scholarly journals Insights into the structure and role of seed-borne bacteriome during maize germination

2020 ◽  
Author(s):  
Lidiane Figueiredo dos Santos ◽  
Julie Fernandes Souta ◽  
Cleiton de Paula Soares ◽  
Letícia Oliveira da Rocha ◽  
Maria Luiza Carvalho Santos ◽  
...  
Keyword(s):  
Microbial Community ◽  
Growth Performance ◽  
Community Composition ◽  
Seedling Growth ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Selective Reduction ◽  
Community Diversity ◽  
Initial Growth ◽  
Maize Seeds

ABSTRACTSeed germination events modulate microbial community composition, which ultimately influences seed to seedling growth performance. Here we assess the seed-borne bacteria community in disinfected and non-disinfected maize seeds and seedlings. Using a gnotobiotic system, sodium hypochlorite (1.25%, 30 min) treated-seeds showed a reduction of bacteria population size and an increase of bacteria community diversity associated with selective suppression of Burkholderia related taxon. The shift in the bacteria community composition in disinfested-seeds negatively affects germination speed, seedling growth, and reserve mobilization rates in comparison with non-disinfected maize seeds. A synthetic bacteria community formed by twelve isolates (9 Burkholderia spp.; 2 Bacillus spp. and 1 Staphylococcus sp.) obtained from natural microbiota of maize seeds herein were capable of recovering germination and seedling growth when reintroduced in disinfected seeds. Overall results showed that changes in bacterial community composition and selective reduction of Burkholderia related members dominance interfere with germination events and initial growth of the maize plantlets. By cultivation-dependent and independent approaches, we deciphered seed-maize microbiome structure, bacterial niches location, and bacterial taxon with relevant roles in seedlings growth performance. A causal relationship between seed microbial community succession and germination performance open opportunities in seed technologies to build-up microbial communities to boost plant growth and health.One sentence summarypartial removal of the seed-borne microbiota negatively affects maize seedling growth performance and altered bacteria community structure. Partial microbial recomposition, mainly with Burkholderia-related isolates, restores the germination phenotype of disinfested seeds.

scholarly journals Insights into the structure and role of seed-borne bacteriome during maize germination

2021 ◽  
Author(s):  
Lidiane Figueiredo dos Santos ◽  
Julie Fernandes Souta ◽  
Cleiton de Paula Soares ◽  
Letícia Oliveira da Rocha ◽  
Maria Luiza Carvalho Santos ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Growth Performance ◽  
Community Composition ◽  
Seedling Growth ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Selective Reduction ◽  
Community Diversity ◽  
Initial Growth

Abstract Seed germination events modulate microbial community composition, which ultimately influences seed to seedling growth performance. Here we evaluate the germinated maize (variety SHS 5050) root bacterial community of disinfected seed (DS) and non-disinfected seed (NDS). Using a gnotobiotic system, sodium hypochlorite (1.25%, 30 min) treated seeds showed a reduction of bacterial population size and an apparent increase of bacterial community diversity associated with a significant selective reduction of Burkholderia related sequences. The shift in the bacterial community composition in DS negatively affects germination speed, seedling growth, and reserve mobilization rates compared with NDS. A synthetic bacterial community (syncom) formed by twelve isolates (9 Burkholderia spp.; 2 Bacillus spp. and 1 Staphylococcus sp.) obtained from natural microbiota maize seeds herein were capable of recovering germination and seedling growth when reintroduced in DS. Overall results showed that changes in bacterial community composition and selective reduction of Burkholderia related members dominance interfere with germination events and initial growth of the maize plantlets. By cultivation-dependent and independent approaches, we deciphered seed-maize microbiome structure, bacterial niches location, and bacterial taxa with relevant roles in seedlings growth performance. A causal relationship between seed microbial community succession and germination performance open opportunities in seed technologies to build-up microbial communities to boost plant growth and health.

scholarly journals Spatial and Annual Variation in Microbial Abundance, Community Composition, and Diversity Associated With Alpine Surface Snow

2021 ◽  
Vol 12 ◽  
Author(s):  
Lucas Fillinger ◽  
Kerstin Hürkamp ◽  
Christine Stumpp ◽  
Nina Weber ◽  
Dominik Forster ◽  
...  
Keyword(s):  
Climate Change ◽  
Microbial Community ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Alpha Diversity ◽  
Community Diversity ◽  
Taxon Richness ◽  
European Alps ◽  
Prokaryotic Cell ◽  
Surface Snow

Understanding microbial community dynamics in the alpine cryosphere is an important step toward assessing climate change impacts on these fragile ecosystems and meltwater-fed environments downstream. In this study, we analyzed microbial community composition, variation in community alpha and beta diversity, and the number of prokaryotic cells and virus-like particles (VLP) in seasonal snowpack from two consecutive years at three high altitude mountain summits along a longitudinal transect across the European Alps. Numbers of prokaryotic cells and VLP both ranged around 104 and 105 per mL of snow meltwater on average, with variation generally within one order of magnitude between sites and years. VLP-to-prokaryotic cell ratios spanned two orders of magnitude, with median values close to 1, and little variation between sites and years in the majority of cases. Estimates of microbial community alpha diversity inferred from Hill numbers revealed low contributions of common and abundant microbial taxa to the total taxon richness, and thus low community evenness. Similar to prokaryotic cell and VLP numbers, differences in alpha diversity between years and sites were generally relatively modest. In contrast, community composition displayed strong variation between sites and especially between years. Analyses of taxonomic and phylogenetic community composition showed that differences between sites within years were mainly characterized by changes in abundances of microbial taxa from similar phylogenetic clades, whereas shifts between years were due to significant phylogenetic turnover. Our findings on the spatiotemporal dynamics and magnitude of variation of microbial abundances, community diversity, and composition in surface snow may help define baseline levels to assess future impacts of climate change on the alpine cryosphere.

scholarly journals Ecology and Host Identity Outweigh Evolutionary History in Shaping the Bat Microbiome

mSystems ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Holly L. Lutz ◽  
Elliot W. Jackson ◽  
Paul W. Webala ◽  
Waswa S. Babyesiza ◽  
Julian C. Kerbis Peterhans ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Community Composition ◽  
Evolutionary History ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Anatomical Site ◽  
Skin Microbiota ◽  
Host Identity ◽  
Host Ecology

ABSTRACT Recent studies of mammalian microbiomes have identified strong phylogenetic effects on bacterial community composition. Bats (Mammalia: Chiroptera) are among the most speciose mammals on the planet and the only mammal capable of true flight. We examined 1,236 16S rRNA amplicon libraries of the gut, oral, and skin microbiota from 497 Afrotropical bats (representing 9 families, 20 genera, and 31 species) to assess the extent to which host ecology and phylogeny predict microbial community similarity in bats. In contrast to recent studies of host-microbe associations in other mammals, we found no correlation between chiropteran phylogeny and bacterial community dissimilarity across the three anatomical sites sampled. For all anatomical sites, we found host species identity and geographic locality to be strong predictors of microbial community composition and observed a positive correlation between elevation and bacterial richness. Last, we identified significantly different bacterial associations within the gut microbiota of insectivorous and frugivorous bats. We conclude that the gut, oral, and skin microbiota of bats are shaped predominantly by ecological factors and do not exhibit the same degree of phylosymbiosis observed in other mammals. IMPORTANCE This study is the first to provide a comprehensive survey of bacterial symbionts from multiple anatomical sites across a broad taxonomic range of Afrotropical bats, demonstrating significant associations between the bat microbiome and anatomical site, geographic locality, and host identity—but not evolutionary history. This study provides a framework for future systems biology approaches to examine host-symbiont relationships across broad taxonomic scales, emphasizing the need to elucidate the interplay between host ecology and evolutionary history in shaping the microbiome of different anatomical sites.

scholarly journals Microbial Community Composition Affects Soil Fungistasis

2003 ◽  
Vol 69 (2) ◽  
pp. 835-844 ◽  
Author(s):  
Wietse de Boer ◽  
Patrick Verheggen ◽  
Paulien J. A. Klein Gunnewiek ◽  
George A. Kowalchuk ◽  
Johannes A. van Veen
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Fusarium Culmorum ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Carbon Limitation ◽  
Soil Fungistasis

ABSTRACT Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.

scholarly journals Microbial Communities Show Parallels at Sites with Distinct Litter and Soil Characteristics

2011 ◽  
Vol 77 (21) ◽  
pp. 7560-7567 ◽  
Author(s):  
Marketa Sagova-Mareckova ◽  
Marek Omelka ◽  
Ladislav Cermak ◽  
Zdenek Kamenik ◽  
Jana Olsovska ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Soil Ph ◽  
Soil Chemistry ◽  
High Performance ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Carbon Sources ◽  
Soil Extracts

ABSTRACTPlant and microbial community composition in connection with soil chemistry determines soil nutrient cycling. The study aimed at demonstrating links between plant and microbial communities and soil chemistry occurring among and within four sites: two pine forests with contrasting soil pH and two grasslands of dissimilar soil chemistry and vegetation. Soil was characterized by C and N content, particle size, and profiles of low-molecular-weight compounds determined by high-performance liquid chromatography (HPLC) of soil extracts. Bacterial and actinobacterial community composition was assessed by terminal restriction fragment length polymorphism (T-RFLP) and cloning followed by sequencing. Abundances of bacteria, fungi, and actinobacteria were determined by quantitative PCR. In addition, a pool of secondary metabolites was estimated byermresistance genes coding for rRNA methyltransferases. The sites were characterized by a stable proportion of C/N within each site, while on a larger scale, the grasslands had a significantly lower C/N ratio than the forests. A Spearman's test showed that soil pH was correlated with bacterial community composition not only among sites but also within each site. Bacterial, actinobacterial, and fungal abundances were related to carbon sources while T-RFLP-assessed microbial community composition was correlated with the chemical environment represented by HPLC profiles. Actinobacteria community composition was the only studied microbial characteristic correlated to all measured factors. It was concluded that the microbial communities of our sites were influenced primarily not only by soil abiotic characteristics but also by dominant litter quality, particularly, by percentage of recalcitrant compounds.

scholarly journals Application of Methods for Identifying Broiler Chicken Gut Bacterial Species Linked with Increased Energy Metabolism

2007 ◽  
Vol 74 (3) ◽  
pp. 783-791 ◽  
Author(s):  
Valeria A. Torok ◽  
Kathy Ophel-Keller ◽  
Maylene Loo ◽  
Robert J. Hughes
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Bacterial Species ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Metabolizable Energy ◽  
Principal Coordinates ◽  
Improved Performance ◽  
Gut Microbial Community

ABSTRACT A high-throughput microbial profiling tool based on terminal restriction fragment length polymorphism was developed to monitor the poultry gut microbiota in response to dietary manipulations. Gut microbial communities from the duodena, jejuna, ilea, and ceca of 48 birds fed either a barley control diet or barley diet supplemented with exogenous enzymes for degrading nonstarch polysaccharide were characterized by using multivariate statistical methods. Analysis of samples showed that gut microbial communities varied significantly among gut sections, except between the duodenum and jejunum. Significant diet-associated differences in gut microbial communities were detected within the ileum and cecum only. The dissimilarity in bacterial community composition between diets was 73 and 66% within the ileum and cecum, respectively. Operational taxonomic units, representing bacterial species or taxonomically related groups, contributing to diet-associated differences were identified. Several bacterial species contributed to differences between diet-related gut microbial community composition, with no individual bacterial species contributing more than 1 to 5% of the total. Using canonical analysis of principal coordinates biplots, we correlated differences in gut microbial community composition within the ileum and cecum to improved performance, as measured by apparent metabolizable energy. This is the first report that directly links differences in the composition of the gut microbial community with improved performance, which implies that the presence of specific beneficial and/or absence of specific detrimental bacterial species may contribute to the improved performance in these birds.

scholarly journals Seasonal Dynamics and Persistency of Endophyte Communities in Kalidium schrenkianum Shifts Under Radiation Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Jing Zhu ◽  
Xiang Sun ◽  
Qi-Yong Tang ◽  
Zhi-Dong Zhang
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Community Dynamics ◽  
Microbial Community Composition ◽  
Northwest China ◽  
Community Diversity ◽  
Radiation Stress ◽  
Core Microbiome ◽  
Essential Components

Endophytes are essential components of plant microbiota. Studies have shown that environmental factors and seasonal alternation can change the microbial community composition of plants. However, most studies have mainly emphasized the transitive endophyte communities and seasonal alternation but paid less attention to their persistence through multiple seasons. Kalidium schrenkianum is a perennial halophyte growing in an arid habitat with radiation stress (137Cs) in northwest China. In this study, K. schrenkianum growing under different environmental stresses were selected to investigate the dynamics and persistency of endophytic microbial communities amid seasons in a year. The results showed that Gammaproteobacteria and unassigned Actinobacteria were the most dominant bacterial communities, while the most dominant fungal communities were Dothideomycetes, unassigned Fungi, and Sodariomycetes. The bacterial community diversity in roots was higher than that in aerial tissues, and root communities had higher diversity in summer and autumn. In contrast, the fungal community diversity was higher in aerial tissues comparing to roots, and the highest diversity was in spring. Season was a determinant factor in the microbial community composition in the roots but not in the aerial tissues. RaupCrick index suggested that the bacterial communities were mainly shaped by stochastic processes. Our research investigated the community traits and members with temporal persistency. For example, bacterial taxa Afipia, Delftia, Stenotrophomonas, Xanthomonadaceae_B_OTU_211, and fungal taxa Neocamarosporium F_OTU_388, F_OTU_404, F_OTU_445, and unassigned Fungi F_OTU_704, F_OTU_767 showed higher frequencies than predicted in all the four seasons tested with neutral community model. The networks of co-occurrence associations presented in two or more seasons were visualized which suggested potential time-continuous core modules in most communities. In addition, the community dynamics and persistency also showed different patterns by radiation levels. Our findings would enhance our understanding of the microbial community assembly under environmental stress, and be promising to improve the development of integrated concept of core microbiome in future.

scholarly journals Protists and collembolans alter microbial community composition, C dynamics and soil aggregation in simplified consumer–prey systems

2020 ◽  
Vol 17 (20) ◽  
pp. 4961-4980
Author(s):  
Amandine Erktan ◽  
Matthias C. Rillig ◽  
Andrea Carminati ◽  
Alexandre Jousset ◽  
Stefan Scheu
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Fungal Biomass ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Soil Aggregation ◽  
The Body ◽  
Trophic Levels ◽  
Soil Functioning ◽  
C Dynamics

Abstract. Microbes play an essential role in soil functioning including biogeochemical cycling and soil aggregate formation. Yet, a major challenge is to link microbes to higher trophic levels and assess consequences for soil functioning. Here, we aimed to assess how microbial consumers modify microbial community composition (PLFA markers), as well as C dynamics (microbial C use, SOC concentration and CO2 emission) and soil aggregation. We rebuilt two simplified soil consumer–prey systems: a bacterial-based system comprising amoebae (Acanthamoeba castellanii) feeding on a microbial community dominated by the free-living bacterium Pseudomonas fluorescens and a fungal-based system comprising collembolans (Heteromurus nitidus) grazing on a microbial community dominated by the saprotrophic fungus Chaetomium globosum. The amoeba A. castellanii did not affect microbial biomass and composition, but it enhanced the formation of soil aggregates and tended to reduce their stability. Presumably, the dominance of P. fluorescens, able to produce antibiotic toxins in response to the attack by A. castellanii, was the main cause of the unchanged microbial community composition, and the release of bacterial extracellular compounds, such as long-chained polymeric substances or proteases, in reaction to predation was responsible for the changes in soil aggregation as a side effect. In the fungal system, collembolans significantly modified microbial community composition via consumptive and non-consumptive effects including the transport of microbes on the body surface. As expected, fungal biomass promoted soil aggregation and was reduced in the presence of H. nitidus. Remarkably, we also found an unexpected contribution of changes in bacterial community composition to soil aggregation. In both the bacterial and fungal systems, bacterial and fungal communities mainly consumed C from soil organic matter (rather than the litter added). Increased fungal biomass was associated with an increased capture of C from added litter, and the presence of collembolans levelled off this effect. Neither amoebae nor collembolans altered SOC concentrations and CO2 production. Overall, the results demonstrated that trophic interactions are important for achieving a mechanistic understanding of biological contributions to soil aggregation and may occur without major changes in C dynamics and with or without changes in the composition of the microbial community.

scholarly journals Colonization in the Photic Zone and Subsequent Changes during Sinking Determine Bacterial Community Composition in Marine Snow

2014 ◽  
Vol 81 (4) ◽  
pp. 1463-1471 ◽  
Author(s):  
Stefan Thiele ◽  
Bernhard M. Fuchs ◽  
Rudolf Amann ◽  
Morten H. Iversen
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Marine Snow ◽  
Free Living ◽  
Fluorescence Maximum

ABSTRACTDue to sampling difficulties, little is known about microbial communities associated with sinking marine snow in the twilight zone. A drifting sediment trap was equipped with a viscous cryogel and deployed to collect intact marine snow from depths of 100 and 400 m off Cape Blanc (Mauritania). Marine snow aggregates were fixed and washedin situto prevent changes in microbial community composition and to enable subsequent analysis using catalyzed reporter deposition fluorescencein situhybridization (CARD-FISH). The attached microbial communities collected at 100 m were similar to the free-living community at the depth of the fluorescence maximum (20 m) but different from those at other depths (150, 400, 550, and 700 m). Therefore, the attached microbial community seemed to be “inherited” from that at the fluorescence maximum. The attached microbial community structure at 400 m differed from that of the attached community at 100 m and from that of any free-living community at the tested depths, except that collected near the sediment at 700 m. The differences between the particle-associated communities at 400 m and 100 m appeared to be due to internal changes in the attached microbial community rather thande novocolonization, detachment, or grazing during the sinking of marine snow. The new sampling method presented here will facilitate future investigations into the mechanisms that shape the bacterial community within sinking marine snow, leading to better understanding of the mechanisms which regulate biogeochemical cycling of settling organic matter.

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