Bio-Fertilizer Affects Structural Dynamics, Function and Network Patterns of the Sugarcane Rhizospheric Microbiota

2021 ◽  
Author(s):  
Nathan Liu ◽  
Ziqin Pang ◽  
Zuli Yang ◽  
Fallah Nyumah ◽  
Chaohua Hu ◽  
...  
Keyword(s):  
Community Composition ◽  
Pathogenic Bacteria ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Fertilizer Application ◽  
Fertilizer Efficiency ◽  
Size Analysis ◽  
Support Vector ◽  
Linear Discriminant ◽  
Network Patterns

Abstract Fertilizers and the microbial communities that determine fertilizer efficiency are key to sustainable agricultural development. Sugarcane is an important sugar cash crop in China, and using bio-fertilizers is important for the sustainable development of China's sugar industry. However, information on the effects of bio-fertilizers on sugarcane soil microbiota has rarely been studied. In this study, the effects of bio-fertilizer application on rhizosphere soil physicochemical indicators, microbial community composition, function and network patterns of sugarcane were discussed using a high-throughput sequencing approach. Experimental design: CK: no fertilizer application (0 kg/ha), CF: compound fertilizer (100 kg/ha, BF1: bio-fertilizer (100 kg/ha of biofertilizer + 3.8 kg/ha of urea), BF2: biofertilizer (150 kg/ha of biofertilizer + 3.8 kg/ha of urea). The results showed that bio-fertilizer was effective in increasing sugarcane yield by 7–17%, reducing soil acidification, changing the diversity of fungi and bacteria, and greatly altering the community composition and structure of rhizosphere microorganisms. Variance partitioning canonical correspondence (VPA) analysis showed that soil physicochemical variables explained 80.09% and 73.31% of the variation in bacteria and fungi, respectively. Redundancy analysis and correlation heatmap showed that soil pH, total nitrogen and available potassium were the main factors influencing bacterial community composition, while total soil phosphorus, available phosphorus, pH and available nitrogen were the main drivers of fungal communities. Volcano plots showed that using bio-fertilizers contributed to the accumulation of more beneficial bacteria at the sugarcane rhizosphere level and the decline of pathogenic bacteria (e.g. Leifsonia), which may slow down or suppress the occurrence of diseases. Linear discriminant analysis (LDA) and effect size analysis (LEfSe) searched for biomarkers under different fertilizer treatments. Meanwhile, support vector machine (SVM) assessed the importance of the microbial genera contributing to the variability between fertilizers, of interest were the bacteria Anaerolineace, Vulgatibacter and Paenibacillus; the fungi Cochliobolus, Sordariales and Dothideomycetes between CF and BF2, compared to the other genera contributing to the variability. Network analysis (co-occurrence network) showed that the network structure of bio-fertilizers was closer to the network characteristics of healthy soils, indicating that bio-fertilizers can improve soil health to some extent, and therefore if bio-fertilizers can be used as an alternative to chemical fertilizers in the future alternative, it is important to achieve green soil development and improve the climate.

scholarly journals Bio-fertilizer Affects Structural Dynamics, Function, and Network Patterns of the Sugarcane Rhizospheric Microbiota

2021 ◽  
Author(s):  
Qiang Liu ◽  
Ziqin Pang ◽  
Zuli Yang ◽  
Fallah Nyumah ◽  
Chaohua Hu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Pathogenic Bacteria ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Fertilizer Efficiency ◽  
Size Analysis ◽  
Support Vector ◽  
Linear Discriminant ◽  
Network Patterns

AbstractFertilizers and microbial communities that determine fertilizer efficiency are key to sustainable agricultural development. Sugarcane is an important sugar cash crop in China, and using bio-fertilizers is important for the sustainable development of China’s sugar industry. However, information on the effects of bio-fertilizers on sugarcane soil microbiota has rarely been studied. In this study, the effects of bio-fertilizer application on rhizosphere soil physicochemical indicators, microbial community composition, function, and network patterns of sugarcane were discussed using a high-throughput sequencing approach. The experimental design is as follows: CK: urea application (57 kg/ha), CF: compound fertilizer (450 kg/ha), BF1: bio-fertilizer (1500 kg/ha of bio-fertilizer + 57 kg/ha of urea), and BF2: bio-fertilizer (2250 kg/ha of bio-fertilizer + 57 kg/ha of urea). The results showed that the bio-fertilizer was effective in increasing sugarcane yield by 3–12% compared to the CF treatment group, while reducing soil acidification, changing the diversity of fungi and bacteria, and greatly altering the composition and structure of the inter-root microbial community. Variance partitioning canonical correspondence (VPA) analysis showed that soil physicochemical variables explained 80.09% and 73.31% of the variation in bacteria and fungi, respectively. Redundancy analysis and correlation heatmap showed that soil pH, total nitrogen, and available potassium were the main factors influencing bacterial community composition, while total soil phosphorus, available phosphorus, pH, and available nitrogen were the main drivers of fungal communities. Volcano plots showed that using bio-fertilizers contributed to the accumulation of more beneficial bacteria in the sugarcane rhizosphere level and the decline of pathogenic bacteria (e.g., Leifsonia), which may slow down or suppress the occurrence of diseases. Linear discriminant analysis (LDA) and effect size analysis (LEfSe) searched for biomarkers under different fertilizer treatments. Meanwhile, support vector machine (SVM) assessed the importance of the microbial genera contributing to the variability between fertilizers, of interest were the bacteria Anaerolineace, Vulgatibacter, and Paenibacillus and the fungi Cochliobolus, Sordariales, and Dothideomycetes between CF and BF2, compared to the other genera contributing to the variability. Network analysis (co-occurrence network) showed that the network structure of bio-fertilizers was closer to the network characteristics of healthy soils, indicating that bio-fertilizers can improve soil health to some extent, and therefore if bio-fertilizers can be used as an alternative to chemical fertilizers in the future alternative, it is important to achieve green soil development and improve the climate.

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 Effects of Magnetic Minerals Exposure and Microbial Responses in Surface Sediment across the Bohai Sea

2021 ◽  
Vol 10 (1) ◽  
pp. 6
Author(s):  
Lei Chen ◽  
Mingpeng Wang ◽  
Yuntao Li ◽  
Weitao Shang ◽  
Jianhui Tang ◽  
...  
Keyword(s):  
Community Composition ◽  
Surface Sediment ◽  
Bohai Sea ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Magnetic Minerals ◽  
The Bohai Sea ◽  
Α Diversity

Extensive production and application of magnetic minerals introduces significant amounts of magnetic wastes into the environment. Exposure to magnetic minerals could affect microbial community composition and geographic distribution. Here, we report that magnetic susceptibility is involved in determining bacterial α-diversity and community composition in surface sediment across the Bohai Sea by high-throughput sequencing analysis of the 16S rRNA gene. The results showed that environmental factors (explained 9.80%) played a larger role than spatial variables (explained 6.72%) in conditioning the bacterial community composition. Exposure to a magnetite center may shape the geographical distribution of five dissimilatory iron reducing bacteria. The microbial iron reduction ability and electroactive activity in sediment close to a magnetite center are stronger than those far away. Our study provides a novel understanding for the response of DIRB and electroactive bacteria to magnetic minerals exposure.

scholarly journals Integrating morphology and metagenomics to understand taxonomic variability of Amphisorus (Foraminifera, Miliolida) from Western Australia and Indonesia

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0244616
Author(s):  
Jan-Niklas Macher ◽  
Martina Prazeres ◽  
Sarah Taudien ◽  
Jamaluddin Jompa ◽  
Aleksey Sadekov ◽  
...  
Keyword(s):  
Community Composition ◽  
Western Australia ◽  
Bacterial Community Composition ◽  
Morphological Variability ◽  
Microbial Community Composition ◽  
Integrated Approach ◽  
Taxonomic Diversity ◽  
Integrative Approach ◽  
Sampling Location ◽  
Metagenomic Sequencing

Foraminifera are a group of mostly marine protists with high taxonomic diversity. Species identification is often complex, as both morphological and molecular approaches can be challenging due to a lack of unique characters and reference sequences. An integrative approach combining state of the art morphological and molecular tools is therefore promising. In this study, we analysed large benthic Foraminifera of the genus Amphisorus from Western Australia and Indonesia. Based on previous findings on high morphological variability observed in the Soritidae and the discontinuous distribution of Amphisorus along the coast of western Australia, we expected to find multiple morphologically and genetically unique Amphisorus types. In order to gain detailed insights into the diversity of Amphisorus, we applied micro CT scanning and shotgun metagenomic sequencing. We identified four distinct morphotypes of Amphisorus, two each in Australia and Indonesia, and showed that each morphotype is a distinct genotype. Furthermore, metagenomics revealed the presence of three dinoflagellate symbiont clades. The most common symbiont was Fugacium Fr5, and we could show that its genotypes were mostly specific to Amphisorus morphotypes. Finally, we assembled the microbial taxa associated with the two Western Australian morphotypes, and analysed their microbial community composition. Even though each Amphisorus morphotype harboured distinct bacterial communities, sampling location had a stronger influence on bacterial community composition, and we infer that the prokaryotic community is primarily shaped by the microhabitat rather than host identity. The integrated approach combining analyses of host morphology and genetics, dinoflagellate symbionts, and associated microbes leads to the conclusion that we identified distinct, yet undescribed taxa of Amphisorus. We argue that the combination of morphological and molecular methods provides unprecedented insights into the diversity of foraminifera, which paves the way for a deeper understanding of their biodiversity, and facilitates future taxonomic and ecological work.

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 Assessing the microbiota of recycled bedding sand on a Wisconsin dairy farm

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hannah E. Pilch ◽  
Andrew J. Steinberger ◽  
Donald C. Sockett ◽  
Nicole Aulik ◽  
Garret Suen ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Pathogenic Bacteria ◽  
Bacterial Community Composition ◽  
Dairy Farm ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Recycling System ◽  
Core Microbiota ◽  
Relative Abundances

Abstract Background Sand is often considered the preferred bedding material for dairy cows as it is thought to have lower bacterial counts than organic bedding materials and cows bedded on sand experience fewer cases of lameness and disease. Sand can also be efficiently recycled and reused, making it cost-effective. However, some studies have suggested that the residual organic material present in recycled sand can serve as a reservoir for commensal and pathogenic bacteria, although no studies have yet characterized the total bacterial community composition. Here we sought to characterize the bacterial community composition of a Wisconsin dairy farm bedding sand recycling system and its dynamics across several stages of the recycling process during both summer and winter using 16S rRNA gene amplicon sequencing. Results Bacterial community compositions of the sand recycling system differed by both seasons and stage. Summer samples had higher richness and distinct community compositions, relative to winter samples. In both summer and winter samples, the diversity of recycled sand decreased with time drying in the recycling room. Compositionally, summer sand 14 d post-recycling was enriched in operational taxonomic units (OTUs) belonging to the genera Acinetobacter and Pseudomonas, relative to freshly washed sand and sand from cow pens. In contrast, no OTUs were found to be enriched in winter sand. The sand recycling system contained an overall core microbiota of 141 OTUs representing 68.45% ± 10.33% SD of the total bacterial relative abundance at each sampled stage. The 4 most abundant genera in this core microbiota included Acinetobacter, Psychrobacter, Corynebacterium, and Pseudomonas. Acinetobacter was present in greater abundance in summer samples, whereas Psychrobacter and Corynebacterium had higher relative abundances in winter samples. Pseudomonas had consistent relative abundances across both seasons. Conclusions These findings highlight the potential of recycled bedding sand as a bacterial reservoir that warrants further study.

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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