Soil Microsite Outweighs Cultivar Genotype Contribution to Brassica Rhizobacterial Community Structure

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.

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

10.1101/2020.03.31.018416 ◽

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

FEMS Microbiology Letters ◽

10.1093/femsle/fnab010 ◽

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.

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

Microorganisms ◽

10.3390/microorganisms8060834 ◽

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.

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Divergent Patterns of Bacterial Community Structure and Function in Response to Estuarine Output in the Middle of the Bohai Sea

Frontiers in Microbiology ◽

10.3389/fmicb.2021.630741 ◽

2021 ◽

Vol 12 ◽

Author(s):

Caixia Wang ◽

Haikun Zhang ◽

Pengyuan Liu ◽

Yibo Wang ◽

Yanyu Sun ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Microbial Communities ◽

Environmental Conditions ◽

Bacterial Community Structure ◽

Bohai Sea ◽

Bacterial Community Composition ◽

Nucleotide Metabolism ◽

The Yellow Sea ◽

The Bohai Sea

Understanding environment-community relationships under shifting environmental conditions helps uncover mechanisms by which environmental microbial communities manage to improve ecosystem functioning. This study investigated the microbial community and structure near the Yellow Sea River estuary in 12 stations across the middle of the Bohai Sea for over two seasons to elucidate the influence of estuarine output on them. We found that the dominant phyla in all stations were Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, and Planctomycetes. Alpha-diversity increased near the estuary and bacterial community structure differed with variation of spatiotemporal gradients. Among all the environmental factors surveyed, temperature, salinity, phosphate, silicon, nitrate, and total virioplankton abundance played crucial roles in controlling the bacterial community composition. Some inferred that community functions such as carbohydrate, lipid, amino acid metabolism, xenobiotics biodegradation, membrane transport, and environmental adaptation were much higher in winter; energy and nucleotide metabolism were lower in winter. Our results suggested that estuarine output had a great influence on the Bohai Sea environment and changes in the water environmental conditions caused by estuarine output developed distinctive microbial communities in the middle of the Bohai Sea. The distinctive microbial communities in winter demonstrated that the shifting water environment may stimulate changes in the diversity and then strengthen the predicted functions.

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

10.1101/2020.06.25.171660 ◽

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.

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

Applied and Environmental Microbiology ◽

10.1128/aem.01464-06 ◽

2006 ◽

Vol 72 (12) ◽

pp. 7804-7812 ◽

Cited By ~ 104

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.

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Structural and Functional Responses of Soil Microbial Communities to Biodegradable Plastic Film Mulching in Two Agroecosystems

10.1101/650317 ◽

2019 ◽

Author(s):

Sreejata Bandopadhyay ◽

Henry Y. Sintim ◽

Jennifer M. DeBruyn

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Microbial Communities ◽

Bacterial Community Structure ◽

Crop Production ◽

Soil Microbial Communities ◽

Plastic Film ◽

Plastic Mulch ◽

Soil Microbial ◽

Mulch Films

AbstractPolyethylene (PE) 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 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 inadequate research regarding the impacts of repeated 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. Treatments included four plastic BDMs, a completely biodegradable cellulose mulch, a non-biodegradable PE mulch and a no mulch plot. Bacterial community structure determined using 16S rRNA 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 rate 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. Limited effects of BDM incorporation on soil bacterial community structure and soil enzyme activities when compared to PE suggest that BDMs have comparable influences on soil microbial communities, and therefore could be considered an alternative to PE.ImportancePlastic film mulches increase crop yields and improve fruit quality. Most plastic mulches are made of polyethylene (PE), which is poorly degradable, resulting in undesirable end-of-life outcomes. Biodegradable mulches (BDMs) may be a sustainable alternative to PE. BDMs are made of polymers which can be degraded by soil microbial enzymes, and are meant to be tilled into soil after use. However, uncertainty about impacts of tilled-in BDMs on soil health has restricted adoption of BDMs. Our previous research showed BDMs did not have a major effect on a wide range of soil quality indicators (Sintim et al. 2019); here we focus on soil microbial communities, showing that BDMs do not have detectable effects on soil microbial communities and their functions, at least over the short term. This informs growers and regulators about use of BDMs in crop production, paving a way for an agricultural practice that reduces environmental plastic pollution.

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Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition

Nature Communications ◽

10.1038/s41467-021-26543-x ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

C. E. Dubé ◽

M. Ziegler ◽

A. Mercière ◽

E. Boissin ◽

S. Planes ◽

...

Keyword(s):

Bacterial Community ◽

Microbial Communities ◽

Metabolic Network ◽

Community Composition ◽

Bacterial Community Composition ◽

Twin Studies ◽

Host Genotype ◽

Microbiome Composition ◽

Relative Contribution ◽

Naturally Occurring

AbstractCoral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.

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Organic Amendments to Avocado Crops Induce Suppressiveness and Influence the Composition and Activity of Soil Microbial Communities

Applied and Environmental Microbiology ◽

10.1128/aem.03787-14 ◽

2015 ◽

Vol 81 (10) ◽

pp. 3405-3418 ◽

Cited By ~ 24

Author(s):

Nuria Bonilla ◽

Carmen Vida ◽

Maira Martínez-Alonso ◽

Blanca B. Landa ◽

Nuria Gaju ◽

...

Keyword(s):

Bacterial Community ◽

Microbial Communities ◽

Root Rot ◽

Bacterial Community Composition ◽

Soil Microbial Communities ◽

Organic Amendments ◽

Bulk Soil ◽

White Root Rot ◽

Content Type ◽

Soil Microbial

ABSTRACTOne of the main avocado diseases in southern Spain is white root rot caused by the fungusRosellinia necatrixPrill. The use of organic soil amendments to enhance the suppressiveness of natural soil is an inviting approach that has successfully controlled other soilborne pathogens. This study tested the suppressive capacity of different organic amendments againstR. necatrixand analyzed their effects on soil microbial communities and enzymatic activities. Two-year-old avocado trees were grown in soil treated with composted organic amendments and then used for inoculation assays. All of the organic treatments reduced disease development in comparison to unamended control soil, especially yard waste (YW) and almond shells (AS). The YW had a strong effect on microbial communities in bulk soil and produced larger population levels and diversity, higher hydrolytic activity and strong changes in the bacterial community composition of bulk soil, suggesting a mechanism of general suppression. Amendment with AS induced more subtle changes in bacterial community composition and specific enzymatic activities, with the strongest effects observed in the rhizosphere. Even if the effect was not strong, the changes caused by AS in bulk soil microbiota were related to the direct inhibition ofR. necatrixby this amendment, most likely being connected to specific populations able to recolonize conducive soil after pasteurization. All of the organic amendments assayed in this study were able to suppress white root rot, although their suppressiveness appears to be mediated differentially.

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Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

Applied and Environmental Microbiology ◽

10.1128/aem.00335-09 ◽

2009 ◽

Vol 75 (15) ◽

pp. 5111-5120 ◽

Cited By ~ 1989

Author(s):

Christian L. Lauber ◽

Micah Hamady ◽

Rob Knight ◽

Noah Fierer

Keyword(s):

Bacterial Community ◽

Soil Ph ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Spatial Scales ◽

Bacterial Community Composition ◽

Phylogenetic Structure ◽

Soil Bacterial Communities ◽

Soil Bacterial Community Structure ◽

Soil Bacterial

ABSTRACT Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R2 = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.

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