Different Soil Salinity Imparts Clear Alteration in Rhizospheric Bacterial Community Dynamics in Rice and Peanut.

Abstract The rhizospheric microbiome is capable of changing the physio-chemical properties of its own micro-environment and found to be indispensable in overall health of the host-plant. The interplay between the rhizospheric environment and the microbiota residing therein tune the physiology of the associated plant. In this study, we have determined how the soil properties and the host-plant remains as an important parameter for microbial community-dynamics in the rhizosphere of rice and peanut. In addition to check the physio-chemical parameters of the rhizospheric soil, we have also prepared the metagenomic DNA from each rhizospheric soil followed by high-throughput sequencing and sequence-analysis to predict the OTUs that represents the community structure. The alpha-diversity of the bacterial community in the RRN sample was highest, while the lowest was in PRS sample. Actinobacteria is the most predominant phylum in PRN, PRS and RRN whereas Acidobacteria in RRS. We found a clear shift in bacterial community over the rice and peanut rhizosphere and also over these host-rhizospheres from normal and high saline region. The rhizospheric bacterial community composition found to be affected by the close-by environmental factors. Thus, the rhizospheric bacterial community-structure is related to both the adjoining soil characters and the type of the hosts.

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Different Soil Salinity Imparts Clear Alteration In Rhizospheric Bacterial Community Dynamics In Rice And Peanut.

10.21203/rs.3.rs-646600/v1 ◽

2021 ◽

Author(s):

Md Majharul Islam ◽

Rajarshi Bhattacharya ◽

Biraj Sarkar ◽

Pulak Kumar Maiti ◽

Shouvik Mahanty ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Host Plant ◽

High Throughput Sequencing ◽

Community Dynamics ◽

Bacterial Community Composition ◽

Chemical Properties ◽

Alpha Diversity ◽

Rhizospheric Soil ◽

Bacterial Community Dynamics

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Divergence in Gut Bacterial Community Among Life Stages of the Rainbow Stag Beetle Phalacrognathus muelleri (Coleptera: Lucanidae)

Insects ◽

10.3390/insects11100719 ◽

2020 ◽

Vol 11 (10) ◽

pp. 719

Author(s):

Miaomiao Wang ◽

Xingjia Xiang ◽

Xia Wan

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Community Structure ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Alpha Diversity ◽

Illumina Miseq ◽

Life Stages ◽

Early Instar

Although stag beetles are popular saprophytic insects, there are few studies about their gut bacterial community. This study focused on the gut bacterial community structure of the rainbow stag beetle (i.e., Phalacrognathus muelleri) in its larvae (three instars) and adult stages, using high throughput sequencing (Illumina Miseq). Our aim was to compare the gut bacterial community structure among different life stages. The results revealed that bacterial alpha diversity increased from the 1st instar to the 3rd instar larvae. Adults showed the lowest gut bacterial alpha diversity. Bacterial community composition was significantly different between larvae and adults (p = 0.001), and 1st instar larvae (early instar) had significant differences with the 2nd (p= 0.007) and 3rd (p = 0.001) instar larvae (final instar). However, there was little difference in the bacterial community composition between the 2nd and 3rd instar larvae (p = 0.059). Our study demonstrated dramatic shifts in gut bacterial community structure between larvae and adults. Larvae fed on decaying wood and adults fed on beetle jelly, suggesting that diet is a crucial factor shaping the gut bacterial community structure. There were significant differences in bacterial community structure between early instar and final instars larvae, suggesting that certain life stages are associated with a defined gut bacterial community.

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Effects of Continuous Cropping on Bacterial Community Structure in Rhizospheric Soil of Sweet Potato

10.21203/rs.3.rs-61006/v1 ◽

2020 ◽

Author(s):

Zhiyuan Gao ◽

Yaya Hu ◽

Meikun Han ◽

Junjie Xu ◽

Xue Wang ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Sweet Potato ◽

Soil Ph ◽

Bacterial Community Structure ◽

High Throughput Sequencing ◽

Potato Industry ◽

Continuous Cropping ◽

Rhizospheric Soil ◽

Potato Varieties

Abstract Background: Continuous cropping obstacles from sweet potato are widespread, which seriously reduce the yield and quality, restrict the sustainable development of sweet potato industry. Bacteria are the most abundant in rhizospheric soil and have a certain relationship with continuous cropping obstacles. However, there are few reports on how continuous cropping affected the bacterial community structure in the rhizospheric soil of sweet potato. In this study, high-throughput sequencing technique was used to explore the changes of rhizospheric soil bacterial community structure of different sweet potato varieties, and the correlation between soil characteristics and this bacterial community after continuous cropping, so as to provide a theoretical basis for the prevention and control of sweet potato continuous cropping obstacles.Results: After two years of continuous cropping, the results showed that (1) the dominant bacteria phlya in rhizospheric soils from both Xushu18 and Yizi138 were Proteobacteria, Acidobacteria, and Actinobacteria. The most dominant genus was Subgroup 6_norank. Significant changes in the relative abundance of rhizospheric soil bacteria were observed for two sweet potato varieties. (2) Bacterial richness and diversity indexes of rhizospheric soil from Xushu18 were higher than those from Yizi138 after continuous cropping. Moreover, the beneficial Lysobacter and Bacillus were more prevalent in Xushu18, but Yizi138 contained more harmful Gemmatimonadetes. (3) Soil pH decreased after continuous cropping, and redundancy analysis showed that soil pH was significantly correlated with bacterial community. Spearman’s rank correlations coefficients analysis demonstrated that pH was positively correlated with Planctomycetes and Acidobacteria, and negatively correlated with Actinobacteria and Firmicutes.Conclusions: After continuous cropping of sweet potato, the bacterial community structure and physicochemical properties in the rhizospheric soil were unbalanced, and the changes of different sweet potato varieties were different. The contents of Lysobacter and Bacillus were higher in the sweet potato variety resistant to continuous cropping. It provides a basis for the development of special microbial fertilizer for sweet potatoes to alleviate continuous cropping obstacle.

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Bacterial community characteristics and enzyme activities in Imperata cylindrica litter as phytoremediation progresses in a copper tailings dam

PeerJ ◽

10.7717/peerj.9612 ◽

2020 ◽

Vol 8 ◽

pp. e9612

Author(s):

Tong Jia ◽

Tingyan Guo ◽

Baofeng Chai

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Chemical Properties ◽

Alpha Diversity ◽

Imperata Cylindrica ◽

Copper Tailings ◽

Α Diversity ◽

Degraded Ecosystems ◽

And Function

This study analyzed Imperata cylindrica litter to determine variation in bacterial community composition and function along with enzyme activity as phytoremediation progresses. We found significant differences in physical and chemical properties of soil and litter in the different sub-dams investigated. The Actinobacteria, Gammaproteobacteria and Alphaproteobacteria were the dominant bacteria found in the litter of the different sub-dams. The alpha diversity (α-diversity) of litter bacterial community increased over as phytoremediation progressed, while total soil carbon and total litter carbon content were positively correlated to bacterial α-diversity. Total litter carbon and total nitrogen were the key factors that influenced bacterial community structure. Heavy metal can influence the degradation of litters by altering the composition of the microbial community. Furthermore, bacterial communities encoded with alpha-amylase (α-amylase) dominated during the initial phytoremediation stage; however, bacterial communities encoded with hemicellulase and peroxidase gradually dominated as phytoremediation progressed. Findings from this study provide a basis for exploring litter decomposition mechanisms in degraded ecosystems, which is critically important to understand the circulation of substances in copper tailings dams.

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16S rRNA gene amplicon-based metagenomic analysis of bacterial communities in the rhizospheres of selected mangrove species from Mida Creek and Gazi Bay, Kenya

PLoS ONE ◽

10.1371/journal.pone.0248485 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0248485

Author(s):

Edith M. Muwawa ◽

Chinedu C. Obieze ◽

Huxley M. Makonde ◽

Joyce M. Jefwa ◽

James H. P. Kahindi ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Community Structure ◽

Bacterial Community Composition ◽

Geographical Location ◽

Alpha Diversity ◽

Rrna Gene ◽

Chemical Parameters ◽

Mangrove Species ◽

Gazi Bay

Prokaryotic communities play key roles in biogeochemical transformation and cycling of nutrients in the productive mangrove ecosystem. In this study, the vertical distribution of rhizosphere bacteria was evaluated by profiling the bacterial diversity and community structure in the rhizospheres of four mangrove species (Sonneratia alba, Rhizophora mucronata, Ceriops tagal and Avicennia marina) from Mida Creek and Gazi Bay, Kenya, using DNA-metabarcoding. Alpha diversity was not significantly different between sites, but, significantly higher in the rhizospheres of S. alba and R. mucronata in Gazi Bay than in Mida Creek. Chemical parameters of the mangrove sediments significantly correlated inversely with alpha diversity metrics. The bacterial community structure was significantly differentiated by geographical location, mangrove species and sampling depth, however, differences in mangrove species and sediment chemical parameters explained more the variation in bacterial community structure. Proteobacteria (mainly Deltaproteobacteria and Gammaproteobacteria) was the dominant phylum while the families Desulfobacteraceae, Pirellulaceae and Syntrophobacteraceae were dominant in both study sites and across all mangrove species. Constrained redundancy analysis indicated that calcium, potassium, magnesium, electrical conductivity, pH, nitrogen, sodium, carbon and salinity contributed significantly to the species–environment relationship. Predicted functional profiling using PICRUSt2 revealed that pathways for sulfur and carbon metabolism were significantly enriched in Gazi Bay than Mida Creek. Overall, the results indicate that bacterial community composition and their potential function are influenced by mangrove species and a fluctuating influx of nutrients in the mangrove ecosystems of Gazi Bay and Mida Creek.

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Divergence in Gut Bacterial Community Structure between Male and Female Stag Beetles Odontolabis fallaciosa (Coleoptera, Lucanidae)

Animals ◽

10.3390/ani10122352 ◽

2020 ◽

Vol 10 (12) ◽

pp. 2352

Author(s):

Xia Wan ◽

Yu Jiang ◽

Yuyan Cao ◽

Binghua Sun ◽

Xingjia Xiang

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Community Structure ◽

High Throughput Sequencing ◽

Alpha Diversity ◽

Illumina Miseq ◽

Bacterial Interactions ◽

Intestinal Bacterial Community ◽

Males And Females ◽

Stag Beetles

Odontolabis fallaciosa (Coleoptera: Lucanidae) is a giant and popular stag beetle with striking sexual dimorphism and male trimorphism. However, little is known about their intestinal microbiota, which might play an indispensable role in shaping the health of their hosts. The aim of this study was to investigate the intestinal bacterial community structure between the two sexes and among three male morphs of O. fallaciosa from China using high-throughput sequencing (Illumina MiSeq). The gut bacterial community structure was significantly different between males and females, suggesting that sex appeared to be the crucial factor shaping the intestinal bacterial community. Females had higher bacterial alpha-diversity than males. There was little difference in gut bacterial community structure among the three male morphs. However, compared to medium and small males, large individuals were associated with the higher relative abundance of Firmicutes and Firmicutes/Bacteroides (F/B) ratio, which might contribute to nutritional efficiency. Overall, these results might help to further our understanding of beetle–bacterial interactions of O. fallaciosa between the two sexes, and among the three male morphs.

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Dynamics of Bacterial Community Composition and Activity during a Mesocosm Diatom Bloom

Applied and Environmental Microbiology ◽

10.1128/aem.66.2.578-587.2000 ◽

2000 ◽

Vol 66 (2) ◽

pp. 578-587 ◽

Cited By ~ 403

Author(s):

Lasse Riemann ◽

Grieg F. Steward ◽

Farooq Azam

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Growth Rates ◽

Community Dynamics ◽

Bacterial Community Composition ◽

Size Fraction ◽

Microbial Colonization ◽

Rrna Gene ◽

Bacterial Community Dynamics ◽

Diatom Blooms

ABSTRACT Bacterial community composition, enzymatic activities, and carbon dynamics were examined during diatom blooms in four 200-liter laboratory seawater mesocosms. The objective was to determine whether the dramatic shifts in growth rates and ectoenzyme activities, which are commonly observed during the course of phytoplankton blooms and their subsequent demise, could result from shifts in bacterial community composition. Nutrient enrichment of metazoan-free seawater resulted in diatom blooms dominated by a Thalassiosira sp., which peaked 9 days after enrichment (≈24 μg of chlorophylla liter−1). At this time bacterial abundance abruptly decreased from 2.8 × 106 to 0.75 × 106 ml−1, and an analysis of bacterial community composition, by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments, revealed the disappearance of three dominant phylotypes. Increased viral and flagellate abundances suggested that both lysis and grazing could have played a role in the observed phylotype-specific mortality. Subsequently, new phylotypes appeared and bacterial production, abundance, and enzyme activities shifted from being predominantly associated with the <1.0-μm size fraction towards the >1.0-μm size fraction, indicating a pronounced microbial colonization of particles. Sequencing of DGGE bands suggested that the observed rapid and extensive colonization of particulate matter was mainly by specialized α-Proteobacteria- andCytophagales-related phylotypes. These particle-associated bacteria had high growth rates as well as high cell-specific aminopeptidase, β-glucosidase, and lipase activities. Rate measurements as well as bacterial population dynamics were almost identical among the mesocosms indicating that the observed bacterial community dynamics were systematic and repeatable responses to the manipulated conditions.

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Influence of intramuscular depot-medroxyprogesterone acetate initiation on vaginal microbiota in the postpartum period

Clinical Infectious Diseases ◽

10.1093/cid/ciaa1876 ◽

2020 ◽

Author(s):

Bridget M Whitney ◽

Sujatha Srinivasan ◽

Kenneth Tapia ◽

Eric Munene Muriuki ◽

Bhavna H Chohan ◽

...

Keyword(s):

Bacterial Community ◽

Medroxyprogesterone Acetate ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Bacterial Load ◽

Alpha Diversity ◽

Rrna Gene ◽

Nugent Score ◽

Depot Medroxyprogesterone Acetate ◽

Significant Difference

Abstract Background The vaginal microbiome plays a key role in women’s reproductive health. Use of exogenous hormones, such as intramuscular depot-medroxyprogesterone acetate (DMPA-IM), may alter the composition of vaginal bacterial community. Methods Vaginal swabs were collected from postpartum Kenyan women initiating DMPA-IM or non-hormonal contraception (non-HC). Bacterial vaginosis was assessed by Nugent score (Nugent-BV) and bacterial community composition was evaluated using broad-range 16S rRNA gene PCR with high-throughput sequencing. Changes in Nugent score, alpha diversity (Shannon diversity index), and total bacterial load between contraceptive groups from enrollment to three-months post-initiation were estimated using multivariable linear mixed effects regression. Results Among 54 HIV-negative women, 33 choosing DMPA-IM and 21 choosing non-HC, Nugent-BV was more common among DMPA-IM users at enrollment. At follow-up, Nugent score had decreased significantly among DMPA-IM users (Δ=-1.89 (95%CI:-3.53, -0.25; p=0.02) while alpha diversity remained stable (Δ=0.03, 95%CI:-0.24, 0.30; p=0.83). Conversely, Nugent score remained relatively stable among non-HC users (Δ=-0.73, 95%CI:-2.18, 0.73; p=0.33) while alpha diversity decreased (Δ=-0.34, 95%CI:-0.67, -0.001; p=0.05). Total bacterial load decreased slightly in DMPA-IM users and increased slightly among non-HC users, resulting in a significant difference in change between the contraceptive groups (difference=-0.64 log10 gene copies/swab, 95%CI:-1.19, -0.08; p=0.02). While significant changes in Nugent score and alpha diversity were observed within contraceptive groups, changes between groups were not significantly different. Conclusions Postpartum vaginal bacterial diversity did not change in DMPA-IM users despite a reduction in Nugent-BV, but decreased significantly among women using non-HC. Choice of contraception may influence Lactobacillus recovery in postpartum women.

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Temporal Changes in the Function of Bacterial Assemblages Associated With Decomposing Earthworms

Frontiers in Microbiology ◽

10.3389/fmicb.2021.682224 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yao-Qin Sun ◽

Yuan Ge

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Time Course ◽

Community Dynamics ◽

Early Stage ◽

Bacterial Community Composition ◽

Terrestrial Ecosystems ◽

Community Change ◽

Soil Invertebrate ◽

Bacterial Community Dynamics

Soil invertebrate corpse decomposition is an ecologically significant, yet poorly understood, process affecting nutrient biogeochemical cycling in terrestrial ecosystems. Here, we attempted to answer how the substrate chemistry and microbial community change during soil invertebrate (earthworm) decomposition and what roles microbes play in this process. Specifically, the dead earthworms (Amynthas corticis) were buried in two soils where the earthworms inhabited, or not, until more than 50% of the earthworm mass was lost. For both soils, earthworms decomposed faster during the early stage (between 0 and 3 days), as reflected by the higher rate of decomposition and increased accumulation of dissolved organic matter (DOM). This decomposition pattern was paralleled by bacterial community dynamics, where bacterial richness and diversity were significantly higher during early decomposition (p < 0.05) with the relative abundances of many genera decreasing as decomposition progressed. The succession of the bacterial community composition was significantly correlated with time-course changes in DOM composition (p < 0.05). Particularly, more functional groups (e.g., microbes associated with carbon, nitrogen, and sulfur cycling) were identified to be linked with the change of a specific DOM type during the early decomposition phase. By exploring the ecologically important process of soil invertebrate decomposition and its associated bacterial communities, this study provides evidence, e.g., a statistically significant positive correlation between bacterial community and DOM compositions, which supports the widely recognized yet less-tested microbial community structure–function relationship hypothesis in invertebrate decomposition.

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Bacterial Community Dynamics during Start-Up of a Trickle-Bed Bioreactor Degrading Aromatic Compounds

Applied and Environmental Microbiology ◽

10.1128/aem.64.3.930-939.1998 ◽

1998 ◽

Vol 64 (3) ◽

pp. 930-939 ◽

Cited By ~ 56

Author(s):

Marion Stoffels ◽

Rudolf Amann ◽

Wolfgang Ludwig ◽

Dariusch Hekmat ◽

Karl-Heinz Schleifer

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Aromatic Compounds ◽

Community Dynamics ◽

23S Rrna ◽

Significant Shift ◽

Wastewater Sample ◽

Bacterial Community Dynamics ◽

Trickle Bed ◽

Trickle Bed Bioreactor

ABSTRACT This study was performed with a laboratory-scale fixed-bed bioreactor degrading a mixture of aromatic compounds (Solvesso100). The starter culture for the bioreactor was prepared in a fermentor with a wastewater sample of a car painting facility as the inoculum and Solvesso100 as the sole carbon source. The bacterial community dynamics in the fermentor and the bioreactor were examined by a conventional isolation procedure and in situ hybridization with fluorescently labeled rRNA-targeted oligonucleotides. Two significant shifts in the bacterial community structure could be demonstrated. The original inoculum from the wastewater of the car factory was rich in proteobacteria of the alpha and beta subclasses, while the final fermentor enrichment was dominated by bacteria closely related toPseudomonas putida or Pseudomonas mendocina, which both belong to the gamma subclass of the classProteobacteria. A second significant shift was observed when the fermentor culture was transferred as inoculum to the trickle-bed bioreactor. The community structure in the bioreactor gradually returned to a higher complexity, with the dominance of beta and alpha subclass proteobacteria, whereas the gamma subclass proteobacteria sharply declined. Obviously, the preceded pollutant adaptant did not lead to a significant enrichment of bacteria that finally dominated in the trickle-bed bioreactor. In the course of experiments, three new 16S as well as 23S rRNA-targeted probes for beta subclass proteobacteria were designed, probe SUBU1237 for the generaBurkholderia and Sutterella, probe ALBO34a for the genera Alcaligenes and Bordetella, and probe Bcv13b for Burkholderia cepacia andBurkholderia vietnamiensis. Bacteria hybridizing with the probe Bcv13b represented the main Solvesso100-degrading population in the reactor.

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