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 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 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.

scholarly journals Distinct bacterial community structure and composition along different cowpea producing ecoregions in Northeastern Brazil

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Luciana de Sousa Lopes ◽  
Lucas William Mendes ◽  
Jadson Emanuel Lopes Antunes ◽  
Louise Melo de Souza Oliveira ◽  
Vania Maria Maciel Melo ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Plant Growth ◽  
Growth Promotion ◽  
Soil Microbial Communities ◽  
Northeastern Brazil ◽  
Soil Microbiome ◽  
Rrna Gene ◽  
Soil Factors ◽  
Organic C

AbstractSoil microbial communities represent the largest biodiversity on Earth, holding an important role in promoting plant growth and productivity. However, the knowledge about how soil factors modulate the bacteria community structure and distribution in tropical regions remain poorly understood, mainly in different cowpea producing ecoregions belonging to Northeastern Brazil. This study addressed the bacterial community along three different ecoregions (Mata, Sertão, and Agreste) through the16S rRNA gene sequencing. The results showed that soil factors, such as Al3+, sand, Na+, cation exchange excel, and total organic C, influenced the bacterial community and could be a predictor of the distinct performance of cowpea production. Also, the bacterial community changed between different ecoregions, and some keystone groups related to plant-growth promotion, such as Bradyrhizobium, Bacillales, Rhizobiales, and Solibacillus, were correlated to cowpea yield, so revealing that the soil microbiome has a primordial role in plant productivity. Here, we provide evidence that bacterial groups related to nutrient cycling can help us to increase cowpea efficiency and we suggest that a better microbiome knowledge can contribute to improving the agricultural performance.

scholarly journals Assessment of the bacterial community structure in shallow and deep sediments of the Perdido Fold Belt region in the Gulf of Mexico

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5583 ◽  
Author(s):  
Ma. Fernanda Sánchez-Soto Jiménez ◽  
Daniel Cerqueda-García ◽  
Jorge L. Montero-Muñoz ◽  
Ma. Leopoldina Aguirre-Macedo ◽  
José Q. García-Maldonado
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Gulf Of Mexico ◽  
Microbial Communities ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Hydrocarbon Contamination ◽  
Rrna Gene ◽  
Fold Belt ◽  
Abundant Otus

The Mexican region of the Perdido Fold Belt (PFB), in northwestern Gulf of Mexico (GoM), is a geological province with important oil reservoirs that will be subjected to forthcoming oil exploration and extraction activities. To date, little is known about the native microbial communities of this region, and how these change relative to water depth. In this study we assessed the bacterial community structure of surficial sediments by high-throughput sequencing of the 16S rRNA gene at 11 sites in the PFB, along a water column depth gradient from 20 to 3,700 m, including five shallow (20–600 m) and six deep (2,800–3,700 m) samples. The results indicated that OTUs richness and diversity were higher for shallow sites (OTUs = 2,888.2 ± 567.88;H′ = 9.6 ± 0.85) than for deep sites (OTUs = 1,884.7 ± 464.2;H′ = 7.74 ± 1.02). Nonmetric multidimensional scaling (NMDS) ordination revealed that shallow microbial communities grouped separately from deep samples. Additionally, the shallow sites plotted further from each other on the NMDS whereas samples from the deeper sites (abyssal plains) plotted much more closely to each other. These differences were related to depth, redox potential, sulfur concentration, and grain size (lime and clay), based on the environmental variables fitted with the axis of the NMDS ordination. In addition, differential abundance analysis identified 147 OTUs with significant fold changes among the zones (107 from shallow and 40 from deep sites), which constituted 10 to 40% of the total relative abundances of the microbial communities. The most abundant OTUs with significant fold changes in shallow samples corresponded toKordiimonadales, Rhodospirillales,Desulfobacterales(Desulfococcus), Syntrophobacterales and Nitrospirales(GOUTA 19,BD2-6,LCP-6), whilstChromatiales,Oceanospirillales(Amphritea,Alcanivorax),Methylococcales,Flavobacteriales,Alteromonadales(Shewanella,ZD0117) andRhodobacteraleswere the better represented taxa in deep samples. Several of the OTUs detected in both deep and shallow sites have been previously related to hydrocarbons consumption. Thus, this metabolism seems to be well represented in the studied sites, and it could abate future hydrocarbon contamination in this ecosystem. The results presented herein, along with biological and physicochemical data, constitute an available reference for further monitoring of the bacterial communities in this economically important region in the GoM.

scholarly journals Variation of soil bacterial communities along a chronosequence of Eucalyptus plantation

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5648 ◽  
Author(s):  
Jiayu Li ◽  
Jiayi Lin ◽  
Chenyu Pei ◽  
Kaitao Lai ◽  
Thomas C. Jeffries ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Communities ◽  
Secondary Forest ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Phosphorus Concentration ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Soil Microbial ◽  
Local Soil

Eucalyptus is harvested for wood and fiber production in many tropical and sub-tropical habitats globally. Plantation has been controversial because of its influence on the surrounding environment, however, the influence of massive Eucalyptus planting on soil microbial communities is unclear. Here we applied high-throughput sequencing of the 16S rRNA gene to assess the microbial community composition and diversity of planting chronosequences, involving two, five and ten years of Eucalyptus plantation, comparing to that of secondary-forest in South China. We found that significant changes in the composition of soil bacteria occurred when the forests were converted from secondary-forest to Eucalyptus. The bacterial community structure was clearly distinct from control and five year samples after Eucalyptus was grown for 2 and 10 years, highlighting the influence of this plantation on local soil microbial communities. These groupings indicated a cycle of impact (2 and 10 year plantations) and low impact (5-year plantations) in this chronosequence of Eucalyptus plantation. Community patterns were underpinned by shifts in soil properties such as pH and phosphorus concentration. Concurrently, key soil taxonomic groups such as Actinobacteria showed abundance shifts, increasing in impacted plantations and decreasing in low impacted samples. Shifts in taxonomy were reflected in a shift in metabolic potential, including pathways for nutrient cycles such as carbon fixation, which changed in abundance over time following Eucalyptus plantation. Combined these results confirm that Eucalyptus plantation can change the community structure and diversity of soil microorganisms with strong implications for land-management and maintaining the health of these ecosystems.

scholarly journals Community Structure Analyses Are More Sensitive to Differences in Soil Bacterial Communities than Anonymous Diversity Indices

2006 ◽  
Vol 72 (12) ◽  
pp. 7804-7812 ◽  
Author(s):  
Martin Hartmann ◽  
Franco Widmer
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Rflp Analysis ◽  
Diversity Indices ◽  
Soil Bacterial Community ◽  
Community Structures ◽  
Soil Microbial ◽  
Soil Bacterial

ABSTRACT Changes in the diversity and structure of soil microbial communities may offer a key to understanding the impact of environmental factors on soil quality in agriculturally managed systems. Twenty-five years of biodynamic, bio-organic, or conventional management in the DOK long-term experiment in Switzerland significantly altered soil bacterial community structures, as assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. To evaluate these results, the relation between bacterial diversity and bacterial community structures and their discrimination potential were investigated by sequence and T-RFLP analyses of 1,904 bacterial 16S rRNA gene clones derived from the DOK soils. Standard anonymous diversity indices such as Shannon, Chao1, and ACE or rarefaction analysis did not allow detection of management-dependent influences on the soil bacterial community. Bacterial community structures determined by sequence and T-RFLP analyses of the three gene libraries substantiated changes previously observed by soil bacterial community level T-RFLP profiling. This supported the value of high-throughput monitoring tools such as T-RFLP analysis for assessment of differences in soil microbial communities. The gene library approach also allowed identification of potential management-specific indicator taxa, which were derived from nine different bacterial phyla. These results clearly demonstrate the advantages of community structure analyses over those based on anonymous diversity indices when analyzing complex soil microbial communities.

scholarly journals Effects of biodegradable plastic film mulching on soil microbial communities in two agroecosystems

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9015 ◽  
Author(s):  
Sreejata Bandopadhyay ◽  
Henry Y. Sintim ◽  
Jennifer M. DeBruyn
Keyword(s):  
Community Structure ◽  
Microbial Communities ◽  
Crop Production ◽  
Soil Microbial Communities ◽  
Biodegradable Plastic ◽  
Rrna Gene ◽  
Plastic Mulch ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Mulch Films

Plastic mulch films are used globally in crop production but incur considerable disposal and environmental pollution issues. Biodegradable plastic mulch films (BDMs), an alternative to polyethylene (PE)-based films, are designed to be tilled into the soil where they are expected to be mineralized to carbon dioxide, water and microbial biomass. However, insufficient research regarding the impacts of repeated soil incorporation of BDMs on soil microbial communities has partly contributed to limited adoption of BDMs. In this study, we evaluated the effects of BDM incorporation on soil microbial community structure and function over two years in two geographical locations: Knoxville, TN, and in Mount Vernon, WA, USA. Treatments included four plastic BDMs (three commercially available and one experimental film), a biodegradable cellulose paper mulch, a non-biodegradable PE mulch and a no mulch plot. Bacterial community structure determined using 16S rRNA gene amplicon sequencing revealed significant differences by location and season. Differences in bacterial communities by mulch treatment were not significant for any season in either location, except for Fall 2015 in WA where differences were observed between BDMs and no-mulch plots. Extracellular enzyme assays were used to characterize communities functionally, revealing significant differences by location and sampling season in both TN and WA but minimal differences between BDMs and PE treatments. Overall, BDMs had comparable influences on soil microbial communities to PE mulch films.

Seasonal effects of river flow on microbial community coalescence and diversity in a riverine network

2020 ◽  
Vol 96 (8) ◽  
Author(s):  
Xia Luo ◽  
Xinyi Xiang ◽  
Yuanhao Yang ◽  
Guoyi Huang ◽  
Kaidao Fu ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Flow Rate ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Rrna Gene ◽  
Strong Impact ◽  
Running Waters

ABSTRACT Terrestrial microbial communities may take advantage of running waters and runoff to enter rivers and mix with aquatic microorganisms. However, the environmental factors governing the interchange of the microbial community within a watercourse and its surrounding environment and the composition of the resulting community are often underestimated. The present study investigated the effect of flow rate on the mixing of water, soil, sediment and biofilm at four sites along the Lancang River and one branch of the river in winter and summer and, in turn, the resultant changes in the microbial community within each habitat. 16S rRNA gene-based Illumina high-throughput sequencing illustrated that bacterial communities were apparently distinct among biofilm, water, soil and sediment. Biofilms had the lowest richness, Shannon diversity and evenness indices compared with other habitats, and those three indices in all habitats increased significantly from winter to summer. SourceTracker analysis showed a significant coalescence between the bacterial communities of sediment, water and biofilm samples at lower flow rates. Additionally, the proportion of Betaproteobacteria in sediment and biofilms increased with a decrease in flow rate, suggesting the flow rate had a strong impact on microbial community composition and exchange among aquatic habitats. These results were further confirmed by a Mantel test and linear regression analysis. Microbial communities in all samples exhibited a significant but very weak distance–decay relationship (r = 0.093, P = 0.024). Turbidity played a much more important role on water bacterial community structure in summer (i.e. rainy season) (BIOENV, r = 0.92). Together, these results suggest that dispersal is an important factor affecting bacterial community structure in this system.

scholarly journals The effects of soil depth on the structure of microbial communities in agricultural soils in Iowa, USA

2020 ◽  
Author(s):  
Jingjie Hao ◽  
Yen Ning Chai ◽  
Raziel A. Ordóñez ◽  
Emily E. Wright ◽  
Sotirios Archontoulis ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Structure ◽  
Soil Depth ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Soil Microbial

AbstractThe determination of how microbial community structure changes within the soil profile, will be beneficial to understanding the long-term health of agricultural soil ecosystems and will provide a first step towards elucidating how deep soil microbial communities contribute to carbon sequestration. This study aimed to investigate the differences in the microbial community abundance, composition and diversity throughout from the surface layers down to deep soils in corn and soybean fields in Iowa, USA. We used 16S rRNA amplicon sequencing of soil samples to characterize the change in microbial community structure. Our results revealed decreased richness and diversity in bacterial community structure with increasing soil depth. We also observed distinct distribution patterns of bacterial community composition along soil profiles. Soil and root data at different depths enabled us to demonstrate that the soil organic matter, soil bulk density and plant water availability were all significant factors in explaining the variation in soil microbial community composition. Our findings provide valuable insights in the changes in microbial community structure to depths of 180 cm in one of the most productive agricultural regions in the world. This knowledge will be important for future management and productivity of agroecosystems in the face of increasing demand for food and climate change.

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