scholarly journals Bacterial Community in the Skin Microbiome of Frogs in a Coldspot of Chytridiomycosis Infection

2021 ◽  
Author(s):  
Milind C. Mutnale ◽  
Gundlapally S. Reddy ◽  
Karthikeyan Vasudevan
Keyword(s):  
Bacterial Community ◽  
Relative Abundance ◽  
Frog Skin ◽  
Batrachochytrium Dendrobatidis ◽  
Bacterial Community Composition ◽  
Skin Microbiome ◽  
Bacterial Phyla ◽  
Frog Species ◽  
Generation Sequencing

AbstractChytridiomycosis is a fungal disease caused by the pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), which has caused declines in amphibian populations worldwide. Asia is considered as a coldspot of infection, since adult frogs are less susceptible to Bd-induced mortality or morbidity. Using the next-generation sequencing approach, we assessed the cutaneous bacterial community composition and presence of anti-Bd bacteria in six frog species from India using DNA isolated from skin swabs. All the six frog species sampled were tested using nested PCR and found Bd negative. We found a total of 551 OTUs on frog skin, of which the bacterial phyla such as Proteobacteria (56.15% average relative abundance) was dominated followed by Actinobacteria (21.98% average relative abundance) and Firmicutes (13.7% average relative abundance). The contribution of Proteobacteria in the anti-Bd community was highest and represented by 175 OTUs. Overall, the anti-Bd bacterial community dominated (51.7% anti-Bd OTUs) the skin microbiome of the frogs. The study highlights the putative role of frog skin microbiome in affording resistance to Bd infections in coldspots of infection.

scholarly journals Bacterial Community Composition and Chromophoric Dissolved Organic Matter Differs with Culture Time of Skeletonema dohrnii

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 150
Author(s):  
Yang Liu ◽  
Jinjun Kan ◽  
Jing Yang ◽  
Md Abu Noman ◽  
Jun Sun
Keyword(s):  
Organic Matter ◽  
Bacterial Community ◽  
Dissolved Organic Matter ◽  
Community Composition ◽  
Relative Abundance ◽  
Bacterial Community Composition ◽  
Algal Growth ◽  
Chromophoric Dissolved Organic Matter ◽  
Bacterial Phyla ◽  
Culture Time

Skeletonema dohrnii is a common red tide microalgae occurring in the coastal waters and throughout the world. The associated heterotrophic or autotrophic bacteria play vital roles in regulating algal growth, production, and physiology. In this study, we investigated the detailed bacterial community structure associated with the growth of S. dohrnii’s using high-throughput sequencing-based on 16S rDNA. Our results demonstrated that Bacteroidetes (48.04%) and Proteobacteria (40.66%) in all samples accounted for the majority of bacterial populations. There was a significant linear regression relationship between the abundance of bacterial phyla and culture time. Notable shifts in bacterial community composition were observed during algal growth: Flavobacteriales accounted for the vast majority of sequences at the order level. Furthermore, the relative abundance of Rhodobacterales was gradually reduced during the whole growth process of S. dohrnii (0–12 days). However, beyond that, the relative abundance of Marinobacter was slowly increasing. It is noteworthy that five fluorophores (Peaks T1, T2, I, M, and A) were detected during the growth stage of S. dohrnii. The characteristic indexes (fluorescence index, humification index, and biological index) of chromophoric dissolved organic matter (CDOM) also varied with the culture time. In addition, the taxa of bacteria had certain effects on CDOM and they were inextricably linked to each other.

scholarly journals Synchrony Degree of Dietary Energy and Nitrogen Release Influences Microbial Community, Fermentation, and Protein Synthesis in a Rumen Simulation System

2020 ◽  
Vol 8 (2) ◽  
pp. 231 ◽  
Author(s):  
Jun Zhang ◽  
Nan Zheng ◽  
Weijun Shen ◽  
Shengguo Zhao ◽  
Jiaqi Wang
Keyword(s):  
Protein Synthesis ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Volatile Fatty Acids ◽  
Bacterial Community Composition ◽  
Simulation System ◽  
Lower Degree ◽  
Ammonia Assimilation ◽  
Nitrogen Release ◽  
Post Feeding

Synchrony of energy and nitrogen release in rumen has been proposed to maximize ruminal microbial fermentation. However, the information regarding bacterial community composition and its metabolism under a higher or lower degree of synchronization is limited. In our study, a 0 to 6 h post-feeding infusion (first half infusion, FHI), 6 to 12 h post-feeding infusion (second half infusion, SHI), and 0 to 12 h post-feeding infusion (continuous infusion, CI) of maltodextrin were used to simulate varying degrees of synchronization of energy and nitrogen release in a rumen simulation system. In addition, the bacterial community, metabolite, enzyme activity, and microbial protein synthesis (MPS) were evaluated. Compared with the FHI and CI, the relative abundance of Fibrobacter, Ruminobacter, BF311, and CF231 decreased in the SHI, but that of Klebsiella and Succinivibrio increased in the SHI. The NH3-N and branched-chain volatile fatty acids were significantly higher, but propionate content and activities of glutamate dehydrogenase (GDH) and alanine dehydrogenase were significantly lower in the SHI than those in the FHI and CI. The SHI had lower MPS and less efficiency of MPS than the FHI and CI, which indicated that the SHI had a lower degree of synchronization. Correlation analysis showed that MPS was positively related to GDH activity and relative abundance of Fibrobacter but negatively related to NH3-N and relative abundance of Klebsiella. Therefore, a higher degree of synchronization of energy and nitrogen release increased MPS partly via influencing the bacterial community, metabolism, and enzyme activities of ammonia assimilation in the in vitro fermenters.

scholarly journals The Role of Microbial Mats in the Removal of Hexavalent Chromium and Associated Shifts in Their Bacterial Community Composition

2020 ◽  
Vol 11 ◽  
Author(s):  
Raeid M. M. Abed ◽  
Mary Shanti ◽  
Thirumahal Muthukrishnan ◽  
Zayana Al-Riyami ◽  
Bernhard Pracejus ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Hexavalent Chromium ◽  
Microbial Mats ◽  
Bacterial Community Composition

scholarly journals Impact of Biochar Application to Soil on the Root-Associated Bacterial Community Structure of Fully Developed Greenhouse Pepper Plants

2011 ◽  
Vol 77 (14) ◽  
pp. 4924-4930 ◽  
Author(s):  
Max Kolton ◽  
Yael Meller Harel ◽  
Zohar Pasternak ◽  
Ellen R. Graber ◽  
Yigal Elad ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Relative Abundance ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Systemic Resistance ◽  
Rrna Gene ◽  
Molecular Fingerprinting ◽  
Content Type ◽  
Biochar Amendment

ABSTRACTAdding biochar to soil has environmental and agricultural potential due to its long-term carbon sequestration capacity and its ability to improve crop productivity. Recent studies have demonstrated that soil-applied biochar promotes the systemic resistance of plants to several prominent foliar pathogens. One potential mechanism for this phenomenon is root-associated microbial elicitors whose presence is somehow augmented in the biochar-amended soils. The objective of this study was to assess the effect of biochar amendment on the root-associated bacterial community composition of mature sweet pepper (Capsicum annuumL.) plants. Molecular fingerprinting (denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism) of 16S rRNA gene fragments showed a clear differentiation between the root-associated bacterial community structures of biochar-amended and control plants. The pyrosequencing of 16S rRNA amplicons from the rhizoplane of both treatments generated a total of 20,142 sequences, 92 to 95% of which were affiliated with theProteobacteria,Bacteroidetes,Actinobacteria, andFirmicutesphyla. The relative abundance of members of theBacteroidetesphylum increased from 12 to 30% as a result of biochar amendment, while that of theProteobacteriadecreased from 71 to 47%. TheBacteroidetes-affiliatedFlavobacteriumwas the strongest biochar-induced genus. The relative abundance of this group increased from 4.2% of total root-associated operational taxonomic units (OTUs) in control samples to 19.6% in biochar-amended samples. Additional biochar-induced genera included chitin and cellulose degraders (ChitinophagaandCellvibrio, respectively) and aromatic compound degraders (HydrogenophagaandDechloromonas). We hypothesize that these biochar-augmented genera may be at least partially responsible for the beneficial effect of biochar amendment on plant growth and viability.

scholarly journals Metagenomics reveals diet-specific specialization of bacterial communities in fungus gardens of grass- and dicot-cutter ants

2018 ◽  
Author(s):  
Lily Khadempour ◽  
Huan Fan ◽  
Ken Keefover-Ring ◽  
Camila Carlos ◽  
Nilson S. Nagamoto ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Potential Role ◽  
Sequence Data ◽  
Bacterial Community Composition ◽  
Fungus Garden ◽  
Functional Profiles ◽  
Ant Fungus

AbstractLeaf-cutter ants in the genusAttaare dominant herbivores in the Neotropics. While most species ofAttacut dicots to incorporate into their fungus gardens, some species specialize on grasses. Here we examine the bacterial community associated with the fungus gardens of grass- and dicot-cutter ants to examine how changes in substrate input affect the bacterial community. We sequenced the metagenomes of 12Attafungus gardens, across four species of ants, with a total of 5.316 Gbp of sequence data. We show significant differences in the fungus garden bacterial community composition between dicot- and grass-cutter ants, with grass-cutter ants having lower diversity. Reflecting this difference in community composition, the bacterial functional profiles between the fungus gardens are significantly different. Specifically, grass-cutter ant fungus garden metagenomes are particularly enriched for genes responsible for amino acid, siderophore, and terpenoid biosynthesis while dicot-cutter ant fungus gardens metagenomes are enriched in genes involved in membrane transport. These differences in bacterial community composition and functional capacity show that different substrate inputs matter for fungus garden bacteria, and sheds light on the potential role of bacteria in mediating the ants’ transition to the use of a novel substrate.

Metagenome analyses reveal the role of Clostridium perfringens in alfalfa silage anaerobic deterioration

2020 ◽  
Vol 367 (8) ◽  
Author(s):  
Mingli Zheng ◽  
Dongze Niu ◽  
Di Jiang ◽  
Rongrong Li ◽  
Lin Meng ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Clostridium Perfringens ◽  
Relative Abundance ◽  
Dominant Role ◽  
Ammonia Nitrogen ◽  
Fermentation Products ◽  
Microbial Community Analyses ◽  
Alfalfa Silage

ABSTRACT The clostridial fermentation caused by the outgrowth of Clostridia was mainly responsible for the silage anaerobic deterioration. Our previous results showed that Clostridium perfringens dominated the clostridial community in poor-fermented alfalfa silage. This study was conducted to further examine the role of C. perfringens in silage anaerobic deterioration through fermentation products and the microbial community analyses. Direct-cut alfalfa was ensiled with C. perfringens contamination (CKC) or with the addition of Lactobacillus plantarum, sucrose and C. perfringens (LSC). Contamination with C. perfringens enhanced the clostridial fermentation in CKC silage, as indicated by high contents of butyric acid, ammonia nitrogen and Clostridia, while LSC silage was well preserved. The genera Bifidobacterium, Garciella and Clostridium dominated the bacterial community in CKC silage, while predominate genus was replaced by Lactobacillus in LSC silage. The clostridial community in CKC silage was dominated by Garciella sp. (26.9 to 58.1%) and C. tyrobutyricum (24.4 to 48.6%), while the relative abundance of C. perfringens was below 5.0%. Therefore, the effect of Clostridia contamination on ensiling fermentation was dependent on the ensilability of the silage material. Garciella sp. and C. tyrobutyricum, rather than C. perfringens, played dominant role in the clostridial fermentation in CKC silage.

scholarly journals Seasonal and ontogenetic variation of skin microbial communities and relationships to natural disease dynamics in declining amphibians

2015 ◽  
Vol 2 (7) ◽  
pp. 140377 ◽  
Author(s):  
Ana V. Longo ◽  
Anna E. Savage ◽  
Ian Hewson ◽  
Kelly R. Zamudio
Keyword(s):  
Bacterial Diversity ◽  
Batrachochytrium Dendrobatidis ◽  
Developmental Stages ◽  
Pathogenic Fungus ◽  
Natural Populations ◽  
Amplicon Sequencing ◽  
Protective Role ◽  
Skin Microbiome ◽  
Skin Bacteria

Recently, microbiologists have focused on characterizing the probiotic role of skin bacteria for amphibians threatened by the fungal disease chytridiomycosis. However, the specific characteristics of microbial diversity required to maintain health or trigger disease are still not well understood in natural populations. We hypothesized that seasonal and developmental transitions affecting susceptibility to chytridiomycosis could also alter the stability of microbial assemblages. To test our hypothesis, we examined patterns of skin bacterial diversity in two species of declining amphibians ( Lithobates yavapaiensis and Eleutherodactylus coqui ) affected by the pathogenic fungus Batrachochytrium dendrobatidis ( Bd ). We focused on two important transitions that affect Bd susceptibility: ontogenetic (from juvenile to adult) shifts in E. coqui and seasonal (from summer to winter) shifts in  L. yavapaiensis . We used a combination of community-fingerprinting analyses and 16S rRNA amplicon sequencing to quantify changes in bacterial diversity and assemblage composition between seasons and developmental stages, and to investigate the relationship between bacterial diversity and pathogen load. We found that winter-sampled frogs and juveniles, two states associated with increased Bd susceptibility, exhibited higher diversity compared with summer-sampled frogs and adult individuals. Our findings also revealed that hosts harbouring higher bacterial diversity carried lower Bd infections, providing support for the protective role of bacterial communities. Ongoing work to understand skin microbiome resilience after pathogen disturbance has the potential to identify key taxa involved in disease resistance.

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