse conditions. Results showed that the intercropping with potato-onion increased tomato seedling biomass. Compared with monoculture system, the alpha diversity of soil bacterial and fungal communities, beta diversity and abundance of bacterial community were increased in the intercropping system. Nevertheless, the beta-diversity and abundance of fungal community had no difference between the intercropping and monoculture systems. The relative abundances of some taxa (i.e., Acidobacteria-Subgroup-6, Arthrobacter, Bacillus, Pseudomonas) and several OTUs with the potential to promote plant growth were increased, while the relative abundances of some potential plant pathogens (i.e., Cladosporium) were decreased in the intercropping system. Redundancy analysis indicated that bacterial community structure was significantly influenced by soil organic carbon and pH, the fungal community structure was related to changes in soil organic carbon and available phosphorus. Overall, our results suggested that the tomato/potato-onion intercropping system altered soil microbial communities and improved the soil environment, which may be the main factor in promoting tomato growth.

Community structure of micro- and macroflocs in pin-point sludge and the influence of sludge age and potassium addition on microfloc formation

2002 ◽  
Vol 46 (1-2) ◽  
pp. 405-412 ◽  
Author(s):  
E. Müller ◽  
K. Kriebitzsch ◽  
P.A. Wilderer ◽  
S. Wuertz
Keyword(s):  
Community Structure ◽  
Microbial Communities ◽  
Extracellular Polymeric Substances ◽  
Point Of View ◽  
Sludge Formation ◽  
Industrial Plants ◽  
Noticeable Improvement ◽  
Lower Protein ◽  
Utilization Patterns ◽  
The Impact

Settling problems caused by pin-point sludge constitute a serious problem in biological wastewater treatment, particularly in many industrial plants. Until now, most studies focused on the relationship between pin-point sludge formation and either shearing forces or the impact of toxicants. This study deals with the community structure in both the micro- and macrofloc fraction which was analyzed by fluorescent in situ hybridization (FISH) and BIOLOG substrate utilization patterns. It was shown that each fraction consisted of different microbial communities with unique metabolic profiles suggesting that pin-point sludge formation is not due to dispersal of intact flocs but to microcolonies growing separately. Alternatively, macroflocs may have an architecture leading to segregation of microbial communities after floc dispersal. Further it could be shown that the formation of microflocs was influenced by sludge age. The best sludge sedimentation was obtained for a sludge age of 5 and 10 days. Additional analysis of extracellular polymeric substances (EPS) suggested that the lower protein to carbohydrate ratio of 10-day-old sludge led to better flocculation compared to 20-day-old sludge containing similar total amounts of EPS. From a practical point of view, addition of potassium (0.1 g/l) effected a noticeable improvement of sludge settleability.

Host fruit as a suitable bacteria growth substrate that promotes larval development of Bactrocera dorsalis (Diptera: Tephritidae)

2019 ◽  
Author(s):  
Mazarin Akami ◽  
Xueming Ren ◽  
Yaohui Wang ◽  
Abdelaziz Mansour ◽  
Shuai Cao ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Larval Development ◽  
Bacterial Growth ◽  
Bacterial Community Structure ◽  
Fruit Fly ◽  
Bactrocera Dorsalis ◽  
Significant Shift ◽  
Bacteria Growth

AbstractThe ability of a host plant to act as a substrate or media for larval development may depend on how good it is at offering suitable nutrients for bacterial growth. In this study, we hypothesized that the suitability of a fruit type for fruit fly larval development is positively correlated with the ability of that fruit to act as a substrate/media for fruit fly symbiotic bacterial growth. We allowed a single female fruit fly to lay eggs on five different host fruits, then we monitored the larval development parameters across five generations and analyzed the bacterial community structure of larvae developing in 2 of these hosts (apple and banana) at the first and fifth generations. Results indicate that the larval length and dry weight did not vary significantly across experimental generations, but were greatly affected by fruit types and larval stages. The larval development time was extended considerably in apple and tomato but shortened in banana and mango. There was a significant shift in bacterial community structure and composition across fruits and generations. The bacterial community of larvae within the same fruit (apple and banana) clustered and was similar to the parental female (with the predominance of Proteobacteria), but there was a shift at the fifth generation (dominance of Firmicutes). Banana offered a suitable better development and growth to larvae and bacteria, respectively, compared to apple in which reduced larval development and bacterial growth were recorded. Although additional experiments are needed to adequately show that the differences in microbiome seen in fruit fly larval guts are the actual driver of different developmental outcomes of larvae on the different fruits, at the very least, our study has provided intriguing data suggesting interaction between the diets and gut microbial communities on insect development.Importance and Significance of the studyTephritid fruit flies entertain complex interactions with gut bacteria. These bacteria are known to provide nutritional benefits to their hosts, by supplementing missing nutrients from the host diets and regulating energy balance. Foraging for food is a risky exercise for the insect which is exposed to ecological adversities, including predators. Therefore, making beneficial choice among available food substrates is a question of survival for the flies and bacteria as well. Our study demonstrates interactions between the host fly and its intestinal bacteria in sustaining the larval development while foraging optimally on different fruit types. These findings add a novel step into our understanding of the interactions between the gut microbial communities and B. dorsalis and provide avenues for developing control strategies to limit the devastative incidence of the fly.

scholarly journals Survival Rates of Microbial Communities from Livestock Waste to Soils: A Comparison between Compost and Digestate

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Maiko Akari ◽  
Yoshitaka Uchida
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Soil Microbial Community ◽  
Survival Rates ◽  
Chemical Fertilizer ◽  
Livestock Waste ◽  
Soil Microbial Community Structure ◽  
Soil Microbial

Livestock waste-based products, such as composted manure, are often used in crop production systems. The products’ microbial characteristics differ depending on animal waste treatment methods used (e.g., biogas production/composting). The question remains whether different livestock waste-based products differently impact soil microbiota. A pot experiment with five treatments (control, chemical fertilizer, digestate + chemical fertilizer, wheat straw compost + chemical fertilizer, and woodchip compost + chemical fertilizer) was conducted to compare the survival rates of microbial communities from digestate and composted manure, after their application to agricultural soil. Potatoes were planted in each pot. The changes in soil pH, the concentration of ammonium and nitrate, and the microbial community properties were monitored after 1, 6, 10, and 14 weeks of the application of livestock waste-based products. The application of composted manure, especially woodchip compost, showed a relatively more extensive impact on the soil microbial community structure than the other treatments. Woodchip compost contained a relatively more abundant and diverse bacterial community than digestate, and its family-level bacterial community structure was similar to that of the soil. These characteristics might determine the extent of the impact of livestock waste-based products on soil microbial communities. Digestate markedly influenced the inorganic nitrogen concentrations in soils but did not affect the soil microbial community. In conclusion, the survival rate of microbes of livestock waste-based products varies depending on the product type. Further investigation is needed to fully understand their impact on soils’ microbial functions.

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