Taxonomic Compositions and Co-occurrence Relationships of Protists in Bulk Soil and Rhizosphere of Soybean Fields in Different Regions of China

As the main consumers of bacteria and fungi in farmed soils, protists remain poorly understood. The aim of this study was to explore protist community assembly and ecological roles in soybean fields. Here, we investigated differences in protist communities using high-throughput sequencing and their inferred potential interactions with bacteria and fungi between the bulk soil and rhizosphere compartments of three soybean cultivars collected from six ecological regions in China. Distinct protist community structures characterized the bulk soil and rhizosphere of soybean plants. A significantly higher relative abundance of phagotrophs was observed in the rhizosphere (25.1%) than in the bulk soil (11.3%). Spatial location (R2 = 0.37–0.51) explained more of the variation in protist community structures of soybean fields than either the compartment (R2 = 0.08–0.09) or cultivar type (R2 = 0.02–0.03). The rhizosphere protist network (76 nodes and 414 edges) was smaller and less complex than the bulk soil network (147 nodes and 880 edges), indicating a smaller potential of niche overlap and interactions in the rhizosphere due to the increased resources in the rhizosphere. Furthermore, more inferred potential predator-prey interactions occur in the rhizosphere. We conclude that protists have a crucial ecological role to play as an integral part of microbial co-occurrence networks in soybean fields.

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Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes

10.1101/332403 ◽

2018 ◽

Author(s):

Hirokazu Toju ◽

Yu Tanaka

Keyword(s):

Crop Production ◽

High Throughput Sequencing ◽

Infected Plant ◽

Agricultural Practices ◽

Root Knot Nematodes ◽

Indigenous Resident ◽

Agroecosystem Management ◽

Soybean Plants ◽

Bacteria And Fungi ◽

Taxonomic Groups

AbstractCyst and root-knot nematodes are major risk factors of agroecosystem management, often causing devastating impacts on crop production. The use of microbes that parasitize or prey on nematodes has been considered as a promising approach for suppressing phytopathogenic nematode populations. However, as effects and persistence of those biological control agents often vary substantially depending on regions, soil characteristics, and agricultural practices, more insights into microbial community processes are required to develop reproducible control of nematode populations. By performing high-throughput sequencing profiling of bacteria and fungi, we examined how root and soil microbiomes differ between benign and nematode-infected plant individuals in a soybean field in Japan. Results indicated that various taxonomic groups of bacteria and fungi occurred preferentially on the soybean individuals infected by root-knot nematodes. Based on a network analysis of potential microbe–microbe associations, we further found that several fungal taxa potentially preying on nematodes [Dactylellina (Orbiliales), Rhizophydium (Rhizophydiales), Clonostachys (Hypocreales), Pochonia (Hypocreales), and Purpureocillium (Hypocreales)] co-occurred in the soybean rhizosphere at a small spatial scale. Overall, this study suggests how “consortia” of anti-nematode microbes can derive from indigenous (resident) microbiomes, thereby providing basic information for managing anti-nematode microbial communities in agroecosystems.

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Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes

Royal Society Open Science ◽

10.1098/rsos.181693 ◽

2019 ◽

Vol 6 (3) ◽

pp. 181693 ◽

Cited By ~ 8

Author(s):

Hirokazu Toju ◽

Yu Tanaka

Keyword(s):

Crop Production ◽

High Throughput Sequencing ◽

Infected Plant ◽

Agricultural Practices ◽

Root Knot Nematodes ◽

Indigenous Resident ◽

Agroecosystem Management ◽

Soybean Plants ◽

Bacteria And Fungi ◽

Taxonomic Groups

Cyst and root-knot nematodes are major risk factors of agroecosystem management, often causing devastating impacts on crop production. The use of microbes that parasitize or prey on nematodes has been considered as a promising approach for suppressing phytopathogenic nematode populations. However, effects and persistence of those biological control agents often vary substantially depending on regions, soil characteristics and agricultural practices: more insights into microbial community processes are required to develop reproducible control of nematode populations. By performing high-throughput sequencing profiling of bacteria and fungi, we examined how root and soil microbiomes differ between benign and nematode-infected plant individuals in a soybean field in Japan. Results indicated that various taxonomic groups of bacteria and fungi occurred preferentially on the soybean individuals infected by root-knot nematodes or those uninfected by nematodes. Based on a network analysis of potential microbe–microbe associations, we further found that several fungal taxa potentially preying on nematodes ( Dactylellina (Orbiliales), Rhizophydium (Rhizophydiales), Clonostachys (Hypocreales), Pochonia (Hypocreales) and Purpureocillium (Hypocreales)) co-occurred in the soybean rhizosphere at a small spatial scale. This study suggests how ‘consortia’ of anti-nematode microbes can derive from indigenous (resident) microbiomes, providing basic information for managing anti-nematode microbial communities in agroecosystems.

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Seasonal Variation Characteristics of Bacteria and Fungi in PM2.5 in Typical Basin Cities of Xi’an and Linfen, China

Atmosphere ◽

10.3390/atmos12070809 ◽

2021 ◽

Vol 12 (7) ◽

pp. 809

Author(s):

Sen Wang ◽

Wanyu Liu ◽

Jun Li ◽

Haotian Sun ◽

Yali Qian ◽

...

Keyword(s):

Seasonal Variation ◽

Relative Abundance ◽

Pathogenic Bacteria ◽

High Throughput Sequencing ◽

Fine Particulate Matter ◽

Ecological Functions ◽

Factors Affecting ◽

Bacterial Phyla ◽

Variation Characteristics ◽

Bacteria And Fungi

Microorganisms existing in airborne fine particulate matter (PM2.5) have key implications in biogeochemical cycling and human health. In this study, PM2.5 samples, collected in the typical basin cities of Xi’an and Linfen, China, were analyzed through high-throughput sequencing to understand microbial seasonal variation characteristics and ecological functions. For bacteria, the highest richness and diversity were identified in autumn. The bacterial phyla were dominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Metabolism was the most abundant pathway, with the highest relative abundance found in autumn. Pathogenic bacteria (Pseudomonas, Acinetobacter, Serratia, and Delftia) were positively correlated with most disease-related pathways. Besides, C cycling dominated in spring and summer, while N cycling dominated in autumn and winter. The relative abundance of S cycling was highest during winter in Linfen. For fungi, the highest richness was found in summer. Basidiomycota and Ascomycota mainly constituted the fungal phyla. Moreover, temperature (T) and sulfur dioxide (SO2) in Xi’an, and T, SO2, and nitrogen dioxide (NO2) in Linfen were the key factors affecting microbial community structures, which were associated with different pollution characteristics in Xi’an and Linfen. Overall, these results provide an important reference for the research into airborne microbial seasonal variations, along with their ecological functions and health impacts.

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Denitrifying bacterial communities in surface-flow constructed wetlands during different seasons: characteristics and relationships with environment factors

Scientific Reports ◽

10.1038/s41598-021-82438-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jia-ming Wei ◽

Li-juan Cui ◽

Wei Li ◽

Yun-mei Ping ◽

Wan Li

Keyword(s):

Environmental Factors ◽

High Throughput Sequencing ◽

Bacterial Abundance ◽

Flow Direction ◽

Denitrifying Bacteria ◽

Surface Flow ◽

Strongly Correlated ◽

Community Structures ◽

Oxidation Reduction ◽

Different Seasons

AbstractDenitrification is an important part of the nitrogen cycle and the key step to removal of nitrogen in surface-flow wetlands. In this study, we explored space–time analysis with high-throughput sequencing to elucidate the relationships between denitrifying bacteria community structures and environmental factors during different seasons. Our results showed that along the flow direction of different processing units, there were dynamic changes in physical and chemical indicators. The bacterial abundance indexes (ACEs) in May, August, and October were 686.8, 686.8, and 996.2, respectively, whereas the Shannon-Weiner indexes were 3.718, 4.303, and 4.432, respectively. Along the flow direction, the denitrifying bacterial abundance initially increased and then decreased subsequently during the same months, although diversity tended to increase. The abundance showed similar changes during the different months. Surface flow wetlands mainly contained the following denitrifying bacteria genus: unclassified Bacteria (37.12%), unclassified Proteobacteria (18.16%), Dechloromonas (16.21%), unranked environmental samples (12.51%), unclassified Betaproteobacteria (9.73%), unclassified Rhodocyclaceae (2.14%), and Rhodanobacter (1.51%). During different seasons, the same unit showed alternating changes, and during the same season, bacterial community structures were influenced by the second genus proportion in different processing units. ACEs were strongly correlated with temperature, dissolved oxygen, and pH. Bacterial diversity was strongly correlated with temperature, electrical conductivity, pH, and oxidation reduction potential. Denitrifying bacteria are greatly affected by environmental factors such as temperature and pH.

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Urban community structure detection based on the OD of traffic analysis zones

Modern Physics Letters B ◽

10.1142/s0217984919501641 ◽

2019 ◽

Vol 33 (13) ◽

pp. 1950164

Author(s):

Qing-Feng Dong ◽

Dian-Kun Chen ◽

Ting Wang

Keyword(s):

Community Structure ◽

Quantitative Methods ◽

Urban Community ◽

Spatial Location ◽

Traffic Analysis ◽

Association Mining ◽

Community Structures ◽

City Community ◽

Traffic Characteristics ◽

Structure Detection

At present, the detection of urban community structures is mainly based on existing administrative divisions, and is performed using qualitative methods. The lack of quantitative methods makes it difficult to judge the rationality of urban community divisions. In this study, we used complex network association mining methods to detect a city community structure by using the Origin-Destinations (OD) at traffic analysis zone (TAZ) level, and successively assigned all the TAZs into different communities. Based on the community results, we calculated the community core degree of each TAZ within every community, and then calculated the Traffic Core Degree and Location Core Degree indicators of the community based on OD passenger flow and spatial location relationship between communities. Finally, we analyzed the correlation among three indicators to ensure the rationality of the community structure. We used the city of Zhengzhou in 2016 as an example case study. For Zhengzhou, we detected a total of six communities. We found a relatively low correlation between Traffic Core Degree and Location Core Degree. Within each group, the correlation between community core degree and Traffic Core Degree was higher than that between community core degree and Location Core Degree, indicating that the urban community structure is more reasonably based on traffic characteristics. The development of a quantitative approach for determining reasonable city community structures has important implications for transportation planning and industrial layout.

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Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape

Applied and Environmental Microbiology ◽

10.1128/aem.01938-17 ◽

2017 ◽

Vol 83 (22) ◽

Cited By ~ 40

Author(s):

Konstantia Gkarmiri ◽

Shahid Mahmood ◽

Alf Ekblad ◽

Sadhna Alström ◽

Nils Högberg ◽

...

Keyword(s):

Brassica Napus ◽

Stable Isotope ◽

Oilseed Rape ◽

High Throughput ◽

High Throughput Sequencing ◽

Rhizosphere Soil ◽

Stable Isotope Probing ◽

Biofuel Production ◽

Content Type ◽

Bacteria And Fungi

ABSTRACT RNA stable isotope probing and high-throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing the roots and rhizosphere soil of oilseed rape to identify taxa assimilating plant-derived carbon following 13CO2 labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other, and there were highly significant differences between their DNA- and RNA-based community profiles. Verrucomicrobia, Proteobacteria, Planctomycetes, Acidobacteria, Gemmatimonadetes, Actinobacteria, and Chloroflexi were the most active bacterial phyla in the rhizosphere soil. Bacteroidetes were more active in roots. The most abundant bacterial genera were well represented in both the 13C- and 12C-RNA fractions, while the fungal taxa were more differentiated. Streptomyces, Rhizobium, and Flavobacterium were dominant in roots, whereas Rhodoplanes and Sphingomonas (Kaistobacter) were dominant in rhizosphere soil. “Candidatus Nitrososphaera” was enriched in 13C in rhizosphere soil. Olpidium and Dendryphion were abundant in the 12C-RNA fraction of roots; Clonostachys was abundant in both roots and rhizosphere soil and heavily 13C enriched. Cryptococcus was dominant in rhizosphere soil and less abundant, but was 13C enriched in roots. The patterns of colonization and C acquisition revealed in this study assist in identifying microbial taxa that may be superior competitors for plant-derived carbon in the rhizosphere of Brassica napus. IMPORTANCE This microbiome study characterizes the active bacteria and fungi colonizing the roots and rhizosphere soil of Brassica napus using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following 13CO2 labeling and compares these with other less active groups not incorporating a plant assimilate. Brassica napus is an economically and globally important oilseed crop, cultivated for edible oil, biofuel production, and phytoextraction of heavy metals; however, it is susceptible to several diseases. The identification of the fungal and bacterial species successfully competing for plant-derived carbon, enabling them to colonize the roots and rhizosphere soil of this plant, should enable the identification of microorganisms that can be evaluated in more detailed functional studies and ultimately be used to improve plant health and productivity in sustainable agriculture.

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Evaluation of the Relationship among Biogenic Amines, Nitrite and Microbial Diversity in Fermented Mustard

Molecules ◽

10.3390/molecules26206173 ◽

2021 ◽

Vol 26 (20) ◽

pp. 6173

Author(s):

Yangyang Yu ◽

Lu Li ◽

Yujuan Xu ◽

Kejing An ◽

Qiao Shi ◽

...

Keyword(s):

Biogenic Amines ◽

High Throughput Sequencing ◽

Starter Cultures ◽

Sequencing Analysis ◽

Maximum Residue Limit ◽

Safety Standard ◽

Bacteria And Fungi ◽

High Level ◽

Degradation Properties ◽

The Relationship

Biogenic amines (BAs) and nitrites are both considered harmful compounds for customer health, and are closely correlated with the microorganisms in fermented mustard (FM). In this study, BAs and nitrite contents in fifteen FM samples from different brands were analyzed. The concentrations of cadaverine in one sample and of histamine in one sample were above the toxic level. Moreover, five FM samples contained a high level of nitrite, exceeding the maximum residue limit (20 mg/kg) suggested by the National Food Safety Standard. Then, this study investigated bacterial and fungal communities by high-throughput sequencing analysis. Firmicutes and Basidiomycota were identified as the major bacteria and fungi phylum, respectively. The correlations among microorganisms, BAs and nitrite were analyzed. Typtamine showed a positive correlation with Lactobacillus and Pseudomonas. Cadaverine and nitrite is positively correlated with Leuconostoc. Furthermore, thirteen strains were selected from the samples to evaluate the accumulation and degradation properties of their BAs and nitrite. The results indicated that the Lactobacillus isolates, including L. plantarum GZ-2 and L. brevis SC-2, can significantly reduce BAs and nitrite in FM model experiments. This study not only assessed the contents of BAs and nitrite in FM samples, but also provided potential starter cultures for BAs and nitrite control in the FM products industry.

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Exploring Microbial Resource of Different Rhizocompartments of Dominant Plants Along the Salinity Gradient Around the Hypersaline Lake Ejinur

Frontiers in Microbiology ◽

10.3389/fmicb.2021.698479 ◽

2021 ◽

Vol 12 ◽

Author(s):

Junqing Luo ◽

Zhechao Zhang ◽

Yazhou Hou ◽

Fengwei Diao ◽

Baihui Hao ◽

...

Keyword(s):

High Throughput Sequencing ◽

Salt Lake ◽

Salinity Gradient ◽

Salt Lakes ◽

Hypersaline Environment ◽

Hypersaline Lake ◽

Littoral Zones ◽

Microbial Resources ◽

Bacteria And Fungi

Lake littoral zones can also be regarded as another extremely hypersaline environment due to hypersaline properties of salt lakes. In this study, high-throughput sequencing technique was used to analyze bacteria and fungi from different rhizocompartments (rhizosphere and endosphere) of four dominant plants along the salinity gradient in the littoral zones of Ejinur Salt Lake. The study found that microbial α-diversity did not increase with the decrease of salinity, indicating that salinity was not the main factor on the effect of microbial diversity. Distance-based redundancy analysis and regression analysis were used to further reveal the relationship between microorganisms from different rhizocompartments and plant species and soil physicochemical properties. Bacteria and fungi in the rhizosphere and endosphere were the most significantly affected by SO42–, SOC, HCO3–, and SOC, respectively. Correlation network analysis revealed the potential role of microorganisms in different root compartments on the regulation of salt stress through synergistic and antagonistic interactions. LEfSe analysis further indicated that dominant microbial taxa in different rhizocompartments had a positive response to plants, such as Marinobacter, Palleronia, Arthrobacter, and Penicillium. This study was of great significance and practical value for understanding salt environments around salt lakes to excavate the potential microbial resources.

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Comparative Analysis of the Bacterial and Fungal Communities in the Gut and the Crop of Aedes albopictus Mosquitoes: A Preliminary Study

Pathogens ◽

10.3390/pathogens9080628 ◽

2020 ◽

Vol 9 (8) ◽

pp. 628

Author(s):

Morgane Guégan ◽

Edwige Martin ◽

Claire Valiente Moro

Keyword(s):

Aedes Albopictus ◽

High Throughput Sequencing ◽

Fungal Communities ◽

Nectar Feeding ◽

Composition And Structure ◽

Asian Tiger ◽

Males And Females ◽

Preliminary Study ◽

Bacteria And Fungi ◽

Pathogen Vector

The Asian tiger mosquito Aedes albopictus is a major pathogen vector and one of the world’s most invasive species. In recent years, the study of mosquito-associated microbiota has received growing interest for reducing transmission of mosquito-borne pathogens. Most of studies on mosquito microbiota mainly focused on the gut bacteria. However, microorganisms can also colonize other organs and are not restricted to bacteria. In mosquitoes, the crop is the primary storage organ for sugars from the nectar feeding before it is transferred into the midgut for digestion. No study has yet investigated whether this organ can harbor microorganisms in Ae. albopictus. By using high-throughput sequencing, this study is the first to describe the microbiota including both bacteria and fungi in sugar-fed Ae. albopictus males and females. The results showed the presence of diverse and rich bacterial and fungal communities in the crop of both sexes that did not strongly differ from the community composition and structure found in the gut. Altogether, our results provide a thorough description of the crop-associated microbiota in Ae. albopictus which can open new avenues for further studies on trophic interactions between the mosquito and its microbiota.

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Analyses of Aerosol Concentrations and Bacterial Community Structures for Closed Cage Broiler Houses at Different Broiler Growth Stages in Winter

Journal of Food Protection ◽

10.4315/0362-028x.jfp-17-524 ◽

2018 ◽

Vol 81 (9) ◽

pp. 1557-1564

Author(s):

LINLIN JIANG ◽

JIANLONG ZHANG ◽

JINXIU TANG ◽

MENG LI ◽

XIAOYU ZHAO ◽

...

Keyword(s):

Bacterial Community ◽

High Throughput ◽

High Throughput Sequencing ◽

Total Concentration ◽

Growth Period ◽

Growth Cycle ◽

Growth Stages ◽

Community Structures ◽

Dynamic Pattern ◽

Different Growth Stages

ABSTRACT The aim of the present study was to analyze the aerosol concentrations and microbial community structures in closed cage broiler houses at different broiler growth stages to assess the dynamic pattern of microbial aerosols in closed cage systems. Our results revealed that the total concentration of bacterial aerosols gradually increased during the growth cycle of broilers. High-throughput sequencing of 16S rDNA revealed that microbial compositions differed tremendously during different growth stages, although Firmicutes and Proteobacteria were the dominant taxa in samples from all broiler growth stages. At the genus level, dominant phylotypes displayed great variation during different growth stages. Escherichia and Shigella were the most dominant taxa throughout the growth cycle, increasing from 4.3 to 12.4% as the broilers grew. The alpha index revealed that the microbial diversity displayed significant differences between the different growth stages and that the bacterial community had the highest diversity when broilers were 22 days old. High-throughput sequencing analyses revealed that environmental microbes and opportunistic pathogens had relatively high abundances during the winter growth period. The data revealed the composition and aerodynamic diameters of microbial aerosols in closed cage broiler houses at different broiler growth stages in winter. The results also enabled us to elucidate the dynamic pattern of microbial aerosols in broiler houses in response to bacterial communities. Our results may provide a basis for developing technologies for air quality control in caged poultry houses.

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