Effect of the combination of bio-organic fertiliser with Bacillus amyloliquefaciens NJN-6 on the control of banana Fusarium wilt disease,crop production and banana rhizosphere culturable microflora

Soil amended with organic amendments has been suggested to be a strategy for managing the Fusarium wilt disease which severely hindered the banana production. The effects of four fertilisation regimes, including chemical fertiliser, manure composts and bio-organic fertiliser (BIO) containing Bacillus amyloliquefaciens NJN-6 for 2-year continuous application on the banana Fusarium wilt disease incidence, crop yield and rhizosphere culturable microbial community were investigated. To explore the soil microflora, plate counting method, in vitro screening method for antagonism, eco-physiological index and culture-dependent denaturing gradient gel electrophoresis method (CD DGGE) were used. The highest banana yield, culturable bacteria, actinobacteria and Bacillus populations, culturable bacteria to fungi (B/F) value, antagonistic Bacillus ratio and lowest Fusarium wilt disease incidence were observed in the BIO treatment. Based on CD DGGE results, the BIO application significantly altered the soil bacteria structure and showed highest richness and diversity. The phylogenetic analysis of the selected bands showed that the most abundant phyla were Proteobacteria and Bacteroidetes and BIO application enriched the genera Comamonas, Chitinophaga, the species Bacillus flexus and uncultured Bacillus. All the results showed that 2-year continuous application of BIO containing B. amyloliquefaciens NJN-6 more effectively controlled Fusarium wilt disease and improved fruit yields under field conditions and modulated banana rhizosphere microflora.     

The rhizosphere microbial community response to a bio-organic fertilizer: finding the mechanisms behind the suppression of watermelon <Emphasis Type="Italic">Fusarium</Emphasis> wilt disease

We aimed to evaluate the capability of bio-organic fertilizer suppressing watermelon Fusarium wilt disease, compare the variations of the rhizosphere bacterial and fungal community compositions after treatment with different fertilizers, and explore mechanisms causing disease suppression in rhizosphere microbial community. A rhizobacterium (Bacillus amyloliquefaciens JDF35) was identified to control watermelon Fusarium wilt disease. Bio-organic fertilizer JDF35 (BOF) was generated by inoculating JDF35 into the organic fertilizer (OF) composed of cow and chicken manure compost (1:50 v/w). A three successive growing season pot experiment was designed to evaluate the effects of BOF compared with OF and chemical fertilizer (CF). Next-generation sequencing using the Illumina MiSeq platform was used to investigate the variations in rhizosphere microbial community composition. The growth of the watermelon plants, soil pH, and available N, P and K concentrations were the highest in the BOF treatment. The Fusarium wilt incidence in the BOF treatment was lower than that in the CF and OF treatment, and the differences for disease incidence were significant (P < 0.001). The diversity of the rhizosphere bacterial community was higher, and that of the fungal was lower in the BOF treatment. Most importantly, the BOF treatment had lowest abundances of Fusarium. The application of the BOF altered the composition of rhizosphere microbial community, suppressing Fusarium wilt disease and promoting plant growth.     

健康与感染青枯病烟株根际土壤与茎秆细菌群落结构与多样性

【目的】了解健康烟株与感染青枯病烟株在根际土壤、茎杆发病部位、茎杆病健交界部位以及未发病茎杆的细菌群落结构与多样性。【方法】分别对土壤与茎杆样品中细菌的16S rRNA基因V3-V4区进行扩增,采用Illumina MiSeq测序技术对扩增片段进行高通量测序,然后对健康烟株与感染青枯病烟株不同部位细菌群落结构与多样性进行分析。【结果】感染青枯病烟株发病茎杆及根际土壤的细菌群落多样性高于健康烟株茎杆及其根际土壤样品,病健交界茎杆样品细菌群落多样性低于健康烟株。变形菌门(Proteobacteria)在所有样品中均为优势菌门;所有烟株根际土壤的优势菌门为拟杆菌门(Bacteroidetes)、酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)和绿弯菌门(Chloroflexi);健康烟株茎杆部位的优势菌门为蓝细菌门(Cyanobacteria);感染青枯病烟株发病茎杆和病健交界茎杆部位的优势菌门为蓝细菌门(Cyanobacteria)和厚壁菌门(Firmicutes)。所有根际土壤样品的优势菌属为劳尔氏菌属(Ralstonia)、假单胞菌属(Pseudomonas)、鞘脂单胞菌属(Sphingomonas)、黄杆菌属(Flavobacterium)和代尔夫特菌属(Delftia),而感染青枯病烟株根际土壤的劳尔氏菌属(Ralstonia)和假单胞菌属(Pseudomonas)相对丰度显著高于健康烟株根际土壤,鞘脂单胞菌属相对丰度显著低于健康烟株根际土壤。烟株茎杆的优势菌属为劳尔氏菌属和假单胞菌属等。感染青枯病烟株病健交界茎杆中劳尔氏菌属、肠杆菌属(Enterobacter)和泛菌属(Pantoea)相对丰度显著低于健康烟株样品。【结论】健康与感染青枯病烟株茎杆样品细菌群落的丰富度和多样性明显低于相应的根际土壤样品。较健康烟株而言,感染青枯病烟株根际土壤和茎杆样品细菌群落丰富度和多样性均表现出不同程度地增加,且根际土壤细菌群落结构变化较茎杆样品明显,而病健交界茎杆样品细菌群落丰富度和多样性降低。烟草青枯病为典型土传病害,其病原茄科劳尔氏菌尽管能在烟株维管束中蔓延扩增,但主要还是分布于土壤中;它的存在似乎对土壤细菌群落的影响大于茎杆样品的。该研究结果提示对于青枯病的防治不能局限于烟株本身,田间土壤也应加大防治力度。     

Vertical distribution of bacterial community is associated with the degree of soil organic matter decomposition in the active layer of moist acidic tundra

The increasing temperature in Arctic tundra deepens the active layer, which is the upper layer of permafrost soil that experiences repeated thawing and freezing. The increasing of soil temperature and the deepening of active layer seem to affect soil microbial communities. Therefore, information on soil microbial communities at various soil depths is essential to understand their potential responses to climate change in the active layer soil. We investigated the community structure of soil bacteria in the active layer from moist acidic tundra in Council, Alaska. We also interpreted their relationship with some relevant soil physicochemical characteristics along soil depth with a fine scale (5 cm depth interval). The bacterial community structure was found to change along soil depth. The relative abundances of Acidobacteria, Gammaproteobacteria, Planctomycetes, and candidate phylum WPS-2 rapidly decreased with soil depth, while those of Bacteroidetes, Chloroflexi, Gemmatimonadetes, and candidate AD3 rapidly increased. A structural shift was also found in the soil bacterial communities around 20 cm depth, where two organic (upper Oi and lower Oa) horizons are subdivided. The quality and the decomposition degree of organic matter might have influenced the bacterial community structure. Besides the organic matter quality, the vertical distribution of bacterial communities was also found to be related to soil pH and total phosphorus content. This study showed the vertical change of bacterial community in the active layer with a fine scale resolution and the possible influence of the quality of soil organic matter on shaping bacterial community structure.     

米修链霉菌TF78对香蕉枯萎病的田间防效及根际土壤微生物的影响

【背景】香蕉枯萎病是香蕉生产上的毁灭性病害,生物防治是遏制该病害发生的有效手段。在前期的研究中,从健康香蕉根际土壤中分离获得一株对香蕉枯萎病具有良好盆栽防治效果的生防菌——米修链霉菌(Streptomyces misionensis) TF78,但其对香蕉枯萎病的田间生防潜力和对土壤微生物环境的影响尚不清楚。【目的】评价米修链霉菌TF78对香蕉枯萎病的田间防治效果,明确其对香蕉根际土壤微生物群落的影响。【方法】选取两块发病香蕉园,测定该生防菌株对香蕉枯萎病的防治效果,并利用扩增子测序技术分析施用菌剂组和空白对照组共12份香蕉根际土壤的微生物多样性和丰度。【结果】米修链霉菌TF78对两块香蕉园的田间防效分别达55.30%和45.32%。该生防菌株处理组的物种稀释曲线坡度大于空白对照组,并显著富集了优势种群梳霉门(Kickxellomycota),消减了绿弯菌门(Chloroflexi)、酸杆菌门(Acidobacteria)和苔藓杆菌(Bryobacter)的丰度,对土壤中优势种群变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)、放线菌门(Actinobacteria)、芽单胞菌门(Gemmatimonadetes)及木霉属(Trichoderma)、鞘氨醇单胞菌属(Sphingomonas)、寡养单胞菌属(Stenotrophomonas)和芽孢杆菌属(Bacillus)的相对丰度影响不显著。【结论】米修链霉菌TF78塑造了不利于香蕉枯萎病菌Fusarium oxysporum f.sp.cubense存活的土壤环境,有效降低了田间香蕉枯萎病的发生,同时对土壤中大部分具有重要生态功能和抑菌功能的优势微生物种群影响不显著。该研究结果为米修链霉菌TF78的进一步开发应用奠定了基础。     

Lime and ammonium carbonate fumigation coupled with bio-organic fertilizer application steered banana rhizosphere to assemble a unique microbiome against Panama disease

Microbiome plays a key role in determining soil suppressiveness against invading pathogens. Our previous study revealed that microbial community of bulk soil could be manipulated by lime and ammonium bicarbonate fumigation followed by biofertilizer application. However, the assembly of microbial community suppressive to banana Panama disease in the rhizosphere is still unclear. In this study, we used high-throughput sequencing and quantitative PCR to explore the assembly of rhizosphere microbiome associated with banana Panama disease suppression in a two-seasonal pot experiment. We found biofertilizer applied to lime and ammonium bicarbonate fumigated soil significantly (P < 0.05) reduced the abundance of rhizosphere Fusarium oxysporum compared to biofertilizer applied to non-fumigated soil. Principal coordinate analysis revealed that biofertilizer applied to lime and ammonium bicarbonate fumigated soil re-shaped the rhizosphere bacterial community composition by increasing the phylogenetic relatedness, and stimulating indigenous microbes, for example, Gemmatimonas, Sphingomonas, Pseudomonas, Lysobacter and Bacillus. Co-occurrence analysis revealed that potential species involved in disease suppression were more interrelated in disease-suppressive soils. Taken together, lime and ammonium bicarbonate fumigation followed by biofertilizer application could induce banana rhizosphere to assemble beneficial microbes dominated consortia to suppress banana Panama disease.     

Use of mulberry–soybean intercropping in salt–alkali soil impacts the diversity of the soil bacterial community

Diverse intercropping system has been used to control disease and improve productivity in the field. In this research, the bacterial communities in salt–alkali soils of monoculture and intercropping mulberry and soybean were studied using 454‐pyrosequencing of the 16S rDNA gene. The dominant taxonomic groups were Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Planctomycetes and Gemmatimonadetes and these were present across all samples. However, the diversity and composition of bacterial communities varied between monoculture and intercropping samples. The estimated bacterial diversity (H') was higher with intercropping soybean than in monoculture soybean, whereas H' showed an opposite pattern in monoculture and intercropping mulberry. Populations of Actinobacteria, Acidobacteria, and Proteobacteria were variable, depending on growth of plants as monoculture or intercropped. Most of Actinobacteria and Chloroflexi were found in intercropping samples, while Acidobacteria and Proteobacteria were present at a higher percentage in monoculture samples. The plant diversity of aboveground and microbial diversity of belowground was linked and soil pH seemed to influence the bacterial community. Finally, the specific plant species was the major factor that determined the bacterial community in the salt–alkali soils.     

Development of a mode of application of bioorganic fertilizer for improving the biocontrol efficacy to <Emphasis Type="Italic">Fusarium</Emphasis> wilt

More effective ways of applying biocontrol products should be developed based both on the characteristics of the biocontrol agents and the normal practices of the agricultural producer. A new system was developed to improve the biocontrol efficacy of Fusarium wilt for watermelon production, and this system was tested in pot and field experiments. Biocontrol was achieved by applying a novel bioorganic fertilizer product (BIO) to Fusarium-infested soil. The best biocontrol was obtained by application of a bioorganic fertilizer, BIO, into soil during the nursery phase of watermelon seedling followed by a second application to Fusarium-infested soil when watermelon seedlings were transplanted. In comparison with the controls, the incidence of the disease was reduced by 60–100% in the pot experiment and by 59–73% in the field experiment when the BIO was applied during the nursery stage. After application of BIO during the nursery stage, the number of colony-forming units of Fusarium oxysporum in rhizospheric soil was significantly (P < 0.05) inhibited compared to the controls. An in vitro experiment showed that the antagonist Paenibacillus polymyxa in the BIO could effectively colonize the rhizosphere of watermelon and proliferate along the extending plant roots. This inhibited growth of Fusarium oxysporum in the rhizosphere of watermelon and protected the watermelon roots from attack by the pathogens. The method used for biocontrol Fusarium wilt disease in watermelon should be a useful strategy to improve field efficacy of other biocontrol agents.     

生物有机肥对土壤微生物群落结构变化及西瓜枯萎病的调控

【目的】研究施用生物有机肥处理土壤后对西瓜枯萎病发生的影响,明确可能与西瓜枯萎病发病密切相关的土壤微生物群落结构。【方法】设置2组不同年份材料对比,依次为施用生物有机肥后2016年发病期(CK2016、T12016)和2017年发病期(CK2017、T12017)。基于16S r RNA序列测定,利用Illumina Miseq高通量测序平台对施用生物有机肥后不同年份的土壤微生物群落组成和差异进行测序分析。【结果】试验结果发现,不同年份的土壤微生物群落中alpha多样性指数并无明显的差异,但是施用生物有机肥后的土壤相比对照土壤中细菌群落多样性略有增高。不同年份土壤细菌群落结构在门水平上差异不显著,其中变形菌门和硬壁菌门是构成这两个年份土壤细菌的重要组成部分,同时也是比较稳定的微生物类群。在属水平上分析发现主要动态变化菌属为芽孢杆菌属、肠球菌属、乳球菌属及水恒杆菌属。通过Spearman分析发现它们与西瓜枯萎病发生率的关系均为负相关。【结论】施用生物有机肥可帮助西瓜连作土壤的生态修复,对枯萎病防治起到一定的作用。通过对施用生物有机肥的不同年份土壤微生物种群结构动态变化及对枯萎病发生率呈正负相关的微生物菌属的分析研究,为如何利用调节土壤微生物群落结构来防治西瓜枯萎病提供了新的思路。     

Evaluation of rhizosphere bacteria and derived bio-organic fertilizers as potential biocontrol agents against bacterial wilt (Ralstonia solanacearum) of potato

Aims

Potato bacterial wilt (Ralstonia solanacearum) is a soil-borne disease that affects the potato plant (Solanum tuberosum) worldwide and causes serious economic losses in southern China. The objective of this study is to study the effect of bacterial antagonists and bio-organic fertilizers on potato bacterial wilt and rhizosphere soil microbial population.

Methods

In the present study, pot and field experiments were conducted to evaluate the LH23 (Bacillus amyloliquefaciens) and LH36 (Bacillus subtilis) strains and their derived bio-organic fertilizers (BIO23 and BIO36) as potential biocontrol agents against potato bacterial wilt.

Results

BIO23 and BIO36 decreased the incidence of bacterial wilt disease and increased potato yields. In pot experiments, the disease incidence of BIO23 and BIO36 was 8.9 % and 11.1 % respectively, much lower than the control (57.7 %). The biocontrol efficiency of BIO23 was 84.6 %, which was the most successful treatment and BIO36 was the second with a biocontrol efficiency of 80.8 %. The increased percentages of potato yields when compared with the control were 63.5 % (BIO23), 64.7 % (BIO36) 34.8 % (LH23), 33.6 % (LH36) and 20.7 % (OF). The counts of antagonists, bacteria and actinobacteria in the rhizosphere soil were significantly increased in BIO23 and BIO36 treatments, whereas the counts of R. solanacearum and fungi in the soil in the both treatments decreased. In field experiments, 70 days after treatment, the biocontrol efficacies of BIO23 and BIO36 treatments were 92.0 % and 84.0 %, and the yield increases of BIO23 and BIO36 treatments were 42.3 % and 28.8 %, respectively, when compared with the organic fertilizer treatment. In addition, the changes in the microbial populations were the same as those observed in the greenhouse experiment.

Conclusions

Potato bacterial wilt could be well controlled by the application bio-organic fertilizer containing a specific antagonist, mainly through the alternation of soil microbial community     

Microbial Community Diversities and Taxa Abundances in Soils along a Seven-Year Gradient of Potato Monoculture Using High Throughput Pyrosequencing Approach

Background

Previous studies have focused on linking soil community structure, diversity, or specific taxa to disturbances. Relatively little attention has been directed to crop monoculture soils, particularly potato monoculture. Information about microbial community changes over time between monoculture and non-monoculture treatments is lacking. Furthermore, few studies have examined microbial communities in potato monoculture soils using a high throughput pyrosequencing approach.

Methodology/Principal Findings

Soils along a seven-year gradient of potato monoculture were collected and microbial communities were characterized using high throughput pyrosequencing approach. Principal findings are as follows. First, diversity (H _Shannon) and richness (S _Chao1) indices of bacterial community, but not of fungal community, were linearly decreased over time and corresponded to a decline of soil sustainability represented by yield decline and disease incidence increase. Second, Fusarium, the only soilborne pathogen-associated fungal genus substantially detected, was linearly increased over time in abundance and was closely associated with yield decline. Third, Fusarium abundance was negatively correlated with soil organic matter (OM) and total nitrogen (TN) but positively with electrical conductivity (EC). Fourth, Fusarium was correlated in abundances with 6 bacterial taxa over time.

Conclusions

Soil bacterial and fungal communities exhibited differential responses to the potato monoculture. The overall soil bacterial communities were shaped by potato monoculture. Fusarium was the only soilborne pathogen-associated genus associated with disease incidence increase and yield decline. The changes of soil OM, TN and EC were responsible for Fusarium enrichment, in addition to selections by the monoculture crop. Acidobacteria and Nitrospirae were linearly decreased over time in abundance, corresponding to the decrease of OM, suggesting their similar ecophysiologial trait. Correlations between abundance of Fusarium with several other bacterial taxa suggested their similar behaviors in responses to potato monoculture and/or soil variables, providing insights into the ecological behaviors of these taxa in the environment.     

Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices

Fertilization and the response of the soil microbial community to the process significantly affect crop yield and the environment. In this study, the seasonal variation in the bacterial communities in rice field soil subjected to different fertilization treatments for more than 50 years was investigated using 16S rRNA sequencing. The simultaneous application of inorganic fertilizers and rice straw compost (CAPK) maintained the species richness of the bacterial communities at levels higher than that in the case of non-fertilization (NF) and application of inorganic fertilizers only (APK) in the initial period of rice growth. The seasonal variation in the bacterial community structure in the NF and APK plots showed cyclic behavior, suggesting that the effect of season was important; however, no such trend was observed in the CAPK plot. In the CAPK plot, the relative abundances of putative copiotrophs such as Bacteroidetes, Firmicutes, and Proteobacteria were higher and those of putative oligotrophs such as Acidobacteria and Plactomycetes were lower than those in the other plots. The relative abundances of organotrophs with respiratory metabolism, such as Actinobacteria, were lower and those of chemoautotrophs that oxidize reduced iron and sulfur compounds were higher in the CAPK plot, suggesting greater carbon storage in this plot. Increased methane emission and nitrogen deficiency, which were inferred from the higher abundances of Methylocystis and Bradyrhizobium in the CAPK plot, may be a negative effect of rice straw application; thus, a solution for these should be considered to increase the use of renewable resources in agricultural lands.     

Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils

Background

Soil bacteria are important drivers for nearly all biogeochemical cycles in terrestrial ecosystems and participate in most nutrient transformations in soil. In contrast to the importance of soil bacteria for ecosystem functioning, we understand little how different management types affect the soil bacterial community composition.

Methodology/Principal Findings

We used pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to identify changes in bacterial diversity and community structure in nine forest and nine grassland soils from the Schwäbische Alb that covered six different management types. The dataset comprised 598,962 sequences that were affiliated to the domain Bacteria. The number of classified sequences per sample ranged from 23,515 to 39,259. Bacterial diversity was more phylum rich in grassland soils than in forest soils. The dominant taxonomic groups across all samples (>1% of all sequences) were Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Firmicutes. Significant variations in relative abundances of bacterial phyla and proteobacterial classes, including Actinobacteria, Firmicutes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes and Alphaproteobacteria, between the land use types forest and grassland were observed. At the genus level, significant differences were also recorded for the dominant genera Phenylobacter, Bacillus, Kribbella, Streptomyces, Agromyces, and Defluviicoccus. In addition, soil bacterial community structure showed significant differences between beech and spruce forest soils. The relative abundances of bacterial groups at different taxonomic levels correlated with soil pH, but little or no relationships to management type and other soil properties were found.

Conclusions/Significance

Soil bacterial community composition and diversity of the six analyzed management types showed significant differences between the land use types grassland and forest. Furthermore, bacterial community structure was largely driven by tree species and soil pH.     

The combination of biochar and PGPBs stimulates the differentiation in rhizosphere soil microbiome and metabolites to suppress soil-borne pathogens under consecutive monoculture regimes

The application of biochar and plant-growth-promoting bacteria (PGPBs) in biocontrol soil-borne pathogens has garnered worldwide interest recently. However, how agricultural replanting disease is alleviated by a combination of biochar and PGPBs treatment (SYBB) remains largely unexplored. In this study, we investigated the beneficial effects of single biochar addition and the combination of biochar and PGPBs on alleviating replanting disease by altering the rhizosphere microbiome and metabolites. Our field experiment showed that the SYBB treatment had a better alleviating effect on replanting disease than the single biochar addition. The study indicated the dominant effect of deterministic processes on the bacterial community and of stochastic processes on the fungal community under biochar and PGPBs treatment. The combination of biochar and PGPBs tended to convert the stochastic processes of fungal community assembly into deterministic processes. We found SYBB treatment increased the abundance of potentially beneficial Pseudomonas, Lysobacter, Gemmatimonadetes and Nitrospira, and decreasing the abundance of potentially pathogenic Fusarium, Talaromyces and Fusarium oxysporum. Moreover, the SYBB treatment increased the abundances of carbohydrates, fatty acids and plant hormones, and decreased the abundances of amino acids in the rhizosphere soil. Co-occurrence network analysis indicated that SYBB treatment increased the connections within the microbial communities and drove the alteration of co-occurrence network among the microbial communities and metabolites, which increased positive correlations in bacteria-metabolite networks and decreased positive correlations in fungi-metabolite networks. Spearman correlation analysis showed the abundances of beneficial Streptomyces, Pseudomonas and Lysobacter were significantly and positively correlated to the metabolites most increased under SYBB treatment. The combination of biochar and PGPBs alleviated replanting disease by mediating the change of rhizosphere soil metabolites, and stimulating the proliferation of indigenous and beneficial soil microbes. The research results are intended to provide the basis for new strategies for green and sustainable remediation of soil-borne pathogens.     

Analyses of dryland biological soil crusts highlight lichens as an important regulator of microbial communities

Biological soil crusts (BSCs) provide important ecosystem services in dryland regions, including erosion control and contribution to nitrogen and CO₂ fixation. As soil microorganisms are still rarely studied within the context of biodiversity planning, we describe, as a contribution to the Soil Crust International project, an approach that addresses this gap in biodiversity assessments. The purpose of the present study was a characterization of prokaryotic communities of BSCs formed by two species of lichenized fungi, Psora decipiens and Toninia sedifolia, in relation to surrounding BSCs and the below-crust soil layer from Tabernas basin (Almería, Spain). Microbial community profiles were determined using 454 pyrosequencing targeting the V4 hypervariable region of the bacterial and archaeal 16S rRNA gene. The majority of the 65,497 sequences obtained belonged to Proteobacteria (mainly Alphaproteobacteria), Actinobacteria, Bacteroidetes and Cyanobacteria. Cyanobacteria were more abundant at the soil surface but rare in below-crust soils, whilst below-crust soils harbored significantly more Acidobacteria, Verrucomicrobia, Gemmatimonadetes, Planctomycetes and Armatimonadetes. Additionally, terricolous lichens were investigated using fluorescence in situ hybridization in conjunction with confocal laser scanning microscopy, the objective being to illustrate bacterial niches in BSC-forming lichens. Bacteria were mainly present at the upper cortex of the squamules and attachment organs. Our findings indicate that the composition of soil prokaryotes varies at a small scale not only in adjacent soil layers but also in BSC-forming lichen species. Furthermore, bacteria were shown to be attached to fungal structures, probably representing a case of fungal-bacterial interaction.     

Liquid Serial Dilution Is Inferior to Solid Media for Isolation of Cultures Representative of the Phylum-Level Diversity of Soil Bacteria

Representatives of only four well-characterized bacterial phyla were isolated from a pasture soil by using liquid serial dilution culture. In contrast, members of Acidobacteria, Verrucomicrobia, and Gemmatimonadetes and of other poorly represented bacterial lineages were isolated in earlier experiments with solidified versions of the same media. We conclude that, contrary to expectation, liquid serial dilution culture is inferior to culturing on solid media for isolating representatives of many bacterial phyla from soil.     

干旱区高寒湿地逆行演替下土壤微生物群落结构的研究

【目的】探究高寒湿地逆行演替对土壤性质与微生物群落结构的影响。【方法】以新疆巴音布鲁克天鹅湖高寒湿地为研究对象,依托逆行演替典型样带(沼泽-沼泽化草甸-草甸),利用高通量测序技术分析各演替区土壤微生物群落结构。【结果】高寒湿地逆行演替改变了土壤微生物在分类操作单元(operational taxonomic unit,OTU)水平上的物种组成,致使草甸区的微生物ACE、Chao1、Simpson、Shannon多样性指数显著低于沼泽区和沼泽化草甸区(P<0.05);随着演替发生,变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)、拟杆菌门(Bacteroidetes)、子囊菌门(Ascomycota)的相对丰度均减少,放线菌门(Actinobacteria)、芽单胞菌门(Gemmatimonadetes)、担子菌门(Basidiomycota)、被孢霉门(Mortierellomycota)的相对丰度增加;主坐标法分析(principal coordinates analysis,PCoA)排序分析显示,土壤微生物群落在各逆行演替都出现不同程度的离散...     

Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt

Soil-borne plant diseases are increasingly causing devastating losses in agricultural production. The development of a more refined model for disease prediction can aid in reducing crop losses through the use of preventative control measures or soil fallowing for a planting season. The emergence of high-throughput DNA sequencing technology has provided unprecedented insight into the microbial composition of diseased versus healthy soils. However, a single independent case study rarely yields a general conclusion predictive of the disease in a particular soil. Here, we attempt to account for the differences among various studies and plant varieties using a machine-learning approach based on 24 independent bacterial data sets comprising 758 samples and 22 independent fungal data sets comprising 279 samples of healthy or Fusarium wilt-diseased soils from eight different countries. We found that soil bacterial and fungal communities were both clearly separated between diseased and healthy soil samples that originated from six crops across nine countries or regions. Alpha diversity was consistently greater in the fungal community of healthy soils. While diseased soil microbiomes harbored higher abundances of Xanthomonadaceae, Bacillaceae, Gibberella, and Fusarium oxysporum, the healthy soil microbiome contained more Streptomyces Mirabilis, Bradyrhizobiaceae, Comamonadaceae, Mortierella, and nonpathogenic fungi of Fusarium. Furthermore, a random forest method identified 45 bacterial OTUs and 40 fungal OTUs that categorized the health status of the soil with an accuracy >80%. We conclude that these models can be applied to predict the potential for occurrence of F. oxysporum wilt by revealing key biological indicators and features common to the wilt-diseased soil microbiome.Subject terms: Molecular ecology, Infectious-disease diagnostics     

Spatial distribution of bacterial communities in high-altitude freshwater wetland sediment

Sediment microorganisms play a crucial role in a variety of biogeochemical processes in freshwater ecosystems. The objective of the current study was to investigate the spatial distribution of sediment bacterial community structure in Luoshijiang Wetland, located in Yunnan–Kweichow Plateau (China). Wetland sediments at different sites and depths were collected. Clone library analysis indicates bacterial communities varied with both sampling site and sediment depth. A total of fourteen bacterial phyla were identified in sediment samples, including Proteobacteria, Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Spirochaetes, and Verrucomicrobia. Proteobacteria (mainly Betaproteobacteria and Deltaproteobacteria) predominated in wetland sediments. Moreover, the proportions of Alphaproteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadete, and Planctomycetes were significantly correlated with chemical properties.     

Cell Size Distributions of Soil Bacterial and Archaeal Taxa

Cell size is a key ecological trait of soil microorganisms that determines a wide range of life history attributes, including the efficiency of nutrient acquisition. However, because of the methodological issues associated with determining cell sizes in situ, we have a limited understanding of how cell abundances vary across cell size fractions and whether certain microbial taxa have consistently smaller cells than other taxa. In this study, we extracted cells from three distinct soils and fractionated them into seven size ranges (5 μm to 0.2 μm) by filtration. Cell abundances in each size fraction were determined by direct microscopy, with the taxonomic composition of each size fraction determined by high-throughput sequencing of the 16S rRNA gene. Most of the cells were smaller than cells typically grown in culture, with 59 to 67% of cells <1.2 μm in diameter. Furthermore, each size fraction harbored distinct bacterial and archaeal communities in each of the three soils, and many of the taxa exhibited distinct size distribution patterns, with the smaller size fractions having higher relative abundances of taxa that are rare or poorly characterized (including Acidobacteria, Gemmatimonadetes, Crenarchaeota, Verrucomicrobia, and Elusimicrobia). In general, there was a direct relationship between average cell size and culturability, with those soil taxa that are poorly represented in culture collections tending to be smaller. Size fractionation not only provides important insight into the life history strategies of soil microbial taxa but also is a useful tool to enable more focused investigations into those taxa that remain poorly characterized.