OTUs Of Bacteria Research Articles

Characteristics of inter-root soil bacterial community structure and diversity of different sand-fixing shrubs at the southeastern edge of the Mu Us Desert, China

PurposeThis study aimed to investigate the effects of different shrub plants on the structure and diversity of inter-root soil bacterial communities, in order to provide scientific support for ecological restoration and revegetation of the Mu Us Desert.MethodsThree major shrub plants (Artemisia ordosica, Salix psammophila, Caragana microphylla) in the Mu Us Desert were selected for this study. Using high-throughput sequencing technology, the bacterial community structure and diversity in the inter-root soils of these plants were analysed in depth, and combined with the determination of soil physicochemical and microbiological properties, the response characteristics of the bacterial diversity in the inter-root soils of the different plants were assessed comprehensively.ResultsIt was found that although the soil pH did not show significant differences among different plant growths, the SOC, TN and TP contents were higher in Salix psammophila sample plot and Artemisia ordosica sample plot, which indicated that the plant growths had a positive effect on the soil nutrient contents. Through Venn diagram analysis, it was observed that the number of OTUs of bacteria in the soils of different shrubland sites varied, and all of them were higher than those in the soils of the sample sites where no plants grew, which indicated that plants had an effect on soil bacterial diversity. The bacterial Chao1 index were higher in the Artemisia ordosica sample plot sample site, suggesting that the growth of Artemisia ordosica contributes to the enhancement of soil bacterial richness. Soil bacterial communities showed compositional differences among different sample plots, especially the higher relative abundance of Betaproteobacteria in the Artemisia ordosica sample plot sample plot, which may be related to the increase of soil organic matter content.ConclusionThe results of the study revealed that specific plants, such as Artemisia ordosica, can significantly improve the soil nutrient status of windy sandy soils, increase soil organic matter and nitrogen content, and thus enhance the diversity and abundance of soil microorganisms. The bacterial community structure in the inter-root soils of different plants differed significantly, with changes in the relative abundance of the dominant phyla, such as Alphaproteobacteria, Betaproteobacteria and Actinobacteria, reflecting the differences in soil nutrient status. These findings emphasise the important role of plants on soil chemical properties and microbial community structure, providing an important basis for soil management and ecological restoration.

A dataset of micro biodiversity in benthic sediment at a global scale

Microorganisms, occupying the largest biomass in deep sea, play essential roles in deep-sea ecosystem. It is believed that the microbes in deep-sea sediments are more representative of deep-sea microbial communities, the microbial composition of which is seldom affected by ocean currents. However, the community of benthic microbes on a global scale has not been adequately explored. Herein, we build a comprehensive global dataset determined by 16S rRNA gene sequencing to characterize the biodiversity of microorganisms in benthic sediment. The dataset comprised 212 records from 106 sites, included sequencing of bacteria and archaea for each site and yielded 4,766,502 and 1,562,989 reads, respectively. Through annotation, a total of 110,073 and 15,795 OTUs of bacteria and archaea were obtained, and 61 bacterial phyla and 15 archaeal phyla were identified, of which the dominant phyla were Proteobacteria and Thaumarchaeota in deep-sea sediment. Therefore, our findings provided a biodiversity data of microbial communities in deep-sea sediment at global-scale and laid a foundation to further reveal the structures of microorganism communities in deep sea.

Larval gut microbiome of Pelidnota luridipes (Coleoptera: Scarabaeidae): high bacterial diversity, different metabolic profiles on gut chambers and species with probiotic potential.

Pelidnota luridipes Blanchard (1850) is a tropical beetle of the family Scarabaeidae, whose larvae live on wood without parental care. Microbiota of mid- and hindgut of larvae was evaluated by culture-dependent and independent methods, and the results show a diverse microbiota, with most species of bacteria and fungi shared between midgut and hindgut. We isolated 272 bacterial and 29 yeast isolates, identified in 57 and 7 species, respectively, while using metabarcoding, we accessed 1,481 and 267 OTUs of bacteria and fungi, respectively. The composition and abundance of bacteria and fungi differed between mid- and hindgut, with a tendency for higher richness and diversity of yeasts in the midgut, and bacteria on the hindgut. Some taxa are abundant in the intestine of P. luridipes larvae, such as Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria; as well as Saccharomycetales and Trichosporonales yeasts. Mid- and hindgut metabolic profiles differ (e.g. biosynthesis of amino acids, cofactors, and lipopolysaccharides) with higher functional diversity in the hindgut. Isolates have different functional traits such as secretion of hydrolytic enzymes and antibiosis against pathogens. Apiotrichum siamense L29A and Bacillus sp. BL17B protected larvae of the moth Galleria mellonella, against infection by the pathogens Listeria monocytogenes ATCC19111 and Pseudomonas aeruginosa ATCC 9027. This is the first work with the larval microbiome of a Rutelini beetle, demonstrating its diversity and potential in prospecting microbial products as probiotics. The functional role of microbiota for the nutrition and adaptability of P. luridipes larvae needs to be evaluated in the future.

Insights into gut microbiota communities of Poecilobdella manillensis, a prevalent Asian medicinal leech.

Medicinal leeches (Annelida: Hirudinea) are fresh water ectoparasitic species which have been applied as traditional therapy. However, gut microbiota could bring high risks of opportunistic infections after leeching and arouses great interests. Here, gut bacterial and fungal communities of an Asian prevalent leech Poecilobdella manillensis were characterized and analysed through culture-independent sequencing. With high coverage in 18 samples (>0.999), a more complicated community was apparent after comparing with previous leech studies. A total of 779/939 OTUs of bacteria and fungi were detected from leech guts. The bacterial community was dominated by the phylum Bacteroidetes and Synergistetes. Genera Mucinivorans and Fretibacterium accounted mostly at the genus level, and genus Aeromonas showed an extremely low abundance (2.02%) on average. The fungal community was dominated by the phylum Ascomycota and Basidiomycota. At the genus level, the dominant OTUs included Mortierella, Geminibasidium and Fusarium. The analysis of core taxa included those above dominant genera and some low-abundance genera (>1%). The functional annotation of the bacterial community showed a close correlation with metabolism (34.8±0.6%). Some fungal species were predicted as opportunistic human pathogens including Fusarium and Chaetomiaceae. The present study provides fundamental rationales for further studies of such issues as bacteria-fungi-host interactions, host fitness, potential pathogens, and infecting risks after leeching. It shall facilitate in-depth explorations on the safe utilization of leech therapy. Present paper is the first-ever exploration on microbiota of a prevalent Asian medicinal leech based on culture-independent technical. And it is also the first report of gut fungi community of medicinal leech. The diversity and composition of bacteria in P. manillensis was far different from that of the European leech. The main components and core OTUs indicate a particular gut environment of medicinal leech. Unknown bacterial and fungal species were also recovered from leech gut.

Testing selectivity of bacterial and fungal culture media compared to original silage samples using next generation sequencing

Plate counts using selective culture media is still the most frequently used method for the enumeration of the different microbial groups that colonize silage, including lactic acid bacteria, yeasts and molds. Since different culture media have specific composition, they may allow the growth of specific populations. To date, no study has used next generation sequencing technology to compare the selective capacity of these different culture media although this approach could provide comprehensive insight into the relevance of using one culture medium over another. Sequencing of the 16S rDNA and ITS amplicon were performed to compare the selectivity of different culture media used in silage microbiology. Corn silage, grass-alfalfa silage and total mixed ration extracts were plated on five selective media for lactic acid bacteria, incubated under aerobic and anaerobic conditions, and on eight selective media for yeast and molds to compare their selectivity. Ensiling provided a pre-selection environment for specific microorganisms over forage and reduced the number of observed OTUs: only 12 OTUs of bacteria were observed in corn silage sampled in the center of a bunker silo, while the mean number of OTUs identified in samples taken closer to the side of the silo, influenced by higher oxygen and humidity level, increased to 79. Still, MRS and Rogosa plates had less than 12 different OTUs in the center and 24 at the side, mainly Lactobacillaceae, Acetobacteraceae, and Leuconostocaceae. Incubating the plates under anaerobic conditions was selective against Acetobacteraceae. MRS supplemented with acetic acid increased selectivity of lactic acid bacteria. When plated on culture media specific for yeast and molds, from 17 to 68 different OTUs were observed in corn silage. Mixed grass-alfalfa silage and total mixed ration samples usually had more observed OTUs and the diversity profile of the corresponding culture media was similar to that of the original samples. For yeasts and molds, Dichloran Rose Bengal Chloramphenicol Agar revealed a diversity profile close to the that of the corn silage.

Soil Microbial Community Structure and Composition in Chinese Fir Plantations of Different Ages in Fujian, Southeast China

ABSTRACT What effects the stand age has on the soil microbial structure and composition remains unclear. The topsoil (0–20 cm) of 3- (YF), 12- (MAF), and 38-year-old (MF) Chinese fir plantations were selected as research objects. We found that the phospholipid fatty acid (PLFA) concentration and OTUs of bacteria and fungi exhibited an uptrend as the stand age increased. Among dominant bacterial and fungal phyla, the relative abundance of Actinobacteria in YF was significantly higher than that in MF and MAF and the relative abundance of Basidiomycota in MF was significantly higher than that in MAF and YF. Interestingly, the relative abundance of three predominant fungal phyla Ascomycota, Basidiomycota, and Zygomycota in MAF were lower than those in MF and YF. The significant difference in the relative abundance of some bacterial phyla (e.g., Ignavibacteriae, Latescibacteria, Nitrospirae, and Tectomicrobia) was also found with stand age, and organic matter, pH, available P, available N, and available K were the main factors for the variances in the biomass and structure of soil microbial communities. These findings showed that considering the shift in the structure and composition of microbial communities might improve our understanding of soil fertility maintenance and sustainable management of these plantations.

The Midgut Microbiota of Colombian Aedes aegypti Populations with Different Levels of Resistance to the Insecticide Lambda-cyhalothrin

Simple SummaryAedes aegypti is a mosquito capable of transmitting many viral diseases such as dengue, Zika, and chikungunya. Since no effective treatments are available for these viruses, eliminating the mosquito with insecticides is vital to combat these diseases. However, the mosquito can generate resistance to the insecticide by changing its genes or its physiology. It has been recognized that the type of bacteria that live inside the mosquito’s gut can contribute to this resistance. In this study, we evaluated Ae. aegypti mosquitoes from six locations in Colombia to determine if they are resistant to lambda-cyhalothrin insecticide, and we analyze their gut microbiota. We observed resistance in five of the six areas. We compared the gut microbiota from susceptible and resistant mosquitoes and found specific bacteria in resistant mosquitoes that may play a role in insecticide resistance. Overall, our findings contribute to the understanding of insecticide resistance in Ae. aegypti that will generate alternatives for interventions to control this mosquito in Colombia.Insecticide resistance in Aedes aegypti populations is a problem that hinders vector control and dengue prevention programs. In this study, we determined the susceptibility of Ae. aegypti populations from six Colombian regions to the pyrethroid lambda-cyhalothrin and evaluated the presence of the V1016I mutation in the sodium channel gene, which has been broadly involved in the resistance to this insecticide. The diversity of the gut microbiota of these mosquito populations was also analyzed. Only mosquitoes from Bello were susceptible to lambda-cyhalothrin and presented a lower allelic frequency of the V1016I mutation. Remarkably, there was not an important change in allelic frequencies among populations with different resistance ratios, indicating that other factors or mechanisms contributed to the resistant phenotype. Treatment of mosquitoes with antibiotics led us to hypothesize that the intestinal microbiota could contribute to the resistance to lambda-cyhalothrin. Beta diversity analysis showed significant differences in the species of bacteria present between susceptible and resistant populations. We identified 14 OTUs of bacteria that were unique in resistant mosquitoes. We propose that kdr mutations are important in the development of resistance to lambda-cyhalothrin at low insecticide concentrations but insect symbionts could play an essential role in the metabolization of pyrethroid insecticides at higher concentrations, contributing to the resistant phenotype in Ae. aegypti.

Diversity and spoilage potential of microbial communities associated with grape sour rot in eastern coastal areas of China.

As a polymicrobial disease, sour rot decreases grape berry yield and wine quality. The diversity of microbial communities in sour rot-affected grapes depends on the cultivation site, but the microbes responsible for this disease in eastern coastal China, has not been reported. To identify the microbes that cause sour grape rot in this important grape-producing region, the diversity and abundance of bacteria and fungi were assessed by metagenomic analysis and cultivation-dependent techniques. A total of 15 bacteria and 10 fungi were isolated from sour rot-affected grapes. High-throughput sequencing of PCR-amplicons generated from diseased grapes revealed 1343 OTUs of bacteria and 1038 OTUs of fungi. Proteobacteria and Firmicutes were dominant phyla among the 19 bacterial phyla identified. Ascomycota was the dominant fungal phylum and the fungi Issatchenkia terricola, Colletotrichum viniferum, Hanseniaspora vineae, Saprochaete gigas, and Candida diversa represented the vast majority ofmicrobial species associated with sour rot-affected grapes. An in vitro spoilage assay confirmed that four of the isolated bacteria strains (two Cronobacter species, Serratia marcescens and Lysinibacillus fusiformis) and five of the isolated fungi strains (three Aspergillus species, Alternaria tenuissima, and Fusarium proliferatum) spoiled grapes. These microorganisms, which appear responsible for spoiling grapes in eastern China, appear closely related to microbes that cause this plant disease around the world.

Effect of canopy gap size on soil respiration in a mixed broadleaved-Korean pine forest: Evidence from biotic and abiotic factors

Understanding the effects of forest structure, the frequency and size of canopy gaps is pivotal for precisely modelling forest soil carbon budgets. We aimed to determine the differences in soil respiration between closed canopy areas and canopy gaps with various sizes and how soil respiration is affected by biotic and abiotic factors, e.g., soil nutrients, soil microbial biomass and community composition, enzyme activities and fine root biomass. Soil respiration and these environmental factors were measured in eleven tree fall gaps (separated into small, medium and large with sizes ranging from 20 m2 to 450 m2) and three control plots in a mixed broadleaved-Korean pine forest during the growing season. Our results showed that soil respiration was similar between the control and small canopy gaps, while it was 17–49% lower in the medium and large canopy gaps compared to that of the control. There was a significant parabolic relationship between soil respiration and soil moisture, and the optimum moisture was approximately 40%. Fine root biomass and soil enzyme activities showed positive effects on soil respiration across different levels of canopy gaps. Furthermore, soil respiration was significantly declined with increasing soil microbial diversity (OTUs of bacteria). Our findings demonstrate that canopy gap has significant impact on soil CO2 emission in a temperate mixed forest, however, further studies concerning other forest ecosystem types and larger scale are warranted.

Divergent patterns of microbial community composition shift under two fertilization regimes revealed by responding species

Using patterns of belowground biodiversity to predict ecological functions and to manage productivity has been a longstanding objective for agronomists and ecologists. However, inconsistent associations between microbial diversity and fertilization have been found in frequency, which can be partly due to the dilution effect of immense silent species in microbial communities. Therefore, we studied the responding pool of the microbial communities, which was determined by filtering out taxa that did not vary significantly between fertilization treatments and the control. With responding species, we hypothesized that the difference of microbial response to different fertilization regimes and between bacterial and fungal response to treatments can be enlarged. In this study, bacterial and fungal community compositions and networks were characterized from soils with chemical fertilization (F), the combined application of chemical fertilizers and organic residues (MRF) and without fertilization (Control) in a 7-year experiment located at the Fengqiu Agroecological Experimental Station. As a result, >90% of the phyla, 75% of the genera and 92% of the OTUs were silent microbes. When filtering out these species, 9 phyla, 88 genera and 185 OTUs of bacteria responded significantly to the MRF treatment compared with those of the Control with an average abundance variation of 0.06% in responding OTUs. In contrast, only 2 phyla, 9 genera and 30 OTUs of bacteria significantly responded to the F treatment with an average amplitude of 0.11%. The higher connectedness and the lower average geodesic distance under the MRF treatment showed a more connective and closer bacterial network compared with the F treatment. Similar but stronger responses were detected in the fungal community composition and networks. To conclude, combined fertilization exerted a moderate impact on many microbial taxa (MM pattern), and chemical fertilization showed a substantial effect on a small amount of taxa (SS pattern). It was further inferred that a variation of the “MM” pattern can result in a more stable, harmonious and efficient ecosystem via maintenance of microbial diversity, stimulation of beneficial species, and exhibition of a more efficient microbial network. Our study showed explicit patterns of microbial communities under fertilization regimes revealed by responding species and highlighted the advantages of combined fertilization with organic matter in agroecosystems.

Shift of the microbial communities from exposed sandstone rocks to forest soils during pedogenesis

Microbial community structure and their biochemical activities have a significant impact on rock weathering, pedogenesis, and the development and succession of terrestrial biodiversity. In this study, microbial diversity of exposed rock and soils covered by different organisms were analysed through high-throughput sequencing. The results showed that microbial diversity was low in the naked or lichen-covered rock samples, with Cyanobacteria, Chloroflexi, Proteobacteria, and Ascomycota being dominant. The abundance of Ascomycota showed a clear predominance in the lichen-covered surface rock samples (89.30 ± 0.03%). For the soil samples with growing vascular plants, the observed OTUs of bacteria and fungi increased significantly, and the community structure and metabolic types of bacteria became more complex. The bacteria changed gradually from rock weathering pioneers to soil organic decomposers and ecological relation maintainers. In addition, fungi belonging to Basidiomycota, Zygomycota, and Glomeromycota were present in these soil samples, some of them formed mycorrhiza with plant roots. Analysis of the correlation between environmental factors and microbial communities indicates that the total organic carbon (TOC) and content of exchangeable iron exerted the most significant effects on the microbial communities. This study advances our understanding of the microbial community succession process during rock weathering and pedogenesis, and provides a reference for the stabilization and improvement of different soil ecosystems.

Pollutants degradation performance and microbial community structure of aerobic granular sludge systems using inoculums adapted at mild and low temperature

Three aerobic granular sequencing batch reactors were inoculated using different inocula from Finland, Spain and a mix of both in order to investigate the effect over the degradation performance and the microbial community structure. The Finnish inoculum achieved a faster granulation and a higher depollution performance within the first two month of operation. However, after 90 days of operation, similar physico-chemical values were observed. On the other hand, the Real-time PCR showed that Archaea diminished from inoculum to granular biomass, while Bacteria and Fungi numbers remained stable. All granular biomass massive parallel sequencing studies were similar regardless of the inocula from which they formed, as confirmed by singular value decomposition principal coordinates analysis, expected effect size of OTUs, and β-diversity analyses. Thermoproteaceae, Meganema and a Trischosporonaceae members were the dominant phylotypes for the three domains studied. The analysis of oligotype distribution demonstrated that a fungal oligotype was ubiquitous. The dominant OTUs of Bacteria were correlated with bioreactors performance. The results obtained determined that the microbial community structure of aerobic granular sludge was similar regardless of their inocula, showing that the granulation of biomass is related to several phylotypes. This will be of future importance for the implementation of aerobic granular sludge to full-scale systems.

Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain

BackgroundThe relative importance of stochasticity versus determinism in soil bacterial communities is unclear, as are the possible influences that alter the balance between these. Here, we investigated the influence of spatial scale on the relative role of stochasticity and determinism in agricultural monocultures consisting only of wheat, thereby minimizing the influence of differences in plant species cover and in cultivation/disturbance regime, extending across a wide range of soils and climates of the North China Plain (NCP). We sampled 243 sites across 1092 km and sequenced the 16S rRNA bacterial gene using MiSeq. We hypothesized that determinism would play a relatively stronger role at the broadest scales, due to the strong influence of climate and soil differences in selecting many distinct OTUs of bacteria adapted to the different environments. In order to test the more general applicability of the hypothesis, we also compared with a natural ecosystem on the Tibetan Plateau.ResultsOur results revealed that the relative importance of stochasticity vs. determinism did vary with spatial scale, in the direction predicted. On the North China Plain, stochasticity played a dominant role from 150 to 900 km (separation between pairs of sites) and determinism dominated at more than 900 km (broad scale). On the Tibetan Plateau, determinism played a dominant role from 130 to 1200 km and stochasticity dominated at less than 130 km. Among the identifiable deterministic factors, soil pH showed the strongest influence on soil bacterial community structure and diversity across the North China Plain. Together, 23.9% of variation in soil microbial community composition could be explained, with environmental factors accounting for 19.7% and spatial parameters 4.1%.ConclusionsOur findings revealed that (1) stochastic processes are relatively more important on the North China Plain, while deterministic processes are more important on the Tibetan Plateau; (2) soil pH was the major factor in shaping soil bacterial community structure of the North China Plain; and (3) most variation in soil microbial community composition could not be explained with existing environmental and spatial factors. Further studies are needed to dissect the influence of stochastic factors (e.g., mutations or extinctions) on soil microbial community distribution, which might make it easier to predictably manipulate the microbial community to produce better yield and soil sustainability outcomes.

Bacterial Diversity and Community Structure in the Pine Wood Nematode Bursaphelenchus xylophilus and B. mucronatus with Different Virulence by High-Throughput Sequencing of the 16S rDNA.

Bursaphelenchus xylophilus is the pathogen of pine wilt disease. Bursaphelenchus mucronatus is similar to B. xylophilus in morphology. Both species share a common niche, but they are quite different in pathogenicity. Presently, the role of bacteria in pine wilt disease development has been widely speculated. The diversity of bacteria associated with B. xylophilus and B. mucronatus with different virulence remains unclear. In this study, virulence of four B. xylophilus and four B. mucronatus strains were evaluated by inoculating Pinus thunbergii. High-throughput sequencing targeted 16S rDNA of different virulence nematode strains was carried out. The associated bacterial community structures of the eight strains were analyzed. The results showed that 634,051 high-quality sequences were obtained from the eight nematode strains. The number of OTUs of bacteria associated with B. mucronatus was generally greater than those of B. xylophilus. The richness of the community of bacteria associated with high virulent B. xylophilus ZL1 and AmA3 was higher than moderately virulent B. xylophilus AA3, HE2, and all B. mucronatus strains. While the diversity of bacteria associated with B. mucronatus was higher than B. xylophilus. Stenotrophomonas, Pseudomonadaceae_Unclassified or Rhizobiaceae_Unclassified were predominant in the nematode strains with different virulence. Oxalobacteraceae and Achromobacter were found more abundant in the low virulent B. xylophilus and non-virulent B. mucronatus strains.

Study on diversity of endophytic bacterial communities in seeds of hybrid maize and their parental lines

The seeds of plants are carriers of a variety of beneficial bacteria and pathogens. Using the non-culture methods of building 16S rDNA libraries, we investigated the endophytic bacterial communities of seeds of four hybrid maize offspring and their respective parents. The results of this study show that the hybrid offspring Yuyu 23, Zhengdan958, Jingdan 28 and Jingyu 11 had 3, 33, 38 and 2 OTUs of bacteria, respectively. The parents Ye 478, Chang 7-2, Zheng 58, Jing 24 and Jing 89 had 12, 36, 6, 12 and 2 OTUs, respectively. In the hybrid Yuyu 23, the dominant bacterium Pantoea (73.38%) was detected in its female parent Ye 478, and the second dominant bacterium of Sphingomonas (26.62%) was detected in both its female (Ye 478) and male (Chang 7-2) parent. In the hybrid Zhengdan 958, the first dominant bacterium Stenotrophomonas (41.67%) was detected in both the female (Zheng 58) and male (Chang 7-2) parent. The second dominant bacterium Acinetobacter (9.26%) was also the second dominant bacterium of its male parent. In the hybrid Jingdan 28, the second dominant bacterium Pseudomonas (12.78%) was also the second dominant bacterium of its female parent, and its third dominant bacterium Sphingomonas (9.90%) was the second dominant bacterium of its male parent and detected in its female parent. In the hybrid Jingyu 11, the first dominant bacterium Leclercia (73.85%) was the third dominant bacterium of its male parent, and the second dominant bacterium Enterobacter (26.15%) was detected in its male parent. As far as we know, this was the first research reported in China on the diversity of the endophytic bacterial communities of the seeds of various maize hybrids with different genotypes.