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

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.

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

10.21203/rs.3.rs-881107/v1 ◽

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.

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

mSystems ◽

10.1128/msystems.00511-19 ◽

2019 ◽

Vol 4 (6) ◽

Cited By ~ 5

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.

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Microbial Community Composition Affects Soil Fungistasis

Applied and Environmental Microbiology ◽

10.1128/aem.69.2.835-844.2003 ◽

2003 ◽

Vol 69 (2) ◽

pp. 835-844 ◽

Cited By ~ 99

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.

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

Applied and Environmental Microbiology ◽

10.1128/aem.00527-11 ◽

2011 ◽

Vol 77 (21) ◽

pp. 7560-7567 ◽

Cited By ~ 17

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.

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

Applied and Environmental Microbiology ◽

10.1128/aem.01384-07 ◽

2007 ◽

Vol 74 (3) ◽

pp. 783-791 ◽

Cited By ~ 105

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.

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

Biogeosciences ◽

10.5194/bg-17-4961-2020 ◽

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.

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

Applied and Environmental Microbiology ◽

10.1128/aem.02570-14 ◽

2014 ◽

Vol 81 (4) ◽

pp. 1463-1471 ◽

Cited By ~ 45

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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Persistence, loss and appearance of bacteria upstream and downstream of a river system

Marine and Freshwater Research ◽

10.1071/mf16010 ◽

2017 ◽

Vol 68 (5) ◽

pp. 851 ◽

Cited By ~ 8

Author(s):

Lisa M. Dann ◽

Renee J. Smith ◽

Thomas C. Jeffries ◽

Jody C. McKerral ◽

Peter G. Fairweather ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Anthropogenic Impacts ◽

Bacterial Species ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Ecosystem Dynamics ◽

Source Tracking ◽

Freshwater Species ◽

Rdna Sequencing

Bacterial taxa shape microbial community composition and influence aquatic ecosystem dynamics. Studies on bacterial persistence in rivers have primarily focussed on microbial-source tracking as an indicator for faecal-source contamination, whereas archetypal freshwater species have received minimal attention. The present study describes the river microbial communities upstream and 3.3km downstream of a small rural town. By 16S rDNA sequencing, we report three patterns in microbial community composition, namely, persistence, loss and appearance. Persistence was observed as 46% inter-site similarity, perhaps owing to generalists that have information lengths that exceed 3.3km and are capable of adapting to system fluctuations. Loss was observed as 10% site exclusivity upstream, perhaps owing to removal processes such as predation and lysis during transport downstream. Last, appearance was observed as 44% site exclusivity downstream, indicating potential anthropogenic impacts from land run-off on bacterial community composition. High multivariate dispersion among downstream samples, as well as overall sample dissimilarity, present as microscale hotspots of discrete Firmicutes and Cyanobacteria species, indicated higher heterogeneity downstream, and therefore increased patchiness from downstream transport and inputs of bacterial genotypes. These findings suggest relativities among three fates for bacterial species of fluvial systems, persistence, loss and appearance, with each having different effects on system dynamics.

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Elevated salinity inhibits nitrogen removal by changing the microbial community composition in constructed wetlands during the cold season

Marine and Freshwater Research ◽

10.1071/mf17171 ◽

2018 ◽

Vol 69 (5) ◽

pp. 802

Author(s):

Yajun Qiao ◽

Penghe Wang ◽

Wenjuan Zhang ◽

Guangfang Sun ◽

Dehua Zhao ◽

...

Keyword(s):

Waste Water ◽

Microbial Community ◽

Community Composition ◽

Constructed Wetlands ◽

Nitrogen Removal ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Cold Season ◽

Saline Waste ◽

Elevated Salinity

In the present study we investigated whether subsurface flow constructed wetlands (SSF-CWs) can remove nitrogen from saline waste water and whether salinity affects nitrogen removal during the cold season (mean water temperature <10°C). Eight Iris pseudacorus-planted SSF-CWs were fed with normal (salinity 1.3–1.5‰; CWP) or saline (salinity 6.3–6.5‰; CWP+) waste water; similarly, eight unplanted SSF-CWs were fed with normal (CWU) or saline waste water (CWU+). The systems were run continuously at a hydraulic loading rate of 187.5mmday–1 and a hydraulic retention time of 4 days. Nitrogen removal efficiency, plant parameters and bacterial abundance and community composition were measured. In CWP, 80% of NH4+-N and 52% of total nitrogen (TN) were removed. In contrast, the removal rates of NH4+-N and TN in CWP+ were reduced by 27 and 37% respectively. In the presence of higher salinity, not only were there decreases in plant biomass (32.1%) and nitrogen uptake (50.1%), but the growth, activity and oxygen release of roots were also reduced (by 37.8, 68.0 and 62.9% respectively). Bacterial community composition also differed under conditions of elevated salinity. Elevated salinity is associated with lower nitrogen removal in SSF-CWs, which we speculate is a result of suppressed wetland macrophyte growth and activity, as well as changes in microbial community composition.

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Reduction of Perchlorate and Nitrate by Microbial Communities in Vadose Soil

Applied and Environmental Microbiology ◽

10.1128/aem.71.7.3928-3934.2005 ◽

2005 ◽

Vol 71 (7) ◽

pp. 3928-3934 ◽

Cited By ~ 46

Author(s):

Mamie Nozawa-Inoue ◽

Kate M. Scow ◽

Dennis E. Rolston

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Denaturing Gradient Gel Electrophoresis ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Human Thyroid ◽

Perchlorate Reduction

ABSTRACT Perchlorate contamination is a concern because of the increasing frequency of its detection in soils and groundwater and its presumed inhibitory effect on human thyroid hormone production. Although significant perchlorate contamination occurs in the vadose (unsaturated) zone, little is known about perchlorate biodegradation potential by indigenous microorganisms in these soils. We measured the effects of electron donor (acetate and hydrogen) and nitrate addition on perchlorate reduction rates and microbial community composition in microcosm incubations of vadose soil. Acetate and hydrogen addition enhanced perchlorate reduction, and a longer lag period was observed for hydrogen (41 days) than for acetate (14 days). Initially, nitrate suppressed perchlorate reduction, but once perchlorate started to be degraded, the process was stimulated by nitrate. Changes in the bacterial community composition were observed in microcosms enriched with perchlorate and either acetate or hydrogen. Denaturing gradient gel electrophoresis analysis and partial sequencing of 16S rRNA genes recovered from these microcosms indicated that formerly reported perchlorate-reducing bacteria were present in the soil and that microbial community compositions were different between acetate- and hydrogen-amended microcosms. These results indicate that there is potential for perchlorate bioremediation by native microbial communities in vadose soil.

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